WorldWideScience

Sample records for efficient likelihood-based tree

  1. Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood.

    Science.gov (United States)

    Wu, Yufeng

    2012-03-01

    Incomplete lineage sorting can cause incongruence between the phylogenetic history of genes (the gene tree) and that of the species (the species tree), which can complicate the inference of phylogenies. In this article, I present a new coalescent-based algorithm for species tree inference with maximum likelihood. I first describe an improved method for computing the probability of a gene tree topology given a species tree, which is much faster than an existing algorithm by Degnan and Salter (2005). Based on this method, I develop a practical algorithm that takes a set of gene tree topologies and infers species trees with maximum likelihood. This algorithm searches for the best species tree by starting from initial species trees and performing heuristic search to obtain better trees with higher likelihood. This algorithm, called STELLS (which stands for Species Tree InfErence with Likelihood for Lineage Sorting), has been implemented in a program that is downloadable from the author's web page. The simulation results show that the STELLS algorithm is more accurate than an existing maximum likelihood method for many datasets, especially when there is noise in gene trees. I also show that the STELLS algorithm is efficient and can be applied to real biological datasets. © 2011 The Author. Evolution© 2011 The Society for the Study of Evolution.

  2. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

    Directory of Open Access Journals (Sweden)

    Kodner Robin B

    2010-10-01

    Full Text Available Abstract Background Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from next-generation sequencing due to computational complexity issues and lack of phylogenetic signal. "Phylogenetic placement," where a reference tree is fixed and the unknown query sequences are placed onto the tree via a reference alignment, is a way to bring the inferential power offered by likelihood-based approaches to large data sets. Results This paper introduces pplacer, a software package for phylogenetic placement and subsequent visualization. The algorithm can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor, has essentially linear time and memory complexity in the number of reference taxa, and is easy to run in parallel. Pplacer features calculation of the posterior probability of a placement on an edge, which is a statistically rigorous way of quantifying uncertainty on an edge-by-edge basis. It also can inform the user of the positional uncertainty for query sequences by calculating expected distance between placement locations, which is crucial in the estimation of uncertainty with a well-sampled reference tree. The software provides visualizations using branch thickness and color to represent number of placements and their uncertainty. A simulation study using reads generated from 631 COG alignments shows a high level of accuracy for phylogenetic placement over a wide range of alignment diversity, and the power of edge uncertainty estimates to measure placement confidence. Conclusions Pplacer enables efficient phylogenetic placement and subsequent visualization, making likelihood-based phylogenetics methodology practical for large collections of reads; it is freely available as source code, binaries, and a web service.

  3. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

    Directory of Open Access Journals (Sweden)

    Edwards Scott V

    2010-10-01

    Full Text Available Abstract Background Several phylogenetic approaches have been developed to estimate species trees from collections of gene trees. However, maximum likelihood approaches for estimating species trees under the coalescent model are limited. Although the likelihood of a species tree under the multispecies coalescent model has already been derived by Rannala and Yang, it can be shown that the maximum likelihood estimate (MLE of the species tree (topology, branch lengths, and population sizes from gene trees under this formula does not exist. In this paper, we develop a pseudo-likelihood function of the species tree to obtain maximum pseudo-likelihood estimates (MPE of species trees, with branch lengths of the species tree in coalescent units. Results We show that the MPE of the species tree is statistically consistent as the number M of genes goes to infinity. In addition, the probability that the MPE of the species tree matches the true species tree converges to 1 at rate O(M -1. The simulation results confirm that the maximum pseudo-likelihood approach is statistically consistent even when the species tree is in the anomaly zone. We applied our method, Maximum Pseudo-likelihood for Estimating Species Trees (MP-EST to a mammal dataset. The four major clades found in the MP-EST tree are consistent with those in the Bayesian concatenation tree. The bootstrap supports for the species tree estimated by the MP-EST method are more reasonable than the posterior probability supports given by the Bayesian concatenation method in reflecting the level of uncertainty in gene trees and controversies over the relationship of four major groups of placental mammals. Conclusions MP-EST can consistently estimate the topology and branch lengths (in coalescent units of the species tree. Although the pseudo-likelihood is derived from coalescent theory, and assumes no gene flow or horizontal gene transfer (HGT, the MP-EST method is robust to a small amount of HGT in the

  4. Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets

    Science.gov (United States)

    Zhou, Xiaofan; Shen, Xing-Xing; Hittinger, Chris Todd

    2018-01-01

    Abstract The sizes of the data matrices assembled to resolve branches of the tree of life have increased dramatically, motivating the development of programs for fast, yet accurate, inference. For example, several different fast programs have been developed in the very popular maximum likelihood framework, including RAxML/ExaML, PhyML, IQ-TREE, and FastTree. Although these programs are widely used, a systematic evaluation and comparison of their performance using empirical genome-scale data matrices has so far been lacking. To address this question, we evaluated these four programs on 19 empirical phylogenomic data sets with hundreds to thousands of genes and up to 200 taxa with respect to likelihood maximization, tree topology, and computational speed. For single-gene tree inference, we found that the more exhaustive and slower strategies (ten searches per alignment) outperformed faster strategies (one tree search per alignment) using RAxML, PhyML, or IQ-TREE. Interestingly, single-gene trees inferred by the three programs yielded comparable coalescent-based species tree estimations. For concatenation-based species tree inference, IQ-TREE consistently achieved the best-observed likelihoods for all data sets, and RAxML/ExaML was a close second. In contrast, PhyML often failed to complete concatenation-based analyses, whereas FastTree was the fastest but generated lower likelihood values and more dissimilar tree topologies in both types of analyses. Finally, data matrix properties, such as the number of taxa and the strength of phylogenetic signal, sometimes substantially influenced the programs’ relative performance. Our results provide real-world gene and species tree phylogenetic inference benchmarks to inform the design and execution of large-scale phylogenomic data analyses. PMID:29177474

  5. An Efficient UD-Based Algorithm for the Computation of Maximum Likelihood Sensitivity of Continuous-Discrete Systems

    DEFF Research Database (Denmark)

    Boiroux, Dimitri; Juhl, Rune; Madsen, Henrik

    2016-01-01

    This paper addresses maximum likelihood parameter estimation of continuous-time nonlinear systems with discrete-time measurements. We derive an efficient algorithm for the computation of the log-likelihood function and its gradient, which can be used in gradient-based optimization algorithms....... This algorithm uses UD decomposition of symmetric matrices and the array algorithm for covariance update and gradient computation. We test our algorithm on the Lotka-Volterra equations. Compared to the maximum likelihood estimation based on finite difference gradient computation, we get a significant speedup...

  6. A short proof that phylogenetic tree reconstruction by maximum likelihood is hard.

    Science.gov (United States)

    Roch, Sebastien

    2006-01-01

    Maximum likelihood is one of the most widely used techniques to infer evolutionary histories. Although it is thought to be intractable, a proof of its hardness has been lacking. Here, we give a short proof that computing the maximum likelihood tree is NP-hard by exploiting a connection between likelihood and parsimony observed by Tuffley and Steel.

  7. A Short Proof that Phylogenetic Tree Reconstruction by Maximum Likelihood is Hard

    OpenAIRE

    Roch, S.

    2005-01-01

    Maximum likelihood is one of the most widely used techniques to infer evolutionary histories. Although it is thought to be intractable, a proof of its hardness has been lacking. Here, we give a short proof that computing the maximum likelihood tree is NP-hard by exploiting a connection between likelihood and parsimony observed by Tuffley and Steel.

  8. Nearly Efficient Likelihood Ratio Tests for Seasonal Unit Roots

    DEFF Research Database (Denmark)

    Jansson, Michael; Nielsen, Morten Ørregaard

    In an important generalization of zero frequency autore- gressive unit root tests, Hylleberg, Engle, Granger, and Yoo (1990) developed regression-based tests for unit roots at the seasonal frequencies in quarterly time series. We develop likelihood ratio tests for seasonal unit roots and show...... that these tests are "nearly efficient" in the sense of Elliott, Rothenberg, and Stock (1996), i.e. that their local asymptotic power functions are indistinguishable from the Gaussian power envelope. Currently available nearly efficient testing procedures for seasonal unit roots are regression-based and require...... the choice of a GLS detrending parameter, which our likelihood ratio tests do not....

  9. Efficient Detection of Repeating Sites to Accelerate Phylogenetic Likelihood Calculations.

    Science.gov (United States)

    Kobert, K; Stamatakis, A; Flouri, T

    2017-03-01

    The phylogenetic likelihood function (PLF) is the major computational bottleneck in several applications of evolutionary biology such as phylogenetic inference, species delimitation, model selection, and divergence times estimation. Given the alignment, a tree and the evolutionary model parameters, the likelihood function computes the conditional likelihood vectors for every node of the tree. Vector entries for which all input data are identical result in redundant likelihood operations which, in turn, yield identical conditional values. Such operations can be omitted for improving run-time and, using appropriate data structures, reducing memory usage. We present a fast, novel method for identifying and omitting such redundant operations in phylogenetic likelihood calculations, and assess the performance improvement and memory savings attained by our method. Using empirical and simulated data sets, we show that a prototype implementation of our method yields up to 12-fold speedups and uses up to 78% less memory than one of the fastest and most highly tuned implementations of the PLF currently available. Our method is generic and can seamlessly be integrated into any phylogenetic likelihood implementation. [Algorithms; maximum likelihood; phylogenetic likelihood function; phylogenetics]. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

  10. OBEST: The Object-Based Event Scenario Tree Methodology

    International Nuclear Information System (INIS)

    WYSS, GREGORY D.; DURAN, FELICIA A.

    2001-01-01

    Event tree analysis and Monte Carlo-based discrete event simulation have been used in risk assessment studies for many years. This report details how features of these two methods can be combined with concepts from object-oriented analysis to develop a new risk assessment methodology with some of the best features of each. The resultant Object-Based Event Scenarios Tree (OBEST) methodology enables an analyst to rapidly construct realistic models for scenarios for which an a priori discovery of event ordering is either cumbersome or impossible (especially those that exhibit inconsistent or variable event ordering, which are difficult to represent in an event tree analysis). Each scenario produced by OBEST is automatically associated with a likelihood estimate because probabilistic branching is integral to the object model definition. The OBEST method uses a recursive algorithm to solve the object model and identify all possible scenarios and their associated probabilities. Since scenario likelihoods are developed directly by the solution algorithm, they need not be computed by statistical inference based on Monte Carlo observations (as required by some discrete event simulation methods). Thus, OBEST is not only much more computationally efficient than these simulation methods, but it also discovers scenarios that have extremely low probabilities as a natural analytical result--scenarios that would likely be missed by a Monte Carlo-based method. This report documents the OBEST methodology, the demonstration software that implements it, and provides example OBEST models for several different application domains, including interactions among failing interdependent infrastructure systems, circuit analysis for fire risk evaluation in nuclear power plants, and aviation safety studies

  11. Phylogenetic analysis using parsimony and likelihood methods.

    Science.gov (United States)

    Yang, Z

    1996-02-01

    The assumptions underlying the maximum-parsimony (MP) method of phylogenetic tree reconstruction were intuitively examined by studying the way the method works. Computer simulations were performed to corroborate the intuitive examination. Parsimony appears to involve very stringent assumptions concerning the process of sequence evolution, such as constancy of substitution rates between nucleotides, constancy of rates across nucleotide sites, and equal branch lengths in the tree. For practical data analysis, the requirement of equal branch lengths means similar substitution rates among lineages (the existence of an approximate molecular clock), relatively long interior branches, and also few species in the data. However, a small amount of evolution is neither a necessary nor a sufficient requirement of the method. The difficulties involved in the application of current statistical estimation theory to tree reconstruction were discussed, and it was suggested that the approach proposed by Felsenstein (1981, J. Mol. Evol. 17: 368-376) for topology estimation, as well as its many variations and extensions, differs fundamentally from the maximum likelihood estimation of a conventional statistical parameter. Evidence was presented showing that the Felsenstein approach does not share the asymptotic efficiency of the maximum likelihood estimator of a statistical parameter. Computer simulations were performed to study the probability that MP recovers the true tree under a hierarchy of models of nucleotide substitution; its performance relative to the likelihood method was especially noted. The results appeared to support the intuitive examination of the assumptions underlying MP. When a simple model of nucleotide substitution was assumed to generate data, the probability that MP recovers the true topology could be as high as, or even higher than, that for the likelihood method. When the assumed model became more complex and realistic, e.g., when substitution rates were

  12. Query and Update Efficient B+-Tree Based Indexing of Moving Objects

    DEFF Research Database (Denmark)

    Jensen, Christian Søndergaard; Lin, Dan; Ooi, Beng Chin

    2004-01-01

    . This motivates the design of a solution that enables the B+-tree to manage moving objects. We represent moving-object locations as vectors that are timestamped based on their update time. By applying a novel linearization technique to these values, it is possible to index the resulting values using a single B...... are streamed to a database. Indexes for moving objects must support queries efficiently, but must also support frequent updates. Indexes based on minimum bounding regions (MBRs) such as the R-tree exhibit high concurrency overheads during node splitting, and each individual update is known to be quite costly......+-tree that partitions values according to their timestamp and otherwise preserves spatial proximity. We develop algorithms for range and k nearest neighbor queries, as well as continuous queries. The proposal can be grafted into existing database systems cost effectively. An extensive experimental study explores...

  13. Efficient Bit-to-Symbol Likelihood Mappings

    Science.gov (United States)

    Moision, Bruce E.; Nakashima, Michael A.

    2010-01-01

    This innovation is an efficient algorithm designed to perform bit-to-symbol and symbol-to-bit likelihood mappings that represent a significant portion of the complexity of an error-correction code decoder for high-order constellations. Recent implementation of the algorithm in hardware has yielded an 8- percent reduction in overall area relative to the prior design.

  14. Maximum likelihood of phylogenetic networks.

    Science.gov (United States)

    Jin, Guohua; Nakhleh, Luay; Snir, Sagi; Tuller, Tamir

    2006-11-01

    Horizontal gene transfer (HGT) is believed to be ubiquitous among bacteria, and plays a major role in their genome diversification as well as their ability to develop resistance to antibiotics. In light of its evolutionary significance and implications for human health, developing accurate and efficient methods for detecting and reconstructing HGT is imperative. In this article we provide a new HGT-oriented likelihood framework for many problems that involve phylogeny-based HGT detection and reconstruction. Beside the formulation of various likelihood criteria, we show that most of these problems are NP-hard, and offer heuristics for efficient and accurate reconstruction of HGT under these criteria. We implemented our heuristics and used them to analyze biological as well as synthetic data. In both cases, our criteria and heuristics exhibited very good performance with respect to identifying the correct number of HGT events as well as inferring their correct location on the species tree. Implementation of the criteria as well as heuristics and hardness proofs are available from the authors upon request. Hardness proofs can also be downloaded at http://www.cs.tau.ac.il/~tamirtul/MLNET/Supp-ML.pdf

  15. Nearly Efficient Likelihood Ratio Tests of the Unit Root Hypothesis

    DEFF Research Database (Denmark)

    Jansson, Michael; Nielsen, Morten Ørregaard

    Seemingly absent from the arsenal of currently available "nearly efficient" testing procedures for the unit root hypothesis, i.e. tests whose local asymptotic power functions are indistinguishable from the Gaussian power envelope, is a test admitting a (quasi-)likelihood ratio interpretation. We...... show that the likelihood ratio unit root test derived in a Gaussian AR(1) model with standard normal innovations is nearly efficient in that model. Moreover, these desirable properties carry over to more complicated models allowing for serially correlated and/or non-Gaussian innovations....

  16. New approaches to phylogenetic tree search and their application to large numbers of protein alignments.

    Science.gov (United States)

    Whelan, Simon

    2007-10-01

    Phylogenetic tree estimation plays a critical role in a wide variety of molecular studies, including molecular systematics, phylogenetics, and comparative genomics. Finding the optimal tree relating a set of sequences using score-based (optimality criterion) methods, such as maximum likelihood and maximum parsimony, may require all possible trees to be considered, which is not feasible even for modest numbers of sequences. In practice, trees are estimated using heuristics that represent a trade-off between topological accuracy and speed. I present a series of novel algorithms suitable for score-based phylogenetic tree reconstruction that demonstrably improve the accuracy of tree estimates while maintaining high computational speeds. The heuristics function by allowing the efficient exploration of large numbers of trees through novel hill-climbing and resampling strategies. These heuristics, and other computational approximations, are implemented for maximum likelihood estimation of trees in the program Leaphy, and its performance is compared to other popular phylogenetic programs. Trees are estimated from 4059 different protein alignments using a selection of phylogenetic programs and the likelihoods of the tree estimates are compared. Trees estimated using Leaphy are found to have equal to or better likelihoods than trees estimated using other phylogenetic programs in 4004 (98.6%) families and provide a unique best tree that no other program found in 1102 (27.1%) families. The improvement is particularly marked for larger families (80 to 100 sequences), where Leaphy finds a unique best tree in 81.7% of families.

  17. Accurate phylogenetic tree reconstruction from quartets: a heuristic approach.

    Science.gov (United States)

    Reaz, Rezwana; Bayzid, Md Shamsuzzoha; Rahman, M Sohel

    2014-01-01

    Supertree methods construct trees on a set of taxa (species) combining many smaller trees on the overlapping subsets of the entire set of taxa. A 'quartet' is an unrooted tree over 4 taxa, hence the quartet-based supertree methods combine many 4-taxon unrooted trees into a single and coherent tree over the complete set of taxa. Quartet-based phylogeny reconstruction methods have been receiving considerable attentions in the recent years. An accurate and efficient quartet-based method might be competitive with the current best phylogenetic tree reconstruction methods (such as maximum likelihood or Bayesian MCMC analyses), without being as computationally intensive. In this paper, we present a novel and highly accurate quartet-based phylogenetic tree reconstruction method. We performed an extensive experimental study to evaluate the accuracy and scalability of our approach on both simulated and biological datasets.

  18. The phylogenetic likelihood library.

    Science.gov (United States)

    Flouri, T; Izquierdo-Carrasco, F; Darriba, D; Aberer, A J; Nguyen, L-T; Minh, B Q; Von Haeseler, A; Stamatakis, A

    2015-03-01

    We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, error-prone, and labor-intensive tasks, such as likelihood calculations, model parameter as well as branch length optimization, and tree space exploration. The highly optimized and parallelized implementation of the phylogenetic likelihood function and a thorough documentation provide a framework for rapid development of scalable parallel phylogenetic software. By example of two likelihood-based phylogenetic codes we show that the PLL improves the sequential performance of current software by a factor of 2-10 while requiring only 1 month of programming time for integration. We show that, when numerical scaling for preventing floating point underflow is enabled, the double precision likelihood calculations in the PLL are up to 1.9 times faster than those in BEAGLE. On an empirical DNA dataset with 2000 taxa the AVX version of PLL is 4 times faster than BEAGLE (scaling enabled and required). The PLL is available at http://www.libpll.org under the GNU General Public License (GPL). © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

  19. Maximum likelihood inference of small trees in the presence of long branches.

    Science.gov (United States)

    Parks, Sarah L; Goldman, Nick

    2014-09-01

    The statistical basis of maximum likelihood (ML), its robustness, and the fact that it appears to suffer less from biases lead to it being one of the most popular methods for tree reconstruction. Despite its popularity, very few analytical solutions for ML exist, so biases suffered by ML are not well understood. One possible bias is long branch attraction (LBA), a regularly cited term generally used to describe a propensity for long branches to be joined together in estimated trees. Although initially mentioned in connection with inconsistency of parsimony, LBA has been claimed to affect all major phylogenetic reconstruction methods, including ML. Despite the widespread use of this term in the literature, exactly what LBA is and what may be causing it is poorly understood, even for simple evolutionary models and small model trees. Studies looking at LBA have focused on the effect of two long branches on tree reconstruction. However, to understand the effect of two long branches it is also important to understand the effect of just one long branch. If ML struggles to reconstruct one long branch, then this may have an impact on LBA. In this study, we look at the effect of one long branch on three-taxon tree reconstruction. We show that, counterintuitively, long branches are preferentially placed at the tips of the tree. This can be understood through the use of analytical solutions to the ML equation and distance matrix methods. We go on to look at the placement of two long branches on four-taxon trees, showing that there is no attraction between long branches, but that for extreme branch lengths long branches are joined together disproportionally often. These results illustrate that even small model trees are still interesting to help understand how ML phylogenetic reconstruction works, and that LBA is a complicated phenomenon that deserves further study. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

  20. Energy-efficient multicast traffic grooming strategy based on light-tree splitting for elastic optical networks

    Science.gov (United States)

    Liu, Huanlin; Yin, Yarui; Chen, Yong

    2017-07-01

    In order to address the problem of optimizing the spectrum resources and power consumption in elastic optical networks (EONs), we investigate the potential gains by jointly employing the light-tree splitting and traffic grooming for multicast requests. An energy-efficient multicast traffic grooming strategy based on light-tree splitting (EED-MTGS-LS) is proposed in this paper. Firstly, we design a traffic pre-processing mechanism to decide the multicast requests' routing order, which considers the request's bandwidth requirement and physical hops synthetically. Then, by dividing a light-tree to some sub-light-trees and grooming the request to these sub-light-trees, the light-tree sharing ratios of multicast requests can be improved. What's more, a priority scheduling vector is constructed, which aims to improve the success rate of spectrum assignment for grooming requests. Finally, a grooming strategy is designed to optimize the total power consumption by reducing the use of transponders and IP routers during routing. Simulation results show that the proposed strategy can significantly improve the spectrum utilization and save the power consumption.

  1. Laser-Based Slam with Efficient Occupancy Likelihood Map Learning for Dynamic Indoor Scenes

    Science.gov (United States)

    Li, Li; Yao, Jian; Xie, Renping; Tu, Jinge; Feng, Chen

    2016-06-01

    Location-Based Services (LBS) have attracted growing attention in recent years, especially in indoor environments. The fundamental technique of LBS is the map building for unknown environments, this technique also named as simultaneous localization and mapping (SLAM) in robotic society. In this paper, we propose a novel approach for SLAMin dynamic indoor scenes based on a 2D laser scanner mounted on a mobile Unmanned Ground Vehicle (UGV) with the help of the grid-based occupancy likelihood map. Instead of applying scan matching in two adjacent scans, we propose to match current scan with the occupancy likelihood map learned from all previous scans in multiple scales to avoid the accumulation of matching errors. Due to that the acquisition of the points in a scan is sequential but not simultaneous, there unavoidably exists the scan distortion at different extents. To compensate the scan distortion caused by the motion of the UGV, we propose to integrate a velocity of a laser range finder (LRF) into the scan matching optimization framework. Besides, to reduce the effect of dynamic objects such as walking pedestrians often existed in indoor scenes as much as possible, we propose a new occupancy likelihood map learning strategy by increasing or decreasing the probability of each occupancy grid after each scan matching. Experimental results in several challenged indoor scenes demonstrate that our proposed approach is capable of providing high-precision SLAM results.

  2. Probabilistic atlas based labeling of the cerebral vessel tree

    Science.gov (United States)

    Van de Giessen, Martijn; Janssen, Jasper P.; Brouwer, Patrick A.; Reiber, Johan H. C.; Lelieveldt, Boudewijn P. F.; Dijkstra, Jouke

    2015-03-01

    Preoperative imaging of the cerebral vessel tree is essential for planning therapy on intracranial stenoses and aneurysms. Usually, a magnetic resonance angiography (MRA) or computed tomography angiography (CTA) is acquired from which the cerebral vessel tree is segmented. Accurate analysis is helped by the labeling of the cerebral vessels, but labeling is non-trivial due to anatomical topological variability and missing branches due to acquisition issues. In recent literature, labeling the cerebral vasculature around the Circle of Willis has mainly been approached as a graph-based problem. The most successful method, however, requires the definition of all possible permutations of missing vessels, which limits application to subsets of the tree and ignores spatial information about the vessel locations. This research aims to perform labeling using probabilistic atlases that model spatial vessel and label likelihoods. A cerebral vessel tree is aligned to a probabilistic atlas and subsequently each vessel is labeled by computing the maximum label likelihood per segment from label-specific atlases. The proposed method was validated on 25 segmented cerebral vessel trees. Labeling accuracies were close to 100% for large vessels, but dropped to 50-60% for small vessels that were only present in less than 50% of the set. With this work we showed that using solely spatial information of the vessel labels, vessel segments from stable vessels (>50% presence) were reliably classified. This spatial information will form the basis for a future labeling strategy with a very loose topological model.

  3. An efficient implementation of maximum likelihood identification of LTI state-space models by local gradient search

    NARCIS (Netherlands)

    Bergboer, N.H.; Verdult, V.; Verhaegen, M.H.G.

    2002-01-01

    We present a numerically efficient implementation of the nonlinear least squares and maximum likelihood identification of multivariable linear time-invariant (LTI) state-space models. This implementation is based on a local parameterization of the system and a gradient search in the resulting

  4. L.U.St: a tool for approximated maximum likelihood supertree reconstruction.

    Science.gov (United States)

    Akanni, Wasiu A; Creevey, Christopher J; Wilkinson, Mark; Pisani, Davide

    2014-06-12

    Supertrees combine disparate, partially overlapping trees to generate a synthesis that provides a high level perspective that cannot be attained from the inspection of individual phylogenies. Supertrees can be seen as meta-analytical tools that can be used to make inferences based on results of previous scientific studies. Their meta-analytical application has increased in popularity since it was realised that the power of statistical tests for the study of evolutionary trends critically depends on the use of taxon-dense phylogenies. Further to that, supertrees have found applications in phylogenomics where they are used to combine gene trees and recover species phylogenies based on genome-scale data sets. Here, we present the L.U.St package, a python tool for approximate maximum likelihood supertree inference and illustrate its application using a genomic data set for the placental mammals. L.U.St allows the calculation of the approximate likelihood of a supertree, given a set of input trees, performs heuristic searches to look for the supertree of highest likelihood, and performs statistical tests of two or more supertrees. To this end, L.U.St implements a winning sites test allowing ranking of a collection of a-priori selected hypotheses, given as a collection of input supertree topologies. It also outputs a file of input-tree-wise likelihood scores that can be used as input to CONSEL for calculation of standard tests of two trees (e.g. Kishino-Hasegawa, Shimidoara-Hasegawa and Approximately Unbiased tests). This is the first fully parametric implementation of a supertree method, it has clearly understood properties, and provides several advantages over currently available supertree approaches. It is easy to implement and works on any platform that has python installed. bitBucket page - https://afro-juju@bitbucket.org/afro-juju/l.u.st.git. Davide.Pisani@bristol.ac.uk.

  5. Cases in which ancestral maximum likelihood will be confusingly misleading.

    Science.gov (United States)

    Handelman, Tomer; Chor, Benny

    2017-05-07

    Ancestral maximum likelihood (AML) is a phylogenetic tree reconstruction criteria that "lies between" maximum parsimony (MP) and maximum likelihood (ML). ML has long been known to be statistically consistent. On the other hand, Felsenstein (1978) showed that MP is statistically inconsistent, and even positively misleading: There are cases where the parsimony criteria, applied to data generated according to one tree topology, will be optimized on a different tree topology. The question of weather AML is statistically consistent or not has been open for a long time. Mossel et al. (2009) have shown that AML can "shrink" short tree edges, resulting in a star tree with no internal resolution, which yields a better AML score than the original (resolved) model. This result implies that AML is statistically inconsistent, but not that it is positively misleading, because the star tree is compatible with any other topology. We show that AML is confusingly misleading: For some simple, four taxa (resolved) tree, the ancestral likelihood optimization criteria is maximized on an incorrect (resolved) tree topology, as well as on a star tree (both with specific edge lengths), while the tree with the original, correct topology, has strictly lower ancestral likelihood. Interestingly, the two short edges in the incorrect, resolved tree topology are of length zero, and are not adjacent, so this resolved tree is in fact a simple path. While for MP, the underlying phenomenon can be described as long edge attraction, it turns out that here we have long edge repulsion. Copyright © 2017. Published by Elsevier Ltd.

  6. Automated reasoning with dynamic event trees: a real-time, knowledge-based decision aide

    International Nuclear Information System (INIS)

    Touchton, R.A.; Gunter, A.D.; Subramanyan, N.

    1988-01-01

    The models and data contained in a probabilistic risk assessment (PRA) Event Sequence Analysis represent a wealth of information that can be used for dynamic calculation of event sequence likelihood. In this paper we report a new and unique computerization methodology which utilizes these data. This sub-system (referred to as PREDICTOR) has been developed and tested as part of a larger system. PREDICTOR performs a real-time (re)calculation of the estimated likelihood of core-melt as a function of plant status. This methodology uses object-oriented programming techniques from the artificial intelligence discipline that enable one to codify event tree and fault tree logic models and associated probabilities developed in a PRA study. Existence of off-normal conditions is reported to PREDICTOR, which then updates the relevant failure probabilities throughout the event tree and fault tree models by dynamically replacing the off-the-shelf (or prior) probabilities with new probabilities based on the current situation. The new event probabilities are immediately propagated through the models (using 'demons') and an updated core-melt probability is calculated. Along the way, the dominant non-success path of each event tree is determined and highlighted. (author)

  7. A knowledge-based approach to the evaluation of fault trees

    International Nuclear Information System (INIS)

    Hwang, Yann-Jong; Chow, Louis R.; Huang, Henry C.

    1996-01-01

    A list of critical components is useful for determining the potential problems of a complex system. However, to find this list through evaluating the fault trees is expensive and time consuming. This paper intends to propose an integrated software program which consists of a fault tree constructor, a knowledge base, and an efficient algorithm for evaluating minimal cut sets of a large fault tree. The proposed algorithm uses the approaches of top-down heuristic searching and the probability-based truncation. That makes the evaluation of fault trees obviously efficient and provides critical components for solving the potential problems in complex systems. Finally, some practical fault trees are included to illustrate the results

  8. Using an implicit min/max KD-Tree for doing efficient terrain line of sight calculations

    CSIR Research Space (South Africa)

    Duvenhage, B

    2009-02-01

    Full Text Available -dimensional tree (kd-tree) based raytracing approach, to calculating LOS information, is efficient. A new implicit min/max kd-tree algorithm is discussed for evaluating LOS queries on large scale spherical terrain. In particular the value of low resolution boundary...

  9. An efficient and extensible approach for compressing phylogenetic trees

    KAUST Repository

    Matthews, Suzanne J; Williams, Tiffani L

    2011-01-01

    Background: Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend

  10. Fuzzy probability based fault tree analysis to propagate and quantify epistemic uncertainty

    International Nuclear Information System (INIS)

    Purba, Julwan Hendry; Sony Tjahyani, D.T.; Ekariansyah, Andi Sofrany; Tjahjono, Hendro

    2015-01-01

    Highlights: • Fuzzy probability based fault tree analysis is to evaluate epistemic uncertainty in fuzzy fault tree analysis. • Fuzzy probabilities represent likelihood occurrences of all events in a fault tree. • A fuzzy multiplication rule quantifies epistemic uncertainty of minimal cut sets. • A fuzzy complement rule estimate epistemic uncertainty of the top event. • The proposed FPFTA has successfully evaluated the U.S. Combustion Engineering RPS. - Abstract: A number of fuzzy fault tree analysis approaches, which integrate fuzzy concepts into the quantitative phase of conventional fault tree analysis, have been proposed to study reliabilities of engineering systems. Those new approaches apply expert judgments to overcome the limitation of the conventional fault tree analysis when basic events do not have probability distributions. Since expert judgments might come with epistemic uncertainty, it is important to quantify the overall uncertainties of the fuzzy fault tree analysis. Monte Carlo simulation is commonly used to quantify the overall uncertainties of conventional fault tree analysis. However, since Monte Carlo simulation is based on probability distribution, this technique is not appropriate for fuzzy fault tree analysis, which is based on fuzzy probabilities. The objective of this study is to develop a fuzzy probability based fault tree analysis to overcome the limitation of fuzzy fault tree analysis. To demonstrate the applicability of the proposed approach, a case study is performed and its results are then compared to the results analyzed by a conventional fault tree analysis. The results confirm that the proposed fuzzy probability based fault tree analysis is feasible to propagate and quantify epistemic uncertainties in fault tree analysis

  11. An efficient and extensible approach for compressing phylogenetic trees.

    Science.gov (United States)

    Matthews, Suzanne J; Williams, Tiffani L

    2011-10-18

    Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as input, we have designed an extensible decompressor that can extract subcollections of trees, compute majority and strict consensus trees, and merge tree collections using set operations such as union, intersection, and set difference. On unweighted phylogenetic trees, TreeZip is able to compress Newick files in excess of 98%. On weighted phylogenetic trees, TreeZip is able to compress a Newick file by at least 73%. TreeZip can be combined with 7zip with little overhead, allowing space savings in excess of 99% (unweighted) and 92%(weighted). Unlike TreeZip, 7zip is not immune to branch rotations, and performs worse as the level of variability in the Newick string representation increases. Finally, since the TreeZip compressed text (TRZ) file contains all the semantic information in a collection of trees, we can easily filter and decompress a subset of trees of interest (such as the set of unique trees), or build the resulting consensus tree in a matter of seconds. We also show the ease of which set operations can be performed on TRZ files, at speeds quicker than those performed on Newick or 7zip compressed Newick files, and without loss of space savings. TreeZip is an efficient approach for compressing large collections of phylogenetic trees. The semantic and compact nature of the TRZ file allow it to be operated upon directly and quickly, without a need to decompress the original Newick file. We believe that TreeZip will be vital for compressing and archiving trees in the biological community.

  12. Efficient Bulk Operations on Dynamic R-Trees

    DEFF Research Database (Denmark)

    Arge, Lars Allan; Hinrichs, Klaus; Vahrenhold, Jan

    2002-01-01

    In recent years there has been an upsurge of interest in spatial databases. A major issue is how to manipulate efficiently massive amounts of spatial data stored on disk in multidimensional spatial indexes (data structures). Construction of spatial indexes (bulk loading ) has been studied...... intensively in the database community. The continuous arrival of massive amounts of new data makes it important to update existing indexes (bulk updating ) efficiently. In this paper we present a simple, yet efficient, technique for performing bulk update and query operations on multidimensional indexes. We...... present our technique in terms of the so-called R-tree and its variants, as they have emerged as practically efficient indexing methods for spatial data. Our method uses ideas from the buffer tree lazy buffering technique and fully utilizes the available internal memory and the page size of the operating...

  13. Failed refutations: further comments on parsimony and likelihood methods and their relationship to Popper's degree of corroboration.

    Science.gov (United States)

    de Queiroz, Kevin; Poe, Steven

    2003-06-01

    Kluge's (2001, Syst. Biol. 50:322-330) continued arguments that phylogenetic methods based on the statistical principle of likelihood are incompatible with the philosophy of science described by Karl Popper are based on false premises related to Kluge's misrepresentations of Popper's philosophy. Contrary to Kluge's conjectures, likelihood methods are not inherently verificationist; they do not treat every instance of a hypothesis as confirmation of that hypothesis. The historical nature of phylogeny does not preclude phylogenetic hypotheses from being evaluated using the probability of evidence. The low absolute probabilities of hypotheses are irrelevant to the correct interpretation of Popper's concept termed degree of corroboration, which is defined entirely in terms of relative probabilities. Popper did not advocate minimizing background knowledge; in any case, the background knowledge of both parsimony and likelihood methods consists of the general assumption of descent with modification and additional assumptions that are deterministic, concerning which tree is considered most highly corroborated. Although parsimony methods do not assume (in the sense of entailing) that homoplasy is rare, they do assume (in the sense of requiring to obtain a correct phylogenetic inference) certain things about patterns of homoplasy. Both parsimony and likelihood methods assume (in the sense of implying by the manner in which they operate) various things about evolutionary processes, although violation of those assumptions does not always cause the methods to yield incorrect phylogenetic inferences. Test severity is increased by sampling additional relevant characters rather than by character reanalysis, although either interpretation is compatible with the use of phylogenetic likelihood methods. Neither parsimony nor likelihood methods assess test severity (critical evidence) when used to identify a most highly corroborated tree(s) based on a single method or model and a

  14. An efficient and extensible approach for compressing phylogenetic trees

    KAUST Repository

    Matthews, Suzanne J

    2011-01-01

    Background: Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as input, we have designed an extensible decompressor that can extract subcollections of trees, compute majority and strict consensus trees, and merge tree collections using set operations such as union, intersection, and set difference.Results: On unweighted phylogenetic trees, TreeZip is able to compress Newick files in excess of 98%. On weighted phylogenetic trees, TreeZip is able to compress a Newick file by at least 73%. TreeZip can be combined with 7zip with little overhead, allowing space savings in excess of 99% (unweighted) and 92%(weighted). Unlike TreeZip, 7zip is not immune to branch rotations, and performs worse as the level of variability in the Newick string representation increases. Finally, since the TreeZip compressed text (TRZ) file contains all the semantic information in a collection of trees, we can easily filter and decompress a subset of trees of interest (such as the set of unique trees), or build the resulting consensus tree in a matter of seconds. We also show the ease of which set operations can be performed on TRZ files, at speeds quicker than those performed on Newick or 7zip compressed Newick files, and without loss of space savings.Conclusions: TreeZip is an efficient approach for compressing large collections of phylogenetic trees. The semantic and compact nature of the TRZ file allow it to be operated upon directly and quickly, without a need to decompress the original Newick file. We believe that TreeZip will be vital for compressing and archiving trees in the biological community. © 2011 Matthews and Williams; licensee BioMed Central Ltd.

  15. Efficient estimators for likelihood ratio sensitivity indices of complex stochastic dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Arampatzis, Georgios; Katsoulakis, Markos A.; Rey-Bellet, Luc [Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003 (United States)

    2016-03-14

    We demonstrate that centered likelihood ratio estimators for the sensitivity indices of complex stochastic dynamics are highly efficient with low, constant in time variance and consequently they are suitable for sensitivity analysis in long-time and steady-state regimes. These estimators rely on a new covariance formulation of the likelihood ratio that includes as a submatrix a Fisher information matrix for stochastic dynamics and can also be used for fast screening of insensitive parameters and parameter combinations. The proposed methods are applicable to broad classes of stochastic dynamics such as chemical reaction networks, Langevin-type equations and stochastic models in finance, including systems with a high dimensional parameter space and/or disparate decorrelation times between different observables. Furthermore, they are simple to implement as a standard observable in any existing simulation algorithm without additional modifications.

  16. Prediction of strontium bromide laser efficiency using cluster and decision tree analysis

    Directory of Open Access Journals (Sweden)

    Iliev Iliycho

    2018-01-01

    Full Text Available Subject of investigation is a new high-powered strontium bromide (SrBr2 vapor laser emitting in multiline region of wavelengths. The laser is an alternative to the atom strontium lasers and electron free lasers, especially at the line 6.45 μm which line is used in surgery for medical processing of biological tissues and bones with minimal damage. In this paper the experimental data from measurements of operational and output characteristics of the laser are statistically processed by means of cluster analysis and tree-based regression techniques. The aim is to extract the more important relationships and dependences from the available data which influence the increase of the overall laser efficiency. There are constructed and analyzed a set of cluster models. It is shown by using different cluster methods that the seven investigated operational characteristics (laser tube diameter, length, supplied electrical power, and others and laser efficiency are combined in 2 clusters. By the built regression tree models using Classification and Regression Trees (CART technique there are obtained dependences to predict the values of efficiency, and especially the maximum efficiency with over 95% accuracy.

  17. Genetic distances and phylogenetic trees of different Awassi sheep populations based on DNA sequencing.

    Science.gov (United States)

    Al-Atiyat, R M; Aljumaah, R S

    2014-08-27

    This study aimed to estimate evolutionary distances and to reconstruct phylogeny trees between different Awassi sheep populations. Thirty-two sheep individuals from three different geographical areas of Jordan and the Kingdom of Saudi Arabia (KSA) were randomly sampled. DNA was extracted from the tissue samples and sequenced using the T7 promoter universal primer. Different phylogenetic trees were reconstructed from 0.64-kb DNA sequences using the MEGA software with the best general time reverse distance model. Three methods of distance estimation were then used. The maximum composite likelihood test was considered for reconstructing maximum likelihood, neighbor-joining and UPGMA trees. The maximum likelihood tree indicated three major clusters separated by cytosine (C) and thymine (T). The greatest distance was shown between the South sheep and North sheep. On the other hand, the KSA sheep as an outgroup showed shorter evolutionary distance to the North sheep population than to the others. The neighbor-joining and UPGMA trees showed quite reliable clusters of evolutionary differentiation of Jordan sheep populations from the Saudi population. The overall results support geographical information and ecological types of the sheep populations studied. Summing up, the resulting phylogeny trees may contribute to the limited information about the genetic relatedness and phylogeny of Awassi sheep in nearby Arab countries.

  18. Likelihood-based methods for evaluating principal surrogacy in augmented vaccine trials.

    Science.gov (United States)

    Liu, Wei; Zhang, Bo; Zhang, Hui; Zhang, Zhiwei

    2017-04-01

    There is growing interest in assessing immune biomarkers, which are quick to measure and potentially predictive of long-term efficacy, as surrogate endpoints in randomized, placebo-controlled vaccine trials. This can be done under a principal stratification approach, with principal strata defined using a subject's potential immune responses to vaccine and placebo (the latter may be assumed to be zero). In this context, principal surrogacy refers to the extent to which vaccine efficacy varies across principal strata. Because a placebo recipient's potential immune response to vaccine is unobserved in a standard vaccine trial, augmented vaccine trials have been proposed to produce the information needed to evaluate principal surrogacy. This article reviews existing methods based on an estimated likelihood and a pseudo-score (PS) and proposes two new methods based on a semiparametric likelihood (SL) and a pseudo-likelihood (PL), for analyzing augmented vaccine trials. Unlike the PS method, the SL method does not require a model for missingness, which can be advantageous when immune response data are missing by happenstance. The SL method is shown to be asymptotically efficient, and it performs similarly to the PS and PL methods in simulation experiments. The PL method appears to have a computational advantage over the PS and SL methods.

  19. Moment Conditions Selection Based on Adaptive Penalized Empirical Likelihood

    Directory of Open Access Journals (Sweden)

    Yunquan Song

    2014-01-01

    Full Text Available Empirical likelihood is a very popular method and has been widely used in the fields of artificial intelligence (AI and data mining as tablets and mobile application and social media dominate the technology landscape. This paper proposes an empirical likelihood shrinkage method to efficiently estimate unknown parameters and select correct moment conditions simultaneously, when the model is defined by moment restrictions in which some are possibly misspecified. We show that our method enjoys oracle-like properties; that is, it consistently selects the correct moment conditions and at the same time its estimator is as efficient as the empirical likelihood estimator obtained by all correct moment conditions. Moreover, unlike the GMM, our proposed method allows us to carry out confidence regions for the parameters included in the model without estimating the covariances of the estimators. For empirical implementation, we provide some data-driven procedures for selecting the tuning parameter of the penalty function. The simulation results show that the method works remarkably well in terms of correct moment selection and the finite sample properties of the estimators. Also, a real-life example is carried out to illustrate the new methodology.

  20. Likelihood-ratio-based biometric verification

    NARCIS (Netherlands)

    Bazen, A.M.; Veldhuis, Raymond N.J.

    2002-01-01

    This paper presents results on optimal similarity measures for biometric verification based on fixed-length feature vectors. First, we show that the verification of a single user is equivalent to the detection problem, which implies that for single-user verification the likelihood ratio is optimal.

  1. Likelihood Ratio-Based Biometric Verification

    NARCIS (Netherlands)

    Bazen, A.M.; Veldhuis, Raymond N.J.

    The paper presents results on optimal similarity measures for biometric verification based on fixed-length feature vectors. First, we show that the verification of a single user is equivalent to the detection problem, which implies that, for single-user verification, the likelihood ratio is optimal.

  2. Object-based methods for individual tree identification and tree species classification from high-spatial resolution imagery

    Science.gov (United States)

    Wang, Le

    2003-10-01

    textures occurring due to branches and twigs. As a result from the inverse wavelet transform, the tree crown boundary is enhanced while the unwanted textures are suppressed. Based on the enhanced image, an improvement is achieved when applying the two-stage methods to a high resolution aerial photograph. To improve tree species classification, we develop a new method to choose the optimal scale parameter with the aid of Bhattacharya Distance (BD), a well-known index of class separability in traditional pixel-based classification. The optimal scale parameter is then fed in the process of a region-growing-based segmentation as a break-off value. Our object classification achieves a better accuracy in separating tree species when compared to the conventional Maximum Likelihood Classification (MLC). In summary, we develop two object-based methods for identifying individual trees and classifying tree species from high-spatial resolution imagery. Both methods achieve promising results and will promote integration of Remote Sensing and GIS in forest applications.

  3. Approximate maximum parsimony and ancestral maximum likelihood.

    Science.gov (United States)

    Alon, Noga; Chor, Benny; Pardi, Fabio; Rapoport, Anat

    2010-01-01

    We explore the maximum parsimony (MP) and ancestral maximum likelihood (AML) criteria in phylogenetic tree reconstruction. Both problems are NP-hard, so we seek approximate solutions. We formulate the two problems as Steiner tree problems under appropriate distances. The gist of our approach is the succinct characterization of Steiner trees for a small number of leaves for the two distances. This enables the use of known Steiner tree approximation algorithms. The approach leads to a 16/9 approximation ratio for AML and asymptotically to a 1.55 approximation ratio for MP.

  4. Optimized Large-scale CMB Likelihood and Quadratic Maximum Likelihood Power Spectrum Estimation

    Science.gov (United States)

    Gjerløw, E.; Colombo, L. P. L.; Eriksen, H. K.; Górski, K. M.; Gruppuso, A.; Jewell, J. B.; Plaszczynski, S.; Wehus, I. K.

    2015-11-01

    We revisit the problem of exact cosmic microwave background (CMB) likelihood and power spectrum estimation with the goal of minimizing computational costs through linear compression. This idea was originally proposed for CMB purposes by Tegmark et al., and here we develop it into a fully functioning computational framework for large-scale polarization analysis, adopting WMAP as a working example. We compare five different linear bases (pixel space, harmonic space, noise covariance eigenvectors, signal-to-noise covariance eigenvectors, and signal-plus-noise covariance eigenvectors) in terms of compression efficiency, and find that the computationally most efficient basis is the signal-to-noise eigenvector basis, which is closely related to the Karhunen-Loeve and Principal Component transforms, in agreement with previous suggestions. For this basis, the information in 6836 unmasked WMAP sky map pixels can be compressed into a smaller set of 3102 modes, with a maximum error increase of any single multipole of 3.8% at ℓ ≤ 32 and a maximum shift in the mean values of a joint distribution of an amplitude-tilt model of 0.006σ. This compression reduces the computational cost of a single likelihood evaluation by a factor of 5, from 38 to 7.5 CPU seconds, and it also results in a more robust likelihood by implicitly regularizing nearly degenerate modes. Finally, we use the same compression framework to formulate a numerically stable and computationally efficient variation of the Quadratic Maximum Likelihood implementation, which requires less than 3 GB of memory and 2 CPU minutes per iteration for ℓ ≤ 32, rendering low-ℓ QML CMB power spectrum analysis fully tractable on a standard laptop.

  5. Assessing the predictive capability of randomized tree-based ensembles in streamflow modelling

    Science.gov (United States)

    Galelli, S.; Castelletti, A.

    2013-07-01

    Combining randomization methods with ensemble prediction is emerging as an effective option to balance accuracy and computational efficiency in data-driven modelling. In this paper, we investigate the prediction capability of extremely randomized trees (Extra-Trees), in terms of accuracy, explanation ability and computational efficiency, in a streamflow modelling exercise. Extra-Trees are a totally randomized tree-based ensemble method that (i) alleviates the poor generalisation property and tendency to overfitting of traditional standalone decision trees (e.g. CART); (ii) is computationally efficient; and, (iii) allows to infer the relative importance of the input variables, which might help in the ex-post physical interpretation of the model. The Extra-Trees potential is analysed on two real-world case studies - Marina catchment (Singapore) and Canning River (Western Australia) - representing two different morphoclimatic contexts. The evaluation is performed against other tree-based methods (CART and M5) and parametric data-driven approaches (ANNs and multiple linear regression). Results show that Extra-Trees perform comparatively well to the best of the benchmarks (i.e. M5) in both the watersheds, while outperforming the other approaches in terms of computational requirement when adopted on large datasets. In addition, the ranking of the input variable provided can be given a physically meaningful interpretation.

  6. (Almost) practical tree codes

    KAUST Repository

    Khina, Anatoly

    2016-08-15

    We consider the problem of stabilizing an unstable plant driven by bounded noise over a digital noisy communication link, a scenario at the heart of networked control. To stabilize such a plant, one needs real-time encoding and decoding with an error probability profile that decays exponentially with the decoding delay. The works of Schulman and Sahai over the past two decades have developed the notions of tree codes and anytime capacity, and provided the theoretical framework for studying such problems. Nonetheless, there has been little practical progress in this area due to the absence of explicit constructions of tree codes with efficient encoding and decoding algorithms. Recently, linear time-invariant tree codes were proposed to achieve the desired result under maximum-likelihood decoding. In this work, we take one more step towards practicality, by showing that these codes can be efficiently decoded using sequential decoding algorithms, up to some loss in performance (and with some practical complexity caveats). We supplement our theoretical results with numerical simulations that demonstrate the effectiveness of the decoder in a control system setting.

  7. Validation of DNA-based identification software by computation of pedigree likelihood ratios.

    Science.gov (United States)

    Slooten, K

    2011-08-01

    Disaster victim identification (DVI) can be aided by DNA-evidence, by comparing the DNA-profiles of unidentified individuals with those of surviving relatives. The DNA-evidence is used optimally when such a comparison is done by calculating the appropriate likelihood ratios. Though conceptually simple, the calculations can be quite involved, especially with large pedigrees, precise mutation models etc. In this article we describe a series of test cases designed to check if software designed to calculate such likelihood ratios computes them correctly. The cases include both simple and more complicated pedigrees, among which inbred ones. We show how to calculate the likelihood ratio numerically and algebraically, including a general mutation model and possibility of allelic dropout. In Appendix A we show how to derive such algebraic expressions mathematically. We have set up these cases to validate new software, called Bonaparte, which performs pedigree likelihood ratio calculations in a DVI context. Bonaparte has been developed by SNN Nijmegen (The Netherlands) for the Netherlands Forensic Institute (NFI). It is available free of charge for non-commercial purposes (see www.dnadvi.nl for details). Commercial licenses can also be obtained. The software uses Bayesian networks and the junction tree algorithm to perform its calculations. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  8. Benefit-based tree valuation

    Science.gov (United States)

    E.G. McPherson

    2007-01-01

    Benefit-based tree valuation provides alternative estimates of the fair and reasonable value of trees while illustrating the relative contribution of different benefit types. This study compared estimates of tree value obtained using cost- and benefit-based approaches. The cost-based approach used the Council of Landscape and Tree Appraisers trunk formula method, and...

  9. ERA: Efficient serial and parallel suffix tree construction for very long strings

    KAUST Repository

    Mansour, Essam

    2011-09-01

    The suffix tree is a data structure for indexing strings. It is used in a variety of applications such as bioinformatics, time series analysis, clustering, text editing and data compression. However, when the string and the resulting suffix tree are too large to fit into the main memory, most existing construction algorithms become very inefficient. This paper presents a disk-based suffix tree construction method, called Elastic Range (ERa), which works efficiently with very long strings that are much larger than the available memory. ERa partitions the tree construction process horizontally and vertically and minimizes I/Os by dynamically adjusting the horizontal partitions independently for each vertical partition, based on the evolving shape of the tree and the available memory. Where appropriate, ERa also groups vertical partitions together to amortize the I/O cost. We developed a serial version; a parallel version for shared-memory and shared-disk multi-core systems; and a parallel version for shared-nothing architectures. ERa indexes the entire human genome in 19 minutes on an ordinary desktop computer. For comparison, the fastest existing method needs 15 minutes using 1024 CPUs on an IBM BlueGene supercomputer.

  10. Dominant clonal Eucalyptus grandis x urophylla trees use water more efficiently

    Science.gov (United States)

    Marina Shinkai Gentil Otto; Robert M. Hubbard; Dan Binkley; Jose Luis Stape

    2014-01-01

    Wood growth in trees depends on the acquisition of resources, and can vary with tree size leading to a variety of stand dynamics. Typically, larger trees obtain more resources and grow faster than smaller trees, but while light has been addressed more often, few case studies have investigated the contributions of water use and water use efficiency (WUE) within stands...

  11. Comparison of water-use efficiency estimates based on tree-ring carbon isotopes with simulations of a dynamic vegetation model

    Science.gov (United States)

    Saurer, Matthias; Renato, Spahni; Fortunat, Joos; David, Frank; Kerstin, Treydte; Rolf, Siegwolf

    2015-04-01

    Tree-ring d13C-based estimates of intrinsic water-use efficiency (iWUE, reflecting the ratio of assimilation A to stomatal conductance gs) generally show a strong increase during the industrial period, likely associated with the increase in atmospheric CO2. However, it is not clear, first, if tree-ring d13C-derived iWUE-values indeed reflect actual plant and ecosystem-scale variability in fluxes and, second, what physiological changes were the drivers of the observed iWUE increase, changes in A or gs or both. To address these questions, we used a complex dynamic vegetation model (LPX) that combines process-based vegetation dynamics with land-atmosphere carbon and water exchange. The analysis was conducted for three functional types, representing conifers, oaks, larch, and various sites in Europe, where tree-ring isotope data are available. The increase in iWUE over the 20th century was comparable in LPX-simulations as in tree-ring-estimates, strengthening confidence in these results. Furthermore, the results from the LPX model suggest that the cause of the iWUE increase was reduced stomatal conductance during recent decades rather than increased assimilation. High-frequency variation reflects the influence of climate, like for example the 1976 summer drought, resulting in strongly reduced A and g in the model, particularly for oak.

  12. A fault tree analysis strategy using binary decision diagrams

    International Nuclear Information System (INIS)

    Reay, Karen A.; Andrews, John D.

    2002-01-01

    The use of binary decision diagrams (BDDs) in fault tree analysis provides both an accurate and efficient means of analysing a system. There is a problem, however, with the conversion process of the fault tree to the BDD. The variable ordering scheme chosen for the construction of the BDD has a crucial effect on its resulting size and previous research has failed to identify any scheme that is capable of producing BDDs for all fault trees. This paper proposes an analysis strategy aimed at increasing the likelihood of obtaining a BDD for any given fault tree, by ensuring the associated calculations are as efficient as possible. The method implements simplification techniques, which are applied to the fault tree to obtain a set of 'minimal' subtrees, equivalent to the original fault tree structure. BDDs are constructed for each, using ordering schemes most suited to their particular characteristics. Quantitative analysis is performed simultaneously on the set of BDDs to obtain the top event probability, the system unconditional failure intensity and the criticality of the basic events

  13. HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing.

    Science.gov (United States)

    Wan, Shixiang; Zou, Quan

    2017-01-01

    Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient ultra-large biological sequence alignment approaches for coping with different sequence types. Distributed and parallel computing represents a crucial technique for accelerating ultra-large (e.g. files more than 1 GB) sequence analyses. Based on HAlign and Spark distributed computing system, we implement a highly cost-efficient and time-efficient HAlign-II tool to address ultra-large multiple biological sequence alignment and phylogenetic tree construction. The experiments in the DNA and protein large scale data sets, which are more than 1GB files, showed that HAlign II could save time and space. It outperformed the current software tools. HAlign-II can efficiently carry out MSA and construct phylogenetic trees with ultra-large numbers of biological sequences. HAlign-II shows extremely high memory efficiency and scales well with increases in computing resource. THAlign-II provides a user-friendly web server based on our distributed computing infrastructure. HAlign-II with open-source codes and datasets was established at http://lab.malab.cn/soft/halign.

  14. Improved EDELWEISS-III sensitivity for low-mass WIMPs using a profile likelihood approach

    Energy Technology Data Exchange (ETDEWEB)

    Hehn, L. [Karlsruher Institut fuer Technologie, Institut fuer Kernphysik, Karlsruhe (Germany); Armengaud, E.; Boissiere, T. de; Gros, M.; Navick, X.F.; Nones, C.; Paul, B. [CEA Saclay, DSM/IRFU, Gif-sur-Yvette Cedex (France); Arnaud, Q. [Univ Lyon, Universite Claude Bernard Lyon 1, CNRS/IN2P3, Institut de Physique Nucleaire de Lyon, Lyon (France); Queen' s University, Kingston (Canada); Augier, C.; Billard, J.; Cazes, A.; Charlieux, F.; Jesus, M. de; Gascon, J.; Juillard, A.; Queguiner, E.; Sanglard, V.; Vagneron, L. [Univ Lyon, Universite Claude Bernard Lyon 1, CNRS/IN2P3, Institut de Physique Nucleaire de Lyon, Lyon (France); Benoit, A.; Camus, P. [Institut Neel, CNRS/UJF, Grenoble (France); Berge, L.; Chapellier, M.; Dumoulin, L.; Giuliani, A.; Le-Sueur, H.; Marnieros, S.; Olivieri, E.; Poda, D. [CSNSM, Univ. Paris-Sud, CNRS/IN2P3, Universite Paris-Saclay, Orsay (France); Bluemer, J. [Karlsruher Institut fuer Technologie, Institut fuer Kernphysik, Karlsruhe (Germany); Karlsruher Institut fuer Technologie, Institut fuer Experimentelle Kernphysik, Karlsruhe (Germany); Broniatowski, A. [CSNSM, Univ. Paris-Sud, CNRS/IN2P3, Universite Paris-Saclay, Orsay (France); Karlsruher Institut fuer Technologie, Institut fuer Experimentelle Kernphysik, Karlsruhe (Germany); Eitel, K.; Kozlov, V.; Siebenborn, B. [Karlsruher Institut fuer Technologie, Institut fuer Kernphysik, Karlsruhe (Germany); Foerster, N.; Heuermann, G.; Scorza, S. [Karlsruher Institut fuer Technologie, Institut fuer Experimentelle Kernphysik, Karlsruhe (Germany); Jin, Y. [Laboratoire de Photonique et de Nanostructures, CNRS, Route de Nozay, Marcoussis (France); Kefelian, C. [Univ Lyon, Universite Claude Bernard Lyon 1, CNRS/IN2P3, Institut de Physique Nucleaire de Lyon, Lyon (France); Karlsruher Institut fuer Technologie, Institut fuer Experimentelle Kernphysik, Karlsruhe (Germany); Kleifges, M.; Tcherniakhovski, D.; Weber, M. [Karlsruher Institut fuer Technologie, Institut fuer Prozessdatenverarbeitung und Elektronik, Karlsruhe (Germany); Kraus, H. [University of Oxford, Department of Physics, Oxford (United Kingdom); Kudryavtsev, V.A. [University of Sheffield, Department of Physics and Astronomy, Sheffield (United Kingdom); Pari, P. [CEA Saclay, DSM/IRAMIS, Gif-sur-Yvette (France); Piro, M.C. [CSNSM, Univ. Paris-Sud, CNRS/IN2P3, Universite Paris-Saclay, Orsay (France); Rensselaer Polytechnic Institute, Troy, NY (United States); Rozov, S.; Yakushev, E. [JINR, Laboratory of Nuclear Problems, Dubna, Moscow Region (Russian Federation); Schmidt, B. [Karlsruher Institut fuer Technologie, Institut fuer Kernphysik, Karlsruhe (Germany); Lawrence Berkeley National Laboratory, Berkeley, CA (United States)

    2016-10-15

    We report on a dark matter search for a Weakly Interacting Massive Particle (WIMP) in the mass range m{sub χ} element of [4, 30] GeV/c{sup 2} with the EDELWEISS-III experiment. A 2D profile likelihood analysis is performed on data from eight selected detectors with the lowest energy thresholds leading to a combined fiducial exposure of 496 kg-days. External backgrounds from γ- and β-radiation, recoils from {sup 206}Pb and neutrons as well as detector intrinsic backgrounds were modelled from data outside the region of interest and constrained in the analysis. The basic data selection and most of the background models are the same as those used in a previously published analysis based on boosted decision trees (BDT) [1]. For the likelihood approach applied in the analysis presented here, a larger signal efficiency and a subtraction of the expected background lead to a higher sensitivity, especially for the lowest WIMP masses probed. No statistically significant signal was found and upper limits on the spin-independent WIMP-nucleon scattering cross section can be set with a hypothesis test based on the profile likelihood test statistics. The 90 % C.L. exclusion limit set for WIMPs with m{sub χ} = 4 GeV/c{sup 2} is 1.6 x 10{sup -39} cm{sup 2}, which is an improvement of a factor of seven with respect to the BDT-based analysis. For WIMP masses above 15 GeV/c{sup 2} the exclusion limits found with both analyses are in good agreement. (orig.)

  15. Pareto Efficient Solutions of Attack-Defence Trees

    DEFF Research Database (Denmark)

    Aslanyan, Zaruhi; Nielson, Flemming

    2015-01-01

    Attack-defence trees are a promising approach for representing threat scenarios and possible countermeasures in a concise and intuitive manner. An attack-defence tree describes the interaction between an attacker and a defender, and is evaluated by assigning parameters to the nodes, such as proba......Attack-defence trees are a promising approach for representing threat scenarios and possible countermeasures in a concise and intuitive manner. An attack-defence tree describes the interaction between an attacker and a defender, and is evaluated by assigning parameters to the nodes......, such as probability or cost of attacks and defences. In case of multiple parameters most analytical methods optimise one parameter at a time, e.g., minimise cost or maximise probability of an attack. Such methods may lead to sub-optimal solutions when optimising conflicting parameters, e.g., minimising cost while...... maximising probability. In order to tackle this challenge, we devise automated techniques that optimise all parameters at once. Moreover, in the case of conflicting parameters our techniques compute the set of all optimal solutions, defined in terms of Pareto efficiency. The developments are carried out...

  16. Generalized empirical likelihood methods for analyzing longitudinal data

    KAUST Repository

    Wang, S.

    2010-02-16

    Efficient estimation of parameters is a major objective in analyzing longitudinal data. We propose two generalized empirical likelihood based methods that take into consideration within-subject correlations. A nonparametric version of the Wilks theorem for the limiting distributions of the empirical likelihood ratios is derived. It is shown that one of the proposed methods is locally efficient among a class of within-subject variance-covariance matrices. A simulation study is conducted to investigate the finite sample properties of the proposed methods and compare them with the block empirical likelihood method by You et al. (2006) and the normal approximation with a correctly estimated variance-covariance. The results suggest that the proposed methods are generally more efficient than existing methods which ignore the correlation structure, and better in coverage compared to the normal approximation with correctly specified within-subject correlation. An application illustrating our methods and supporting the simulation study results is also presented.

  17. On Tree-Based Phylogenetic Networks.

    Science.gov (United States)

    Zhang, Louxin

    2016-07-01

    A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree-based networks. We present a simple necessary and sufficient condition for tree-based networks and prove that a universal tree-based network exists for any number of taxa that contains as its base every phylogenetic tree on the same set of taxa. This answers two problems posted by Francis and Steel recently. A byproduct is a computer program for generating random binary phylogenetic networks under the uniform distribution model.

  18. ELB-trees an efficient and lock-free B-tree derivative

    DEFF Research Database (Denmark)

    Bonnichsen, Lars Frydendal; Karlsson, Sven; Probst, Christian W.

    2013-01-01

    overhead. All lock-free data structures are based on simple atomic operations that, though supported by modern processors, are expensive in execution time. We present a lock-free data structure, ELB-trees, which under certain assumptions can be used as multimaps as well as priority queues. Specifically...... it cannot store duplicate key-value pairs, and it is not linearizable. Compared to existing data structures, ELB-trees require fewer atomic operations leading to improved performance. We measure the parallel performance of ELB-trees using a set of benchmarks and observe that ELB-trees are up to almost 30......As computer systems scale in the number of processors, scalable data structures with good parallel performance become increasingly important. Lock-free data structures promise such improved parallel performance at the expense of higher algorithmic complexity and higher sequential execution time...

  19. Species trees for the tree swallows (Genus Tachycineta): an alternative phylogenetic hypothesis to the mitochondrial gene tree.

    Science.gov (United States)

    Dor, Roi; Carling, Matthew D; Lovette, Irby J; Sheldon, Frederick H; Winkler, David W

    2012-10-01

    The New World swallow genus Tachycineta comprises nine species that collectively have a wide geographic distribution and remarkable variation both within- and among-species in ecologically important traits. Existing phylogenetic hypotheses for Tachycineta are based on mitochondrial DNA sequences, thus they provide estimates of a single gene tree. In this study we sequenced multiple individuals from each species at 16 nuclear intron loci. We used gene concatenated approaches (Bayesian and maximum likelihood) as well as coalescent-based species tree inference to reconstruct phylogenetic relationships of the genus. We examined the concordance and conflict between the nuclear and mitochondrial trees and between concatenated and coalescent-based inferences. Our results provide an alternative phylogenetic hypothesis to the existing mitochondrial DNA estimate of phylogeny. This new hypothesis provides a more accurate framework in which to explore trait evolution and examine the evolution of the mitochondrial genome in this group. Copyright © 2012 Elsevier Inc. All rights reserved.

  20. Nonbinary Tree-Based Phylogenetic Networks.

    Science.gov (United States)

    Jetten, Laura; van Iersel, Leo

    2018-01-01

    Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can, for example, represent gene transfer events. Such phylogenetic networks are called tree-based. Here, we consider two possible generalizations of this concept to nonbinary networks, which we call tree-based and strictly-tree-based nonbinary phylogenetic networks. We give simple graph-theoretic characterizations of tree-based and strictly-tree-based nonbinary phylogenetic networks. Moreover, we show for each of these two classes that it can be decided in polynomial time whether a given network is contained in the class. Our approach also provides a new view on tree-based binary phylogenetic networks. Finally, we discuss two examples of nonbinary phylogenetic networks in biology and show how our results can be applied to them.

  1. Maximum likelihood phylogenetic reconstruction from high-resolution whole-genome data and a tree of 68 eukaryotes.

    Science.gov (United States)

    Lin, Yu; Hu, Fei; Tang, Jijun; Moret, Bernard M E

    2013-01-01

    The rapid accumulation of whole-genome data has renewed interest in the study of the evolution of genomic architecture, under such events as rearrangements, duplications, losses. Comparative genomics, evolutionary biology, and cancer research all require tools to elucidate the mechanisms, history, and consequences of those evolutionary events, while phylogenetics could use whole-genome data to enhance its picture of the Tree of Life. Current approaches in the area of phylogenetic analysis are limited to very small collections of closely related genomes using low-resolution data (typically a few hundred syntenic blocks); moreover, these approaches typically do not include duplication and loss events. We describe a maximum likelihood (ML) approach for phylogenetic analysis that takes into account genome rearrangements as well as duplications, insertions, and losses. Our approach can handle high-resolution genomes (with 40,000 or more markers) and can use in the same analysis genomes with very different numbers of markers. Because our approach uses a standard ML reconstruction program (RAxML), it scales up to large trees. We present the results of extensive testing on both simulated and real data showing that our approach returns very accurate results very quickly. In particular, we analyze a dataset of 68 high-resolution eukaryotic genomes, with from 3,000 to 42,000 genes, from the eGOB database; the analysis, including bootstrapping, takes just 3 hours on a desktop system and returns a tree in agreement with all well supported branches, while also suggesting resolutions for some disputed placements.

  2. SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

    Science.gov (United States)

    Liu, Kevin; Warnow, Tandy J; Holder, Mark T; Nelesen, Serita M; Yu, Jiaye; Stamatakis, Alexandros P; Linder, C Randal

    2012-01-01

    Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Coestimation of alignments and trees has been attempted but currently only SATé estimates reasonably accurate trees and alignments for large data sets in practical time frames (Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I) in terms of speed and of phylogenetic and alignment accuracy. SATé-II uses a different divide-and-conquer strategy than SATé-I and so produces smaller more closely related subsets than SATé-I; as a result, SATé-II produces more accurate alignments and trees, can analyze larger data sets, and runs more efficiently than SATé-I. Generally, SATé is a metamethod that takes an existing multiple sequence alignment method as an input parameter and boosts the quality of that alignment method. SATé-II-boosted alignment methods are significantly more accurate than their unboosted versions, and trees based upon these improved alignments are more accurate than trees based upon the original alignments. Because SATé-I used maximum likelihood (ML) methods that treat gaps as missing data to estimate trees and because we found a correlation between the quality of tree/alignment pairs and ML scores, we explored the degree to which SATé's performance depends on using ML with gaps treated as missing data to determine the best tree/alignment pair. We present two lines of evidence that using ML with gaps treated as missing data to optimize the alignment and tree produces very poor results. First, we show that the optimization problem where a set of unaligned DNA sequences is given and the output is the tree and alignment of

  3. Generalized empirical likelihood methods for analyzing longitudinal data

    KAUST Repository

    Wang, S.; Qian, L.; Carroll, R. J.

    2010-01-01

    Efficient estimation of parameters is a major objective in analyzing longitudinal data. We propose two generalized empirical likelihood based methods that take into consideration within-subject correlations. A nonparametric version of the Wilks

  4. Real Time Animation of Trees Based on BBSC in Computer Games

    Directory of Open Access Journals (Sweden)

    Xuefeng Ao

    2009-01-01

    Full Text Available That researchers in the field of computer games usually find it is difficult to simulate the motion of actual 3D model trees lies in the fact that the tree model itself has very complicated structure, and many sophisticated factors need to be considered during the simulation. Though there are some works on simulating 3D tree and its motion, few of them are used in computer games due to the high demand for real-time in computer games. In this paper, an approach of animating trees in computer games based on a novel tree model representation—Ball B-Spline Curves (BBSCs are proposed. By taking advantage of the good features of the BBSC-based model, physical simulation of the motion of leafless trees with wind blowing becomes easier and more efficient. The method can generate realistic 3D tree animation in real-time, which meets the high requirement for real time in computer games.

  5. IcyTree: rapid browser-based visualization for phylogenetic trees and networks.

    Science.gov (United States)

    Vaughan, Timothy G

    2017-08-01

    IcyTree is an easy-to-use application which can be used to visualize a wide variety of phylogenetic trees and networks. While numerous phylogenetic tree viewers exist already, IcyTree distinguishes itself by being a purely online tool, having a responsive user interface, supporting phylogenetic networks (ancestral recombination graphs in particular), and efficiently drawing trees that include information such as ancestral locations or trait values. IcyTree also provides intuitive panning and zooming utilities that make exploring large phylogenetic trees of many thousands of taxa feasible. IcyTree is a web application and can be accessed directly at http://tgvaughan.github.com/icytree . Currently supported web browsers include Mozilla Firefox and Google Chrome. IcyTree is written entirely in client-side JavaScript (no plugin required) and, once loaded, does not require network access to run. IcyTree is free software, and the source code is made available at http://github.com/tgvaughan/icytree under version 3 of the GNU General Public License. tgvaughan@gmail.com. © The Author(s) 2017. Published by Oxford University Press.

  6. PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis

    Directory of Open Access Journals (Sweden)

    Wang Huai-Chun

    2009-09-01

    Full Text Available Abstract Background The covarion hypothesis of molecular evolution holds that selective pressures on a given amino acid or nucleotide site are dependent on the identity of other sites in the molecule that change throughout time, resulting in changes of evolutionary rates of sites along the branches of a phylogenetic tree. At the sequence level, covarion-like evolution at a site manifests as conservation of nucleotide or amino acid states among some homologs where the states are not conserved in other homologs (or groups of homologs. Covarion-like evolution has been shown to relate to changes in functions at sites in different clades, and, if ignored, can adversely affect the accuracy of phylogenetic inference. Results PROCOV (protein covarion analysis is a software tool that implements a number of previously proposed covarion models of protein evolution for phylogenetic inference in a maximum likelihood framework. Several algorithmic and implementation improvements in this tool over previous versions make computationally expensive tree searches with covarion models more efficient and analyses of large phylogenomic data sets tractable. PROCOV can be used to identify covarion sites by comparing the site likelihoods under the covarion process to the corresponding site likelihoods under a rates-across-sites (RAS process. Those sites with the greatest log-likelihood difference between a 'covarion' and an RAS process were found to be of functional or structural significance in a dataset of bacterial and eukaryotic elongation factors. Conclusion Covarion models implemented in PROCOV may be especially useful for phylogenetic estimation when ancient divergences between sequences have occurred and rates of evolution at sites are likely to have changed over the tree. It can also be used to study lineage-specific functional shifts in protein families that result in changes in the patterns of site variability among subtrees.

  7. PALM: a paralleled and integrated framework for phylogenetic inference with automatic likelihood model selectors.

    Directory of Open Access Journals (Sweden)

    Shu-Hwa Chen

    Full Text Available BACKGROUND: Selecting an appropriate substitution model and deriving a tree topology for a given sequence set are essential in phylogenetic analysis. However, such time consuming, computationally intensive tasks rely on knowledge of substitution model theories and related expertise to run through all possible combinations of several separate programs. To ensure a thorough and efficient analysis and avert tedious manipulations of various programs, this work presents an intuitive framework, the phylogenetic reconstruction with automatic likelihood model selectors (PALM, with convincing, updated algorithms and a best-fit model selection mechanism for seamless phylogenetic analysis. METHODOLOGY: As an integrated framework of ClustalW, PhyML, MODELTEST, ProtTest, and several in-house programs, PALM evaluates the fitness of 56 substitution models for nucleotide sequences and 112 substitution models for protein sequences with scores in various criteria. The input for PALM can be either sequences in FASTA format or a sequence alignment file in PHYLIP format. To accelerate the computing of maximum likelihood and bootstrapping, this work integrates MPICH2/PhyML, PalmMonitor and Palm job controller across several machines with multiple processors and adopts the task parallelism approach. Moreover, an intuitive and interactive web component, PalmTree, is developed for displaying and operating the output tree with options of tree rooting, branches swapping, viewing the branch length values, and viewing bootstrapping score, as well as removing nodes to restart analysis iteratively. SIGNIFICANCE: The workflow of PALM is straightforward and coherent. Via a succinct, user-friendly interface, researchers unfamiliar with phylogenetic analysis can easily use this server to submit sequences, retrieve the output, and re-submit a job based on a previous result if some sequences are to be deleted or added for phylogenetic reconstruction. PALM results in an inference of

  8. Tapered composite likelihood for spatial max-stable models

    KAUST Repository

    Sang, Huiyan

    2014-05-01

    Spatial extreme value analysis is useful to environmental studies, in which extreme value phenomena are of interest and meaningful spatial patterns can be discerned. Max-stable process models are able to describe such phenomena. This class of models is asymptotically justified to characterize the spatial dependence among extremes. However, likelihood inference is challenging for such models because their corresponding joint likelihood is unavailable and only bivariate or trivariate distributions are known. In this paper, we propose a tapered composite likelihood approach by utilizing lower dimensional marginal likelihoods for inference on parameters of various max-stable process models. We consider a weighting strategy based on a "taper range" to exclude distant pairs or triples. The "optimal taper range" is selected to maximize various measures of the Godambe information associated with the tapered composite likelihood function. This method substantially reduces the computational cost and improves the efficiency over equally weighted composite likelihood estimators. We illustrate its utility with simulation experiments and an analysis of rainfall data in Switzerland.

  9. Tapered composite likelihood for spatial max-stable models

    KAUST Repository

    Sang, Huiyan; Genton, Marc G.

    2014-01-01

    Spatial extreme value analysis is useful to environmental studies, in which extreme value phenomena are of interest and meaningful spatial patterns can be discerned. Max-stable process models are able to describe such phenomena. This class of models is asymptotically justified to characterize the spatial dependence among extremes. However, likelihood inference is challenging for such models because their corresponding joint likelihood is unavailable and only bivariate or trivariate distributions are known. In this paper, we propose a tapered composite likelihood approach by utilizing lower dimensional marginal likelihoods for inference on parameters of various max-stable process models. We consider a weighting strategy based on a "taper range" to exclude distant pairs or triples. The "optimal taper range" is selected to maximize various measures of the Godambe information associated with the tapered composite likelihood function. This method substantially reduces the computational cost and improves the efficiency over equally weighted composite likelihood estimators. We illustrate its utility with simulation experiments and an analysis of rainfall data in Switzerland.

  10. Maximum likelihood-based analysis of photon arrival trajectories in single-molecule FRET

    Energy Technology Data Exchange (ETDEWEB)

    Waligorska, Marta [Adam Mickiewicz University, Faculty of Chemistry, Grunwaldzka 6, 60-780 Poznan (Poland); Molski, Andrzej, E-mail: amolski@amu.edu.pl [Adam Mickiewicz University, Faculty of Chemistry, Grunwaldzka 6, 60-780 Poznan (Poland)

    2012-07-25

    Highlights: Black-Right-Pointing-Pointer We study model selection and parameter recovery from single-molecule FRET experiments. Black-Right-Pointing-Pointer We examine the maximum likelihood-based analysis of two-color photon trajectories. Black-Right-Pointing-Pointer The number of observed photons determines the performance of the method. Black-Right-Pointing-Pointer For long trajectories, one can extract mean dwell times that are comparable to inter-photon times. -- Abstract: When two fluorophores (donor and acceptor) are attached to an immobilized biomolecule, anti-correlated fluctuations of the donor and acceptor fluorescence caused by Foerster resonance energy transfer (FRET) report on the conformational kinetics of the molecule. Here we assess the maximum likelihood-based analysis of donor and acceptor photon arrival trajectories as a method for extracting the conformational kinetics. Using computer generated data we quantify the accuracy and precision of parameter estimates and the efficiency of the Akaike information criterion (AIC) and the Bayesian information criterion (BIC) in selecting the true kinetic model. We find that the number of observed photons is the key parameter determining parameter estimation and model selection. For long trajectories, one can extract mean dwell times that are comparable to inter-photon times.

  11. Efficient fault tree handling - the Asea-Atom approach

    International Nuclear Information System (INIS)

    Ericsson, G.; Knochenhauer, M.; Mills, R.

    1985-01-01

    In recent years there has been a trend in Swedish Probabilistic Safety Analysis (PSA) work towards coordination of the tools and methods used, in order to facilitate exchange of information and review. Thus, standardized methods for fault tree drawing and basic event coding have been developed as well as a number of computer codes for fault tree handling. The computer code used by Asea-Atom is called SUPER-TREE. As indicated by the name, the key feature is the concept of one super tree containing all the information necessary in the fault tree analysis, i.e. system fault trees, sequence fault trees and component data base. The code has proved to allow great flexibility in the choice of level of detail in the analysis

  12. Likelihood functions for the analysis of single-molecule binned photon sequences

    Energy Technology Data Exchange (ETDEWEB)

    Gopich, Irina V., E-mail: irinag@niddk.nih.gov [Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 (United States)

    2012-03-02

    Graphical abstract: Folding of a protein with attached fluorescent dyes, the underlying conformational trajectory of interest, and the observed binned photon trajectory. Highlights: Black-Right-Pointing-Pointer A sequence of photon counts can be analyzed using a likelihood function. Black-Right-Pointing-Pointer The exact likelihood function for a two-state kinetic model is provided. Black-Right-Pointing-Pointer Several approximations are considered for an arbitrary kinetic model. Black-Right-Pointing-Pointer Improved likelihood functions are obtained to treat sequences of FRET efficiencies. - Abstract: We consider the analysis of a class of experiments in which the number of photons in consecutive time intervals is recorded. Sequence of photon counts or, alternatively, of FRET efficiencies can be studied using likelihood-based methods. For a kinetic model of the conformational dynamics and state-dependent Poisson photon statistics, the formalism to calculate the exact likelihood that this model describes such sequences of photons or FRET efficiencies is developed. Explicit analytic expressions for the likelihood function for a two-state kinetic model are provided. The important special case when conformational dynamics are so slow that at most a single transition occurs in a time bin is considered. By making a series of approximations, we eventually recover the likelihood function used in hidden Markov models. In this way, not only is insight gained into the range of validity of this procedure, but also an improved likelihood function can be obtained.

  13. Decision-Tree Program

    Science.gov (United States)

    Buntine, Wray

    1994-01-01

    IND computer program introduces Bayesian and Markov/maximum-likelihood (MML) methods and more-sophisticated methods of searching in growing trees. Produces more-accurate class-probability estimates important in applications like diagnosis. Provides range of features and styles with convenience for casual user, fine-tuning for advanced user or for those interested in research. Consists of four basic kinds of routines: data-manipulation, tree-generation, tree-testing, and tree-display. Written in C language.

  14. TreePOD: Sensitivity-Aware Selection of Pareto-Optimal Decision Trees.

    Science.gov (United States)

    Muhlbacher, Thomas; Linhardt, Lorenz; Moller, Torsten; Piringer, Harald

    2018-01-01

    Balancing accuracy gains with other objectives such as interpretability is a key challenge when building decision trees. However, this process is difficult to automate because it involves know-how about the domain as well as the purpose of the model. This paper presents TreePOD, a new approach for sensitivity-aware model selection along trade-offs. TreePOD is based on exploring a large set of candidate trees generated by sampling the parameters of tree construction algorithms. Based on this set, visualizations of quantitative and qualitative tree aspects provide a comprehensive overview of possible tree characteristics. Along trade-offs between two objectives, TreePOD provides efficient selection guidance by focusing on Pareto-optimal tree candidates. TreePOD also conveys the sensitivities of tree characteristics on variations of selected parameters by extending the tree generation process with a full-factorial sampling. We demonstrate how TreePOD supports a variety of tasks involved in decision tree selection and describe its integration in a holistic workflow for building and selecting decision trees. For evaluation, we illustrate a case study for predicting critical power grid states, and we report qualitative feedback from domain experts in the energy sector. This feedback suggests that TreePOD enables users with and without statistical background a confident and efficient identification of suitable decision trees.

  15. Zero-inflated Poisson model based likelihood ratio test for drug safety signal detection.

    Science.gov (United States)

    Huang, Lan; Zheng, Dan; Zalkikar, Jyoti; Tiwari, Ram

    2017-02-01

    In recent decades, numerous methods have been developed for data mining of large drug safety databases, such as Food and Drug Administration's (FDA's) Adverse Event Reporting System, where data matrices are formed by drugs such as columns and adverse events as rows. Often, a large number of cells in these data matrices have zero cell counts and some of them are "true zeros" indicating that the drug-adverse event pairs cannot occur, and these zero counts are distinguished from the other zero counts that are modeled zero counts and simply indicate that the drug-adverse event pairs have not occurred yet or have not been reported yet. In this paper, a zero-inflated Poisson model based likelihood ratio test method is proposed to identify drug-adverse event pairs that have disproportionately high reporting rates, which are also called signals. The maximum likelihood estimates of the model parameters of zero-inflated Poisson model based likelihood ratio test are obtained using the expectation and maximization algorithm. The zero-inflated Poisson model based likelihood ratio test is also modified to handle the stratified analyses for binary and categorical covariates (e.g. gender and age) in the data. The proposed zero-inflated Poisson model based likelihood ratio test method is shown to asymptotically control the type I error and false discovery rate, and its finite sample performance for signal detection is evaluated through a simulation study. The simulation results show that the zero-inflated Poisson model based likelihood ratio test method performs similar to Poisson model based likelihood ratio test method when the estimated percentage of true zeros in the database is small. Both the zero-inflated Poisson model based likelihood ratio test and likelihood ratio test methods are applied to six selected drugs, from the 2006 to 2011 Adverse Event Reporting System database, with varying percentages of observed zero-count cells.

  16. Efficiency of Individual Tree Detection Approaches Based on Light-Weight and Low-Cost UAS Imagery in Australian Savannas

    Directory of Open Access Journals (Sweden)

    Grigorijs Goldbergs

    2018-01-01

    Full Text Available The reliability of airborne light detection and ranging (LiDAR for delineating individual trees and estimating aboveground biomass (AGB has been proven in a diverse range of ecosystems, but can be difficult and costly to commission. Point clouds derived from structure from motion (SfM matching techniques obtained from unmanned aerial systems (UAS could be a feasible low-cost alternative to airborne LiDAR scanning for canopy parameter retrieval. This study assesses the extent to which SfM three-dimensional (3D point clouds—obtained from a light-weight mini-UAS quadcopter with an inexpensive consumer action GoPro camera—can efficiently and effectively detect individual trees, measure tree heights, and provide AGB estimates in Australian tropical savannas. Two well-established canopy maxima and watershed segmentation tree detection algorithms were tested on canopy height models (CHM derived from SfM imagery. The influence of CHM spatial resolution on tree detection accuracy was analysed, and the results were validated against existing high-resolution airborne LiDAR data. We found that the canopy maxima and watershed segmentation routines produced similar tree detection rates (~70% for dominant and co-dominant trees, but yielded low detection rates (<35% for suppressed and small trees due to poor representativeness in point clouds and overstory occlusion. Although airborne LiDAR provides higher tree detection rates and more accurate estimates of tree heights, we found SfM image matching to be an adequate low-cost alternative for the detection of dominant and co-dominant tree stands.

  17. The hydrological vulnerability of western North American boreal tree species based on ground-based observations of tree mortality

    Science.gov (United States)

    Hember, R. A.; Kurz, W. A.; Coops, N. C.

    2017-12-01

    Several studies indicate that climate change has increased rates of tree mortality, adversely affecting timber supply and carbon storage in western North American boreal forests. Statistical models of tree mortality can play a complimentary role in detecting and diagnosing forest change. Yet, such models struggle to address real-world complexity, including expectations that hydrological vulnerability arises from both drought stress and excess-water stress, and that these effects vary by species, tree size, and competitive status. Here, we describe models that predict annual probability of tree mortality (Pm) of common boreal tree species based on tree height (H), biomass of larger trees (BLT), soil water content (W), reference evapotranspiration (E), and two-way interactions. We show that interactions among H and hydrological variables are consistently significant. Vulnerability to extreme droughts consistently increases as H approaches maximum observed values of each species, while some species additionally show increasing vulnerability at low H. Some species additionally show increasing vulnerability to low W under high BLT, or increasing drought vulnerability under low BLT. These results suggest that vulnerability of trees to increasingly severe droughts depends on the hydraulic efficiency, competitive status, and microclimate of individual trees. Static simulations of Pm across a 1-km grid (i.e., with time-independent inputs of H, BLT, and species composition) indicate complex spatial patterns in the time trends during 1965-2014 and a mean change in Pm of 42 %. Lastly, we discuss how the size-dependence of hydrological vulnerability, in concert with increasingly severe drought events, may shape future responses of stand-level biomass production to continued warming and increasing carbon dioxide concentration in the region.

  18. Application of Goal Tree-Success Tree model as the knowledge-base of operator advisory systems

    International Nuclear Information System (INIS)

    Kim, I.S.; Modarres, M.

    1987-01-01

    The most important portion of an expert system development is the articulation of knowledge by the expert and its satisfactory formulation in a suitable knowledge representation scheme for mechanization by a computer. A 'deep knowledge' approach called Goal Tree-Success Tree model is devised to represent complex dynamic domain knowledge. This approach can hierarchically model the underlying principles of a given process domain (for example nuclear power plant operations domain). The Goal Tree-Success Tree can then be used to represent the knowledge-base and provide means of selecting an efficient search routine in the inference engine of an expert system. A prototype expert system has been developed to demonstrate the method. This expert system models the operation of a typical system used in the pressurized water reactors. The expert system is modeled for real-time operations if an interface between plant parameters and the expert system is established. The real-time operation provides an ability to quickly remedy minor disturbances that can quickly lead to a system malfunction or trip. A description of both the Goal Tree-Success Tree model and the prototype expert system is presented. (orig.)

  19. Analytical estimates and proof of the scale-free character of efficiency and improvement in Barabasi-Albert trees

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez-Bermejo, B. [Departamento de Fisica, Universidad Rey Juan Carlos, Escuela Superior de Ciencias Experimentales y Tecnologia, Edificio Departamental II, Calle Tulipan S/N, 28933-Mostoles-Madrid (Spain)], E-mail: benito.hernandez@urjc.es; Marco-Blanco, J. [Departamento de Fisica, Universidad Rey Juan Carlos, Escuela Superior de Ciencias Experimentales y Tecnologia, Edificio Departamental II, Calle Tulipan S/N, 28933-Mostoles-Madrid (Spain); Romance, M. [Departamento de Matematica Aplicada, Universidad Rey Juan Carlos, Escuela Superior de Ciencias Experimentales y Tecnologia, Edificio Departamental II, Calle Tulipan S/N, 28933-Mostoles-Madrid (Spain)

    2009-02-23

    Estimates for the efficiency of a tree are derived, leading to new analytical expressions for Barabasi-Albert trees efficiency. These expressions are used to investigate the dynamic behaviour of such networks. It is proved that the preferential attachment leads to an asymptotic conservation of efficiency as the Barabasi-Albert trees grow.

  20. Analytical estimates and proof of the scale-free character of efficiency and improvement in Barabasi-Albert trees

    International Nuclear Information System (INIS)

    Hernandez-Bermejo, B.; Marco-Blanco, J.; Romance, M.

    2009-01-01

    Estimates for the efficiency of a tree are derived, leading to new analytical expressions for Barabasi-Albert trees efficiency. These expressions are used to investigate the dynamic behaviour of such networks. It is proved that the preferential attachment leads to an asymptotic conservation of efficiency as the Barabasi-Albert trees grow

  1. Building Representative-Based Data Aggregation Tree in Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Yanfei Zheng

    2010-01-01

    Full Text Available Data aggregation is an essential operation to reduce energy consumption in large-scale wireless sensor networks (WSNs. A compromised node may forge an aggregation result and mislead base station into trusting a false reading. Efficient and secure aggregation scheme is critical in WSN applications due to the stringent resource constraints. In this paper, we propose a method to build up the representative-based aggregation tree in the WSNs such that the sensing data are aggregated along the route from the leaf cell to the root of the tree. In the cinema of large-scale and high-density sensor nodes, representative-based aggregation tree can reduce the data transmission overhead greatly by directed aggregation and cell-by-cell communications. It also provides security services including the integrity, freshness, and authentication, via detection mechanism in the cells.

  2. On Determining if Tree-based Networks Contain Fixed Trees.

    Science.gov (United States)

    Anaya, Maria; Anipchenko-Ulaj, Olga; Ashfaq, Aisha; Chiu, Joyce; Kaiser, Mahedi; Ohsawa, Max Shoji; Owen, Megan; Pavlechko, Ella; St John, Katherine; Suleria, Shivam; Thompson, Keith; Yap, Corrine

    2016-05-01

    We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is N based on T? We show that it is [Formula: see text]-hard to decide, by reduction from 3-Dimensional Matching (3DM) and further that the problem is fixed-parameter tractable.

  3. An Efficient Method of Vibration Diagnostics For Rotating Machinery Using a Decision Tree

    Directory of Open Access Journals (Sweden)

    Bo Suk Yang

    2000-01-01

    Full Text Available This paper describes an efficient method to automatize vibration diagnosis for rotating machinery using a decision tree, which is applicable to vibration diagnosis expert system. Decision tree is a widely known formalism for expressing classification knowledge and has been used successfully in many diverse areas such as character recognition, medical diagnosis, and expert systems, etc. In order to build a decision tree for vibration diagnosis, we have to define classes and attributes. A set of cases based on past experiences is also needed. This training set is inducted using a result-cause matrix newly developed in the present work instead of using a conventionally implemented cause-result matrix. This method was applied to diagnostics for various cases taken from published work. It is found that the present method predicts causes of the abnormal vibration for test cases with high reliability.

  4. Comparisons of likelihood and machine learning methods of individual classification

    Science.gov (United States)

    Guinand, B.; Topchy, A.; Page, K.S.; Burnham-Curtis, M. K.; Punch, W.F.; Scribner, K.T.

    2002-01-01

    Classification methods used in machine learning (e.g., artificial neural networks, decision trees, and k-nearest neighbor clustering) are rarely used with population genetic data. We compare different nonparametric machine learning techniques with parametric likelihood estimations commonly employed in population genetics for purposes of assigning individuals to their population of origin (“assignment tests”). Classifier accuracy was compared across simulated data sets representing different levels of population differentiation (low and high FST), number of loci surveyed (5 and 10), and allelic diversity (average of three or eight alleles per locus). Empirical data for the lake trout (Salvelinus namaycush) exhibiting levels of population differentiation comparable to those used in simulations were examined to further evaluate and compare classification methods. Classification error rates associated with artificial neural networks and likelihood estimators were lower for simulated data sets compared to k-nearest neighbor and decision tree classifiers over the entire range of parameters considered. Artificial neural networks only marginally outperformed the likelihood method for simulated data (0–2.8% lower error rates). The relative performance of each machine learning classifier improved relative likelihood estimators for empirical data sets, suggesting an ability to “learn” and utilize properties of empirical genotypic arrays intrinsic to each population. Likelihood-based estimation methods provide a more accessible option for reliable assignment of individuals to the population of origin due to the intricacies in development and evaluation of artificial neural networks. In recent years, characterization of highly polymorphic molecular markers such as mini- and microsatellites and development of novel methods of analysis have enabled researchers to extend investigations of ecological and evolutionary processes below the population level to the level of

  5. Drug safety data mining with a tree-based scan statistic.

    Science.gov (United States)

    Kulldorff, Martin; Dashevsky, Inna; Avery, Taliser R; Chan, Arnold K; Davis, Robert L; Graham, David; Platt, Richard; Andrade, Susan E; Boudreau, Denise; Gunter, Margaret J; Herrinton, Lisa J; Pawloski, Pamala A; Raebel, Marsha A; Roblin, Douglas; Brown, Jeffrey S

    2013-05-01

    In post-marketing drug safety surveillance, data mining can potentially detect rare but serious adverse events. Assessing an entire collection of drug-event pairs is traditionally performed on a predefined level of granularity. It is unknown a priori whether a drug causes a very specific or a set of related adverse events, such as mitral valve disorders, all valve disorders, or different types of heart disease. This methodological paper evaluates the tree-based scan statistic data mining method to enhance drug safety surveillance. We use a three-million-member electronic health records database from the HMO Research Network. Using the tree-based scan statistic, we assess the safety of selected antifungal and diabetes drugs, simultaneously evaluating overlapping diagnosis groups at different granularity levels, adjusting for multiple testing. Expected and observed adverse event counts were adjusted for age, sex, and health plan, producing a log likelihood ratio test statistic. Out of 732 evaluated disease groupings, 24 were statistically significant, divided among 10 non-overlapping disease categories. Five of the 10 signals are known adverse effects, four are likely due to confounding by indication, while one may warrant further investigation. The tree-based scan statistic can be successfully applied as a data mining tool in drug safety surveillance using observational data. The total number of statistical signals was modest and does not imply a causal relationship. Rather, data mining results should be used to generate candidate drug-event pairs for rigorous epidemiological studies to evaluate the individual and comparative safety profiles of drugs. Copyright © 2013 John Wiley & Sons, Ltd.

  6. Generalized Empirical Likelihood-Based Focused Information Criterion and Model Averaging

    Directory of Open Access Journals (Sweden)

    Naoya Sueishi

    2013-07-01

    Full Text Available This paper develops model selection and averaging methods for moment restriction models. We first propose a focused information criterion based on the generalized empirical likelihood estimator. We address the issue of selecting an optimal model, rather than a correct model, for estimating a specific parameter of interest. Then, this study investigates a generalized empirical likelihood-based model averaging estimator that minimizes the asymptotic mean squared error. A simulation study suggests that our averaging estimator can be a useful alternative to existing post-selection estimators.

  7. Design and Analysis of Self-Healing Tree-Based Hybrid Spectral Amplitude Coding OCDMA System

    Directory of Open Access Journals (Sweden)

    Waqas A. Imtiaz

    2017-01-01

    Full Text Available This paper presents an efficient tree-based hybrid spectral amplitude coding optical code division multiple access (SAC-OCDMA system that is able to provide high capacity transmission along with fault detection and restoration throughout the passive optical network (PON. Enhanced multidiagonal (EMD code is adapted to elevate system’s performance, which negates multiple access interference and associated phase induced intensity noise through efficient two-matrix structure. Moreover, system connection availability is enhanced through an efficient protection architecture with tree and star-ring topology at the feeder and distribution level, respectively. The proposed hybrid architecture aims to provide seamless transmission of information at minimum cost. Mathematical model based on Gaussian approximation is developed to analyze performance of the proposed setup, followed by simulation analysis for validation. It is observed that the proposed system supports 64 subscribers, operating at the data rates of 2.5 Gbps and above. Moreover, survivability and cost analysis in comparison with existing schemes show that the proposed tree-based hybrid SAC-OCDMA system provides the required redundancy at minimum cost of infrastructure and operation.

  8. Nonbinary tree-based phylogenetic networks

    OpenAIRE

    Jetten, Laura; van Iersel, Leo

    2016-01-01

    Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can for example represent gene transfer events. Such phylogenetic networks are called tree-based. Here, we consider two possible generalizations of this concept to nonbinary networks, which we call tree-based and st...

  9. Carbon Isotope discrimination in acacia auriculiformis - can it be used to select for higher water-use-efficiency in trees?

    International Nuclear Information System (INIS)

    Montagu, K.D.; Woo, K.C.; Puangchit, L.

    1999-01-01

    Full text: Determining the water-use-efficiency of trees in relation lo wood production is problematic due to the sheer size of the plant and the number of years taken to produce the wood. Indirect measures of water-use-efficiency, such as carbon isotope discrimination (Δ), are therefore attractive to tree breeders wishing to select for increased water-use-efficiency. To begin to evaluate the usefulness of Δ as a selection parameter for the tropical tree Acacia auriculiformis we addressed the following questions: 1. Within the tree canopy, how variable is Δ? 2. Is there any genotypic variation in Δ? and 3. Does water availability affect genotypic variation? To address these questions we sampled foliage from pot trials and field trials of A. auriculiformis ranging in age from 3 months lo 8 years in Australia and Thailand. In 16-18m high 8-year-old trees, canopy variation in Δ was large (P>0.01). Foliage Δ values increased down the tree from 22.0 %o at the top to 24.7 %o at the base. The decrease was rapid in the lop 3 m of the canopy thus considerable care must be taken to sampling foliage from the same position in the canopy. Genotype variations in Δ was observed in seedlings and 2 year-old trees (P>0.01) but not in 8 year-old trees (P=0.60). Where genotypic variation were observed the differences between the lowest and highest values were 2.2 - 3.6 %o. Reduced water availability decreased Δ values in both pot and field studies but not in a consistent way across seedlots. Thus it would appear that the Δ of trees grown under favourable conditions does not give an indication of the Δ value which will be obtained under water-limited conditions. This complicates the use of Δ as a screening method. We have clearly shown that genotype variation occurs in A. auriculiformis in both seedlings and young field-grown trees. Considerable care is required when sampling large trees, as variation in Δ within the tree can be as large as between genotypes. The challenge

  10. A likelihood-based time series modeling approach for application in dendrochronology to examine the growth-climate relations and forest disturbance history

    Science.gov (United States)

    A time series intervention analysis (TSIA) of dendrochronological data to infer the tree growth-climate-disturbance relations and forest disturbance history is described. Maximum likelihood is used to estimate the parameters of a structural time series model with components for ...

  11. Metrics for comparing neuronal tree shapes based on persistent homology.

    Directory of Open Access Journals (Sweden)

    Yanjie Li

    Full Text Available As more and more neuroanatomical data are made available through efforts such as NeuroMorpho.Org and FlyCircuit.org, the need to develop computational tools to facilitate automatic knowledge discovery from such large datasets becomes more urgent. One fundamental question is how best to compare neuron structures, for instance to organize and classify large collection of neurons. We aim to develop a flexible yet powerful framework to support comparison and classification of large collection of neuron structures efficiently. Specifically we propose to use a topological persistence-based feature vectorization framework. Existing methods to vectorize a neuron (i.e, convert a neuron to a feature vector so as to support efficient comparison and/or searching typically rely on statistics or summaries of morphometric information, such as the average or maximum local torque angle or partition asymmetry. These simple summaries have limited power in encoding global tree structures. Based on the concept of topological persistence recently developed in the field of computational topology, we vectorize each neuron structure into a simple yet informative summary. In particular, each type of information of interest can be represented as a descriptor function defined on the neuron tree, which is then mapped to a simple persistence-signature. Our framework can encode both local and global tree structure, as well as other information of interest (electrophysiological or dynamical measures, by considering multiple descriptor functions on the neuron. The resulting persistence-based signature is potentially more informative than simple statistical summaries (such as average/mean/max of morphometric quantities-Indeed, we show that using a certain descriptor function will give a persistence-based signature containing strictly more information than the classical Sholl analysis. At the same time, our framework retains the efficiency associated with treating neurons as

  12. LDR: A Package for Likelihood-Based Sufficient Dimension Reduction

    Directory of Open Access Journals (Sweden)

    R. Dennis Cook

    2011-03-01

    Full Text Available We introduce a new mlab software package that implements several recently proposed likelihood-based methods for sufficient dimension reduction. Current capabilities include estimation of reduced subspaces with a fixed dimension d, as well as estimation of d by use of likelihood-ratio testing, permutation testing and information criteria. The methods are suitable for preprocessing data for both regression and classification. Implementations of related estimators are also available. Although the software is more oriented to command-line operation, a graphical user interface is also provided for prototype computations.

  13. Dissimilarity-based classification of anatomical tree structures

    DEFF Research Database (Denmark)

    Sørensen, Lauge; Lo, Pechin Chien Pau; Dirksen, Asger

    2011-01-01

    A novel method for classification of abnormality in anatomical tree structures is presented. A tree is classified based on direct comparisons with other trees in a dissimilarity-based classification scheme. The pair-wise dissimilarity measure between two trees is based on a linear assignment betw...

  14. Dissimilarity-based classification of anatomical tree structures

    DEFF Research Database (Denmark)

    Sørensen, Lauge Emil Borch Laurs; Lo, Pechin Chien Pau; Dirksen, Asger

    2011-01-01

    A novel method for classification of abnormality in anatomical tree structures is presented. A tree is classified based on direct comparisons with other trees in a dissimilarity-based classification scheme. The pair-wise dissimilarity measure between two trees is based on a linear assignment...

  15. Likelihood-based inference for clustered line transect data

    DEFF Research Database (Denmark)

    Waagepetersen, Rasmus Plenge; Schweder, Tore

    The uncertainty in estimation of spatial animal density from line transect surveys depends on the degree of spatial clustering in the animal population. To quantify the clustering we model line transect data as independent thinnings of spatial shot-noise Cox processes. Likelihood-based inference...

  16. Likelihood-based inference for clustered line transect data

    DEFF Research Database (Denmark)

    Waagepetersen, Rasmus; Schweder, Tore

    2006-01-01

    The uncertainty in estimation of spatial animal density from line transect surveys depends on the degree of spatial clustering in the animal population. To quantify the clustering we model line transect data as independent thinnings of spatial shot-noise Cox processes. Likelihood-based inference...

  17. Ringing Artefact Reduction By An Efficient Likelihood Improvement Method

    Science.gov (United States)

    Fuderer, Miha

    1989-10-01

    In MR imaging, the extent of the acquired spatial frequencies of the object is necessarily finite. The resulting image shows artefacts caused by "truncation" of its Fourier components. These are known as Gibbs artefacts or ringing artefacts. These artefacts are particularly. visible when the time-saving reduced acquisition method is used, say, when scanning only the lowest 70% of the 256 data lines. Filtering the data results in loss of resolution. A method is described that estimates the high frequency data from the low-frequency data lines, with the likelihood of the image as criterion. It is a computationally very efficient method, since it requires practically only two extra Fourier transforms, in addition to the normal. reconstruction. The results of this method on MR images of human subjects are promising. Evaluations on a 70% acquisition image show about 20% decrease of the error energy after processing. "Error energy" is defined as the total power of the difference to a 256-data-lines reference image. The elimination of ringing artefacts then appears almost complete..

  18. Photo guide for estimating risk to hardwood trees during prescribed burning operations in eastern oak forests

    Science.gov (United States)

    Patrick H. Brose

    2009-01-01

    A field guide of 40 photographs of common hardwood trees of eastern oak forests and fuel loadings surrounding their bases. The guide contains instructions on how to rapidly assess a tree's likelihood to be damaged or killed by prescribed burning.

  19. Efficient Maximum Likelihood Estimation for Pedigree Data with the Sum-Product Algorithm.

    Science.gov (United States)

    Engelhardt, Alexander; Rieger, Anna; Tresch, Achim; Mansmann, Ulrich

    2016-01-01

    We analyze data sets consisting of pedigrees with age at onset of colorectal cancer (CRC) as phenotype. The occurrence of familial clusters of CRC suggests the existence of a latent, inheritable risk factor. We aimed to compute the probability of a family possessing this risk factor as well as the hazard rate increase for these risk factor carriers. Due to the inheritability of this risk factor, the estimation necessitates a costly marginalization of the likelihood. We propose an improved EM algorithm by applying factor graphs and the sum-product algorithm in the E-step. This reduces the computational complexity from exponential to linear in the number of family members. Our algorithm is as precise as a direct likelihood maximization in a simulation study and a real family study on CRC risk. For 250 simulated families of size 19 and 21, the runtime of our algorithm is faster by a factor of 4 and 29, respectively. On the largest family (23 members) in the real data, our algorithm is 6 times faster. We introduce a flexible and runtime-efficient tool for statistical inference in biomedical event data with latent variables that opens the door for advanced analyses of pedigree data. © 2017 S. Karger AG, Basel.

  20. Measurement of $b$-tagging Efficiency of $c$-jets in $t\\bar{t}$ Events Using a Likelihood Approach with the ATLAS Detector

    CERN Document Server

    The ATLAS collaboration

    2018-01-01

    A new technique is presented to measure the rate at which charm jets are tagged as $b$-jets based on a data sample of single lepton $t\\bar{t}$ events, where one of the $W$-bosons decays leptonically and the other decays to a $c$- and $s$-quark, or other quark pair combinations. The data sample was collected by the ATLAS detector at $\\sqrt{s} = 13$ TeV in 2015 and 2016 and corresponds to an integrated luminosity of 36 fb$^{-1}$. A kinematic likelihood technique is used to assign jets to the corresponding $t\\bar{t}$ decay products. A likelihood fit is used to extract the $c$-jet tagging efficiency from the pair of jets associated to $W$-boson decays. This new technique is used to calibrate the ATLAS MV2c10 $b$-tagging algorithm.

  1. ldr: An R Software Package for Likelihood-Based Su?cient Dimension Reduction

    Directory of Open Access Journals (Sweden)

    Kofi Placid Adragni

    2014-11-01

    Full Text Available In regression settings, a su?cient dimension reduction (SDR method seeks the core information in a p-vector predictor that completely captures its relationship with a response. The reduced predictor may reside in a lower dimension d < p, improving ability to visualize data and predict future observations, and mitigating dimensionality issues when carrying out further analysis. We introduce ldr, a new R software package that implements three recently proposed likelihood-based methods for SDR: covariance reduction, likelihood acquired directions, and principal fitted components. All three methods reduce the dimensionality of the data by pro jection into lower dimensional subspaces. The package also implements a variable screening method built upon principal ?tted components which makes use of ?exible basis functions to capture the dependencies between the predictors and the response. Examples are given to demonstrate likelihood-based SDR analyses using ldr, including estimation of the dimension of reduction subspaces and selection of basis functions. The ldr package provides a framework that we hope to grow into a comprehensive library of likelihood-based SDR methodologies.

  2. Phosphorus use efficiency of the gum arabi tree (Acacia senegal (L) Willd) in Sudan

    International Nuclear Information System (INIS)

    Elamin, K.H.; Mustafa, A.F.

    1996-01-01

    This study was conducted to identify gum arabic tree (Acacia senegal L. Willd) provenances with high efficiency for phosphorus uptake and use. Thirteen provenances were collected from different habitats with the gum belt of the Sudan. A preliminary trial was conducted during the period 1989-1992 at the Gezira Agricultural Research Station in Wad Medani. This study revealed that there are clear genotypic differences in phosphorus use efficiency, nitrogen yield and dry matter production. All the provenances tested also exhibited a high ability for survival under the dry climatic conditions as prevailing in the gum belt of Sudan. Based on differences in phosphorus use efficiency observed in the preliminary study, 4 provenances were selected for a detailed study. Provenance 11 and 2 represented the highly efficient group, provenance 7 the moderately efficient group and provenance 13 the low efficient group. The detailed study revealed that provenance 11 is superior to all others in terms of biomass production as well as in phosphorus use efficiency. Although the ability to take up phosphorus was low, this was compensated by having a high root length density enabling the tree to take up a quantity of phosphorus similar to that taken up by other provenances. The high ability to convert the absorbed phosphorus into a greater quantity of dry matter made this provenance the best in phosphorus use efficiency. These results suggest that provenance 11 may be a suitable candidate to be introduced into the gum belt of Sudan in support of its rehabilitation programme. (author). 13 refs, 4 figs, 5 tabs

  3. Phosphorus use efficiency of the gum arabi tree (Acacia senegal (L) Willd) in Sudan

    Energy Technology Data Exchange (ETDEWEB)

    Elamin, K H; Mustafa, A F [Gezira Agricultural Research Centre, Wad Medani (Sudan). Forestry Research Section

    1996-07-01

    This study was conducted to identify gum arabic tree (Acacia senegal L. Willd) provenances with high efficiency for phosphorus uptake and use. Thirteen provenances were collected from different habitats with the gum belt of the Sudan. A preliminary trial was conducted during the period 1989-1992 at the Gezira Agricultural Research Station in Wad Medani. This study revealed that there are clear genotypic differences in phosphorus use efficiency, nitrogen yield and dry matter production. All the provenances tested also exhibited a high ability for survival under the dry climatic conditions as prevailing in the gum belt of Sudan. Based on differences in phosphorus use efficiency observed in the preliminary study, 4 provenances were selected for a detailed study. Provenance 11 and 2 represented the highly efficient group, provenance 7 the moderately efficient group and provenance 13 the low efficient group. The detailed study revealed that provenance 11 is superior to all others in terms of biomass production as well as in phosphorus use efficiency. Although the ability to take up phosphorus was low, this was compensated by having a high root length density enabling the tree to take up a quantity of phosphorus similar to that taken up by other provenances. The high ability to convert the absorbed phosphorus into a greater quantity of dry matter made this provenance the best in phosphorus use efficiency. These results suggest that provenance 11 may be a suitable candidate to be introduced into the gum belt of Sudan in support of its rehabilitation programme. (author). 13 refs, 4 figs, 5 tabs.

  4. Lidar-based individual tree species classification using convolutional neural network

    Science.gov (United States)

    Mizoguchi, Tomohiro; Ishii, Akira; Nakamura, Hiroyuki; Inoue, Tsuyoshi; Takamatsu, Hisashi

    2017-06-01

    Terrestrial lidar is commonly used for detailed documentation in the field of forest inventory investigation. Recent improvements of point cloud processing techniques enabled efficient and precise computation of an individual tree shape parameters, such as breast-height diameter, height, and volume. However, tree species are manually specified by skilled workers to date. Previous works for automatic tree species classification mainly focused on aerial or satellite images, and few works have been reported for classification techniques using ground-based sensor data. Several candidate sensors can be considered for classification, such as RGB or multi/hyper spectral cameras. Above all candidates, we use terrestrial lidar because it can obtain high resolution point cloud in the dark forest. We selected bark texture for the classification criteria, since they clearly represent unique characteristics of each tree and do not change their appearance under seasonable variation and aged deterioration. In this paper, we propose a new method for automatic individual tree species classification based on terrestrial lidar using Convolutional Neural Network (CNN). The key component is the creation step of a depth image which well describe the characteristics of each species from a point cloud. We focus on Japanese cedar and cypress which cover the large part of domestic forest. Our experimental results demonstrate the effectiveness of our proposed method.

  5. A Walk-based Semantically Enriched Tree Kernel Over Distributed Word Representations

    DEFF Research Database (Denmark)

    Srivastava, Shashank; Hovy, Dirk

    2013-01-01

    We propose a walk-based graph kernel that generalizes the notion of tree-kernels to continuous spaces. Our proposed approach subsumes a general framework for word-similarity, and in particular, provides a flexible way to incorporate distributed representations. Using vector representations......, such an approach captures both distributional semantic similarities among words as well as the structural relations between them (encoded as the structure of the parse tree). We show an efficient formulation to compute this kernel using simple matrix multiplication operations. We present our results on three...

  6. Analysis of large fault trees based on functional decomposition

    International Nuclear Information System (INIS)

    Contini, Sergio; Matuzas, Vaidas

    2011-01-01

    With the advent of the Binary Decision Diagrams (BDD) approach in fault tree analysis, a significant enhancement has been achieved with respect to previous approaches, both in terms of efficiency and accuracy of the overall outcome of the analysis. However, the exponential increase of the number of nodes with the complexity of the fault tree may prevent the construction of the BDD. In these cases, the only way to complete the analysis is to reduce the complexity of the BDD by applying the truncation technique, which nevertheless implies the problem of estimating the truncation error or upper and lower bounds of the top-event unavailability. This paper describes a new method to analyze large coherent fault trees which can be advantageously applied when the working memory is not sufficient to construct the BDD. It is based on the decomposition of the fault tree into simpler disjoint fault trees containing a lower number of variables. The analysis of each simple fault tree is performed by using all the computational resources. The results from the analysis of all simpler fault trees are re-combined to obtain the results for the original fault tree. Two decomposition methods are herewith described: the first aims at determining the minimal cut sets (MCS) and the upper and lower bounds of the top-event unavailability; the second can be applied to determine the exact value of the top-event unavailability. Potentialities, limitations and possible variations of these methods will be discussed with reference to the results of their application to some complex fault trees.

  7. Analysis of large fault trees based on functional decomposition

    Energy Technology Data Exchange (ETDEWEB)

    Contini, Sergio, E-mail: sergio.contini@jrc.i [European Commission, Joint Research Centre, Institute for the Protection and Security of the Citizen, 21020 Ispra (Italy); Matuzas, Vaidas [European Commission, Joint Research Centre, Institute for the Protection and Security of the Citizen, 21020 Ispra (Italy)

    2011-03-15

    With the advent of the Binary Decision Diagrams (BDD) approach in fault tree analysis, a significant enhancement has been achieved with respect to previous approaches, both in terms of efficiency and accuracy of the overall outcome of the analysis. However, the exponential increase of the number of nodes with the complexity of the fault tree may prevent the construction of the BDD. In these cases, the only way to complete the analysis is to reduce the complexity of the BDD by applying the truncation technique, which nevertheless implies the problem of estimating the truncation error or upper and lower bounds of the top-event unavailability. This paper describes a new method to analyze large coherent fault trees which can be advantageously applied when the working memory is not sufficient to construct the BDD. It is based on the decomposition of the fault tree into simpler disjoint fault trees containing a lower number of variables. The analysis of each simple fault tree is performed by using all the computational resources. The results from the analysis of all simpler fault trees are re-combined to obtain the results for the original fault tree. Two decomposition methods are herewith described: the first aims at determining the minimal cut sets (MCS) and the upper and lower bounds of the top-event unavailability; the second can be applied to determine the exact value of the top-event unavailability. Potentialities, limitations and possible variations of these methods will be discussed with reference to the results of their application to some complex fault trees.

  8. Expressive Power of Tree and String Based Wrappers

    OpenAIRE

    Ikeda, Daisuke; Yamada, Yasuhiro; Hirokawa, Sachio

    2003-01-01

    There exist two types of wrappers: the string based wrapper such as the LR wrapper, and the tree based wrapper. A tree based wrapper designates extraction regions by nodes on the trees of semistructured documents. The tree based wrapper seems to be more powerful than the string based one. There exist, however, manyHTML documents on the Web such that a standard tree based wrapper fails to extract contents because they are structured by presentational tags, punctuation symbols, and white spaces...

  9. Efficient, reliable and fast high-level triggering using a bonsai boosted decision tree

    International Nuclear Information System (INIS)

    Gligorov, V V; Williams, M

    2013-01-01

    High-level triggering is a vital component of many modern particle physics experiments. This paper describes a modification to the standard boosted decision tree (BDT) classifier, the so-called bonsai BDT, that has the following important properties: it is more efficient than traditional cut-based approaches; it is robust against detector instabilities, and it is very fast. Thus, it is fit-for-purpose for the online running conditions faced by any large-scale data acquisition system.

  10. Likelihood-based Dynamic Factor Analysis for Measurement and Forecasting

    NARCIS (Netherlands)

    Jungbacker, B.M.J.P.; Koopman, S.J.

    2015-01-01

    We present new results for the likelihood-based analysis of the dynamic factor model. The latent factors are modelled by linear dynamic stochastic processes. The idiosyncratic disturbance series are specified as autoregressive processes with mutually correlated innovations. The new results lead to

  11. FB-Tree: A B+-Tree for Flash-Based SSDs

    DEFF Research Database (Denmark)

    Jørgensen, Martin V.; Rasmussen, René B.; Saltenis, Simonas

    2011-01-01

    Due to their many advantages, flash-based SSDs (Solid-State Drives) have become a mainstream alternative to magnetic disks for database servers. Nevertheless, database systems, designed and optimized for magnetic disks, still do not fully exploit all the benefits of the new technology. We propose....... As a consequence, the FB-tree outperforms a regular B+-tree in all scenarios tested. For instance, the throughput of a random workload of 75% updates increases by a factor of three using only two times the space of the B+-tree....

  12. A structurally based analytic model for estimation of biomass and fuel loads of woodland trees

    Science.gov (United States)

    Robin J. Tausch

    2009-01-01

    Allometric/structural relationships in tree crowns are a consequence of the physical, physiological, and fluid conduction processes of trees, which control the distribution, efficient support, and growth of foliage in the crown. The structural consequences of these processes are used to develop an analytic model based on the concept of branch orders. A set of...

  13. A joint individual-based model coupling growth and mortality reveals that tree vigor is a key component of tropical forest dynamics.

    Science.gov (United States)

    Aubry-Kientz, Mélaine; Rossi, Vivien; Boreux, Jean-Jacques; Hérault, Bruno

    2015-06-01

    Tree vigor is often used as a covariate when tree mortality is predicted from tree growth in tropical forest dynamic models, but it is rarely explicitly accounted for in a coherent modeling framework. We quantify tree vigor at the individual tree level, based on the difference between expected and observed growth. The available methods to join nonlinear tree growth and mortality processes are not commonly used by forest ecologists so that we develop an inference methodology based on an MCMC approach, allowing us to sample the parameters of the growth and mortality model according to their posterior distribution using the joint model likelihood. We apply our framework to a set of data on the 20-year dynamics of a forest in Paracou, French Guiana, taking advantage of functional trait-based growth and mortality models already developed independently. Our results showed that growth and mortality are intimately linked and that the vigor estimator is an essential predictor of mortality, highlighting that trees growing more than expected have a far lower probability of dying. Our joint model methodology is sufficiently generic to be used to join two longitudinal and punctual linked processes and thus may be applied to a wide range of growth and mortality models. In the context of global changes, such joint models are urgently needed in tropical forests to analyze, and then predict, the effects of the ongoing changes on the tree dynamics in hyperdiverse tropical forests.

  14. Efficient random access high resolution region-of-interest (ROI) image retrieval using backward coding of wavelet trees (BCWT)

    Science.gov (United States)

    Corona, Enrique; Nutter, Brian; Mitra, Sunanda; Guo, Jiangling; Karp, Tanja

    2008-03-01

    Efficient retrieval of high quality Regions-Of-Interest (ROI) from high resolution medical images is essential for reliable interpretation and accurate diagnosis. Random access to high quality ROI from codestreams is becoming an essential feature in many still image compression applications, particularly in viewing diseased areas from large medical images. This feature is easier to implement in block based codecs because of the inherent spatial independency of the code blocks. This independency implies that the decoding order of the blocks is unimportant as long as the position for each is properly identified. In contrast, wavelet-tree based codecs naturally use some interdependency that exploits the decaying spectrum model of the wavelet coefficients. Thus one must keep track of the decoding order from level to level with such codecs. We have developed an innovative multi-rate image subband coding scheme using "Backward Coding of Wavelet Trees (BCWT)" which is fast, memory efficient, and resolution scalable. It offers far less complexity than many other existing codecs including both, wavelet-tree, and block based algorithms. The ROI feature in BCWT is implemented through a transcoder stage that generates a new BCWT codestream containing only the information associated with the user-defined ROI. This paper presents an efficient technique that locates a particular ROI within the BCWT coded domain, and decodes it back to the spatial domain. This technique allows better access and proper identification of pathologies in high resolution images since only a small fraction of the codestream is required to be transmitted and analyzed.

  15. TreePics: visualizing trees with pictures

    Directory of Open Access Journals (Sweden)

    Nicolas Puillandre

    2017-09-01

    Full Text Available While many programs are available to edit phylogenetic trees, associating pictures with branch tips in an efficient and automatic way is not an available option. Here, we present TreePics, a standalone software that uses a web browser to visualize phylogenetic trees in Newick format and that associates pictures (typically, pictures of the voucher specimens to the tip of each branch. Pictures are visualized as thumbnails and can be enlarged by a mouse rollover. Further, several pictures can be selected and displayed in a separate window for visual comparison. TreePics works either online or in a full standalone version, where it can display trees with several thousands of pictures (depending on the memory available. We argue that TreePics can be particularly useful in a preliminary stage of research, such as to quickly detect conflicts between a DNA-based phylogenetic tree and morphological variation, that may be due to contamination that needs to be removed prior to final analyses, or the presence of species complexes.

  16. High-order Composite Likelihood Inference for Max-Stable Distributions and Processes

    KAUST Repository

    Castruccio, Stefano; Huser, Raphaë l; Genton, Marc G.

    2015-01-01

    In multivariate or spatial extremes, inference for max-stable processes observed at a large collection of locations is a very challenging problem in computational statistics, and current approaches typically rely on less expensive composite likelihoods constructed from small subsets of data. In this work, we explore the limits of modern state-of-the-art computational facilities to perform full likelihood inference and to efficiently evaluate high-order composite likelihoods. With extensive simulations, we assess the loss of information of composite likelihood estimators with respect to a full likelihood approach for some widely-used multivariate or spatial extreme models, we discuss how to choose composite likelihood truncation to improve the efficiency, and we also provide recommendations for practitioners. This article has supplementary material online.

  17. High-order Composite Likelihood Inference for Max-Stable Distributions and Processes

    KAUST Repository

    Castruccio, Stefano

    2015-09-29

    In multivariate or spatial extremes, inference for max-stable processes observed at a large collection of locations is a very challenging problem in computational statistics, and current approaches typically rely on less expensive composite likelihoods constructed from small subsets of data. In this work, we explore the limits of modern state-of-the-art computational facilities to perform full likelihood inference and to efficiently evaluate high-order composite likelihoods. With extensive simulations, we assess the loss of information of composite likelihood estimators with respect to a full likelihood approach for some widely-used multivariate or spatial extreme models, we discuss how to choose composite likelihood truncation to improve the efficiency, and we also provide recommendations for practitioners. This article has supplementary material online.

  18. Explaining growth of individual trees: Light interception and efficiency of light use by Eucalyptus at four sites in Brazil

    Science.gov (United States)

    Dan Binkley; Jose Luiz Stape; William L. Bauerle; Michael G. Ryan

    2010-01-01

    The growth of wood in trees and forests depends on the acquisition of resources (light, water, and nutrients), the efficiency of using resources for photosynthesis, and subsequent partitioning to woody tissues. Patterns of efficiency over time for individual trees, or between trees at one time, result from changes in rates photosynthesis and shifts in...

  19. Geodesic atlas-based labeling of anatomical trees

    DEFF Research Database (Denmark)

    Feragen, Aasa; Petersen, Jens; Owen, Megan

    2015-01-01

    We present a fast and robust atlas-based algorithm for labeling airway trees, using geodesic distances in a geometric tree-space. Possible branch label configurations for an unlabeled airway tree are evaluated using distances to a training set of labeled airway trees. In tree-space, airway tree t...... equally complete airway trees, and comparable in performance to that of experts in pulmonary medicine, emphasizing the suitability of the labeling algorithm for clinical use....

  20. A Tree Based Broadcast Scheme for (m, k)-firm Real-Time Stream in Wireless Sensor Networks.

    Science.gov (United States)

    Park, HoSung; Kim, Beom-Su; Kim, Kyong Hoon; Shah, Babar; Kim, Ki-Il

    2017-11-09

    Recently, various unicast routing protocols have been proposed to deliver measured data from the sensor node to the sink node within the predetermined deadline in wireless sensor networks. In parallel with their approaches, some applications demand the specific service, which is based on broadcast to all nodes within the deadline, the feasible real-time traffic model and improvements in energy efficiency. However, current protocols based on either flooding or one-to-one unicast cannot meet the above requirements entirely. Moreover, as far as the authors know, there is no study for the real-time broadcast protocol to support the application-specific traffic model in WSN yet. Based on the above analysis, in this paper, we propose a new ( m , k )-firm-based Real-time Broadcast Protocol (FRBP) by constructing a broadcast tree to satisfy the ( m , k )-firm, which is applicable to the real-time model in resource-constrained WSNs. The broadcast tree in FRBP is constructed by the distance-based priority scheme, whereas energy efficiency is improved by selecting as few as nodes on a tree possible. To overcome the unstable network environment, the recovery scheme invokes rapid partial tree reconstruction in order to designate another node as the parent on a tree according to the measured ( m , k )-firm real-time condition and local states monitoring. Finally, simulation results are given to demonstrate the superiority of FRBP compared to the existing schemes in terms of average deadline missing ratio, average throughput and energy consumption.

  1. Semi-Automatic Anatomical Tree Matching for Landmark-Based Elastic Registration of Liver Volumes

    Directory of Open Access Journals (Sweden)

    Klaus Drechsler

    2010-01-01

    Full Text Available One promising approach to register liver volume acquisitions is based on the branching points of the vessel trees as anatomical landmarks inherently available in the liver. Automated tree matching algorithms were proposed to automatically find pair-wise correspondences between two vessel trees. However, to the best of our knowledge, none of the existing automatic methods are completely error free. After a review of current literature and methodologies on the topic, we propose an efficient interaction method that can be employed to support tree matching algorithms with important pre-selected correspondences or after an automatic matching to manually correct wrongly matched nodes. We used this method in combination with a promising automatic tree matching algorithm also presented in this work. The proposed method was evaluated by 4 participants and a CT dataset that we used to derive multiple artificial datasets.

  2. Heterogeneous Compression of Large Collections of Evolutionary Trees.

    Science.gov (United States)

    Matthews, Suzanne J

    2015-01-01

    Compressing heterogeneous collections of trees is an open problem in computational phylogenetics. In a heterogeneous tree collection, each tree can contain a unique set of taxa. An ideal compression method would allow for the efficient archival of large tree collections and enable scientists to identify common evolutionary relationships over disparate analyses. In this paper, we extend TreeZip to compress heterogeneous collections of trees. TreeZip is the most efficient algorithm for compressing homogeneous tree collections. To the best of our knowledge, no other domain-based compression algorithm exists for large heterogeneous tree collections or enable their rapid analysis. Our experimental results indicate that TreeZip averages 89.03 percent (72.69 percent) space savings on unweighted (weighted) collections of trees when the level of heterogeneity in a collection is moderate. The organization of the TRZ file allows for efficient computations over heterogeneous data. For example, consensus trees can be computed in mere seconds. Lastly, combining the TreeZip compressed (TRZ) file with general-purpose compression yields average space savings of 97.34 percent (81.43 percent) on unweighted (weighted) collections of trees. Our results lead us to believe that TreeZip will prove invaluable in the efficient archival of tree collections, and enables scientists to develop novel methods for relating heterogeneous collections of trees.

  3. An efficient connected dominating set algorithm in WSNs based on the induced tree of the crossed cube

    Directory of Open Access Journals (Sweden)

    Zhang Jing

    2015-06-01

    Full Text Available The connected dominating set (CDS has become a well-known approach for constructing a virtual backbone in wireless sensor networks. Then traffic can forwarded by the virtual backbone and other nodes turn off their radios to save energy. Furthermore, a smaller CDS incurs fewer interference problems. However, constructing a minimum CDS is an NP-hard problem, and thus most researchers concentrate on how to derive approximate algorithms. In this paper, a novel algorithm based on the induced tree of the crossed cube (ITCC is presented. The ITCC is to find a maximal independent set (MIS, which is based on building an induced tree of the crossed cube network, and then to connect the MIS nodes to form a CDS. The priority of an induced tree is determined according to a new parameter, the degree of the node in the square of a graph. This paper presents the proof that the ITCC generates a CDS with a lower approximation ratio. Furthermore, it is proved that the cardinality of the induced trees is a Fibonacci sequence, and an upper bound to the number of the dominating set is established. The simulations show that the algorithm provides the smallest CDS size compared with some other traditional algorithms.

  4. A GIS-based tool for estimating tree canopy cover on fixed-radius plots using high-resolution aerial imagery

    Science.gov (United States)

    Sara A. Goeking; Greg C. Liknes; Erik Lindblom; John Chase; Dennis M. Jacobs; Robert. Benton

    2012-01-01

    Recent changes to the Forest Inventory and Analysis (FIA) Program's definition of forest land precipitated the development of a geographic information system (GIS)-based tool for efficiently estimating tree canopy cover for all FIA plots. The FIA definition of forest land has shifted from a density-related criterion based on stocking to a 10 percent tree canopy...

  5. Efficient simulation and likelihood methods for non-neutral multi-allele models.

    Science.gov (United States)

    Joyce, Paul; Genz, Alan; Buzbas, Erkan Ozge

    2012-06-01

    Throughout the 1980s, Simon Tavaré made numerous significant contributions to population genetics theory. As genetic data, in particular DNA sequence, became more readily available, a need to connect population-genetic models to data became the central issue. The seminal work of Griffiths and Tavaré (1994a , 1994b , 1994c) was among the first to develop a likelihood method to estimate the population-genetic parameters using full DNA sequences. Now, we are in the genomics era where methods need to scale-up to handle massive data sets, and Tavaré has led the way to new approaches. However, performing statistical inference under non-neutral models has proved elusive. In tribute to Simon Tavaré, we present an article in spirit of his work that provides a computationally tractable method for simulating and analyzing data under a class of non-neutral population-genetic models. Computational methods for approximating likelihood functions and generating samples under a class of allele-frequency based non-neutral parent-independent mutation models were proposed by Donnelly, Nordborg, and Joyce (DNJ) (Donnelly et al., 2001). DNJ (2001) simulated samples of allele frequencies from non-neutral models using neutral models as auxiliary distribution in a rejection algorithm. However, patterns of allele frequencies produced by neutral models are dissimilar to patterns of allele frequencies produced by non-neutral models, making the rejection method inefficient. For example, in some cases the methods in DNJ (2001) require 10(9) rejections before a sample from the non-neutral model is accepted. Our method simulates samples directly from the distribution of non-neutral models, making simulation methods a practical tool to study the behavior of the likelihood and to perform inference on the strength of selection.

  6. Improvement of testing and maintenance based on fault tree analysis

    International Nuclear Information System (INIS)

    Cepin, M.

    2000-01-01

    Testing and maintenance of safety equipment is an important issue, which significantly contributes to safe and efficient operation of a nuclear power plant. In this paper a method, which extends the classical fault tree with time, is presented. Its mathematical model is represented by a set of equations, which include time requirements defined in the house event matrix. House events matrix is a representation of house events switched on and off through the discrete points of time. It includes house events, which timely switch on and off parts of the fault tree in accordance with the status of the plant configuration. Time dependent top event probability is calculated by the fault tree evaluations. Arrangement of components outages is determined on base of minimization of mean system unavailability. The results show that application of the method may improve the time placement of testing and maintenance activities of safety equipment. (author)

  7. treeman: an R package for efficient and intuitive manipulation of phylogenetic trees.

    Science.gov (United States)

    Bennett, Dominic J; Sutton, Mark D; Turvey, Samuel T

    2017-01-07

    Phylogenetic trees are hierarchical structures used for representing the inter-relationships between biological entities. They are the most common tool for representing evolution and are essential to a range of fields across the life sciences. The manipulation of phylogenetic trees-in terms of adding or removing tips-is often performed by researchers not just for reasons of management but also for performing simulations in order to understand the processes of evolution. Despite this, the most common programming language among biologists, R, has few class structures well suited to these tasks. We present an R package that contains a new class, called TreeMan, for representing the phylogenetic tree. This class has a list structure allowing phylogenetic trees to be manipulated more efficiently. Computational running times are reduced because of the ready ability to vectorise and parallelise methods. Development is also improved due to fewer lines of code being required for performing manipulation processes. We present three use cases-pinning missing taxa to a supertree, simulating evolution with a tree-growth model and detecting significant phylogenetic turnover-that demonstrate the new package's speed and simplicity.

  8. Credibilistic multi-period portfolio optimization based on scenario tree

    Science.gov (United States)

    Mohebbi, Negin; Najafi, Amir Abbas

    2018-02-01

    In this paper, we consider a multi-period fuzzy portfolio optimization model with considering transaction costs and the possibility of risk-free investment. We formulate a bi-objective mean-VaR portfolio selection model based on the integration of fuzzy credibility theory and scenario tree in order to dealing with the markets uncertainty. The scenario tree is also a proper method for modeling multi-period portfolio problems since the length and continuity of their horizon. We take the return and risk as well cardinality, threshold, class, and liquidity constraints into consideration for further compliance of the model with reality. Then, an interactive dynamic programming method, which is based on a two-phase fuzzy interactive approach, is employed to solve the proposed model. In order to verify the proposed model, we present an empirical application in NYSE under different circumstances. The results show that the consideration of data uncertainty and other real-world assumptions lead to more practical and efficient solutions.

  9. Maximum likelihood-based analysis of single-molecule photon arrival trajectories

    Science.gov (United States)

    Hajdziona, Marta; Molski, Andrzej

    2011-02-01

    In this work we explore the statistical properties of the maximum likelihood-based analysis of one-color photon arrival trajectories. This approach does not involve binning and, therefore, all of the information contained in an observed photon strajectory is used. We study the accuracy and precision of parameter estimates and the efficiency of the Akaike information criterion and the Bayesian information criterion (BIC) in selecting the true kinetic model. We focus on the low excitation regime where photon trajectories can be modeled as realizations of Markov modulated Poisson processes. The number of observed photons is the key parameter in determining model selection and parameter estimation. For example, the BIC can select the true three-state model from competing two-, three-, and four-state kinetic models even for relatively short trajectories made up of 2 × 103 photons. When the intensity levels are well-separated and 104 photons are observed, the two-state model parameters can be estimated with about 10% precision and those for a three-state model with about 20% precision.

  10. Maximum likelihood-based analysis of single-molecule photon arrival trajectories.

    Science.gov (United States)

    Hajdziona, Marta; Molski, Andrzej

    2011-02-07

    In this work we explore the statistical properties of the maximum likelihood-based analysis of one-color photon arrival trajectories. This approach does not involve binning and, therefore, all of the information contained in an observed photon strajectory is used. We study the accuracy and precision of parameter estimates and the efficiency of the Akaike information criterion and the Bayesian information criterion (BIC) in selecting the true kinetic model. We focus on the low excitation regime where photon trajectories can be modeled as realizations of Markov modulated Poisson processes. The number of observed photons is the key parameter in determining model selection and parameter estimation. For example, the BIC can select the true three-state model from competing two-, three-, and four-state kinetic models even for relatively short trajectories made up of 2 × 10(3) photons. When the intensity levels are well-separated and 10(4) photons are observed, the two-state model parameters can be estimated with about 10% precision and those for a three-state model with about 20% precision.

  11. ColorTree: a batch customization tool for phylogenic trees.

    Science.gov (United States)

    Chen, Wei-Hua; Lercher, Martin J

    2009-07-31

    Genome sequencing projects and comparative genomics studies typically aim to trace the evolutionary history of large gene sets, often requiring human inspection of hundreds of phylogenetic trees. If trees are checked for compatibility with an explicit null hypothesis (e.g., the monophyly of certain groups), this daunting task is greatly facilitated by an appropriate coloring scheme. In this note, we introduce ColorTree, a simple yet powerful batch customization tool for phylogenic trees. Based on pattern matching rules, ColorTree applies a set of customizations to an input tree file, e.g., coloring labels or branches. The customized trees are saved to an output file, which can then be viewed and further edited by Dendroscope (a freely available tree viewer). ColorTree runs on any Perl installation as a stand-alone command line tool, and its application can thus be easily automated. This way, hundreds of phylogenic trees can be customized for easy visual inspection in a matter of minutes. ColorTree allows efficient and flexible visual customization of large tree sets through the application of a user-supplied configuration file to multiple tree files.

  12. A Tree Based Broadcast Scheme for (m, k-firm Real-Time Stream in Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    HoSung Park

    2017-11-01

    Full Text Available Recently, various unicast routing protocols have been proposed to deliver measured data from the sensor node to the sink node within the predetermined deadline in wireless sensor networks. In parallel with their approaches, some applications demand the specific service, which is based on broadcast to all nodes within the deadline, the feasible real-time traffic model and improvements in energy efficiency. However, current protocols based on either flooding or one-to-one unicast cannot meet the above requirements entirely. Moreover, as far as the authors know, there is no study for the real-time broadcast protocol to support the application-specific traffic model in WSN yet. Based on the above analysis, in this paper, we propose a new (m, k-firm-based Real-time Broadcast Protocol (FRBP by constructing a broadcast tree to satisfy the (m, k-firm, which is applicable to the real-time model in resource-constrained WSNs. The broadcast tree in FRBP is constructed by the distance-based priority scheme, whereas energy efficiency is improved by selecting as few as nodes on a tree possible. To overcome the unstable network environment, the recovery scheme invokes rapid partial tree reconstruction in order to designate another node as the parent on a tree according to the measured (m, k-firm real-time condition and local states monitoring. Finally, simulation results are given to demonstrate the superiority of FRBP compared to the existing schemes in terms of average deadline missing ratio, average throughput and energy consumption.

  13. MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

    Science.gov (United States)

    Tamura, Koichiro; Peterson, Daniel; Peterson, Nicholas; Stecher, Glen; Nei, Masatoshi; Kumar, Sudhir

    2011-01-01

    Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net. PMID:21546353

  14. One tree to link them all: a phylogenetic dataset for the European tetrapoda.

    Science.gov (United States)

    Roquet, Cristina; Lavergne, Sébastien; Thuiller, Wilfried

    2014-08-08

    Since the ever-increasing availability of phylogenetic informative data, the last decade has seen an upsurge of ecological studies incorporating information on evolutionary relationships among species. However, detailed species-level phylogenies are still lacking for many large groups and regions, which are necessary for comprehensive large-scale eco-phylogenetic analyses. Here, we provide a dataset of 100 dated phylogenetic trees for all European tetrapods based on a mixture of supermatrix and supertree approaches. Phylogenetic inference was performed separately for each of the main Tetrapoda groups of Europe except mammals (i.e. amphibians, birds, squamates and turtles) by means of maximum likelihood (ML) analyses of supermatrix applying a tree constraint at the family (amphibians and squamates) or order (birds and turtles) levels based on consensus knowledge. For each group, we inferred 100 ML trees to be able to provide a phylogenetic dataset that accounts for phylogenetic uncertainty, and assessed node support with bootstrap analyses. Each tree was dated using penalized-likelihood and fossil calibration. The trees obtained were well-supported by existing knowledge and previous phylogenetic studies. For mammals, we modified the most complete supertree dataset available on the literature to include a recent update of the Carnivora clade. As a final step, we merged the phylogenetic trees of all groups to obtain a set of 100 phylogenetic trees for all European Tetrapoda species for which data was available (91%). We provide this phylogenetic dataset (100 chronograms) for the purpose of comparative analyses, macro-ecological or community ecology studies aiming to incorporate phylogenetic information while accounting for phylogenetic uncertainty.

  15. Advanced hybrid query tree algorithm based on slotted backoff mechanism in RFID

    Directory of Open Access Journals (Sweden)

    XIE Xiaohui

    2013-12-01

    Full Text Available The merits of performance quality for a RFID system are determined by the effectiveness of tag anti-collision algorithm.Many algorithms for RFID system of tag identification have been proposed,but they all have obvious weaknesses,such as slow speed of identification,unstable and so on.The existing algorithms can be divided into two groups,one is based on ALOHA and another is based on query tree.This article is based on the hybrid query tree algorithm,combined with a slotted backoff mechanism and a specific encoding (Manchester encoding.The number of value“1” in every three consecutive bits of tags is used to determine the tag response time slots,which will greatly reduce the time slot of the collision and improve the recognition efficiency.

  16. Tree-Based Unrooted Phylogenetic Networks.

    Science.gov (United States)

    Francis, A; Huber, K T; Moulton, V

    2018-02-01

    Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An unrooted phylogenetic network on a non-empty, finite set X of taxa, or network, is a connected, simple graph in which every vertex has degree 1 or 3 and whose leaf set is X. It is called a phylogenetic tree if the underlying graph is a tree. In this paper we consider properties of tree-based networks, that is, networks that can be constructed by adding edges into a phylogenetic tree. We show that although they have some properties in common with their rooted analogues which have recently drawn much attention in the literature, they have some striking differences in terms of both their structural and computational properties. We expect that our results could eventually have applications to, for example, detecting horizontal gene transfer or hybridization which are important factors in the evolution of many organisms.

  17. Logic of likelihood

    International Nuclear Information System (INIS)

    Wall, M.J.W.

    1992-01-01

    The notion of open-quotes probabilityclose quotes is generalized to that of open-quotes likelihood,close quotes and a natural logical structure is shown to exist for any physical theory which predicts likelihoods. Two physically based axioms are given for this logical structure to form an orthomodular poset, with an order-determining set of states. The results strengthen the basis of the quantum logic approach to axiomatic quantum theory. 25 refs

  18. Composite likelihood estimation of demographic parameters

    Directory of Open Access Journals (Sweden)

    Garrigan Daniel

    2009-11-01

    Full Text Available Abstract Background Most existing likelihood-based methods for fitting historical demographic models to DNA sequence polymorphism data to do not scale feasibly up to the level of whole-genome data sets. Computational economies can be achieved by incorporating two forms of pseudo-likelihood: composite and approximate likelihood methods. Composite likelihood enables scaling up to large data sets because it takes the product of marginal likelihoods as an estimator of the likelihood of the complete data set. This approach is especially useful when a large number of genomic regions constitutes the data set. Additionally, approximate likelihood methods can reduce the dimensionality of the data by summarizing the information in the original data by either a sufficient statistic, or a set of statistics. Both composite and approximate likelihood methods hold promise for analyzing large data sets or for use in situations where the underlying demographic model is complex and has many parameters. This paper considers a simple demographic model of allopatric divergence between two populations, in which one of the population is hypothesized to have experienced a founder event, or population bottleneck. A large resequencing data set from human populations is summarized by the joint frequency spectrum, which is a matrix of the genomic frequency spectrum of derived base frequencies in two populations. A Bayesian Metropolis-coupled Markov chain Monte Carlo (MCMCMC method for parameter estimation is developed that uses both composite and likelihood methods and is applied to the three different pairwise combinations of the human population resequence data. The accuracy of the method is also tested on data sets sampled from a simulated population model with known parameters. Results The Bayesian MCMCMC method also estimates the ratio of effective population size for the X chromosome versus that of the autosomes. The method is shown to estimate, with reasonable

  19. Rapid maximum likelihood ancestral state reconstruction of continuous characters: A rerooting-free algorithm.

    Science.gov (United States)

    Goolsby, Eric W

    2017-04-01

    Ancestral state reconstruction is a method used to study the evolutionary trajectories of quantitative characters on phylogenies. Although efficient methods for univariate ancestral state reconstruction under a Brownian motion model have been described for at least 25 years, to date no generalization has been described to allow more complex evolutionary models, such as multivariate trait evolution, non-Brownian models, missing data, and within-species variation. Furthermore, even for simple univariate Brownian motion models, most phylogenetic comparative R packages compute ancestral states via inefficient tree rerooting and full tree traversals at each tree node, making ancestral state reconstruction extremely time-consuming for large phylogenies. Here, a computationally efficient method for fast maximum likelihood ancestral state reconstruction of continuous characters is described. The algorithm has linear complexity relative to the number of species and outperforms the fastest existing R implementations by several orders of magnitude. The described algorithm is capable of performing ancestral state reconstruction on a 1,000,000-species phylogeny in fewer than 2 s using a standard laptop, whereas the next fastest R implementation would take several days to complete. The method is generalizable to more complex evolutionary models, such as phylogenetic regression, within-species variation, non-Brownian evolutionary models, and multivariate trait evolution. Because this method enables fast repeated computations on phylogenies of virtually any size, implementation of the described algorithm can drastically alleviate the computational burden of many otherwise prohibitively time-consuming tasks requiring reconstruction of ancestral states, such as phylogenetic imputation of missing data, bootstrapping procedures, Expectation-Maximization algorithms, and Bayesian estimation. The described ancestral state reconstruction algorithm is implemented in the Rphylopars

  20. A well-resolved phylogeny of the trees of Puerto Rico based on DNA barcode sequence data.

    Science.gov (United States)

    Muscarella, Robert; Uriarte, María; Erickson, David L; Swenson, Nathan G; Zimmerman, Jess K; Kress, W John

    2014-01-01

    The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i) low terminal phylogenetic resolution and (ii) arbitrarily defined species pools. We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA) to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%). We used a maximum likelihood (ML) approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with Phylomatic (proportion of internal nodes resolved: constrained ML = 74%, unconstrained ML = 68%, Phylomatic = 52%). We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and Phylomatic phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types) changed some of our results depending on which phylogeny (ML vs. Phylomatic) was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny. With the DNA barcode phylogeny presented here (based on an island-wide species pool), we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i) facilitate stronger inferences about the role of historical processes in governing the assembly and composition of Puerto Rican forests, (ii) provide insight into Caribbean

  1. SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data.

    Science.gov (United States)

    Lee, Tae-Ho; Guo, Hui; Wang, Xiyin; Kim, Changsoo; Paterson, Andrew H

    2014-02-26

    Phylogenetic trees are widely used for genetic and evolutionary studies in various organisms. Advanced sequencing technology has dramatically enriched data available for constructing phylogenetic trees based on single nucleotide polymorphisms (SNPs). However, massive SNP data makes it difficult to perform reliable analysis, and there has been no ready-to-use pipeline to generate phylogenetic trees from these data. We developed a new pipeline, SNPhylo, to construct phylogenetic trees based on large SNP datasets. The pipeline may enable users to construct a phylogenetic tree from three representative SNP data file formats. In addition, in order to increase reliability of a tree, the pipeline has steps such as removing low quality data and considering linkage disequilibrium. A maximum likelihood method for the inference of phylogeny is also adopted in generation of a tree in our pipeline. Using SNPhylo, users can easily produce a reliable phylogenetic tree from a large SNP data file. Thus, this pipeline can help a researcher focus more on interpretation of the results of analysis of voluminous data sets, rather than manipulations necessary to accomplish the analysis.

  2. An object-oriented classification method of high resolution imagery based on improved AdaTree

    International Nuclear Information System (INIS)

    Xiaohe, Zhang; Liang, Zhai; Jixian, Zhang; Huiyong, Sang

    2014-01-01

    With the popularity of the application using high spatial resolution remote sensing image, more and more studies paid attention to object-oriented classification on image segmentation as well as automatic classification after image segmentation. This paper proposed a fast method of object-oriented automatic classification. First, edge-based or FNEA-based segmentation was used to identify image objects and the values of most suitable attributes of image objects for classification were calculated. Then a certain number of samples from the image objects were selected as training data for improved AdaTree algorithm to get classification rules. Finally, the image objects could be classified easily using these rules. In the AdaTree, we mainly modified the final hypothesis to get classification rules. In the experiment with WorldView2 image, the result of the method based on AdaTree showed obvious accuracy and efficient improvement compared with the method based on SVM with the kappa coefficient achieving 0.9242

  3. Increased water-use efficiency does not lead to enhanced tree growth under xeric and mesic conditions

    NARCIS (Netherlands)

    Lévesque, M.; Siegwolf, R.; Saurer, M.; Eilmann, B.; Rigling, A.

    2014-01-01

    Higher atmospheric CO2 concentrations (ca ) can under certain conditions increase tree growth by enhancing photosynthesis, resulting in an increase of intrinsic water-use efficiency (i WUE) in trees. However, the magnitude of these effects and their interactions with changing climatic conditions are

  4. Likelihood-Based Inference of B Cell Clonal Families.

    Directory of Open Access Journals (Sweden)

    Duncan K Ralph

    2016-10-01

    Full Text Available The human immune system depends on a highly diverse collection of antibody-making B cells. B cell receptor sequence diversity is generated by a random recombination process called "rearrangement" forming progenitor B cells, then a Darwinian process of lineage diversification and selection called "affinity maturation." The resulting receptors can be sequenced in high throughput for research and diagnostics. Such a collection of sequences contains a mixture of various lineages, each of which may be quite numerous, or may consist of only a single member. As a step to understanding the process and result of this diversification, one may wish to reconstruct lineage membership, i.e. to cluster sampled sequences according to which came from the same rearrangement events. We call this clustering problem "clonal family inference." In this paper we describe and validate a likelihood-based framework for clonal family inference based on a multi-hidden Markov Model (multi-HMM framework for B cell receptor sequences. We describe an agglomerative algorithm to find a maximum likelihood clustering, two approximate algorithms with various trade-offs of speed versus accuracy, and a third, fast algorithm for finding specific lineages. We show that under simulation these algorithms greatly improve upon existing clonal family inference methods, and that they also give significantly different clusters than previous methods when applied to two real data sets.

  5. Integrating individual trip planning in energy efficiency – Building decision tree models for Danish fisheries

    DEFF Research Database (Denmark)

    Bastardie, Francois; Nielsen, J. Rasmus; Andersen, Bo Sølgaard

    2013-01-01

    efficiency for the value of catch per unit of fuel consumed is analysed by merging the questionnaire, logbook and VMS (vessel monitoring system) information. Logic decision trees and conditional behaviour probabilities are established from the responses of fishermen regarding a range of sequential......-intensive but efficient vessels conducting pelagic or industrial fishing are more inclined to base their decision on fish price only, while numerous smaller and less efficient vessels conducting demersal mixed or crustacean fishery usually consider other flexible factors, e.g., the potential for a large catch, weather...... the adaptations of individual fishermen to resource availability dynamics, increasing fuel prices, changes in regulations, and the consequences of socioeconomic external pressures on harvested stocks. A new methodology is described here to obtain quantitative information on the fishermen’s micro-scale decisions...

  6. GSHR-Tree: a spatial index tree based on dynamic spatial slot and hash table in grid environments

    Science.gov (United States)

    Chen, Zhanlong; Wu, Xin-cai; Wu, Liang

    2008-12-01

    Computation Grids enable the coordinated sharing of large-scale distributed heterogeneous computing resources that can be used to solve computationally intensive problems in science, engineering, and commerce. Grid spatial applications are made possible by high-speed networks and a new generation of Grid middleware that resides between networks and traditional GIS applications. The integration of the multi-sources and heterogeneous spatial information and the management of the distributed spatial resources and the sharing and cooperative of the spatial data and Grid services are the key problems to resolve in the development of the Grid GIS. The performance of the spatial index mechanism is the key technology of the Grid GIS and spatial database affects the holistic performance of the GIS in Grid Environments. In order to improve the efficiency of parallel processing of a spatial mass data under the distributed parallel computing grid environment, this paper presents a new grid slot hash parallel spatial index GSHR-Tree structure established in the parallel spatial indexing mechanism. Based on the hash table and dynamic spatial slot, this paper has improved the structure of the classical parallel R tree index. The GSHR-Tree index makes full use of the good qualities of R-Tree and hash data structure. This paper has constructed a new parallel spatial index that can meet the needs of parallel grid computing about the magnanimous spatial data in the distributed network. This arithmetic splits space in to multi-slots by multiplying and reverting and maps these slots to sites in distributed and parallel system. Each sites constructs the spatial objects in its spatial slot into an R tree. On the basis of this tree structure, the index data was distributed among multiple nodes in the grid networks by using large node R-tree method. The unbalance during process can be quickly adjusted by means of a dynamical adjusting algorithm. This tree structure has considered the

  7. Maximum likelihood estimation for Cox's regression model under nested case-control sampling

    DEFF Research Database (Denmark)

    Scheike, Thomas Harder; Juul, Anders

    2004-01-01

    -like growth factor I was associated with ischemic heart disease. The study was based on a population of 3784 Danes and 231 cases of ischemic heart disease where controls were matched on age and gender. We illustrate the use of the MLE for these data and show how the maximum likelihood framework can be used......Nested case-control sampling is designed to reduce the costs of large cohort studies. It is important to estimate the parameters of interest as efficiently as possible. We present a new maximum likelihood estimator (MLE) for nested case-control sampling in the context of Cox's proportional hazards...... model. The MLE is computed by the EM-algorithm, which is easy to implement in the proportional hazards setting. Standard errors are estimated by a numerical profile likelihood approach based on EM aided differentiation. The work was motivated by a nested case-control study that hypothesized that insulin...

  8. An Efficient Distributed Algorithm for Constructing Spanning Trees in Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Rosana Lachowski

    2015-01-01

    Full Text Available Monitoring and data collection are the two main functions in wireless sensor networks (WSNs. Collected data are generally transmitted via multihop communication to a special node, called the sink. While in a typical WSN, nodes have a sink node as the final destination for the data traffic, in an ad hoc network, nodes need to communicate with each other. For this reason, routing protocols for ad hoc networks are inefficient for WSNs. Trees, on the other hand, are classic routing structures explicitly or implicitly used in WSNs. In this work, we implement and evaluate distributed algorithms for constructing routing trees in WSNs described in the literature. After identifying the drawbacks and advantages of these algorithms, we propose a new algorithm for constructing spanning trees in WSNs. The performance of the proposed algorithm and the quality of the constructed tree were evaluated in different network scenarios. The results showed that the proposed algorithm is a more efficient solution. Furthermore, the algorithm provides multiple routes to the sensor nodes to be used as mechanisms for fault tolerance and load balancing.

  9. Efficient Levenberg-Marquardt minimization of the maximum likelihood estimator for Poisson deviates

    International Nuclear Information System (INIS)

    Laurence, T.; Chromy, B.

    2010-01-01

    Histograms of counted events are Poisson distributed, but are typically fitted without justification using nonlinear least squares fitting. The more appropriate maximum likelihood estimator (MLE) for Poisson distributed data is seldom used. We extend the use of the Levenberg-Marquardt algorithm commonly used for nonlinear least squares minimization for use with the MLE for Poisson distributed data. In so doing, we remove any excuse for not using this more appropriate MLE. We demonstrate the use of the algorithm and the superior performance of the MLE using simulations and experiments in the context of fluorescence lifetime imaging. Scientists commonly form histograms of counted events from their data, and extract parameters by fitting to a specified model. Assuming that the probability of occurrence for each bin is small, event counts in the histogram bins will be distributed according to the Poisson distribution. We develop here an efficient algorithm for fitting event counting histograms using the maximum likelihood estimator (MLE) for Poisson distributed data, rather than the non-linear least squares measure. This algorithm is a simple extension of the common Levenberg-Marquardt (L-M) algorithm, is simple to implement, quick and robust. Fitting using a least squares measure is most common, but it is the maximum likelihood estimator only for Gaussian-distributed data. Non-linear least squares methods may be applied to event counting histograms in cases where the number of events is very large, so that the Poisson distribution is well approximated by a Gaussian. However, it is not easy to satisfy this criterion in practice - which requires a large number of events. It has been well-known for years that least squares procedures lead to biased results when applied to Poisson-distributed data; a recent paper providing extensive characterization of these biases in exponential fitting is given. The more appropriate measure based on the maximum likelihood estimator (MLE

  10. MAXIMUM LIKELIHOOD CLASSIFICATION OF HIGH-RESOLUTION SAR IMAGES IN URBAN AREA

    Directory of Open Access Journals (Sweden)

    M. Soheili Majd

    2012-09-01

    Full Text Available In this work, we propose a state-of-the-art on statistical analysis of polarimetric synthetic aperture radar (SAR data, through the modeling of several indices. We concentrate on eight ground classes which have been carried out from amplitudes, co-polarisation ratio, depolarization ratios, and other polarimetric descriptors. To study their different statistical behaviours, we consider Gauss, log- normal, Beta I, Weibull, Gamma, and Fisher statistical models and estimate their parameters using three methods: method of moments (MoM, maximum-likelihood (ML methodology, and log-cumulants method (MoML. Then, we study the opportunity of introducing this information in an adapted supervised classification scheme based on Maximum–Likelihood and Fisher pdf. Our work relies on an image of a suburban area, acquired by the airborne RAMSES SAR sensor of ONERA. The results prove the potential of such data to discriminate urban surfaces and show the usefulness of adapting any classical classification algorithm however classification maps present a persistant class confusion between flat gravelled or concrete roofs and trees.

  11. Robust B+ -Tree-Based Indexing of Moving Objects

    DEFF Research Database (Denmark)

    Jensen, Christian Søndergaard; Tiesyte, Dalia; Tradisauskas, Nerius

    2006-01-01

    Bx-tree is based on the B+-tree and is relatively easy to integrate into an existing DBMS. However, the Bx-tree is sensitive to data skew. This paper proposes a new query processing algorithm for the Bx-tree that fully exploits the available data statistics to reduce the query enlargement...

  12. A support vector machine based test for incongruence between sets of trees in tree space

    Science.gov (United States)

    2012-01-01

    Background The increased use of multi-locus data sets for phylogenetic reconstruction has increased the need to determine whether a set of gene trees significantly deviate from the phylogenetic patterns of other genes. Such unusual gene trees may have been influenced by other evolutionary processes such as selection, gene duplication, or horizontal gene transfer. Results Motivated by this problem we propose a nonparametric goodness-of-fit test for two empirical distributions of gene trees, and we developed the software GeneOut to estimate a p-value for the test. Our approach maps trees into a multi-dimensional vector space and then applies support vector machines (SVMs) to measure the separation between two sets of pre-defined trees. We use a permutation test to assess the significance of the SVM separation. To demonstrate the performance of GeneOut, we applied it to the comparison of gene trees simulated within different species trees across a range of species tree depths. Applied directly to sets of simulated gene trees with large sample sizes, GeneOut was able to detect very small differences between two set of gene trees generated under different species trees. Our statistical test can also include tree reconstruction into its test framework through a variety of phylogenetic optimality criteria. When applied to DNA sequence data simulated from different sets of gene trees, results in the form of receiver operating characteristic (ROC) curves indicated that GeneOut performed well in the detection of differences between sets of trees with different distributions in a multi-dimensional space. Furthermore, it controlled false positive and false negative rates very well, indicating a high degree of accuracy. Conclusions The non-parametric nature of our statistical test provides fast and efficient analyses, and makes it an applicable test for any scenario where evolutionary or other factors can lead to trees with different multi-dimensional distributions. The

  13. Escaping Depressions in LRTS Based on Incremental Refinement of Encoded Quad-Trees

    Directory of Open Access Journals (Sweden)

    Yue Hu

    2017-01-01

    Full Text Available In the context of robot navigation, game AI, and so on, real-time search is extensively used to undertake motion planning. Though it satisfies the requirement of quick response to users’ commands and environmental changes, learning real-time search (LRTS suffers from the heuristic depressions where agents behave irrationally. There have introduced several effective solutions, such as state abstractions. This paper combines LRTS and encoded quad-tree abstraction which represent the search space in multiresolutions. When exploring the environments, agents are enabled to locally repair the quad-tree models and incrementally refine the spatial cognition. By virtue of the idea of state aggregation and heuristic generalization, our EQ LRTS (encoded quad-tree based LRTS possesses the ability of quickly escaping from heuristic depressions with less state revisitations. Experiments and analysis show that (a our encoding principle for quad-trees is a much more memory-efficient method than other data structures expressing quad-trees, (b EQ LRTS differs a lot in several characteristics from classical PR LRTS which represent the space and refine the paths hierarchically, and (c EQ LRTS substantially reduces the planning amount and curtails heuristic updates compared with LRTS on uniform cells.

  14. A Waterline Extraction Method from Remote Sensing Image Based on Quad-tree and Multiple Active Contour Model

    Directory of Open Access Journals (Sweden)

    YU Jintao

    2016-09-01

    Full Text Available After the characteristics of geodesic active contour model (GAC, Chan-Vese model(CV and local binary fitting model(LBF are analyzed, and the active contour model based on regions and edges is combined with image segmentation method based on quad-tree, a waterline extraction method based on quad-tree and multiple active contour model is proposed in this paper. Firstly, the method provides an initial contour according to quad-tree segmentation. Secondly, a new signed pressure force(SPF function based on global image statistics information of CV model and local image statistics information of LBF model has been defined, and then ,the edge stopping function(ESF is replaced by the proposed SPF function, which solves the problem such as evolution stopped in advance and excessive evolution. Finally, the selective binary and Gaussian filtering level set method is used to avoid reinitializing and regularization to improve the evolution efficiency. The experimental results show that this method can effectively extract the weak edges and serious concave edges, and owns some properties such as sub-pixel accuracy, high efficiency and reliability for waterline extraction.

  15. Likelihood-Based Inference in Nonlinear Error-Correction Models

    DEFF Research Database (Denmark)

    Kristensen, Dennis; Rahbæk, Anders

    We consider a class of vector nonlinear error correction models where the transfer function (or loadings) of the stationary relation- ships is nonlinear. This includes in particular the smooth transition models. A general representation theorem is given which establishes the dynamic properties...... and a linear trend in general. Gaussian likelihood-based estimators are considered for the long- run cointegration parameters, and the short-run parameters. Asymp- totic theory is provided for these and it is discussed to what extend asymptotic normality and mixed normaity can be found. A simulation study...

  16. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

    Science.gov (United States)

    Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent; Anisimova, Maria; Hordijk, Wim; Gascuel, Olivier

    2010-05-01

    PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.

  17. Water-Tree Modelling and Detection for Underground Cables

    Science.gov (United States)

    Chen, Qi

    In recent years, aging infrastructure has become a major concern for the power industry. Since its inception in early 20th century, the electrical system has been the cornerstone of an industrial society. Stable and uninterrupted delivery of electrical power is now a base necessity for the modern world. As the times march-on, however, the electrical infrastructure ages and there is the inevitable need to renew and replace the existing system. Unfortunately, due to time and financial constraints, many electrical systems today are forced to operate beyond their original design and power utilities must find ways to prolong the lifespan of older equipment. Thus, the concept of preventative maintenance arises. Preventative maintenance allows old equipment to operate longer and at better efficiency, but in order to implement preventative maintenance, the operators must know minute details of the electrical system, especially some of the harder to assess issues such water-tree. Water-tree induced insulation degradation is a problem typically associated with older cable systems. It is a very high impedance phenomenon and it is difficult to detect using traditional methods such as Tan-Delta or Partial Discharge. The proposed dissertation studies water-tree development in underground cables, potential methods to detect water-tree location and water-tree severity estimation. The dissertation begins by developing mathematical models of water-tree using finite element analysis. The method focuses on surface-originated vented tree, the most prominent type of water-tree fault in the field. Using the standard operation parameters of North American electrical systems, the water-tree boundary conditions are defined. By applying finite element analysis technique, the complex water-tree structure is broken down to homogeneous components. The result is a generalized representation of water-tree capacitance at different stages of development. The result from the finite element analysis

  18. Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees

    Science.gov (United States)

    Kenah, Eben; Britton, Tom; Halloran, M. Elizabeth; Longini, Ira M.

    2016-01-01

    Recent work has attempted to use whole-genome sequence data from pathogens to reconstruct the transmission trees linking infectors and infectees in outbreaks. However, transmission trees from one outbreak do not generalize to future outbreaks. Reconstruction of transmission trees is most useful to public health if it leads to generalizable scientific insights about disease transmission. In a survival analysis framework, estimation of transmission parameters is based on sums or averages over the possible transmission trees. A phylogeny can increase the precision of these estimates by providing partial information about who infected whom. The leaves of the phylogeny represent sampled pathogens, which have known hosts. The interior nodes represent common ancestors of sampled pathogens, which have unknown hosts. Starting from assumptions about disease biology and epidemiologic study design, we prove that there is a one-to-one correspondence between the possible assignments of interior node hosts and the transmission trees simultaneously consistent with the phylogeny and the epidemiologic data on person, place, and time. We develop algorithms to enumerate these transmission trees and show these can be used to calculate likelihoods that incorporate both epidemiologic data and a phylogeny. A simulation study confirms that this leads to more efficient estimates of hazard ratios for infectiousness and baseline hazards of infectious contact, and we use these methods to analyze data from a foot-and-mouth disease virus outbreak in the United Kingdom in 2001. These results demonstrate the importance of data on individuals who escape infection, which is often overlooked. The combination of survival analysis and algorithms linking phylogenies to transmission trees is a rigorous but flexible statistical foundation for molecular infectious disease epidemiology. PMID:27070316

  19. Efficient Dynamic Adaptation Strategies for Object Tracking Tree in Wireless Sensor Network

    Directory of Open Access Journals (Sweden)

    CHEN, M.

    2012-12-01

    Full Text Available Most object tracking trees are established using the predefined mobility profile. However, when the real object's movement behaviors and query rates are different from the predefined mobility profile and query rates, the update cost and query cost of object tracking tree may increase. To upgrade the object tracking tree, the sink needs to send very large messages to collect the real movement information from the network, introducing a very large message overhead, which is referred to as adaptation cost. The Sub Root Message-Tree Adaptive procedure was proposed to dynamically collect the real movement information under the sub-tree and reconstruct the sub-tree to provide good performance based on the collected information. The simulation results indicates that the Sub Root Message-Tree Adaptive procedure is sufficient to achieve good total cost and lower adaptation cost.

  20. New subsea X tree generation brings innovative features providing efficiency for ultra deep waters

    Energy Technology Data Exchange (ETDEWEB)

    Araujo, Gustavo Bellot de Almeida; Labes, Alan Zaragoza [FMC Technologies, Houston, TX (United States)

    2008-07-01

    The EVDT has been developed for global applications. Based upon the widely field proven 10 K Vertical Tree and 15 K HPHT Tree, the system has incorporated the latest technological advancements. The Tubing Hanger System and installation tooling are available up to a 7 inch bore for 10,000 psi applications and a 5 inch bore for 15,000 psi applications. The Tubing Hanger can be installed using a Tubing Head when flexibility for sequencing of events is required during offshore installations. Or it can simply land into the wellhead, eliminating the Tubing Head. This allows for a more efficient installation when completion and drilling operations are conducted without retrieving the Sub sea Blow Out Preventer (BOP) and Riser. The EVDT incorporates a retrievable Flow Module downstream of the wing valve that can be configured to project specific variances such as production, gas injection and water injection service. The Flow Module can also be configured to include Multi-Phase Flow Meters, sensors, and gauges. This allows an upgrade sub sea without having to pull and re-run the entire Tree system. These features allowed the system to hit the mark regarding what the industry needs today and also allowed to accommodate technologies that will arise in the years to come. (author)

  1. Base tree property

    Czech Academy of Sciences Publication Activity Database

    Balcar, B.; Doucha, Michal; Hrušák, M.

    2015-01-01

    Roč. 32, č. 1 (2015), s. 69-81 ISSN 0167-8094 R&D Projects: GA AV ČR IAA100190902 Institutional support: RVO:67985840 Keywords : forcing * Boolean algebras * base tree Subject RIV: BA - General Mathematics Impact factor: 0.614, year: 2015 http://link.springer.com/article/10.1007/s11083-013-9316-2

  2. Treelink: data integration, clustering and visualization of phylogenetic trees.

    Science.gov (United States)

    Allende, Christian; Sohn, Erik; Little, Cedric

    2015-12-29

    Phylogenetic trees are central to a wide range of biological studies. In many of these studies, tree nodes need to be associated with a variety of attributes. For example, in studies concerned with viral relationships, tree nodes are associated with epidemiological information, such as location, age and subtype. Gene trees used in comparative genomics are usually linked with taxonomic information, such as functional annotations and events. A wide variety of tree visualization and annotation tools have been developed in the past, however none of them are intended for an integrative and comparative analysis. Treelink is a platform-independent software for linking datasets and sequence files to phylogenetic trees. The application allows an automated integration of datasets to trees for operations such as classifying a tree based on a field or showing the distribution of selected data attributes in branches and leafs. Genomic and proteonomic sequences can also be linked to the tree and extracted from internal and external nodes. A novel clustering algorithm to simplify trees and display the most divergent clades was also developed, where validation can be achieved using the data integration and classification function. Integrated geographical information allows ancestral character reconstruction for phylogeographic plotting based on parsimony and likelihood algorithms. Our software can successfully integrate phylogenetic trees with different data sources, and perform operations to differentiate and visualize those differences within a tree. File support includes the most popular formats such as newick and csv. Exporting visualizations as images, cluster outputs and genomic sequences is supported. Treelink is available as a web and desktop application at http://www.treelinkapp.com .

  3. Effects of species-specific leaf characteristics and reduced water availability on fine particle capture efficiency of trees

    International Nuclear Information System (INIS)

    Räsänen, Janne V.; Holopainen, Toini; Joutsensaari, Jorma; Ndam, Collins; Pasanen, Pertti; Rinnan, Åsmund; Kivimäenpää, Minna

    2013-01-01

    Trees can improve air quality by capturing particles in their foliage. We determined the particle capture efficiencies of coniferous Pinus sylvestris and three broadleaved species: Betula pendula, Betula pubescens and Tilia vulgaris in a wind tunnel using NaCl particles. The importance of leaf surface structure, physiology and moderate soil drought on the particle capture efficiencies of the trees were determined. The results confirm earlier findings of more efficient particle capture by conifers compared to broadleaved plants. The particle capture efficiency of P. sylvestris (0.21%) was significantly higher than those of B. pubescens, T. vulgaris and B. pendula (0.083%, 0.047%, 0.043%, respectively). The small leaf size of P. sylvestris was the major characteristic that increased particle capture. Among the broadleaved species, low leaf wettability, low stomatal density and leaf hairiness increased particle capture. Moderate soil drought tended to increase particle capture efficiency of P. sylvestris. -- Highlights: • Coniferous Scots pine was the most efficient particle collector. • Decreasing single leaf size increases particle deposition of the total leaf area. • Hairiness of the leaf increases particle deposition. -- Trees can improve air quality by removing PM 2.5 pollutants carried on the wind at a velocity of 3 m s −1 , the efficiency of which depends on species leaf characteristics and physical factors

  4. A retrospective likelihood approach for efficient integration of multiple omics factors in case-control association studies.

    Science.gov (United States)

    Balliu, Brunilda; Tsonaka, Roula; Boehringer, Stefan; Houwing-Duistermaat, Jeanine

    2015-03-01

    Integrative omics, the joint analysis of outcome and multiple types of omics data, such as genomics, epigenomics, and transcriptomics data, constitute a promising approach for powerful and biologically relevant association studies. These studies often employ a case-control design, and often include nonomics covariates, such as age and gender, that may modify the underlying omics risk factors. An open question is how to best integrate multiple omics and nonomics information to maximize statistical power in case-control studies that ascertain individuals based on the phenotype. Recent work on integrative omics have used prospective approaches, modeling case-control status conditional on omics, and nonomics risk factors. Compared to univariate approaches, jointly analyzing multiple risk factors with a prospective approach increases power in nonascertained cohorts. However, these prospective approaches often lose power in case-control studies. In this article, we propose a novel statistical method for integrating multiple omics and nonomics factors in case-control association studies. Our method is based on a retrospective likelihood function that models the joint distribution of omics and nonomics factors conditional on case-control status. The new method provides accurate control of Type I error rate and has increased efficiency over prospective approaches in both simulated and real data. © 2015 Wiley Periodicals, Inc.

  5. Supplementary Material for: High-Order Composite Likelihood Inference for Max-Stable Distributions and Processes

    KAUST Repository

    Castruccio, Stefano; Huser, Raphaë l; Genton, Marc G.

    2016-01-01

    In multivariate or spatial extremes, inference for max-stable processes observed at a large collection of points is a very challenging problem and current approaches typically rely on less expensive composite likelihoods constructed from small subsets of data. In this work, we explore the limits of modern state-of-the-art computational facilities to perform full likelihood inference and to efficiently evaluate high-order composite likelihoods. With extensive simulations, we assess the loss of information of composite likelihood estimators with respect to a full likelihood approach for some widely used multivariate or spatial extreme models, we discuss how to choose composite likelihood truncation to improve the efficiency, and we also provide recommendations for practitioners. This article has supplementary material online.

  6. Evaluation of Smoking Prevention Television Messages Based on the Elaboration Likelihood Model

    Science.gov (United States)

    Flynn, Brian S.; Worden, John K.; Bunn, Janice Yanushka; Connolly, Scott W.; Dorwaldt, Anne L.

    2011-01-01

    Progress in reducing youth smoking may depend on developing improved methods to communicate with higher risk youth. This study explored the potential of smoking prevention messages based on the Elaboration Likelihood Model (ELM) to address these needs. Structured evaluations of 12 smoking prevention messages based on three strategies derived from…

  7. Simulation-based marginal likelihood for cluster strong lensing cosmology

    Science.gov (United States)

    Killedar, M.; Borgani, S.; Fabjan, D.; Dolag, K.; Granato, G.; Meneghetti, M.; Planelles, S.; Ragone-Figueroa, C.

    2018-01-01

    Comparisons between observed and predicted strong lensing properties of galaxy clusters have been routinely used to claim either tension or consistency with Λ cold dark matter cosmology. However, standard approaches to such cosmological tests are unable to quantify the preference for one cosmology over another. We advocate approximating the relevant Bayes factor using a marginal likelihood that is based on the following summary statistic: the posterior probability distribution function for the parameters of the scaling relation between Einstein radii and cluster mass, α and β. We demonstrate, for the first time, a method of estimating the marginal likelihood using the X-ray selected z > 0.5 Massive Cluster Survey clusters as a case in point and employing both N-body and hydrodynamic simulations of clusters. We investigate the uncertainty in this estimate and consequential ability to compare competing cosmologies, which arises from incomplete descriptions of baryonic processes, discrepancies in cluster selection criteria, redshift distribution and dynamical state. The relation between triaxial cluster masses at various overdensities provides a promising alternative to the strong lensing test.

  8. Section-Based Tree Species Identification Using Airborne LIDAR Point Cloud

    Science.gov (United States)

    Yao, C.; Zhang, X.; Liu, H.

    2017-09-01

    The application of LiDAR data in forestry initially focused on mapping forest community, particularly and primarily intended for largescale forest management and planning. Then with the smaller footprint and higher sampling density LiDAR data available, detecting individual tree overstory, estimating crowns parameters and identifying tree species are demonstrated practicable. This paper proposes a section-based protocol of tree species identification taking palm tree as an example. Section-based method is to detect objects through certain profile among different direction, basically along X-axis or Y-axis. And this method improve the utilization of spatial information to generate accurate results. Firstly, separate the tree points from manmade-object points by decision-tree-based rules, and create Crown Height Mode (CHM) by subtracting the Digital Terrain Model (DTM) from the digital surface model (DSM). Then calculate and extract key points to locate individual trees, thus estimate specific tree parameters related to species information, such as crown height, crown radius, and cross point etc. Finally, with parameters we are able to identify certain tree species. Comparing to species information measured on ground, the portion correctly identified trees on all plots could reach up to 90.65 %. The identification result in this research demonstrate the ability to distinguish palm tree using LiDAR point cloud. Furthermore, with more prior knowledge, section-based method enable the process to classify trees into different classes.

  9. Empirical Likelihood in Nonignorable Covariate-Missing Data Problems.

    Science.gov (United States)

    Xie, Yanmei; Zhang, Biao

    2017-04-20

    Missing covariate data occurs often in regression analysis, which frequently arises in the health and social sciences as well as in survey sampling. We study methods for the analysis of a nonignorable covariate-missing data problem in an assumed conditional mean function when some covariates are completely observed but other covariates are missing for some subjects. We adopt the semiparametric perspective of Bartlett et al. (Improving upon the efficiency of complete case analysis when covariates are MNAR. Biostatistics 2014;15:719-30) on regression analyses with nonignorable missing covariates, in which they have introduced the use of two working models, the working probability model of missingness and the working conditional score model. In this paper, we study an empirical likelihood approach to nonignorable covariate-missing data problems with the objective of effectively utilizing the two working models in the analysis of covariate-missing data. We propose a unified approach to constructing a system of unbiased estimating equations, where there are more equations than unknown parameters of interest. One useful feature of these unbiased estimating equations is that they naturally incorporate the incomplete data into the data analysis, making it possible to seek efficient estimation of the parameter of interest even when the working regression function is not specified to be the optimal regression function. We apply the general methodology of empirical likelihood to optimally combine these unbiased estimating equations. We propose three maximum empirical likelihood estimators of the underlying regression parameters and compare their efficiencies with other existing competitors. We present a simulation study to compare the finite-sample performance of various methods with respect to bias, efficiency, and robustness to model misspecification. The proposed empirical likelihood method is also illustrated by an analysis of a data set from the US National Health and

  10. Transpiration efficiency of a tropical pioneer tree (Ficus insipida) in relation to soil fertility.

    Science.gov (United States)

    Cernusak, Lucas A; Winter, Klaus; Aranda, Jorge; Turner, Benjamin L; Marshall, John D

    2007-01-01

    The response of whole-plant water-use efficiency, termed transpiration efficiency (TE), to variation in soil fertility was assessed in a tropical pioneer tree, Ficus insipida Willd. Measurements of stable isotope ratios (delta(13)C, delta(18)O, delta(15)N), elemental concentrations (C, N, P), plant growth, instantaneous leaf gas exchange, and whole-plant water use were used to analyse the mechanisms controlling TE. Plants were grown individually in 19 l pots with non-limiting soil moisture. Soil fertility was altered by mixing soil with varying proportions of rice husks, and applying a slow release fertilizer. A large variation was observed in leaf photosynthetic rate, mean relative growth rate (RGR), and TE in response to experimental treatments; these traits were well correlated with variation in leaf N concentration. Variation in TE showed a strong dependence on the ratio of intercellular to ambient CO(2) mole fractions (c(i)/c(a)); both for instantaneous measurements of c(i)/c(a) (R(2)=0.69, P <0.0001, n=30), and integrated estimates based on C isotope discrimination (R(2)=0.88, P <0.0001, n=30). On the other hand, variations in the leaf-to-air humidity gradient, unproductive water loss, and respiratory C use probably played only minor roles in modulating TE in the face of variable soil fertility. The pronounced variation in TE resulted from a combination of the strong response of c(i)/c(a) to leaf N, and inherently high values of c(i)/c(a) for this tropical tree species; these two factors conspired to cause a 4-fold variation among treatments in (1-c(i)/c(a)), the term that actually modifies TE. Results suggest that variation in plant N status could have important implications for the coupling between C and water exchange in tropical forest trees.

  11. On the performance of social network and likelihood-based expert weighting schemes

    International Nuclear Information System (INIS)

    Cooke, Roger M.; ElSaadany, Susie; Huang Xinzheng

    2008-01-01

    Using expert judgment data from the TU Delft's expert judgment database, we compare the performance of different weighting schemes, namely equal weighting, performance-based weighting from the classical model [Cooke RM. Experts in uncertainty. Oxford: Oxford University Press; 1991.], social network (SN) weighting and likelihood weighting. The picture that emerges with regard to SN weights is rather mixed. SN theory does not provide an alternative to performance-based combination of expert judgments, since the statistical accuracy of the SN decision maker is sometimes unacceptably low. On the other hand, it does outperform equal weighting in the majority of cases. The results here, though not overwhelmingly positive, do nonetheless motivate further research into social interaction methods for nominating and weighting experts. Indeed, a full expert judgment study with performance measurement requires an investment in time and effort, with a view to securing external validation. If high confidence in a comparable level of validation can be obtained by less intensive methods, this would be very welcome, and would facilitate the application of structured expert judgment in situations where the resources for a full study are not available. Likelihood weights are just as resource intensive as performance-based weights, and the evidence presented here suggests that they are inferior to performance-based weights with regard to those scoring variables which are optimized in performance weights (calibration and information). Perhaps surprisingly, they are also inferior with regard to likelihood. Their use is further discouraged by the fact that they constitute a strongly improper scoring rule

  12. Efficient Algorithms for Computing the Triplet and Quartet Distance Between Trees of Arbitrary Degree

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Fagerberg, Rolf; Mailund, Thomas

    2013-01-01

    ), respectively, and counting how often the induced topologies in the two input trees are different. In this paper we present efficient algorithms for computing these distances. We show how to compute the triplet distance in time O(n log n) and the quartet distance in time O(d n log n), where d is the maximal......The triplet and quartet distances are distance measures to compare two rooted and two unrooted trees, respectively. The leaves of the two trees should have the same set of n labels. The distances are defined by enumerating all subsets of three labels (triplets) and four labels (quartets...... degree of any node in the two trees. Within the same time bounds, our framework also allows us to compute the parameterized triplet and quartet distances, where a parameter is introduced to weight resolved (binary) topologies against unresolved (non-binary) topologies. The previous best algorithm...

  13. Obtaining reliable Likelihood Ratio tests from simulated likelihood functions

    DEFF Research Database (Denmark)

    Andersen, Laura Mørch

    It is standard practice by researchers and the default option in many statistical programs to base test statistics for mixed models on simulations using asymmetric draws (e.g. Halton draws). This paper shows that when the estimated likelihood functions depend on standard deviations of mixed param...

  14. tropiTree: An NGS-Based EST-SSR Resource for 24 Tropical Tree Species

    Science.gov (United States)

    Russell, Joanne R.; Hedley, Peter E.; Cardle, Linda; Dancey, Siobhan; Morris, Jenny; Booth, Allan; Odee, David; Mwaura, Lucy; Omondi, William; Angaine, Peter; Machua, Joseph; Muchugi, Alice; Milne, Iain; Kindt, Roeland; Jamnadass, Ramni; Dawson, Ian K.

    2014-01-01

    The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data. PMID:25025376

  15. Experimental demonstration of the maximum likelihood-based chromatic dispersion estimator for coherent receivers

    DEFF Research Database (Denmark)

    Borkowski, Robert; Johannisson, Pontus; Wymeersch, Henk

    2014-01-01

    We perform an experimental investigation of a maximum likelihood-based (ML-based) algorithm for bulk chromatic dispersion estimation for digital coherent receivers operating in uncompensated optical networks. We demonstrate the robustness of the method at low optical signal-to-noise ratio (OSNR...

  16. Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance

    Science.gov (United States)

    2013-01-01

    Background Constructing species trees from multi-copy gene trees remains a challenging problem in phylogenetics. One difficulty is that the underlying genes can be incongruent due to evolutionary processes such as gene duplication and loss, deep coalescence, or lateral gene transfer. Gene tree estimation errors may further exacerbate the difficulties of species tree estimation. Results We present a new approach for inferring species trees from incongruent multi-copy gene trees that is based on a generalization of the Robinson-Foulds (RF) distance measure to multi-labeled trees (mul-trees). We prove that it is NP-hard to compute the RF distance between two mul-trees; however, it is easy to calculate this distance between a mul-tree and a singly-labeled species tree. Motivated by this, we formulate the RF problem for mul-trees (MulRF) as follows: Given a collection of multi-copy gene trees, find a singly-labeled species tree that minimizes the total RF distance from the input mul-trees. We develop and implement a fast SPR-based heuristic algorithm for the NP-hard MulRF problem. We compare the performance of the MulRF method (available at http://genome.cs.iastate.edu/CBL/MulRF/) with several gene tree parsimony approaches using gene tree simulations that incorporate gene tree error, gene duplications and losses, and/or lateral transfer. The MulRF method produces more accurate species trees than gene tree parsimony approaches. We also demonstrate that the MulRF method infers in minutes a credible plant species tree from a collection of nearly 2,000 gene trees. Conclusions Our new phylogenetic inference method, based on a generalized RF distance, makes it possible to quickly estimate species trees from large genomic data sets. Since the MulRF method, unlike gene tree parsimony, is based on a generic tree distance measure, it is appealing for analyses of genomic data sets, in which many processes such as deep coalescence, recombination, gene duplication and losses as

  17. Fast and accurate estimation of the covariance between pairwise maximum likelihood distances

    Directory of Open Access Journals (Sweden)

    Manuel Gil

    2014-09-01

    Full Text Available Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989 which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error.

  18. Fast and accurate estimation of the covariance between pairwise maximum likelihood distances.

    Science.gov (United States)

    Gil, Manuel

    2014-01-01

    Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error.

  19. Fast method of constructing image correlations to build a free network based on image multivocabulary trees

    Science.gov (United States)

    Zhan, Zongqian; Wang, Xin; Wei, Minglu

    2015-05-01

    In image-based three-dimensional (3-D) reconstruction, one topic of growing importance is how to quickly obtain a 3-D model from a large number of images. The retrieval of the correct and relevant images for the model poses a considerable technological challenge. The "image vocabulary tree" has been proposed as a method to search for similar images. However, a significant drawback of this approach is identified in its low time efficiency and barely satisfactory classification result. The method proposed is inspired by, and improves upon, some recent methods. Specifically, vocabulary quality is considered and multivocabulary trees are designed to improve the classification result. A marked improvement was, indeed, observed in our evaluation of the proposed method. To improve time efficiency, graphics processing unit (GPU) computer unified device architecture parallel computation is applied in the multivocabulary trees. The results of the experiments showed that the GPU was three to four times more efficient than the enumeration matching and CPU methods when the number of images is large. This paper presents a reliable reference method for the rapid construction of a free network to be used for the computing of 3-D information.

  20. The Probabilistic Convolution Tree: Efficient Exact Bayesian Inference for Faster LC-MS/MS Protein Inference

    Science.gov (United States)

    Serang, Oliver

    2014-01-01

    Exact Bayesian inference can sometimes be performed efficiently for special cases where a function has commutative and associative symmetry of its inputs (called “causal independence”). For this reason, it is desirable to exploit such symmetry on big data sets. Here we present a method to exploit a general form of this symmetry on probabilistic adder nodes by transforming those probabilistic adder nodes into a probabilistic convolution tree with which dynamic programming computes exact probabilities. A substantial speedup is demonstrated using an illustration example that can arise when identifying splice forms with bottom-up mass spectrometry-based proteomics. On this example, even state-of-the-art exact inference algorithms require a runtime more than exponential in the number of splice forms considered. By using the probabilistic convolution tree, we reduce the runtime to and the space to where is the number of variables joined by an additive or cardinal operator. This approach, which can also be used with junction tree inference, is applicable to graphs with arbitrary dependency on counting variables or cardinalities and can be used on diverse problems and fields like forward error correcting codes, elemental decomposition, and spectral demixing. The approach also trivially generalizes to multiple dimensions. PMID:24626234

  1. A hierarchical scheme for geodesic anatomical labeling of airway trees

    DEFF Research Database (Denmark)

    Feragen, Aasa; Petersen, Jens; Owen, Megan

    2012-01-01

    We present a fast and robust supervised algorithm for label- ing anatomical airway trees, based on geodesic distances in a geometric tree-space. Possible branch label configurations for a given unlabeled air- way tree are evaluated based on the distances to a training set of labeled airway trees....... In tree-space, the airway tree topology and geometry change continuously, giving a natural way to automatically handle anatomical differences and noise. The algorithm is made efficient using a hierarchical approach, in which labels are assigned from the top down. We only use features of the airway...

  2. Factors Associated with Young Adults’ Pregnancy Likelihood

    Science.gov (United States)

    Kitsantas, Panagiota; Lindley, Lisa L.; Wu, Huichuan

    2014-01-01

    OBJECTIVES While progress has been made to reduce adolescent pregnancies in the United States, rates of unplanned pregnancy among young adults (18–29 years) remain high. In this study, we assessed factors associated with perceived likelihood of pregnancy (likelihood of getting pregnant/getting partner pregnant in the next year) among sexually experienced young adults who were not trying to get pregnant and had ever used contraceptives. METHODS We conducted a secondary analysis of 660 young adults, 18–29 years old in the United States, from the cross-sectional National Survey of Reproductive and Contraceptive Knowledge. Logistic regression and classification tree analyses were conducted to generate profiles of young adults most likely to report anticipating a pregnancy in the next year. RESULTS Nearly one-third (32%) of young adults indicated they believed they had at least some likelihood of becoming pregnant in the next year. Young adults who believed that avoiding pregnancy was not very important were most likely to report pregnancy likelihood (odds ratio [OR], 5.21; 95% CI, 2.80–9.69), as were young adults for whom avoiding a pregnancy was important but not satisfied with their current contraceptive method (OR, 3.93; 95% CI, 1.67–9.24), attended religious services frequently (OR, 3.0; 95% CI, 1.52–5.94), were uninsured (OR, 2.63; 95% CI, 1.31–5.26), and were likely to have unprotected sex in the next three months (OR, 1.77; 95% CI, 1.04–3.01). DISCUSSION These results may help guide future research and the development of pregnancy prevention interventions targeting sexually experienced young adults. PMID:25782849

  3. On the likelihood function of Gaussian max-stable processes

    KAUST Repository

    Genton, M. G.; Ma, Y.; Sang, H.

    2011-01-01

    We derive a closed form expression for the likelihood function of a Gaussian max-stable process indexed by ℝd at p≤d+1 sites, d≥1. We demonstrate the gain in efficiency in the maximum composite likelihood estimators of the covariance matrix from p=2 to p=3 sites in ℝ2 by means of a Monte Carlo simulation study. © 2011 Biometrika Trust.

  4. On the likelihood function of Gaussian max-stable processes

    KAUST Repository

    Genton, M. G.

    2011-05-24

    We derive a closed form expression for the likelihood function of a Gaussian max-stable process indexed by ℝd at p≤d+1 sites, d≥1. We demonstrate the gain in efficiency in the maximum composite likelihood estimators of the covariance matrix from p=2 to p=3 sites in ℝ2 by means of a Monte Carlo simulation study. © 2011 Biometrika Trust.

  5. Likelihood Inference of Nonlinear Models Based on a Class of Flexible Skewed Distributions

    Directory of Open Access Journals (Sweden)

    Xuedong Chen

    2014-01-01

    Full Text Available This paper deals with the issue of the likelihood inference for nonlinear models with a flexible skew-t-normal (FSTN distribution, which is proposed within a general framework of flexible skew-symmetric (FSS distributions by combining with skew-t-normal (STN distribution. In comparison with the common skewed distributions such as skew normal (SN, and skew-t (ST as well as scale mixtures of skew normal (SMSN, the FSTN distribution can accommodate more flexibility and robustness in the presence of skewed, heavy-tailed, especially multimodal outcomes. However, for this distribution, a usual approach of maximum likelihood estimates based on EM algorithm becomes unavailable and an alternative way is to return to the original Newton-Raphson type method. In order to improve the estimation as well as the way for confidence estimation and hypothesis test for the parameters of interest, a modified Newton-Raphson iterative algorithm is presented in this paper, based on profile likelihood for nonlinear regression models with FSTN distribution, and, then, the confidence interval and hypothesis test are also developed. Furthermore, a real example and simulation are conducted to demonstrate the usefulness and the superiority of our approach.

  6. The distribution of weaver ant pheromones on host trees

    DEFF Research Database (Denmark)

    Offenberg, Joachim

    2007-01-01

    The visible anal spots deposited by Oecophylla smaragdina ants have been suggested to deter ant prey, affect interspecific competition and facilitate mutualists and parasites in tracking down Oecophylla ants. I measured the density of anal spots on host trees with and without ants and tested for ...... to leaves. Also there was a positive correlation between spot density and the likelihood of being detected by ants. Anal spots may thus function as reliable cues to interacting species and be an important factor in shaping the community around Oecophylla colonies.......The visible anal spots deposited by Oecophylla smaragdina ants have been suggested to deter ant prey, affect interspecific competition and facilitate mutualists and parasites in tracking down Oecophylla ants. I measured the density of anal spots on host trees with and without ants and tested...... for correlations between spot density, ant activity and the likelihood of being detected by an ant. Spots were only found on trees with ants. On ant-trees, spots were distributed throughout the trees but with higher densities in areas with high ant activity and pheromone densities were higher on twigs compared...

  7. Rule-based detection of intrathoracic airway trees

    International Nuclear Information System (INIS)

    Sonka, M.; Park, W.; Hoffman, E.A.

    1996-01-01

    New sensitive and reliable methods for assessing alterations in regional lung structure and function are critically important for the investigation and treatment of pulmonary diseases. Accurate identification of the airway tree will provide an assessment of airway structure and will provide a means by which multiple volumetric images of the lung at the same lung volume over time can be used to assess regional parenchymal changes. The authors describe a novel rule-based method for the segmentation of airway trees from three-dimensional (3-D) sets of computed tomography (CT) images, and its validation. The presented method takes advantage of a priori anatomical knowledge about pulmonary airway and vascular trees and their interrelationships. The method is based on a combination of 3-D seeded region growing that is used to identify large airways, rule-based two-dimensional (2-D) segmentation of individual CT slices to identify probable locations of smaller diameter airways, and merging of airway regions across the 3-D set of slices resulting in a tree-like airway structure. The method was validated in 40 3-mm-thick CT sections from five data sets of canine lungs scanned via electron beam CT in vivo with lung volume held at a constant pressure. The method's performance was compared with that of the conventional 3-D region growing method. The method substantially outperformed an existing conventional approach to airway tree detection

  8. Two related algorithms for root-to-frontier tree pattern matching

    NARCIS (Netherlands)

    Cleophas, L.G.W.A.; Hemerik, C.; Zwaan, G.

    2006-01-01

    Tree pattern matching (TPM) algorithms on ordered, ranked trees play an important role in applications such as compilers and term rewriting systems. Many TPM algorithms appearing in the literature are based on tree automata. For efficiency, these automata should be deterministic, yet deterministic

  9. Tree decomposition based fast search of RNA structures including pseudoknots in genomes.

    Science.gov (United States)

    Song, Yinglei; Liu, Chunmei; Malmberg, Russell; Pan, Fangfang; Cai, Liming

    2005-01-01

    Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structure-sequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not been available. In this paper, a novel RNA structure profiling model is introduced based on the notion of a conformational graph to specify the consensus structure of an RNA family. Tree decomposition yields a small tree width t for such conformation graphs (e.g., t = 2 for stem loops and only a slight increase for pseudo-knots). Within this modelling framework, the optimal alignment of a sequence to the structure model corresponds to finding a maximum valued isomorphic subgraph and consequently can be accomplished through dynamic programming on the tree decomposition of the conformational graph in time O(k(t)N(2)), where k is a small parameter; and N is the size of the projiled RNA structure. Experiments show that the application of the alignment algorithm to search in genomes yields the same search accuracy as methods based on a Covariance model with a significant reduction in computation time. In particular; very accurate searches of tmRNAs in bacteria genomes and of telomerase RNAs in yeast genomes can be accomplished in days, as opposed to months required by other methods. The tree decomposition based searching tool is free upon request and can be downloaded at our site h t t p ://w.uga.edu/RNA-informatics/software/index.php.

  10. Refining discordant gene trees.

    Science.gov (United States)

    Górecki, Pawel; Eulenstein, Oliver

    2014-01-01

    Evolutionary studies are complicated by discordance between gene trees and the species tree in which they evolved. Dealing with discordant trees often relies on comparison costs between gene and species trees, including the well-established Robinson-Foulds, gene duplication, and deep coalescence costs. While these costs have provided credible results for binary rooted gene trees, corresponding cost definitions for non-binary unrooted gene trees, which are frequently occurring in practice, are challenged by biological realism. We propose a natural extension of the well-established costs for comparing unrooted and non-binary gene trees with rooted binary species trees using a binary refinement model. For the duplication cost we describe an efficient algorithm that is based on a linear time reduction and also computes an optimal rooted binary refinement of the given gene tree. Finally, we show that similar reductions lead to solutions for computing the deep coalescence and the Robinson-Foulds costs. Our binary refinement of Robinson-Foulds, gene duplication, and deep coalescence costs for unrooted and non-binary gene trees together with the linear time reductions provided here for computing these costs significantly extends the range of trees that can be incorporated into approaches dealing with discordance.

  11. A best-first tree-searching approach for ML decoding in MIMO system

    KAUST Repository

    Shen, Chung-An; Eltawil, Ahmed M.; Mondal, Sudip; Salama, Khaled N.

    2012-01-01

    In MIMO communication systems maximum-likelihood (ML) decoding can be formulated as a tree-searching problem. This paper presents a tree-searching approach that combines the features of classical depth-first and breadth-first approaches to achieve

  12. Efficient utilization of short rotation tree biomass for cooking in India

    Science.gov (United States)

    Sharma, R.; Chauhan, S. K.

    2012-04-01

    The human as well as livestock population increase is phenomenal in developing world including India. The survival of this huge population certainly depends on the carrying capacity of the natural systems, which is essentially determined by the nature itself. Present state of the forests can satisfy the needs of certain population and the demand for wood has rapidly outstripped the sustainability of forests. The fuelwood requirements in the developing world is approximately 80 per cent of total wood requirements and is the major cause of forest degradation. Therefore, there is need to maximize the productivity on one hand and protection/extention of the area on another hand. Wood substitution is an option including shifting from fuelwood for cooking to fossil fuels but in the changing climatic situation, this option is short term alternative. There is need to produce more and use the same efficiently to reduce the demands. Millions of households across the country are using crude cooking stoves for their daily needs which are not only energy inefficient but detrimental to women health also. It has been the policy of Government to encourage trees outside forests to minimize the pressure from forests through meeting requirements outside forests, which is possible through intensively managed short rotation forestry and also some initiatives have been taken to increase the fuelwood efficiency through improved cooking stove, which are working successfully. Woodfuel remained the most important source of household energy in India but regular attempts have not been made to improve the efficiency in its use. This paper will focus on potential of short rotation forestry plantations for energy consumption and its efficient use at domestic scale. This has three fold interrelated economic, environmental and social impact. Key words: Short Rotation Forestry, trees outside forests, wood energy, cooking stove

  13. The equivalence of information-theoretic and likelihood-based methods for neural dimensionality reduction.

    Directory of Open Access Journals (Sweden)

    Ross S Williamson

    2015-04-01

    Full Text Available Stimulus dimensionality-reduction methods in neuroscience seek to identify a low-dimensional space of stimulus features that affect a neuron's probability of spiking. One popular method, known as maximally informative dimensions (MID, uses an information-theoretic quantity known as "single-spike information" to identify this space. Here we examine MID from a model-based perspective. We show that MID is a maximum-likelihood estimator for the parameters of a linear-nonlinear-Poisson (LNP model, and that the empirical single-spike information corresponds to the normalized log-likelihood under a Poisson model. This equivalence implies that MID does not necessarily find maximally informative stimulus dimensions when spiking is not well described as Poisson. We provide several examples to illustrate this shortcoming, and derive a lower bound on the information lost when spiking is Bernoulli in discrete time bins. To overcome this limitation, we introduce model-based dimensionality reduction methods for neurons with non-Poisson firing statistics, and show that they can be framed equivalently in likelihood-based or information-theoretic terms. Finally, we show how to overcome practical limitations on the number of stimulus dimensions that MID can estimate by constraining the form of the non-parametric nonlinearity in an LNP model. We illustrate these methods with simulations and data from primate visual cortex.

  14. EEG feature selection method based on decision tree.

    Science.gov (United States)

    Duan, Lijuan; Ge, Hui; Ma, Wei; Miao, Jun

    2015-01-01

    This paper aims to solve automated feature selection problem in brain computer interface (BCI). In order to automate feature selection process, we proposed a novel EEG feature selection method based on decision tree (DT). During the electroencephalogram (EEG) signal processing, a feature extraction method based on principle component analysis (PCA) was used, and the selection process based on decision tree was performed by searching the feature space and automatically selecting optimal features. Considering that EEG signals are a series of non-linear signals, a generalized linear classifier named support vector machine (SVM) was chosen. In order to test the validity of the proposed method, we applied the EEG feature selection method based on decision tree to BCI Competition II datasets Ia, and the experiment showed encouraging results.

  15. A likelihood-based framework for the analysis of discussion threads

    NARCIS (Netherlands)

    Gómez, Vincenc; Kappen, Hilbert J.; Litvak, Nelli; Kaltenbrunner, Andreas

    2013-01-01

    Online discussion threads are conversational cascades in the form of posted messages that can be generally found in social systems that comprise many-to-many interaction such as blogs, news aggregators or bulletin board systems. We propose a framework based on generative models of growing trees to

  16. Likelihood-based inference for cointegration with nonlinear error-correction

    DEFF Research Database (Denmark)

    Kristensen, Dennis; Rahbek, Anders Christian

    2010-01-01

    We consider a class of nonlinear vector error correction models where the transfer function (or loadings) of the stationary relationships is nonlinear. This includes in particular the smooth transition models. A general representation theorem is given which establishes the dynamic properties...... and a linear trend in general. Gaussian likelihood-based estimators are considered for the long-run cointegration parameters, and the short-run parameters. Asymptotic theory is provided for these and it is discussed to what extend asymptotic normality and mixed normality can be found. A simulation study...

  17. PTree: pattern-based, stochastic search for maximum parsimony phylogenies

    Directory of Open Access Journals (Sweden)

    Ivan Gregor

    2013-06-01

    Full Text Available Phylogenetic reconstruction is vital to analyzing the evolutionary relationship of genes within and across populations of different species. Nowadays, with next generation sequencing technologies producing sets comprising thousands of sequences, robust identification of the tree topology, which is optimal according to standard criteria such as maximum parsimony, maximum likelihood or posterior probability, with phylogenetic inference methods is a computationally very demanding task. Here, we describe a stochastic search method for a maximum parsimony tree, implemented in a software package we named PTree. Our method is based on a new pattern-based technique that enables us to infer intermediate sequences efficiently where the incorporation of these sequences in the current tree topology yields a phylogenetic tree with a lower cost. Evaluation across multiple datasets showed that our method is comparable to the algorithms implemented in PAUP* or TNT, which are widely used by the bioinformatics community, in terms of topological accuracy and runtime. We show that our method can process large-scale datasets of 1,000–8,000 sequences. We believe that our novel pattern-based method enriches the current set of tools and methods for phylogenetic tree inference. The software is available under: http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/.

  18. PTree: pattern-based, stochastic search for maximum parsimony phylogenies.

    Science.gov (United States)

    Gregor, Ivan; Steinbrück, Lars; McHardy, Alice C

    2013-01-01

    Phylogenetic reconstruction is vital to analyzing the evolutionary relationship of genes within and across populations of different species. Nowadays, with next generation sequencing technologies producing sets comprising thousands of sequences, robust identification of the tree topology, which is optimal according to standard criteria such as maximum parsimony, maximum likelihood or posterior probability, with phylogenetic inference methods is a computationally very demanding task. Here, we describe a stochastic search method for a maximum parsimony tree, implemented in a software package we named PTree. Our method is based on a new pattern-based technique that enables us to infer intermediate sequences efficiently where the incorporation of these sequences in the current tree topology yields a phylogenetic tree with a lower cost. Evaluation across multiple datasets showed that our method is comparable to the algorithms implemented in PAUP* or TNT, which are widely used by the bioinformatics community, in terms of topological accuracy and runtime. We show that our method can process large-scale datasets of 1,000-8,000 sequences. We believe that our novel pattern-based method enriches the current set of tools and methods for phylogenetic tree inference. The software is available under: http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/.

  19. Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

    Energy Technology Data Exchange (ETDEWEB)

    N. Price, Morgan; S. Dehal, Paramvir; P. Arkin, Adam

    2009-07-31

    Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

  20. Maximum Likelihood and Restricted Likelihood Solutions in Multiple-Method Studies.

    Science.gov (United States)

    Rukhin, Andrew L

    2011-01-01

    A formulation of the problem of combining data from several sources is discussed in terms of random effects models. The unknown measurement precision is assumed not to be the same for all methods. We investigate maximum likelihood solutions in this model. By representing the likelihood equations as simultaneous polynomial equations, the exact form of the Groebner basis for their stationary points is derived when there are two methods. A parametrization of these solutions which allows their comparison is suggested. A numerical method for solving likelihood equations is outlined, and an alternative to the maximum likelihood method, the restricted maximum likelihood, is studied. In the situation when methods variances are considered to be known an upper bound on the between-method variance is obtained. The relationship between likelihood equations and moment-type equations is also discussed.

  1. Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent.

    Science.gov (United States)

    Allman, Elizabeth S; Degnan, James H; Rhodes, John A

    2011-06-01

    Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals-each with many genes-splitting into new populations or species. The coalescent process, which models ancestry of gene copies within populations, is often used to model the probability distribution of gene trees given a fixed species tree. This multispecies coalescent model provides a framework for phylogeneticists to infer species trees from gene trees using maximum likelihood or Bayesian approaches. Because the coalescent models a branching process over time, all trees are typically assumed to be rooted in this setting. Often, however, gene trees inferred by traditional phylogenetic methods are unrooted. We investigate probabilities of unrooted gene trees under the multispecies coalescent model. We show that when there are four species with one gene sampled per species, the distribution of unrooted gene tree topologies identifies the unrooted species tree topology and some, but not all, information in the species tree edges (branch lengths). The location of the root on the species tree is not identifiable in this situation. However, for 5 or more species with one gene sampled per species, we show that the distribution of unrooted gene tree topologies identifies the rooted species tree topology and all its internal branch lengths. The length of any pendant branch leading to a leaf of the species tree is also identifiable for any species from which more than one gene is sampled.

  2. Efficient parsimony-based methods for phylogenetic network reconstruction.

    Science.gov (United States)

    Jin, Guohua; Nakhleh, Luay; Snir, Sagi; Tuller, Tamir

    2007-01-15

    Phylogenies--the evolutionary histories of groups of organisms-play a major role in representing relationships among biological entities. Although many biological processes can be effectively modeled as tree-like relationships, others, such as hybrid speciation and horizontal gene transfer (HGT), result in networks, rather than trees, of relationships. Hybrid speciation is a significant evolutionary mechanism in plants, fish and other groups of species. HGT plays a major role in bacterial genome diversification and is a significant mechanism by which bacteria develop resistance to antibiotics. Maximum parsimony is one of the most commonly used criteria for phylogenetic tree inference. Roughly speaking, inference based on this criterion seeks the tree that minimizes the amount of evolution. In 1990, Jotun Hein proposed using this criterion for inferring the evolution of sequences subject to recombination. Preliminary results on small synthetic datasets. Nakhleh et al. (2005) demonstrated the criterion's application to phylogenetic network reconstruction in general and HGT detection in particular. However, the naive algorithms used by the authors are inapplicable to large datasets due to their demanding computational requirements. Further, no rigorous theoretical analysis of computing the criterion was given, nor was it tested on biological data. In the present work we prove that the problem of scoring the parsimony of a phylogenetic network is NP-hard and provide an improved fixed parameter tractable algorithm for it. Further, we devise efficient heuristics for parsimony-based reconstruction of phylogenetic networks. We test our methods on both synthetic and biological data (rbcL gene in bacteria) and obtain very promising results.

  3. Pareto Efficient Solution of Attack-Defence Trees

    NARCIS (Netherlands)

    Aslanyan, Zaruhi; Nielson, Flemming

    Attack-defence trees are a promising approach for representing threat scenarios and possible countermeasures in a concise and intuitive manner. An attack-defence tree describes the interaction between an attacker and a defender, and is evaluated by assigning parameters to the nodes, such as

  4. Safe semi-supervised learning based on weighted likelihood.

    Science.gov (United States)

    Kawakita, Masanori; Takeuchi, Jun'ichi

    2014-05-01

    We are interested in developing a safe semi-supervised learning that works in any situation. Semi-supervised learning postulates that n(') unlabeled data are available in addition to n labeled data. However, almost all of the previous semi-supervised methods require additional assumptions (not only unlabeled data) to make improvements on supervised learning. If such assumptions are not met, then the methods possibly perform worse than supervised learning. Sokolovska, Cappé, and Yvon (2008) proposed a semi-supervised method based on a weighted likelihood approach. They proved that this method asymptotically never performs worse than supervised learning (i.e., it is safe) without any assumption. Their method is attractive because it is easy to implement and is potentially general. Moreover, it is deeply related to a certain statistical paradox. However, the method of Sokolovska et al. (2008) assumes a very limited situation, i.e., classification, discrete covariates, n(')→∞ and a maximum likelihood estimator. In this paper, we extend their method by modifying the weight. We prove that our proposal is safe in a significantly wide range of situations as long as n≤n('). Further, we give a geometrical interpretation of the proof of safety through the relationship with the above-mentioned statistical paradox. Finally, we show that the above proposal is asymptotically safe even when n(')

  5. Recent trends in the intrinsic water-use efficiency of ringless rainforest trees in Borneo.

    Science.gov (United States)

    Loader, N J; Walsh, R P D; Robertson, I; Bidin, K; Ong, R C; Reynolds, G; McCarroll, D; Gagen, M; Young, G H F

    2011-11-27

    Stable carbon isotope (δ(13)C) series were developed from analysis of sequential radial wood increments from AD 1850 to AD 2009 for four mature primary rainforest trees from the Danum and Imbak areas of Sabah, Malaysia. The aseasonal equatorial climate meant that conventional dendrochronology was not possible as the tree species investigated do not exhibit clear annual rings or dateable growth bands. Chronology was established using radiocarbon dating to model age-growth relationships and date the carbon isotopic series from which the intrinsic water-use efficiency (IWUE) was calculated. The two Eusideroxylon zwageri trees from Imbak yielded ages of their pith/central wood (±1 sigma) of 670 ± 40 and 759 ± 40 years old; the less dense Shorea johorensis and Shorea superba trees at Danum yielded ages of 240 ± 40 and 330 ± 40 years, respectively. All trees studied exhibit an increase in the IWUE since AD 1960. This reflects, in part, a response of the forest to increasing atmospheric carbon dioxide concentration. Unlike studies of some northern European trees, no clear plateau in this response was observed. A change in the IWUE implies an associated modification of the local carbon and/or hydrological cycles. To resolve these uncertainties, a shift in emphasis away from high-resolution studies towards long, well-replicated time series is proposed to develop the environmental data essential for model evaluation. Identification of old (greater than 700 years) ringless trees demonstrates their potential in assessing the impacts of climatic and atmospheric change. It also shows the scientific and applied value of a conservation policy that ensures the survival of primary forest containing particularly old trees (as in Imbak Canyon and Danum).

  6. Improving the water use efficiency of olive trees growing in water harvesting systems

    Science.gov (United States)

    Berliner, Pedro; Leake, Salomon; Carmi, Gennady; Agam, Nurit

    2017-04-01

    Water is a primary limiting factor for agricultural development in many arid and semi-arid regions in which a runoff generation is a rather frequent event. If conveyed to dyke surrounded plots and ponded, runoff water can thereafter be used for tree production. One of the most promising runoff collection configurations is that of micro-catchments in which water is collected close to the area in which runoff was generated and stored in adjacent shallow pits. The objective of this work was to assess the effect of the geometry of runoff water collection area (shallow pit or trench) on direct evaporative water losses and on the water use efficiency of olive trees grown in them. The study was conducted during the summer of 2013 and 2014. In this study regular micro-catchments with basins of 9 m2 (3 x 3 m) by 0.1 m deep were compared with trenches of one meter deep and one meter wide. Each configuration was replicated three times. One tree was planted in each shallow basin and the distance between trees in the 12 m long trench was four meters. Access tubes for neutron probes were installed in the micro-catchments and trenches (four and seven, respectively) to depths of 2.5 m. Soil water content in the soil profile was monitored periodically throughout drying periods in between simulated runoff events. Transpiration of the trees was estimated from half-hourly sap flow measurements using a Granier system. Total transpiration fluxes were computed for time intervals corresponding to consecutive soil water measurements. During the first year, a large runoff event was simulated by applying once four cubic meters to each plot; and in the second year the same volume of water was split into four applications, simulating a series of small runoff events. In both geometries, trees received the same amount of water per tree. Evaporation from trenches and micro-catchments was estimated as the difference between evapotranspiration obtained computing the differences in total soil water

  7. Enhanced photosynthetic efficiency in trees world-wide by rising atmospheric CO2 levels

    Science.gov (United States)

    Ehlers, Ina; Wieloch, Thomas; Groenendijk, Peter; Vlam, Mart; van der Sleen, Peter; Zuidema, Pieter A.; Robertson, Iain; Schleucher, Jürgen

    2014-05-01

    signals is a fundamental advantage of isotopomer ratios (Augusti et al., Chem. Geol 2008). These results demonstrate that increasing [CO2] has reduced the ratio of photorespiration to photosynthesis on a global scale. Photorespiration is a side reaction that decreases the C gain of plants; the suppression of photorespiration in all analyzed trees indicates that increasing atmospheric [CO2] is enhancing the photosynthetic efficiency of trees world-wide. The consensus response of the trees agrees with the response of annual plants in greenhouse experiments, with three important conclusions. First, the generality of the isotopomer shift confirms that the CO2 response reflects the ratio of photosynthesis to photorespiration, and that it creates a robust signal in tree rings. Second, the agreement between greenhouse-grown plants and trees indicates that there has not been an acclimation response of the trees during the past centuries. Third, the results show that the regulation of tree gas exchange has during past centuries been governed by the same rules as observed in manipulative experiments, in contradiction to recent reports (Keenan et al., Nature 2013).

  8. On the quirks of maximum parsimony and likelihood on phylogenetic networks.

    Science.gov (United States)

    Bryant, Christopher; Fischer, Mareike; Linz, Simone; Semple, Charles

    2017-03-21

    Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe evolution accurately. For instance, processes like hybridization or lateral gene transfer that are commonplace in many groups of organisms and result in mosaic patterns of relationships cannot be represented by a single phylogenetic tree. This is why phylogenetic networks, which can display such events, are becoming of more and more interest in phylogenetic research. It is therefore necessary to extend concepts like maximum parsimony from phylogenetic trees to networks. Several suggestions for possible extensions can be found in recent literature, for instance the softwired and the hardwired parsimony concepts. In this paper, we analyze the so-called big parsimony problem under these two concepts, i.e. we investigate maximum parsimonious networks and analyze their properties. In particular, we show that finding a softwired maximum parsimony network is possible in polynomial time. We also show that the set of maximum parsimony networks for the hardwired definition always contains at least one phylogenetic tree. Lastly, we investigate some parallels of parsimony to different likelihood concepts on phylogenetic networks. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Coalescent-Based Analyses of Genomic Sequence Data Provide a Robust Resolution of Phylogenetic Relationships among Major Groups of Gibbons

    Science.gov (United States)

    Shi, Cheng-Min; Yang, Ziheng

    2018-01-01

    Abstract The phylogenetic relationships among extant gibbon species remain unresolved despite numerous efforts using morphological, behavorial, and genetic data and the sequencing of whole genomes. A major challenge in reconstructing the gibbon phylogeny is the radiative speciation process, which resulted in extremely short internal branches in the species phylogeny and extensive incomplete lineage sorting with extensive gene-tree heterogeneity across the genome. Here, we analyze two genomic-scale data sets, with ∼10,000 putative noncoding and exonic loci, respectively, to estimate the species tree for the major groups of gibbons. We used the Bayesian full-likelihood method bpp under the multispecies coalescent model, which naturally accommodates incomplete lineage sorting and uncertainties in the gene trees. For comparison, we included three heuristic coalescent-based methods (mp-est, SVDQuartets, and astral) as well as concatenation. From both data sets, we infer the phylogeny for the four extant gibbon genera to be (Hylobates, (Nomascus, (Hoolock, Symphalangus))). We used simulation guided by the real data to evaluate the accuracy of the methods used. Astral, while not as efficient as bpp, performed well in estimation of the species tree even in presence of excessive incomplete lineage sorting. Concatenation, mp-est and SVDQuartets were unreliable when the species tree contains very short internal branches. Likelihood ratio test of gene flow suggests a small amount of migration from Hylobates moloch to H. pileatus, while cross-genera migration is absent or rare. Our results highlight the utility of coalescent-based methods in addressing challenging species tree problems characterized by short internal branches and rampant gene tree-species tree discordance. PMID:29087487

  10. Generic physical protection logic trees

    International Nuclear Information System (INIS)

    Paulus, W.K.

    1981-10-01

    Generic physical protection logic trees, designed for application to nuclear facilities and materials, are presented together with a method of qualitative evaluation of the trees for design and analysis of physical protection systems. One or more defense zones are defined where adversaries interact with the physical protection system. Logic trees that are needed to describe the possible scenarios within a defense zone are selected. Elements of a postulated or existing physical protection system are tagged to the primary events of the logic tree. The likelihood of adversary success in overcoming these elements is evaluated on a binary, yes/no basis. The effect of these evaluations is propagated through the logic of each tree to determine whether the adversary is likely to accomplish the end event of the tree. The physical protection system must be highly likely to overcome the adversary before he accomplishes his objective. The evaluation must be conducted for all significant states of the site. Deficiencies uncovered become inputs to redesign and further analysis, closing the loop on the design/analysis cycle

  11. Generic physical protection logic trees

    Energy Technology Data Exchange (ETDEWEB)

    Paulus, W.K.

    1981-10-01

    Generic physical protection logic trees, designed for application to nuclear facilities and materials, are presented together with a method of qualitative evaluation of the trees for design and analysis of physical protection systems. One or more defense zones are defined where adversaries interact with the physical protection system. Logic trees that are needed to describe the possible scenarios within a defense zone are selected. Elements of a postulated or existing physical protection system are tagged to the primary events of the logic tree. The likelihood of adversary success in overcoming these elements is evaluated on a binary, yes/no basis. The effect of these evaluations is propagated through the logic of each tree to determine whether the adversary is likely to accomplish the end event of the tree. The physical protection system must be highly likely to overcome the adversary before he accomplishes his objective. The evaluation must be conducted for all significant states of the site. Deficiencies uncovered become inputs to redesign and further analysis, closing the loop on the design/analysis cycle.

  12. A Voxel-Based Method for Automated Identification and Morphological Parameters Estimation of Individual Street Trees from Mobile Laser Scanning Data

    Directory of Open Access Journals (Sweden)

    Hongxing Liu

    2013-01-01

    Full Text Available As an important component of urban vegetation, street trees play an important role in maintenance of environmental quality, aesthetic beauty of urban landscape, and social service for inhabitants. Acquiring accurate and up-to-date inventory information for street trees is required for urban horticultural planning, and municipal urban forest management. This paper presents a new Voxel-based Marked Neighborhood Searching (VMNS method for efficiently identifying street trees and deriving their morphological parameters from Mobile Laser Scanning (MLS point cloud data. The VMNS method consists of six technical components: voxelization, calculating values of voxels, searching and marking neighborhoods, extracting potential trees, deriving morphological parameters, and eliminating pole-like objects other than trees. The method is validated and evaluated through two case studies. The evaluation results show that the completeness and correctness of our method for street tree detection are over 98%. The derived morphological parameters, including tree height, crown diameter, diameter at breast height (DBH, and crown base height (CBH, are in a good agreement with the field measurements. Our method provides an effective tool for extracting various morphological parameters for individual street trees from MLS point cloud data.

  13. Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction.

    Science.gov (United States)

    Sayyari, Erfan; Mirarab, Siavash

    2016-11-11

    Inferring species trees from gene trees using the coalescent-based summary methods has been the subject of much attention, yet new scalable and accurate methods are needed. We introduce DISTIQUE, a new statistically consistent summary method for inferring species trees from gene trees under the coalescent model. We generalize our results to arbitrary phylogenetic inference problems; we show that two arbitrarily chosen leaves, called anchors, can be used to estimate relative distances between all other pairs of leaves by inferring relevant quartet trees. This results in a family of distance-based tree inference methods, with running times ranging between quadratic to quartic in the number of leaves. We show in simulated studies that DISTIQUE has comparable accuracy to leading coalescent-based summary methods and reduced running times.

  14. Efficient method for computing the maximum-likelihood quantum state from measurements with additive Gaussian noise.

    Science.gov (United States)

    Smolin, John A; Gambetta, Jay M; Smith, Graeme

    2012-02-17

    We provide an efficient method for computing the maximum-likelihood mixed quantum state (with density matrix ρ) given a set of measurement outcomes in a complete orthonormal operator basis subject to Gaussian noise. Our method works by first changing basis yielding a candidate density matrix μ which may have nonphysical (negative) eigenvalues, and then finding the nearest physical state under the 2-norm. Our algorithm takes at worst O(d(4)) for the basis change plus O(d(3)) for finding ρ where d is the dimension of the quantum state. In the special case where the measurement basis is strings of Pauli operators, the basis change takes only O(d(3)) as well. The workhorse of the algorithm is a new linear-time method for finding the closest probability distribution (in Euclidean distance) to a set of real numbers summing to one.

  15. A broad scale analysis of tree risk, mitigation and potential habitat for cavity-nesting birds

    Science.gov (United States)

    Brian Kane; Paige S. Warren; Susannah B. Lerman

    2015-01-01

    Trees in towns and cities provide habitat for wildlife. In particular, cavity-nesting birds nest in the deadand decayed stems and branches of these trees. The same dead and decayed stems and branches alsohave a greater likelihood of failure, which, in some circumstances, increases risk. We examined 1760trees in Baltimore, MD, USA and western MA, USA, assessing tree...

  16. Failure diagnosis and fault tree analysis

    International Nuclear Information System (INIS)

    Weber, G.

    1982-07-01

    In this report a methodology of failure diagnosis for complex systems is presented. Systems which can be represented by fault trees are considered. This methodology is based on switching algebra, failure diagnosis of digital circuits and fault tree analysis. Relations between these disciplines are shown. These relations are due to Boolean algebra and Boolean functions used throughout. It will be shown on this basis that techniques of failure diagnosis and fault tree analysis are useful to solve the following problems: 1. describe an efficient search of all failed components if the system is failed. 2. Describe an efficient search of all states which are close to a system failure if the system is still operating. The first technique will improve the availability, the second the reliability and safety. For these problems, the relation to methods of failure diagnosis for combinational circuits is required. Moreover, the techniques are demonstrated for a number of systems which can be represented by fault trees. (orig./RW) [de

  17. Automated detection of microcalcification clusters in digital mammograms based on wavelet domain hidden Markov tree modeling

    International Nuclear Information System (INIS)

    Regentova, E.; Zhang, L.; Veni, G.; Zheng, J.

    2007-01-01

    A system is designed for detecting microcalcification clusters (MCC) in digital mammograms. The system is intended for computer-aided diagnostic prompting. Further discrimination of MCC as benign or malignant is assumed to be performed by radiologists. Processing of mammograms is based on the statistical modeling by means of wavelet domain hidden markov trees (WHMT). Segmentation is performed by the weighted likelihood evaluation followed by the classification based on spatial filters for a single microcalcification (MC) and a cluster of MC detection. The analysis is carried out on FROC curves for 40 mammograms from the mini-MIAS database and for 100 mammograms with 50 cancerous and 50 benign cases from DDSM database. The designed system is capable to detect 100% of true positive cases in these sets. The rate of false positives is 2.9 per case for mini-MIAS dataset; and 0.01 for the DDSM images. (orig.)

  18. Predicting gene function using hierarchical multi-label decision tree ensembles

    Directory of Open Access Journals (Sweden)

    Kocev Dragi

    2010-01-01

    Full Text Available Abstract Background S. cerevisiae, A. thaliana and M. musculus are well-studied organisms in biology and the sequencing of their genomes was completed many years ago. It is still a challenge, however, to develop methods that assign biological functions to the ORFs in these genomes automatically. Different machine learning methods have been proposed to this end, but it remains unclear which method is to be preferred in terms of predictive performance, efficiency and usability. Results We study the use of decision tree based models for predicting the multiple functions of ORFs. First, we describe an algorithm for learning hierarchical multi-label decision trees. These can simultaneously predict all the functions of an ORF, while respecting a given hierarchy of gene functions (such as FunCat or GO. We present new results obtained with this algorithm, showing that the trees found by it exhibit clearly better predictive performance than the trees found by previously described methods. Nevertheless, the predictive performance of individual trees is lower than that of some recently proposed statistical learning methods. We show that ensembles of such trees are more accurate than single trees and are competitive with state-of-the-art statistical learning and functional linkage methods. Moreover, the ensemble method is computationally efficient and easy to use. Conclusions Our results suggest that decision tree based methods are a state-of-the-art, efficient and easy-to-use approach to ORF function prediction.

  19. Nonbinary Tree-Based Phylogenetic Networks

    NARCIS (Netherlands)

    Jetten, L.; van Iersel, L.J.J.

    2018-01-01

    Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can for example

  20. Maximum parsimony, substitution model, and probability phylogenetic trees.

    Science.gov (United States)

    Weng, J F; Thomas, D A; Mareels, I

    2011-01-01

    The problem of inferring phylogenies (phylogenetic trees) is one of the main problems in computational biology. There are three main methods for inferring phylogenies-Maximum Parsimony (MP), Distance Matrix (DM) and Maximum Likelihood (ML), of which the MP method is the most well-studied and popular method. In the MP method the optimization criterion is the number of substitutions of the nucleotides computed by the differences in the investigated nucleotide sequences. However, the MP method is often criticized as it only counts the substitutions observable at the current time and all the unobservable substitutions that really occur in the evolutionary history are omitted. In order to take into account the unobservable substitutions, some substitution models have been established and they are now widely used in the DM and ML methods but these substitution models cannot be used within the classical MP method. Recently the authors proposed a probability representation model for phylogenetic trees and the reconstructed trees in this model are called probability phylogenetic trees. One of the advantages of the probability representation model is that it can include a substitution model to infer phylogenetic trees based on the MP principle. In this paper we explain how to use a substitution model in the reconstruction of probability phylogenetic trees and show the advantage of this approach with examples.

  1. Efficient algorithms for maximum likelihood decoding in the surface code

    Science.gov (United States)

    Bravyi, Sergey; Suchara, Martin; Vargo, Alexander

    2014-09-01

    We describe two implementations of the optimal error correction algorithm known as the maximum likelihood decoder (MLD) for the two-dimensional surface code with a noiseless syndrome extraction. First, we show how to implement MLD exactly in time O (n2), where n is the number of code qubits. Our implementation uses a reduction from MLD to simulation of matchgate quantum circuits. This reduction however requires a special noise model with independent bit-flip and phase-flip errors. Secondly, we show how to implement MLD approximately for more general noise models using matrix product states (MPS). Our implementation has running time O (nχ3), where χ is a parameter that controls the approximation precision. The key step of our algorithm, borrowed from the density matrix renormalization-group method, is a subroutine for contracting a tensor network on the two-dimensional grid. The subroutine uses MPS with a bond dimension χ to approximate the sequence of tensors arising in the course of contraction. We benchmark the MPS-based decoder against the standard minimum weight matching decoder observing a significant reduction of the logical error probability for χ ≥4.

  2. Carbon Sequestration Estimation of Street Trees Based on Point Cloud from Vehicle-Borne Laser Scanning System

    Science.gov (United States)

    Zhao, Y.; Hu, Q.

    2017-09-01

    Continuous development of urban road traffic system requests higher standards of road ecological environment. Ecological benefits of street trees are getting more attention. Carbon sequestration of street trees refers to the carbon stocks of street trees, which can be a measurement for ecological benefits of street trees. Estimating carbon sequestration in a traditional way is costly and inefficient. In order to solve above problems, a carbon sequestration estimation approach for street trees based on 3D point cloud from vehicle-borne laser scanning system is proposed in this paper. The method can measure the geometric parameters of a street tree, including tree height, crown width, diameter at breast height (DBH), by processing and analyzing point cloud data of an individual tree. Four Chinese scholartree trees and four camphor trees are selected for experiment. The root mean square error (RMSE) of tree height is 0.11m for Chinese scholartree and 0.02m for camphor. Crown widths in X direction and Y direction, as well as the average crown width are calculated. And the RMSE of average crown width is 0.22m for Chinese scholartree and 0.10m for camphor. The last calculated parameter is DBH, the RMSE of DBH is 0.5cm for both Chinese scholartree and camphor. Combining the measured geometric parameters and an appropriate carbon sequestration calculation model, the individual tree's carbon sequestration will be estimated. The proposed method can help enlarge application range of vehicle-borne laser point cloud data, improve the efficiency of estimating carbon sequestration, construct urban ecological environment and manage landscape.

  3. A biclustering algorithm for binary matrices based on penalized Bernoulli likelihood

    KAUST Repository

    Lee, Seokho

    2013-01-31

    We propose a new biclustering method for binary data matrices using the maximum penalized Bernoulli likelihood estimation. Our method applies a multi-layer model defined on the logits of the success probabilities, where each layer represents a simple bicluster structure and the combination of multiple layers is able to reveal complicated, multiple biclusters. The method allows for non-pure biclusters, and can simultaneously identify the 1-prevalent blocks and 0-prevalent blocks. A computationally efficient algorithm is developed and guidelines are provided for specifying the tuning parameters, including initial values of model parameters, the number of layers, and the penalty parameters. Missing-data imputation can be handled in the EM framework. The method is tested using synthetic and real datasets and shows good performance. © 2013 Springer Science+Business Media New York.

  4. MixtureTree annotator: a program for automatic colorization and visual annotation of MixtureTree.

    Directory of Open Access Journals (Sweden)

    Shu-Chuan Chen

    Full Text Available The MixtureTree Annotator, written in JAVA, allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides a unique advantage over any other programs which perform a similar function. In addition, the MixtureTree Annotator is the only package that can efficiently annotate the output produced by MixtureTree with mutation information and coalescent time information. In order to visualize the resulting output file, a modified version of FigTree is used. Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy. In addition to allowing the user to automatically color any given Newick tree by sequence name, the MixtureTree Annotator is the only method that allows the user to automatically annotate the resulting tree created by the MixtureTree program. The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.

  5. Fitting Markovian binary trees using global and individual demographic data

    OpenAIRE

    Hautphenne, Sophie; Massaro, Melanie; Turner, Katharine

    2017-01-01

    We consider a class of branching processes called Markovian binary trees, in which the individuals lifetime and reproduction epochs are modeled using a transient Markovian arrival process (TMAP). We estimate the parameters of the TMAP based on population data containing information on age-specific fertility and mortality rates. Depending on the degree of detail of the available data, a weighted non-linear regression method or a maximum likelihood method is applied. We discuss the optimal choi...

  6. Utilising Tree-Based Ensemble Learning for Speaker Segmentation

    DEFF Research Database (Denmark)

    Abou-Zleikha, Mohamed; Tan, Zheng-Hua; Christensen, Mads Græsbøll

    2014-01-01

    In audio and speech processing, accurate detection of the changing points between multiple speakers in speech segments is an important stage for several applications such as speaker identification and tracking. Bayesian Information Criteria (BIC)-based approaches are the most traditionally used...... for a certain condition, the model becomes biased to the data used for training limiting the model’s generalisation ability. In this paper, we propose a BIC-based tuning-free approach for speaker segmentation through the use of ensemble-based learning. A forest of segmentation trees is constructed in which each...... tree is trained using a sampled version of the speech segment. During the tree construction process, a set of randomly selected points in the input sequence is examined as potential segmentation points. The point that yields the highest ΔBIC is chosen and the same process is repeated for the resultant...

  7. Corporate brand extensions based on the purchase likelihood: governance implications

    Directory of Open Access Journals (Sweden)

    Spyridon Goumas

    2018-03-01

    Full Text Available This paper is examining the purchase likelihood of hypothetical service brand extensions from product companies focusing on consumer electronics based on sector categorization and perceptions of fit between the existing product category and image of the company. Prior research has recognized that levels of brand knowledge eases the transference of associations and affect to the new products. Similarity to the existing products of the parent company and perceived image also influence the success of brand extensions. However, sector categorization may interfere with this relationship. The purpose of this study is to examine Greek consumers’ attitudes towards hypothetical brand extensions, and how these are affected by consumers’ existing knowledge about the brand, sector categorization and perceptions of image and category fit of cross-sector extensions. This aim is examined in the context of technological categories, where less-known companies exhibited significance in purchase likelihood, and contradictory with the existing literature, service companies did not perform as positively as expected. Additional insights to the existing literature about sector categorization are provided. The effect of both image and category fit is also examined and predictions regarding the effect of each are made.

  8. Component-based modeling of systems for automated fault tree generation

    International Nuclear Information System (INIS)

    Majdara, Aref; Wakabayashi, Toshio

    2009-01-01

    One of the challenges in the field of automated fault tree construction is to find an efficient modeling approach that can support modeling of different types of systems without ignoring any necessary details. In this paper, we are going to represent a new system of modeling approach for computer-aided fault tree generation. In this method, every system model is composed of some components and different types of flows propagating through them. Each component has a function table that describes its input-output relations. For the components having different operational states, there is also a state transition table. Each component can communicate with other components in the system only through its inputs and outputs. A trace-back algorithm is proposed that can be applied to the system model to generate the required fault trees. The system modeling approach and the fault tree construction algorithm are applied to a fire sprinkler system and the results are presented

  9. Simple street tree sampling

    Science.gov (United States)

    David J. Nowak; Jeffrey T. Walton; James Baldwin; Jerry. Bond

    2015-01-01

    Information on street trees is critical for management of this important resource. Sampling of street tree populations provides an efficient means to obtain street tree population information. Long-term repeat measures of street tree samples supply additional information on street tree changes and can be used to report damages from catastrophic events. Analyses of...

  10. Efficient FPT Algorithms for (Strict) Compatibility of Unrooted Phylogenetic Trees.

    Science.gov (United States)

    Baste, Julien; Paul, Christophe; Sau, Ignasi; Scornavacca, Celine

    2017-04-01

    In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species X; these relationships are often depicted via a phylogenetic tree-a tree having its leaves labeled bijectively by elements of X and without degree-2 nodes-called the "species tree." One common approach for reconstructing a species tree consists in first constructing several phylogenetic trees from primary data (e.g., DNA sequences originating from some species in X), and then constructing a single phylogenetic tree maximizing the "concordance" with the input trees. The obtained tree is our estimation of the species tree and, when the input trees are defined on overlapping-but not identical-sets of labels, is called "supertree." In this paper, we focus on two problems that are central when combining phylogenetic trees into a supertree: the compatibility and the strict compatibility problems for unrooted phylogenetic trees. These problems are strongly related, respectively, to the notions of "containing as a minor" and "containing as a topological minor" in the graph community. Both problems are known to be fixed parameter tractable in the number of input trees k, by using their expressibility in monadic second-order logic and a reduction to graphs of bounded treewidth. Motivated by the fact that the dependency on k of these algorithms is prohibitively large, we give the first explicit dynamic programming algorithms for solving these problems, both running in time [Formula: see text], where n is the total size of the input.

  11. Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies.

    Science.gov (United States)

    Leaché, Adam D; Banbury, Barbara L; Felsenstein, Joseph; de Oca, Adrián Nieto-Montes; Stamatakis, Alexandros

    2015-11-01

    Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD loci for phylogenetic inference. We compare the two primary ways RAD loci are used during phylogenetic analysis, including the analysis of full sequences (i.e., SNPs together with invariant sites), or the analysis of SNPs on their own after excluding invariant sites. We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy, but not of computational time. We introduce two new acquisition bias corrections for dealing with alignments composed exclusively of SNPs, a conditional likelihood method and a reconstituted DNA approach. The conditional likelihood method conditions on the presence of variable characters only (the number of invariant sites that are unsampled but known to exist is not considered), while the reconstituted DNA approach requires the user to specify the exact number of unsampled invariant sites prior to the analysis. Under simulation, branch length biases increase with the amount of missing data for both acquisition bias correction methods, but branch length accuracy is much improved in the reconstituted DNA approach compared to the conditional likelihood approach. Phylogenetic analyses of the empirical data using concatenation or a coalescent-based species tree approach provide strong support for many of the accepted relationships among phrynosomatid lizards, suggesting that RAD loci contain useful phylogenetic signal across a range of divergence times despite the

  12. Coalescent methods for estimating phylogenetic trees.

    Science.gov (United States)

    Liu, Liang; Yu, Lili; Kubatko, Laura; Pearl, Dennis K; Edwards, Scott V

    2009-10-01

    We review recent models to estimate phylogenetic trees under the multispecies coalescent. Although the distinction between gene trees and species trees has come to the fore of phylogenetics, only recently have methods been developed that explicitly estimate species trees. Of the several factors that can cause gene tree heterogeneity and discordance with the species tree, deep coalescence due to random genetic drift in branches of the species tree has been modeled most thoroughly. Bayesian approaches to estimating species trees utilizes two likelihood functions, one of which has been widely used in traditional phylogenetics and involves the model of nucleotide substitution, and the second of which is less familiar to phylogeneticists and involves the probability distribution of gene trees given a species tree. Other recent parametric and nonparametric methods for estimating species trees involve parsimony criteria, summary statistics, supertree and consensus methods. Species tree approaches are an appropriate goal for systematics, appear to work well in some cases where concatenation can be misleading, and suggest that sampling many independent loci will be paramount. Such methods can also be challenging to implement because of the complexity of the models and computational time. In addition, further elaboration of the simplest of coalescent models will be required to incorporate commonly known issues such as deviation from the molecular clock, gene flow and other genetic forces.

  13. Weighted profile likelihood-based confidence interval for the difference between two proportions with paired binomial data.

    Science.gov (United States)

    Pradhan, Vivek; Saha, Krishna K; Banerjee, Tathagata; Evans, John C

    2014-07-30

    Inference on the difference between two binomial proportions in the paired binomial setting is often an important problem in many biomedical investigations. Tang et al. (2010, Statistics in Medicine) discussed six methods to construct confidence intervals (henceforth, we abbreviate it as CI) for the difference between two proportions in paired binomial setting using method of variance estimates recovery. In this article, we propose weighted profile likelihood-based CIs for the difference between proportions of a paired binomial distribution. However, instead of the usual likelihood, we use weighted likelihood that is essentially making adjustments to the cell frequencies of a 2 × 2 table in the spirit of Agresti and Min (2005, Statistics in Medicine). We then conduct numerical studies to compare the performances of the proposed CIs with that of Tang et al. and Agresti and Min in terms of coverage probabilities and expected lengths. Our numerical study clearly indicates that the weighted profile likelihood-based intervals and Jeffreys interval (cf. Tang et al.) are superior in terms of achieving the nominal level, and in terms of expected lengths, they are competitive. Finally, we illustrate the use of the proposed CIs with real-life examples. Copyright © 2014 John Wiley & Sons, Ltd.

  14. Monitoring individual tree-based change with airborne lidar.

    Science.gov (United States)

    Duncanson, Laura; Dubayah, Ralph

    2018-05-01

    Understanding the carbon flux of forests is critical for constraining the global carbon cycle and managing forests to mitigate climate change. Monitoring forest growth and mortality rates is critical to this effort, but has been limited in the past, with estimates relying primarily on field surveys. Advances in remote sensing enable the potential to monitor tree growth and mortality across landscapes. This work presents an approach to measure tree growth and loss using multidate lidar campaigns in a high-biomass forest in California, USA. Individual tree crowns were delineated in 2008 and again in 2013 using a 3D crown segmentation algorithm, with derived heights and crown radii extracted and used to estimate individual tree aboveground biomass. Tree growth, loss, and aboveground biomass were analyzed with respect to tree height and crown radius. Both tree growth and loss rates decrease with increasing tree height, following the expectation that trees slow in growth rate as they age. Additionally, our aboveground biomass analysis suggests that, while the system is a net source of aboveground carbon, these carbon dynamics are governed by size class with the largest sources coming from the loss of a relatively small number of large individuals. This study demonstrates that monitoring individual tree-based growth and loss can be conducted with multidate airborne lidar, but these methods remain relatively immature. Disparities between lidar acquisitions were particularly difficult to overcome and decreased the sample of trees analyzed for growth rate in this study to 21% of the full number of delineated crowns. However, this study illuminates the potential of airborne remote sensing for ecologically meaningful forest monitoring at an individual tree level. As methods continue to improve, airborne multidate lidar will enable a richer understanding of the drivers of tree growth, loss, and aboveground carbon flux.

  15. Algorithmic fault tree construction by component-based system modeling

    International Nuclear Information System (INIS)

    Majdara, Aref; Wakabayashi, Toshio

    2008-01-01

    Computer-aided fault tree generation can be easier, faster and less vulnerable to errors than the conventional manual fault tree construction. In this paper, a new approach for algorithmic fault tree generation is presented. The method mainly consists of a component-based system modeling procedure an a trace-back algorithm for fault tree synthesis. Components, as the building blocks of systems, are modeled using function tables and state transition tables. The proposed method can be used for a wide range of systems with various kinds of components, if an inclusive component database is developed. (author)

  16. Calculating the probability of multitaxon evolutionary trees: bootstrappers Gambit.

    OpenAIRE

    Lake, J A

    1995-01-01

    The reconstruction of multitaxon trees from molecular sequences is confounded by the variety of algorithms and criteria used to evaluate trees, making it difficult to compare the results of different analyses. A global method of multitaxon phylogenetic reconstruction described here, Bootstrappers Gambit, can be used with any four-taxon algorithm, including distance, maximum likelihood, and parsimony methods. It incorporates a Bayesian-Jeffreys'-bootstrap analysis to provide a uniform probabil...

  17. An efficient computational method for global sensitivity analysis and its application to tree growth modelling

    International Nuclear Information System (INIS)

    Wu, Qiong-Li; Cournède, Paul-Henry; Mathieu, Amélie

    2012-01-01

    Global sensitivity analysis has a key role to play in the design and parameterisation of functional–structural plant growth models which combine the description of plant structural development (organogenesis and geometry) and functional growth (biomass accumulation and allocation). We are particularly interested in this study in Sobol's method which decomposes the variance of the output of interest into terms due to individual parameters but also to interactions between parameters. Such information is crucial for systems with potentially high levels of non-linearity and interactions between processes, like plant growth. However, the computation of Sobol's indices relies on Monte Carlo sampling and re-sampling, whose costs can be very high, especially when model evaluation is also expensive, as for tree models. In this paper, we thus propose a new method to compute Sobol's indices inspired by Homma–Saltelli, which improves slightly their use of model evaluations, and then derive for this generic type of computational methods an estimator of the error estimation of sensitivity indices with respect to the sampling size. It allows the detailed control of the balance between accuracy and computing time. Numerical tests on a simple non-linear model are convincing and the method is finally applied to a functional–structural model of tree growth, GreenLab, whose particularity is the strong level of interaction between plant functioning and organogenesis. - Highlights: ► We study global sensitivity analysis in the context of functional–structural plant modelling. ► A new estimator based on Homma–Saltelli method is proposed to compute Sobol indices, based on a more balanced re-sampling strategy. ► The estimation accuracy of sensitivity indices for a class of Sobol's estimators can be controlled by error analysis. ► The proposed algorithm is implemented efficiently to compute Sobol indices for a complex tree growth model.

  18. Maximum Gene-Support Tree

    Directory of Open Access Journals (Sweden)

    Yunfeng Shan

    2008-01-01

    Full Text Available Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced as well as plants that have the fossil-supported true phylogenetic trees available. In this study, we generated single gene trees of seven yeast species as well as single gene trees of nine baculovirus species using all the orthologous genes among the species compared. Homologous genes among seven known plants were used for validation of the finding. Four algorithms—maximum parsimony (MP, minimum evolution (ME, maximum likelihood (ML, and neighbor-joining (NJ—were used. Trees were reconstructed before and after weighting the DNA and protein sequence lengths among genes. Rarely a gene can always generate the “true tree” by all the four algorithms. However, the most frequent gene tree, termed “maximum gene-support tree” (MGS tree, or WMGS tree for the weighted one, in yeasts, baculoviruses, or plants was consistently found to be the “true tree” among the species. The results provide insights into the overall degree of divergence of orthologous genes of the genomes analyzed and suggest the following: 1 The true tree relationship among the species studied is still maintained by the largest group of orthologous genes; 2 There are usually more orthologous genes with higher similarities between genetically closer species than between genetically more distant ones; and 3 The maximum gene-support tree reflects the phylogenetic relationship among species in comparison.

  19. Cross-scale interactions affect tree growth and intrinsic water use efficiency and highlight the importance of spatial context in managing forests under global change

    Science.gov (United States)

    Kenneth J. Ruzicka; Klaus J. Puettmann; J. Renée Brooks

    2017-01-01

    Summary1. We investigated the potential of cross-scale interactions to affect the outcome of density reduction in a large-scale silvicultural experiment to better understand options for managing forests under climate change. 2. We measured tree growth and intrinsic water-use efficiency (iWUE) based on stable carbon isotopes (δ...

  20. Uptake and distribution of soil applied zinc by citrus trees-addressing fertilizer use efficiency with 68Zn labeling.

    Science.gov (United States)

    Hippler, Franz Walter Rieger; Boaretto, Rodrigo Marcelli; Quaggio, José Antônio; Boaretto, Antonio Enedi; Abreu-Junior, Cassio Hamilton; Mattos, Dirceu

    2015-01-01

    The zinc (Zn) supply increases the fruit yield of Citrus trees that are grown, especially in the highly weathered soils of the tropics due to the inherently low nutrient availability in the soil solution. Leaf sprays containing micronutrients are commonly applied to orchards, even though the nutrient supply via soil could be of practical value. This study aimed to evaluate the effect of Zn fertilizers that are applied to the soil surface on absorption and partitioning of the nutrient by citrus trees. A greenhouse experiment was conducted with one-year-old sweet orange trees. The plants were grown in soils with different textures (18.1 or 64.4% clay) that received 1.8 g Zn per plant, in the form of either ZnO or ZnSO4 enriched with the stable isotope 68Zn. Zinc fertilization increased the availability of the nutrient in the soil and the content in the orange trees. Greater responses were obtained when ZnSO4 was applied to the sandy loam soil due to its lower specific metal adsorption compared to that of the clay soil. The trunk and branches accumulated the most fertilizer-derived Zn (Zndff) and thus represent the major reserve organ for this nutrient in the plant. The trees recovered up to 4% of the applied Zndff. Despite this relative low recovery, the Zn requirement of the trees was met with the selected treatment based on the total leaf nutrient content and increased Cu/Zn-SOD activity in the leaves. We conclude that the efficiency of Zn fertilizers depends on the fertilizer source and the soil texture, which must be taken into account by guidelines for fruit crop fertilization via soil, in substitution or complementation of traditional foliar sprays.

  1. Uptake and distribution of soil applied zinc by citrus trees-addressing fertilizer use efficiency with 68Zn labeling.

    Directory of Open Access Journals (Sweden)

    Franz Walter Rieger Hippler

    Full Text Available The zinc (Zn supply increases the fruit yield of Citrus trees that are grown, especially in the highly weathered soils of the tropics due to the inherently low nutrient availability in the soil solution. Leaf sprays containing micronutrients are commonly applied to orchards, even though the nutrient supply via soil could be of practical value. This study aimed to evaluate the effect of Zn fertilizers that are applied to the soil surface on absorption and partitioning of the nutrient by citrus trees. A greenhouse experiment was conducted with one-year-old sweet orange trees. The plants were grown in soils with different textures (18.1 or 64.4% clay that received 1.8 g Zn per plant, in the form of either ZnO or ZnSO4 enriched with the stable isotope 68Zn. Zinc fertilization increased the availability of the nutrient in the soil and the content in the orange trees. Greater responses were obtained when ZnSO4 was applied to the sandy loam soil due to its lower specific metal adsorption compared to that of the clay soil. The trunk and branches accumulated the most fertilizer-derived Zn (Zndff and thus represent the major reserve organ for this nutrient in the plant. The trees recovered up to 4% of the applied Zndff. Despite this relative low recovery, the Zn requirement of the trees was met with the selected treatment based on the total leaf nutrient content and increased Cu/Zn-SOD activity in the leaves. We conclude that the efficiency of Zn fertilizers depends on the fertilizer source and the soil texture, which must be taken into account by guidelines for fruit crop fertilization via soil, in substitution or complementation of traditional foliar sprays.

  2. Empirical likelihood

    CERN Document Server

    Owen, Art B

    2001-01-01

    Empirical likelihood provides inferences whose validity does not depend on specifying a parametric model for the data. Because it uses a likelihood, the method has certain inherent advantages over resampling methods: it uses the data to determine the shape of the confidence regions, and it makes it easy to combined data from multiple sources. It also facilitates incorporating side information, and it simplifies accounting for censored, truncated, or biased sampling.One of the first books published on the subject, Empirical Likelihood offers an in-depth treatment of this method for constructing confidence regions and testing hypotheses. The author applies empirical likelihood to a range of problems, from those as simple as setting a confidence region for a univariate mean under IID sampling, to problems defined through smooth functions of means, regression models, generalized linear models, estimating equations, or kernel smooths, and to sampling with non-identically distributed data. Abundant figures offer vi...

  3. Approximate Likelihood

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    Most physics results at the LHC end in a likelihood ratio test. This includes discovery and exclusion for searches as well as mass, cross-section, and coupling measurements. The use of Machine Learning (multivariate) algorithms in HEP is mainly restricted to searches, which can be reduced to classification between two fixed distributions: signal vs. background. I will show how we can extend the use of ML classifiers to distributions parameterized by physical quantities like masses and couplings as well as nuisance parameters associated to systematic uncertainties. This allows for one to approximate the likelihood ratio while still using a high dimensional feature vector for the data. Both the MEM and ABC approaches mentioned above aim to provide inference on model parameters (like cross-sections, masses, couplings, etc.). ABC is fundamentally tied Bayesian inference and focuses on the “likelihood free” setting where only a simulator is available and one cannot directly compute the likelihood for the dat...

  4. Discrete Discriminant analysis based on tree-structured graphical models

    DEFF Research Database (Denmark)

    Perez de la Cruz, Gonzalo; Eslava, Guillermina

    The purpose of this paper is to illustrate the potential use of discriminant analysis based on tree{structured graphical models for discrete variables. This is done by comparing its empirical performance using estimated error rates for real and simulated data. The results show that discriminant a...... analysis based on tree{structured graphical models is a simple nonlinear method competitive with, and sometimes superior to, other well{known linear methods like those assuming mutual independence between variables and linear logistic regression.......The purpose of this paper is to illustrate the potential use of discriminant analysis based on tree{structured graphical models for discrete variables. This is done by comparing its empirical performance using estimated error rates for real and simulated data. The results show that discriminant...

  5. Comparing forest measurements from tree rings and a space-based index of vegetation activity in Siberia

    International Nuclear Information System (INIS)

    Bunn, Andrew G; Hughes, Malcolm K; Losleben, Mark; Kirdyanov, Alexander V; Shishov, Vladimir V; Vaganov, Eugene A; Berner, Logan T; Oltchev, Alexander

    2013-01-01

    Different methods have been developed for measuring carbon stocks and fluxes in the northern high latitudes, ranging from intensively measured small plots to space-based methods that use reflectance data to drive production efficiency models. The field of dendroecology has used samples of tree growth from radial increments to quantify long-term variability in ecosystem productivity, but these have very limited spatial domains. Since the cambium material in tree cores is itself a product of photosynthesis in the canopy, it would be ideal to link these two approaches. We examine the associations between the normalized differenced vegetation index (NDVI) and tree growth using 19 pairs of tree-ring widths (TRW) and maximum latewood density (MXD) across much of Siberia. We find consistent correlations between NDVI and both measures of tree growth and no systematic difference between MXD and TRW. At the regional level we note strong correspondence between the first principal component of tree growth and NDVI for MXD and TRW in a temperature-limited bioregion, indicating that canopy reflectance and cambial production are broadly linked. Using a network of 21 TRW chronologies from south of Lake Baikal, we find a similarly strong regional correspondence with NDVI in a markedly drier region. We show that tree growth is dominated by variation at decadal and multidecadal time periods, which the satellite record is incapable of recording given its relatively short record. (letter)

  6. Nitrogen release, tree uptake, and ecosystem retention in a mid-rotation loblolly pine plantation following fertilization with 15N-enriched enhanced efficiency fertilizers.

    OpenAIRE

    Werner, Amy

    2013-01-01

    Nitrogen is the most frequently limiting nutrient in southern pine plantations.  Previous studies found that only 10 to 25% of applied urea fertilizer N is taken up by trees.  Enhanced efficiency fertilizers could increase tree uptake efficiency by controlling the release of N and/or stabilize N.  Three enhanced efficiency fertilizers were selected as a representation of fertilizers that could be used in forestry: 1) NBPT treated urea (NBPT urea), 2) polymer coated urea (PC urea), and 3) mono...

  7. Simple method for direct crown base height estimation of individual conifer trees using airborne LiDAR data.

    Science.gov (United States)

    Luo, Laiping; Zhai, Qiuping; Su, Yanjun; Ma, Qin; Kelly, Maggi; Guo, Qinghua

    2018-05-14

    Crown base height (CBH) is an essential tree biophysical parameter for many applications in forest management, forest fuel treatment, wildfire modeling, ecosystem modeling and global climate change studies. Accurate and automatic estimation of CBH for individual trees is still a challenging task. Airborne light detection and ranging (LiDAR) provides reliable and promising data for estimating CBH. Various methods have been developed to calculate CBH indirectly using regression-based means from airborne LiDAR data and field measurements. However, little attention has been paid to directly calculate CBH at the individual tree scale in mixed-species forests without field measurements. In this study, we propose a new method for directly estimating individual-tree CBH from airborne LiDAR data. Our method involves two main strategies: 1) removing noise and understory vegetation for each tree; and 2) estimating CBH by generating percentile ranking profile for each tree and using a spline curve to identify its inflection points. These two strategies lend our method the advantages of no requirement of field measurements and being efficient and effective in mixed-species forests. The proposed method was applied to a mixed conifer forest in the Sierra Nevada, California and was validated by field measurements. The results showed that our method can directly estimate CBH at individual tree level with a root-mean-squared error of 1.62 m, a coefficient of determination of 0.88 and a relative bias of 3.36%. Furthermore, we systematically analyzed the accuracies among different height groups and tree species by comparing with field measurements. Our results implied that taller trees had relatively higher uncertainties than shorter trees. Our findings also show that the accuracy for CBH estimation was the highest for black oak trees, with an RMSE of 0.52 m. The conifer species results were also good with uniformly high R 2 ranging from 0.82 to 0.93. In general, our method has

  8. Likelihood ratio decisions in memory: three implied regularities.

    Science.gov (United States)

    Glanzer, Murray; Hilford, Andrew; Maloney, Laurence T

    2009-06-01

    We analyze four general signal detection models for recognition memory that differ in their distributional assumptions. Our analyses show that a basic assumption of signal detection theory, the likelihood ratio decision axis, implies three regularities in recognition memory: (1) the mirror effect, (2) the variance effect, and (3) the z-ROC length effect. For each model, we present the equations that produce the three regularities and show, in computed examples, how they do so. We then show that the regularities appear in data from a range of recognition studies. The analyses and data in our study support the following generalization: Individuals make efficient recognition decisions on the basis of likelihood ratios.

  9. Efficient chaining of seeds in ordered trees

    OpenAIRE

    Allali, Julien; Chauve, Cédric; Ferraro, Pascal; Gaillard, Anne-Laure

    2010-01-01

    International audience; We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem is a natural extension of a similar problem for sequences, and has applications in computational biology, such as mining a database of RNA secondary structures. For the chaining problem with a set of m constant size seeds, we describe...

  10. 3D Visualization of Trees Based on a Sphere-Board Model

    Directory of Open Access Journals (Sweden)

    Jiangfeng She

    2018-01-01

    Full Text Available Because of the smooth interaction of tree systems, the billboard and crossed-plane techniques of image-based rendering (IBR have been used for tree visualization for many years. However, both the billboard-based tree model (BBTM and the crossed-plane tree model (CPTM have several notable limitations; for example, they give an impression of slicing when viewed from the top side, and they produce an unimpressive stereoscopic effect and insufficient lighted effects. In this study, a sphere-board-based tree model (SBTM is proposed to eliminate these defects and to improve the final visual effects. Compared with the BBTM or CPTM, the proposed SBTM uses one or more sphere-like 3D geometric surfaces covered with a virtual texture, which can present more details about the foliage than can 2D planes, to represent the 3D outline of a tree crown. However, the profile edge presented by a continuous surface is overly smooth and regular, and when used to delineate the outline of a tree crown, it makes the tree appear very unrealistic. To overcome this shortcoming and achieve a more natural final visual effect of the tree model, an additional process is applied to the edge of the surface profile. In addition, the SBTM can better support lighted effects because of its cubic geometrical features. Interactive visualization effects for a single tree and a grove are presented in a case study of Sabina chinensis. The results show that the SBTM can achieve a better compromise between realism and performance than can the BBTM or CPTM.

  11. Genomics-assisted breeding in fruit trees.

    Science.gov (United States)

    Iwata, Hiroyoshi; Minamikawa, Mai F; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

    2016-01-01

    Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding.

  12. Estimation of Tree Cover in an Agricultural Parkland of Senegal Using Rule-Based Regression Tree Modeling

    Directory of Open Access Journals (Sweden)

    Stefanie M. Herrmann

    2013-10-01

    Full Text Available Field trees are an integral part of the farmed parkland landscape in West Africa and provide multiple benefits to the local environment and livelihoods. While field trees have received increasing interest in the context of strengthening resilience to climate variability and change, the actual extent of farmed parkland and spatial patterns of tree cover are largely unknown. We used the rule-based predictive modeling tool Cubist® to estimate field tree cover in the west-central agricultural region of Senegal. A collection of rules and associated multiple linear regression models was constructed from (1 a reference dataset of percent tree cover derived from very high spatial resolution data (2 m Orbview as the dependent variable, and (2 ten years of 10-day 250 m Moderate Resolution Imaging Spectrometer (MODIS Normalized Difference Vegetation Index (NDVI composites and derived phenological metrics as independent variables. Correlation coefficients between modeled and reference percent tree cover of 0.88 and 0.77 were achieved for training and validation data respectively, with absolute mean errors of 1.07 and 1.03 percent tree cover. The resulting map shows a west-east gradient from high tree cover in the peri-urban areas of horticulture and arboriculture to low tree cover in the more sparsely populated eastern part of the study area. A comparison of current (2000s tree cover along this gradient with historic cover as seen on Corona images reveals dynamics of change but also areas of remarkable stability of field tree cover since 1968. The proposed modeling approach can help to identify locations of high and low tree cover in dryland environments and guide ground studies and management interventions aimed at promoting the integration of field trees in agricultural systems.

  13. An Isometric Mapping Based Co-Location Decision Tree Algorithm

    Science.gov (United States)

    Zhou, G.; Wei, J.; Zhou, X.; Zhang, R.; Huang, W.; Sha, H.; Chen, J.

    2018-05-01

    Decision tree (DT) induction has been widely used in different pattern classification. However, most traditional DTs have the disadvantage that they consider only non-spatial attributes (ie, spectral information) as a result of classifying pixels, which can result in objects being misclassified. Therefore, some researchers have proposed a co-location decision tree (Cl-DT) method, which combines co-location and decision tree to solve the above the above-mentioned traditional decision tree problems. Cl-DT overcomes the shortcomings of the existing DT algorithms, which create a node for each value of a given attribute, which has a higher accuracy than the existing decision tree approach. However, for non-linearly distributed data instances, the euclidean distance between instances does not reflect the true positional relationship between them. In order to overcome these shortcomings, this paper proposes an isometric mapping method based on Cl-DT (called, (Isomap-based Cl-DT), which is a method that combines heterogeneous and Cl-DT together. Because isometric mapping methods use geodetic distances instead of Euclidean distances between non-linearly distributed instances, the true distance between instances can be reflected. The experimental results and several comparative analyzes show that: (1) The extraction method of exposed carbonate rocks is of high accuracy. (2) The proposed method has many advantages, because the total number of nodes, the number of leaf nodes and the number of nodes are greatly reduced compared to Cl-DT. Therefore, the Isomap -based Cl-DT algorithm can construct a more accurate and faster decision tree.

  14. AN ISOMETRIC MAPPING BASED CO-LOCATION DECISION TREE ALGORITHM

    Directory of Open Access Journals (Sweden)

    G. Zhou

    2018-05-01

    Full Text Available Decision tree (DT induction has been widely used in different pattern classification. However, most traditional DTs have the disadvantage that they consider only non-spatial attributes (ie, spectral information as a result of classifying pixels, which can result in objects being misclassified. Therefore, some researchers have proposed a co-location decision tree (Cl-DT method, which combines co-location and decision tree to solve the above the above-mentioned traditional decision tree problems. Cl-DT overcomes the shortcomings of the existing DT algorithms, which create a node for each value of a given attribute, which has a higher accuracy than the existing decision tree approach. However, for non-linearly distributed data instances, the euclidean distance between instances does not reflect the true positional relationship between them. In order to overcome these shortcomings, this paper proposes an isometric mapping method based on Cl-DT (called, (Isomap-based Cl-DT, which is a method that combines heterogeneous and Cl-DT together. Because isometric mapping methods use geodetic distances instead of Euclidean distances between non-linearly distributed instances, the true distance between instances can be reflected. The experimental results and several comparative analyzes show that: (1 The extraction method of exposed carbonate rocks is of high accuracy. (2 The proposed method has many advantages, because the total number of nodes, the number of leaf nodes and the number of nodes are greatly reduced compared to Cl-DT. Therefore, the Isomap -based Cl-DT algorithm can construct a more accurate and faster decision tree.

  15. An introduction to tree-structured modeling with application to quality of life data.

    Science.gov (United States)

    Su, Xiaogang; Azuero, Andres; Cho, June; Kvale, Elizabeth; Meneses, Karen M; McNees, M Patrick

    2011-01-01

    Investigators addressing nursing research are faced increasingly with the need to analyze data that involve variables of mixed types and are characterized by complex nonlinearity and interactions. Tree-based methods, also called recursive partitioning, are gaining popularity in various fields. In addition to efficiency and flexibility in handling multifaceted data, tree-based methods offer ease of interpretation. The aims of this study were to introduce tree-based methods, discuss their advantages and pitfalls in application, and describe their potential use in nursing research. In this article, (a) an introduction to tree-structured methods is presented, (b) the technique is illustrated via quality of life (QOL) data collected in the Breast Cancer Education Intervention study, and (c) implications for their potential use in nursing research are discussed. As illustrated by the QOL analysis example, tree methods generate interesting and easily understood findings that cannot be uncovered via traditional linear regression analysis. The expanding breadth and complexity of nursing research may entail the use of new tools to improve efficiency and gain new insights. In certain situations, tree-based methods offer an attractive approach that help address such needs.

  16. Genomics-assisted breeding in fruit trees

    OpenAIRE

    Iwata, Hiroyoshi; Minamikawa, Mai F.; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

    2016-01-01

    Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the pl...

  17. A review and comparison of Bayesian and likelihood-based inferences in beta regression and zero-or-one-inflated beta regression.

    Science.gov (United States)

    Liu, Fang; Eugenio, Evercita C

    2018-04-01

    Beta regression is an increasingly popular statistical technique in medical research for modeling of outcomes that assume values in (0, 1), such as proportions and patient reported outcomes. When outcomes take values in the intervals [0,1), (0,1], or [0,1], zero-or-one-inflated beta (zoib) regression can be used. We provide a thorough review on beta regression and zoib regression in the modeling, inferential, and computational aspects via the likelihood-based and Bayesian approaches. We demonstrate the statistical and practical importance of correctly modeling the inflation at zero/one rather than ad hoc replacing them with values close to zero/one via simulation studies; the latter approach can lead to biased estimates and invalid inferences. We show via simulation studies that the likelihood-based approach is computationally faster in general than MCMC algorithms used in the Bayesian inferences, but runs the risk of non-convergence, large biases, and sensitivity to starting values in the optimization algorithm especially with clustered/correlated data, data with sparse inflation at zero and one, and data that warrant regularization of the likelihood. The disadvantages of the regular likelihood-based approach make the Bayesian approach an attractive alternative in these cases. Software packages and tools for fitting beta and zoib regressions in both the likelihood-based and Bayesian frameworks are also reviewed.

  18. Spray deposition from ground-based applications of carbaryl to protect individual trees from bark beetle attack.

    Science.gov (United States)

    Fettig, Christopher J; Munson, A Steven; McKelvey, Stephen R; Bush, Parshall B; Borys, Robert R

    2008-01-01

    Bark beetles (Coleoptera: Curculionidae, Scolytinae) are recognized as the most important tree mortality agent in western coniferous forests. A common method of protecting trees from bark beetle attack is to saturate the tree bole with carbaryl (1-naphthyl methylcarbamate) using a hydraulic sprayer. In this study, we evaluate the amount of carbaryl drift (ground deposition) occurring at four distances from the tree bole (7.6, 15.2, 22.9, and 38.1 m) during conventional spray applications for protecting individual lodgepole pine (Pinus contorta Dougl. ex Loud.) from mountain pine beetle (Dendroctonus ponderosae Hopkins) attack and Engelmann spruce (Picea engelmannii Parry ex Engelm.) from spruce beetle (D. rufipennis [Kirby]) attack. Mean deposition (carbaryl + alpha-naphthol) did not differ significantly among treatments (nozzle orifices) at any distance from the tree bole. Values ranged from 0.04 +/- 0.02 mg carbaryl m(-2) at 38.1 m to 13.30 +/- 2.54 mg carbaryl m(-2) at 7.6 m. Overall, distance from the tree bole significantly affected the amount of deposition. Deposition was greatest 7.6 m from the tree bole and quickly declined as distance from the tree bole increased. Approximately 97% of total spray deposition occurred within 15.2 m of the tree bole. Application efficiency (i.e., percentage of insecticide applied that is retained on trees) ranged from 80.9 to 87.2%. Based on review of the literature, this amount of drift poses little threat to adjacent aquatic environments. No-spray buffers of 7.6 m should be sufficient to protect freshwater fish, amphibians, crustaceans, bivalves, and most aquatic insects. Buffers >22.9 m appear sufficient to protect the most sensitive aquatic insects (Plecoptera).

  19. Practical likelihood analysis for spatial generalized linear mixed models

    DEFF Research Database (Denmark)

    Bonat, W. H.; Ribeiro, Paulo Justiniano

    2016-01-01

    We investigate an algorithm for maximum likelihood estimation of spatial generalized linear mixed models based on the Laplace approximation. We compare our algorithm with a set of alternative approaches for two datasets from the literature. The Rhizoctonia root rot and the Rongelap are......, respectively, examples of binomial and count datasets modeled by spatial generalized linear mixed models. Our results show that the Laplace approximation provides similar estimates to Markov Chain Monte Carlo likelihood, Monte Carlo expectation maximization, and modified Laplace approximation. Some advantages...... of Laplace approximation include the computation of the maximized log-likelihood value, which can be used for model selection and tests, and the possibility to obtain realistic confidence intervals for model parameters based on profile likelihoods. The Laplace approximation also avoids the tuning...

  20. Efficient Disk-Based Techniques for Manipulating Very Large String Databases

    KAUST Repository

    Allam, Amin

    2017-05-18

    Indexing and processing strings are very important topics in database management. Strings can be database records, DNA sequences, protein sequences, or plain text. Various string operations are required for several application categories, such as bioinformatics and entity resolution. When the string count or sizes become very large, several state-of-the-art techniques for indexing and processing such strings may fail or behave very inefficiently. Modifying an existing technique to overcome these issues is not usually straightforward or even possible. A category of string operations can be facilitated by the suffix tree data structure, which basically indexes a long string to enable efficient finding of any substring of the indexed string, and can be used in other operations as well, such as approximate string matching. In this document, we introduce a novel efficient method to construct the suffix tree index for very long strings using parallel architectures, which is a major challenge in this category. Another category of string operations require clustering similar strings in order to perform application-specific processing on the resulting possibly-overlapping clusters. In this document, based on clustering similar strings, we introduce a novel efficient technique for record linkage and entity resolution, and a novel method for correcting errors in a large number of small strings (read sequences) generated by the DNA sequencing machines.

  1. Wobbling and LSF-based maximum likelihood expectation maximization reconstruction for wobbling PET

    International Nuclear Information System (INIS)

    Kim, Hang-Keun; Son, Young-Don; Kwon, Dae-Hyuk; Joo, Yohan; Cho, Zang-Hee

    2016-01-01

    Positron emission tomography (PET) is a widely used imaging modality; however, the PET spatial resolution is not yet satisfactory for precise anatomical localization of molecular activities. Detector size is the most important factor because it determines the intrinsic resolution, which is approximately half of the detector size and determines the ultimate PET resolution. Detector size, however, cannot be made too small because both the decreased detection efficiency and the increased septal penetration effect degrade the image quality. A wobbling and line spread function (LSF)-based maximum likelihood expectation maximization (WL-MLEM) algorithm, which combined the MLEM iterative reconstruction algorithm with wobbled sampling and LSF-based deconvolution using the system matrix, was proposed for improving the spatial resolution of PET without reducing the scintillator or detector size. The new algorithm was evaluated using a simulation, and its performance was compared with that of the existing algorithms, such as conventional MLEM and LSF-based MLEM. Simulations demonstrated that the WL-MLEM algorithm yielded higher spatial resolution and image quality than the existing algorithms. The WL-MLEM algorithm with wobbling PET yielded substantially improved resolution compared with conventional algorithms with stationary PET. The algorithm can be easily extended to other iterative reconstruction algorithms, such as maximum a priori (MAP) and ordered subset expectation maximization (OSEM). The WL-MLEM algorithm with wobbling PET may offer improvements in both sensitivity and resolution, the two most sought-after features in PET design. - Highlights: • This paper proposed WL-MLEM algorithm for PET and demonstrated its performance. • WL-MLEM algorithm effectively combined wobbling and line spread function based MLEM. • WL-MLEM provided improvements in the spatial resolution and the PET image quality. • WL-MLEM can be easily extended to the other iterative

  2. Classifying dysmorphic syndromes by using artificial neural network based hierarchical decision tree.

    Science.gov (United States)

    Özdemir, Merve Erkınay; Telatar, Ziya; Eroğul, Osman; Tunca, Yusuf

    2018-05-01

    Dysmorphic syndromes have different facial malformations. These malformations are significant to an early diagnosis of dysmorphic syndromes and contain distinctive information for face recognition. In this study we define the certain features of each syndrome by considering facial malformations and classify Fragile X, Hurler, Prader Willi, Down, Wolf Hirschhorn syndromes and healthy groups automatically. The reference points are marked on the face images and ratios between the points' distances are taken into consideration as features. We suggest a neural network based hierarchical decision tree structure in order to classify the syndrome types. We also implement k-nearest neighbor (k-NN) and artificial neural network (ANN) classifiers to compare classification accuracy with our hierarchical decision tree. The classification accuracy is 50, 73 and 86.7% with k-NN, ANN and hierarchical decision tree methods, respectively. Then, the same images are shown to a clinical expert who achieve a recognition rate of 46.7%. We develop an efficient system to recognize different syndrome types automatically in a simple, non-invasive imaging data, which is independent from the patient's age, sex and race at high accuracy. The promising results indicate that our method can be used for pre-diagnosis of the dysmorphic syndromes by clinical experts.

  3. Sequence comparison alignment-free approach based on suffix tree and L-words frequency.

    Science.gov (United States)

    Soares, Inês; Goios, Ana; Amorim, António

    2012-01-01

    The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions). In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L-L-words--in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

  4. A Single Camera Motion Capture System for Human-Computer Interaction

    Science.gov (United States)

    Okada, Ryuzo; Stenger, Björn

    This paper presents a method for markerless human motion capture using a single camera. It uses tree-based filtering to efficiently propagate a probability distribution over poses of a 3D body model. The pose vectors and associated shapes are arranged in a tree, which is constructed by hierarchical pairwise clustering, in order to efficiently evaluate the likelihood in each frame. Anew likelihood function based on silhouette matching is proposed that improves the pose estimation of thinner body parts, i. e. the limbs. The dynamic model takes self-occlusion into account by increasing the variance of occluded body-parts, thus allowing for recovery when the body part reappears. We present two applications of our method that work in real-time on a Cell Broadband Engine™: a computer game and a virtual clothing application.

  5. A Fast Framework for Abrupt Change Detection Based on Binary Search Trees and Kolmogorov Statistic

    Science.gov (United States)

    Qi, Jin-Peng; Qi, Jie; Zhang, Qing

    2016-01-01

    Change-Point (CP) detection has attracted considerable attention in the fields of data mining and statistics; it is very meaningful to discuss how to quickly and efficiently detect abrupt change from large-scale bioelectric signals. Currently, most of the existing methods, like Kolmogorov-Smirnov (KS) statistic and so forth, are time-consuming, especially for large-scale datasets. In this paper, we propose a fast framework for abrupt change detection based on binary search trees (BSTs) and a modified KS statistic, named BSTKS (binary search trees and Kolmogorov statistic). In this method, first, two binary search trees, termed as BSTcA and BSTcD, are constructed by multilevel Haar Wavelet Transform (HWT); second, three search criteria are introduced in terms of the statistic and variance fluctuations in the diagnosed time series; last, an optimal search path is detected from the root to leaf nodes of two BSTs. The studies on both the synthetic time series samples and the real electroencephalograph (EEG) recordings indicate that the proposed BSTKS can detect abrupt change more quickly and efficiently than KS, t-statistic (t), and Singular-Spectrum Analyses (SSA) methods, with the shortest computation time, the highest hit rate, the smallest error, and the highest accuracy out of four methods. This study suggests that the proposed BSTKS is very helpful for useful information inspection on all kinds of bioelectric time series signals. PMID:27413364

  6. A Fast Framework for Abrupt Change Detection Based on Binary Search Trees and Kolmogorov Statistic.

    Science.gov (United States)

    Qi, Jin-Peng; Qi, Jie; Zhang, Qing

    2016-01-01

    Change-Point (CP) detection has attracted considerable attention in the fields of data mining and statistics; it is very meaningful to discuss how to quickly and efficiently detect abrupt change from large-scale bioelectric signals. Currently, most of the existing methods, like Kolmogorov-Smirnov (KS) statistic and so forth, are time-consuming, especially for large-scale datasets. In this paper, we propose a fast framework for abrupt change detection based on binary search trees (BSTs) and a modified KS statistic, named BSTKS (binary search trees and Kolmogorov statistic). In this method, first, two binary search trees, termed as BSTcA and BSTcD, are constructed by multilevel Haar Wavelet Transform (HWT); second, three search criteria are introduced in terms of the statistic and variance fluctuations in the diagnosed time series; last, an optimal search path is detected from the root to leaf nodes of two BSTs. The studies on both the synthetic time series samples and the real electroencephalograph (EEG) recordings indicate that the proposed BSTKS can detect abrupt change more quickly and efficiently than KS, t-statistic (t), and Singular-Spectrum Analyses (SSA) methods, with the shortest computation time, the highest hit rate, the smallest error, and the highest accuracy out of four methods. This study suggests that the proposed BSTKS is very helpful for useful information inspection on all kinds of bioelectric time series signals.

  7. Improved efficiency of maximum likelihood analysis of time series with temporally correlated errors

    Science.gov (United States)

    Langbein, John

    2017-08-01

    Most time series of geophysical phenomena have temporally correlated errors. From these measurements, various parameters are estimated. For instance, from geodetic measurements of positions, the rates and changes in rates are often estimated and are used to model tectonic processes. Along with the estimates of the size of the parameters, the error in these parameters needs to be assessed. If temporal correlations are not taken into account, or each observation is assumed to be independent, it is likely that any estimate of the error of these parameters will be too low and the estimated value of the parameter will be biased. Inclusion of better estimates of uncertainties is limited by several factors, including selection of the correct model for the background noise and the computational requirements to estimate the parameters of the selected noise model for cases where there are numerous observations. Here, I address the second problem of computational efficiency using maximum likelihood estimates (MLE). Most geophysical time series have background noise processes that can be represented as a combination of white and power-law noise, 1/f^{α } with frequency, f. With missing data, standard spectral techniques involving FFTs are not appropriate. Instead, time domain techniques involving construction and inversion of large data covariance matrices are employed. Bos et al. (J Geod, 2013. doi: 10.1007/s00190-012-0605-0) demonstrate one technique that substantially increases the efficiency of the MLE methods, yet is only an approximate solution for power-law indices >1.0 since they require the data covariance matrix to be Toeplitz. That restriction can be removed by simply forming a data filter that adds noise processes rather than combining them in quadrature. Consequently, the inversion of the data covariance matrix is simplified yet provides robust results for a wider range of power-law indices.

  8. Evaluation of properties over phylogenetic trees using stochastic logics.

    Science.gov (United States)

    Requeno, José Ignacio; Colom, José Manuel

    2016-06-14

    Model checking has been recently introduced as an integrated framework for extracting information of the phylogenetic trees using temporal logics as a querying language, an extension of modal logics that imposes restrictions of a boolean formula along a path of events. The phylogenetic tree is considered a transition system modeling the evolution as a sequence of genomic mutations (we understand mutation as different ways that DNA can be changed), while this kind of logics are suitable for traversing it in a strict and exhaustive way. Given a biological property that we desire to inspect over the phylogeny, the verifier returns true if the specification is satisfied or a counterexample that falsifies it. However, this approach has been only considered over qualitative aspects of the phylogeny. In this paper, we repair the limitations of the previous framework for including and handling quantitative information such as explicit time or probability. To this end, we apply current probabilistic continuous-time extensions of model checking to phylogenetics. We reinterpret a catalog of qualitative properties in a numerical way, and we also present new properties that couldn't be analyzed before. For instance, we obtain the likelihood of a tree topology according to a mutation model. As case of study, we analyze several phylogenies in order to obtain the maximum likelihood with the model checking tool PRISM. In addition, we have adapted the software for optimizing the computation of maximum likelihoods. We have shown that probabilistic model checking is a competitive framework for describing and analyzing quantitative properties over phylogenetic trees. This formalism adds soundness and readability to the definition of models and specifications. Besides, the existence of model checking tools hides the underlying technology, omitting the extension, upgrade, debugging and maintenance of a software tool to the biologists. A set of benchmarks justify the feasibility of our

  9. A simulation study of likelihood inference procedures in rayleigh distribution with censored data

    International Nuclear Information System (INIS)

    Baklizi, S. A.; Baker, H. M.

    2001-01-01

    Inference procedures based on the likelihood function are considered for the one parameter Rayleigh distribution with type1 and type 2 censored data. Using simulation techniques, the finite sample performances of the maximum likelihood estimator and the large sample likelihood interval estimation procedures based on the Wald, the Rao, and the likelihood ratio statistics are investigated. It appears that the maximum likelihood estimator is unbiased. The approximate variance estimates obtained from the asymptotic normal distribution of the maximum likelihood estimator are accurate under type 2 censored data while they tend to be smaller than the actual variances when considering type1 censored data of small size. It appears also that interval estimation based on the Wald and Rao statistics need much more sample size than interval estimation based on the likelihood ratio statistic to attain reasonable accuracy. (authors). 15 refs., 4 tabs

  10. Tree architecture and life-history strategies across 200 co-occurring tropical tree species

    NARCIS (Netherlands)

    Iida, Y.; Kohyama, T.S.; Kubo, T.; Kassim, A.R.; Poorter, L.; Sterck, F.J.; Potts, M.D.

    2011-01-01

    1. Tree architecture is thought to allow species to partition horizontal and vertical light gradients in the forest canopy. Tree architecture is closely related to light capture, carbon gain and the efficiency with which trees reach the canopy. Previous studies that investigated how light gradients

  11. Statistical tracking of tree-like tubular structures with efficient branching detection in 3D medical image data

    DEFF Research Database (Denmark)

    Wang, X.; Heimann, T.; Lo, P.

    2012-01-01

    to their robustness against image noise and pathological changes. However, most tracking methods are limited to a specific application and do not support branching structures efficiently. In this work, we present a novel statistical tracking approach for the extraction of different types of tubular structures...... with ringlike cross-sections. Domain-specific knowledge is learned from training data sets and integrated into the tracking process by simple adaption of parameters. In addition, an efficient branching detection algorithm is presented. This approach was evaluated by extracting coronary arteries from 32 CTA data...... for the tracking of coronary arteries were achieved. For the extraction of airway trees, 51.3% of the total tree length, 53.6% of the total number of branches and a 4.98% false positive rate were attained. In both experiments, our approach is comparable to state-of-the-art methods....

  12. Generalising tree traversals and tree transformations to DAGs

    DEFF Research Database (Denmark)

    Bahr, Patrick; Axelsson, Emil

    2017-01-01

    We present a recursion scheme based on attribute grammars that can be transparently applied to trees and acyclic graphs. Our recursion scheme allows the programmer to implement a tree traversal or a tree transformation and then apply it to compact graph representations of trees instead. The resul......We present a recursion scheme based on attribute grammars that can be transparently applied to trees and acyclic graphs. Our recursion scheme allows the programmer to implement a tree traversal or a tree transformation and then apply it to compact graph representations of trees instead...... as the complementing theory with a number of examples....

  13. Robust Gaussian Process Regression with a Student-t Likelihood

    NARCIS (Netherlands)

    Jylänki, P.P.; Vanhatalo, J.; Vehtari, A.

    2011-01-01

    This paper considers the robust and efficient implementation of Gaussian process regression with a Student-t observation model, which has a non-log-concave likelihood. The challenge with the Student-t model is the analytically intractable inference which is why several approximative methods have

  14. The unfolding of NaI(Tl) γ-ray spectrum based on maximum likelihood method

    International Nuclear Information System (INIS)

    Zhang Qingxian; Ge Liangquan; Gu Yi; Zeng Guoqiang; Lin Yanchang; Wang Guangxi

    2011-01-01

    NaI(Tl) detectors, having a good detection efficiency, are used to detect gamma rays in field surveys. But the poor energy resolution hinders their applications, despite the use of traditional methods to resolve the overlapped gamma-ray peaks. In this paper, the maximum likelihood (ML) solution is used to resolve the spectrum. The ML method,which is capable of decomposing the peaks in energy difference of over 2/3 FWHM, is applied to scale NaI(Tl) the spectrometer. The result shows that the net area is in proportion to the content of isotopes and the precision of scaling is better than the stripping ration method. (authors)

  15. Flexible and efficient estimating equations for variogram estimation

    KAUST Repository

    Sun, Ying; Chang, Xiaohui; Guan, Yongtao

    2018-01-01

    Variogram estimation plays a vastly important role in spatial modeling. Different methods for variogram estimation can be largely classified into least squares methods and likelihood based methods. A general framework to estimate the variogram through a set of estimating equations is proposed. This approach serves as an alternative approach to likelihood based methods and includes commonly used least squares approaches as its special cases. The proposed method is highly efficient as a low dimensional representation of the weight matrix is employed. The statistical efficiency of various estimators is explored and the lag effect is examined. An application to a hydrology dataset is also presented.

  16. Flexible and efficient estimating equations for variogram estimation

    KAUST Repository

    Sun, Ying

    2018-01-11

    Variogram estimation plays a vastly important role in spatial modeling. Different methods for variogram estimation can be largely classified into least squares methods and likelihood based methods. A general framework to estimate the variogram through a set of estimating equations is proposed. This approach serves as an alternative approach to likelihood based methods and includes commonly used least squares approaches as its special cases. The proposed method is highly efficient as a low dimensional representation of the weight matrix is employed. The statistical efficiency of various estimators is explored and the lag effect is examined. An application to a hydrology dataset is also presented.

  17. Likelihood ratio sequential sampling models of recognition memory.

    Science.gov (United States)

    Osth, Adam F; Dennis, Simon; Heathcote, Andrew

    2017-02-01

    The mirror effect - a phenomenon whereby a manipulation produces opposite effects on hit and false alarm rates - is benchmark regularity of recognition memory. A likelihood ratio decision process, basing recognition on the relative likelihood that a stimulus is a target or a lure, naturally predicts the mirror effect, and so has been widely adopted in quantitative models of recognition memory. Glanzer, Hilford, and Maloney (2009) demonstrated that likelihood ratio models, assuming Gaussian memory strength, are also capable of explaining regularities observed in receiver-operating characteristics (ROCs), such as greater target than lure variance. Despite its central place in theorising about recognition memory, however, this class of models has not been tested using response time (RT) distributions. In this article, we develop a linear approximation to the likelihood ratio transformation, which we show predicts the same regularities as the exact transformation. This development enabled us to develop a tractable model of recognition-memory RT based on the diffusion decision model (DDM), with inputs (drift rates) provided by an approximate likelihood ratio transformation. We compared this "LR-DDM" to a standard DDM where all targets and lures receive their own drift rate parameters. Both were implemented as hierarchical Bayesian models and applied to four datasets. Model selection taking into account parsimony favored the LR-DDM, which requires fewer parameters than the standard DDM but still fits the data well. These results support log-likelihood based models as providing an elegant explanation of the regularities of recognition memory, not only in terms of choices made but also in terms of the times it takes to make them. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Likelihood inference for unions of interacting discs

    DEFF Research Database (Denmark)

    Møller, Jesper; Helisová, Katarina

    To the best of our knowledge, this is the first paper which discusses likelihood inference or a random set using a germ-grain model, where the individual grains are unobservable edge effects occur, and other complications appear. We consider the case where the grains form a disc process modelled...... is specified with respect to a given marked Poisson model (i.e. a Boolean model). We show how edge effects and other complications can be handled by considering a certain conditional likelihood. Our methodology is illustrated by analyzing Peter Diggle's heather dataset, where we discuss the results...... of simulation-based maximum likelihood inference and the effect of specifying different reference Poisson models....

  19. Testing efficacy of distance and tree-based methods for DNA barcoding of grasses (Poaceae tribe Poeae) in Australia.

    Science.gov (United States)

    Birch, Joanne L; Walsh, Neville G; Cantrill, David J; Holmes, Gareth D; Murphy, Daniel J

    2017-01-01

    In Australia, Poaceae tribe Poeae are represented by 19 genera and 99 species, including economically and environmentally important native and introduced pasture grasses [e.g. Poa (Tussock-grasses) and Lolium (Ryegrasses)]. We used this tribe, which are well characterised in regards to morphological diversity and evolutionary relationships, to test the efficacy of DNA barcoding methods. A reference library was generated that included 93.9% of species in Australia (408 individuals, [Formula: see text] = 3.7 individuals per species). Molecular data were generated for official plant barcoding markers (rbcL, matK) and the nuclear ribosomal internal transcribed spacer (ITS) region. We investigated accuracy of specimen identifications using distance- (nearest neighbour, best-close match, and threshold identification) and tree-based (maximum likelihood, Bayesian inference) methods and applied species discovery methods (automatic barcode gap discovery, Poisson tree processes) based on molecular data to assess congruence with recognised species. Across all methods, success rate for specimen identification of genera was high (87.5-99.5%) and of species was low (25.6-44.6%). Distance- and tree-based methods were equally ineffective in providing accurate identifications for specimens to species rank (26.1-44.6% and 25.6-31.3%, respectively). The ITS marker achieved the highest success rate for specimen identification at both generic and species ranks across the majority of methods. For distance-based analyses the best-close match method provided the greatest accuracy for identification of individuals with a high percentage of "correct" (97.6%) and a low percentage of "incorrect" (0.3%) generic identifications, based on the ITS marker. For tribe Poeae, and likely for other grass lineages, sequence data in the standard DNA barcode markers are not variable enough for accurate identification of specimens to species rank. For recently diverged grass species similar challenges are

  20. MRI-based decision tree model for diagnosis of biliary atresia.

    Science.gov (United States)

    Kim, Yong Hee; Kim, Myung-Joon; Shin, Hyun Joo; Yoon, Haesung; Han, Seok Joo; Koh, Hong; Roh, Yun Ho; Lee, Mi-Jung

    2018-02-23

    To evaluate MRI findings and to generate a decision tree model for diagnosis of biliary atresia (BA) in infants with jaundice. We retrospectively reviewed features of MRI and ultrasonography (US) performed in infants with jaundice between January 2009 and June 2016 under approval of the institutional review board, including the maximum diameter of periportal signal change on MRI (MR triangular cord thickness, MR-TCT) or US (US-TCT), visibility of common bile duct (CBD) and abnormality of gallbladder (GB). Hepatic subcapsular flow was reviewed on Doppler US. We performed conditional inference tree analysis using MRI findings to generate a decision tree model. A total of 208 infants were included, 112 in the BA group and 96 in the non-BA group. Mean age at the time of MRI was 58.7 ± 36.6 days. Visibility of CBD, abnormality of GB and MR-TCT were good discriminators for the diagnosis of BA and the MRI-based decision tree using these findings with MR-TCT cut-off 5.1 mm showed 97.3 % sensitivity, 94.8 % specificity and 96.2 % accuracy. MRI-based decision tree model reliably differentiates BA in infants with jaundice. MRI can be an objective imaging modality for the diagnosis of BA. • MRI-based decision tree model reliably differentiates biliary atresia in neonatal cholestasis. • Common bile duct, gallbladder and periportal signal changes are the discriminators. • MRI has comparable performance to ultrasonography for diagnosis of biliary atresia.

  1. Multiple hypothesis tracking based extraction of airway trees from CT data

    DEFF Research Database (Denmark)

    Raghavendra, Selvan; Petersen, Jens; de Bruijne, Marleen

    Segmentation of airway trees from CT scans of lungs has important clinical applications, in relation to the diagnosis of chronic obstructive pulmonary disease (COPD). Here we present a method based on multiple hypothesis tracking (MHT) and template matching, originally devised for vessel...... segmentation, to extract airway trees. Idealized tubular templates are constructed and ranked using scores assigned based on the image data. Several such regularly spaced hypotheses are used in constructing a hypothesis tree, which is then traversed to obtain improved segmentation results....

  2. Which trees should be removed in thinning?

    Directory of Open Access Journals (Sweden)

    Timo Pukkala

    2015-12-01

    Full Text Available Background: In economically optimal management, trees that are removed in a thinning treatment should be selected on the basis of their value, relative value increment and the effect of removal on the growth of remaining trees. Large valuable trees with decreased value increment should be removed, especially when they overtop smaller trees. Methods: This study optimized the tree selection rule in the thinning treatments of continuous cover management when the aim is to maximize the profitability of forest management. The weights of three criteria (stem value, relative value increment and effect of removal on the competition of remaining trees were optimized together with thinning intervals. Results and conclusions: The results confirmed the hypothesis that optimal thinning involves removing predominantly large trees. Increasing stumpage value, decreasing relative value increment, and increasing competitive influence increased the likelihood that removal is optimal decision. However, if the spatial distribution of trees is irregular, it is optimal to leave large trees in sparse places and remove somewhat smaller trees from dense places. However, the benefit of optimal thinning, as compared to diameter limit cutting is not usually large in pure one-species stands. On the contrary, removing the smallest trees from the stand may lead to significant (30–40 % reductions in the net present value of harvest incomes. Keywords: Continuous cover forestry, Tree selection, High thinning, Optimal management, Spatial distribution, Spatial growth model

  3. Efficient reduction and modularization for large fault trees stored by pages

    International Nuclear Information System (INIS)

    Chen, Shanqi; Wang, Jin; Wang, Jiaqun; Wang, Fang; Hu, Liqin

    2016-01-01

    Highlights: • New fault tree pre-processing methods used in RiskA are presented. • Including the fault tree paging storage, simplification and modularization. • For getting MCS for fault trees containing more than 10,000 gates and events. • Reduce computer resources needs (RAM) and improve computation speed. - Abstract: Fault Tree Analysis (FTA), an indispensable tool used in Probabilistic Risk Assessment (PRA), has been used throughout the commercial nuclear power industry for safety and reliability analyses. However, large fault tree analysis, such as those used in nuclear power plant requires significant computer resources, which makes the analysis of PRA model inefficient and time consuming. This paper describes a fault tree pre-processing method used in the reliability and probabilistic safety assessment program RiskA that is capable of generating minimal cutsets for fault trees containing more than 10,000 gates and basic events. The novel feature of this method is not only that Boolean reduction rules are used but also that a new objective of simplification is proposed. Moreover, since the method aims to find more fault tree modules by the linear-time algorithm, it can optimize fault tree modularization, which further reduces the computational time of large fault tree analysis.

  4. Factors Associated With the Likelihood of Hospitalization Following Emergency Department Visits for Behavioral Health Conditions.

    Science.gov (United States)

    Hamilton, Jane E; Desai, Pratikkumar V; Hoot, Nathan R; Gearing, Robin E; Jeong, Shin; Meyer, Thomas D; Soares, Jair C; Begley, Charles E

    2016-11-01

    following an ED visit. The block of enabling factors was the strongest predictor of hospitalization following an ED visit compared to predisposing and need factors. Our findings also provide evidence of disparities in hospitalization of the uninsured and racial and ethnic minority patients with ED visits for behavioral health conditions. Thus, improved access to community-based behavioral health services and an increased capacity for inpatient psychiatric hospitals for treating indigent patients may be needed to improve the efficiency of ED services in our region for patients with behavioral health conditions. Among need factors, a discharge diagnosis of schizophrenia/psychotic spectrum disorder, an affective disorder, a personality disorder, an impulse control disorder, or dementia as well as secondary diagnoses of suicidal ideation and/or suicidal behavior increased the likelihood of hospitalization following an ED visit, also suggesting an opportunity for improving the efficiency of ED care through the provision of psychiatric services to stabilize and treat patients with serious mental illness. © 2016 by the Society for Academic Emergency Medicine.

  5. A maximum likelihood framework for protein design

    Directory of Open Access Journals (Sweden)

    Philippe Hervé

    2006-06-01

    Full Text Available Abstract Background The aim of protein design is to predict amino-acid sequences compatible with a given target structure. Traditionally envisioned as a purely thermodynamic question, this problem can also be understood in a wider context, where additional constraints are captured by learning the sequence patterns displayed by natural proteins of known conformation. In this latter perspective, however, we still need a theoretical formalization of the question, leading to general and efficient learning methods, and allowing for the selection of fast and accurate objective functions quantifying sequence/structure compatibility. Results We propose a formulation of the protein design problem in terms of model-based statistical inference. Our framework uses the maximum likelihood principle to optimize the unknown parameters of a statistical potential, which we call an inverse potential to contrast with classical potentials used for structure prediction. We propose an implementation based on Markov chain Monte Carlo, in which the likelihood is maximized by gradient descent and is numerically estimated by thermodynamic integration. The fit of the models is evaluated by cross-validation. We apply this to a simple pairwise contact potential, supplemented with a solvent-accessibility term, and show that the resulting models have a better predictive power than currently available pairwise potentials. Furthermore, the model comparison method presented here allows one to measure the relative contribution of each component of the potential, and to choose the optimal number of accessibility classes, which turns out to be much higher than classically considered. Conclusion Altogether, this reformulation makes it possible to test a wide diversity of models, using different forms of potentials, or accounting for other factors than just the constraint of thermodynamic stability. Ultimately, such model-based statistical analyses may help to understand the forces

  6. Tree compression with top trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li; Landau, Gad M.

    2013-01-01

    We introduce a new compression scheme for labeled trees based on top trees [3]. Our compression scheme is the first to simultaneously take advantage of internal repeats in the tree (as opposed to the classical DAG compression that only exploits rooted subtree repeats) while also supporting fast...

  7. Tree compression with top trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li; Landau, Gad M.

    2015-01-01

    We introduce a new compression scheme for labeled trees based on top trees. Our compression scheme is the first to simultaneously take advantage of internal repeats in the tree (as opposed to the classical DAG compression that only exploits rooted subtree repeats) while also supporting fast...

  8. Bridging process-based and empirical approaches to modeling tree growth

    Science.gov (United States)

    Harry T. Valentine; Annikki Makela; Annikki Makela

    2005-01-01

    The gulf between process-based and empirical approaches to modeling tree growth may be bridged, in part, by the use of a common model. To this end, we have formulated a process-based model of tree growth that can be fitted and applied in an empirical mode. The growth model is grounded in pipe model theory and an optimal control model of crown development. Together, the...

  9. A Python-based Interface for Wide Coverage Lexicalized Tree-adjoining Grammars

    Directory of Open Access Journals (Sweden)

    Wang Ziqi

    2015-04-01

    Full Text Available This paper describes the design and implementation of a Python-based interface for wide coverage Lexicalized Tree-adjoining Grammars. The grammars are part of the XTAG Grammar project at the University of Pennsylvania, which were hand-written and semi-automatically curated to parse real-world corpora. We provide an interface to the wide coverage English and Korean XTAG grammars. Each XTAG grammar is lexicalized, which means at least one word selects a tree fragment (called an elementary tree or etree. Derivations for sentences are built by combining etrees using substitution (replacement of a tree node with an etree at the frontier of another etree and adjunction (replacement of an internal tree node in an etree by another etree. Each etree is associated with a feature structure representing constraints on substitution and adjunction. Feature structures are combined using unification during the combination of etrees. We plan to integrate our toolkit for XTAG grammars into the Python-based Natural Language Toolkit (NLTK: nltk.org. We have provided an API capable of searching the lexicalized etrees for a given word or multiple words, searching for a etree by name or function, display the lexicalized etrees to the user using a graphical view, display the feature structure associated with each tree node in an etree, hide or highlight features based on a regular expression, and browsing the entire tree database for each XTAG grammar.

  10. MB3-Miner: efficiently mining eMBedded subTREEs using Tree Model Guided candidate generation

    NARCIS (Netherlands)

    Tan, H.; Dillon, T.; Hadzic, F.; Chang, E.; Feng, L.

    2005-01-01

    Tree mining has many useful applications in areas such as Bioinformatics, XML mining, Web mining, etc. In general, most of the formally represented information in these domains is a tree structured form. In this paper we focus on mining frequent embedded subtrees from databases of rooted labeled

  11. Efficient algorithms to assess component and gate importance in fault tree analysis

    International Nuclear Information System (INIS)

    Dutuit, Y.; Rauzy, A.

    2001-01-01

    One of the principal activities of risk assessment is either the ranking or the categorization of structures, systems and components with respect to their risk-significance or their safety-significance. Several measures, so-called importance factors, of such a significance have been proposed for the case where the support model is a fault tree. In this article, we show how binary decision diagrams can be use to assess efficiently a number of classical importance factors. This work completes the preliminary results obtained recently by Andrews and Sinnamon, and the authors. It deals also with the concept of joint reliability importance

  12. Silviculture and the assessment of climate change genetic risk for southern Appalachian forest tree species

    Science.gov (United States)

    Kevin M. Potter; Barbara S. Crane

    2012-01-01

    Changing climate conditions and increasing insect and pathogen infestations will increase the likelihood that forest trees could experience population-level extirpation or species-level extinction during the next century. Gene conservation and silvicultural efforts to preserve forest tree genetic diversity present a particular challenge in species-rich regions such as...

  13. Long-term CO2 rise has increased photosynthetic efficiency and water use efficiency but did not stimulate diameter growth of tropical trees

    Science.gov (United States)

    Groenendijk, P.; Zuidema, P.; Sleen, P. V. D.; Vlam, M.; Ehlers, I.; Schleucher, J.

    2014-12-01

    Tropical forests are a crucial component of the global carbon cycle, and their responses to atmospheric changes may shift carbon cycling and climate systems. Dynamic Global Vegetation Models (DGVMs) are the major tools to simulate tropical forest responses to climate change. One of the main determinants of these simulated responses is the effect of CO2 on tropical tree physiology and growth, the 'CO2 fertilization effect'. The paucity of CO2 enrichment experiments in the tropics importantly limits insights into the CO2 fertilization effect as well as the validation of DGVMs. However, use can be made of the 40% rise in atmospheric CO2 concentration since the onset of the Industrial Revolution. The effects of the historical CO2 rise on tree physiology and growth can be obtained from stable isotopes, isotopomers and tree diameter increments obtained in tree-ring studies. We studied the physiological and growth responses of 12 tree species in Bolivia, Cameroon and Thailand to 150 years of CO2 enrichment. Analyses of 13C of wood cellulose revealed strong, long-term increases in leaf intercellular CO2 concentrations for all study species and a marked improvement of intrinsic water use efficiency (iWUE). For a subset of one species per site, we studied the Deuterium isotopomers (isomers with isotopic atoms) of glucose in wood to obtain a direct estimate of the photorespiration-to-photosynthesis ratio. We found that this ratio consistently and strongly decreased over the past century, thus increasing the effeciency and rate of photosynthesis. In spite of these strong physiological responses to increased CO2levels, we did not find evidence for increased tree diameter growth for any of the sites, or for sites combined. Possible reasons for the lack of a growth stimulation include increased (leaf) temperature, insufficient availability of nutrients or a shift in biomass investment in trees. Our results suggest that the strong CO2 fertilization of tropical tree growth often

  14. Sequence Comparison Alignment-Free Approach Based on Suffix Tree and L-Words Frequency

    Directory of Open Access Journals (Sweden)

    Inês Soares

    2012-01-01

    Full Text Available The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions. In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L—L-words—in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

  15. Resource-use efficiencies of three indigenous tree species planted in resource islands created by shrubs: implications for reforestation of subtropical degraded shrublands

    Science.gov (United States)

    Nan Liu; Qinfeng Guo

    2012-01-01

    Shrub resource islands are characterized by resources accumulated shrubby areas surrounded by relative barren soils. This research aims to determine resource-use efficiency of native trees species planted on shrub resource islands, and to determine how the planted trees may influence the resource islands in degraded shrublands in South China. Shrub (Rhodomyrtus...

  16. Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia).

    Science.gov (United States)

    Pyron, R Alexander; Hendry, Catriona R; Chou, Vincent M; Lemmon, Emily M; Lemmon, Alan R; Burbrink, Frank T

    2014-12-01

    Next-generation genomic sequencing promises to quickly and cheaply resolve remaining contentious nodes in the Tree of Life, and facilitates species-tree estimation while taking into account stochastic genealogical discordance among loci. Recent methods for estimating species trees bypass full likelihood-based estimates of the multi-species coalescent, and approximate the true species-tree using simpler summary metrics. These methods converge on the true species-tree with sufficient genomic sampling, even in the anomaly zone. However, no studies have yet evaluated their efficacy on a large-scale phylogenomic dataset, and compared them to previous concatenation strategies. Here, we generate such a dataset for Caenophidian snakes, a group with >2500 species that contains several rapid radiations that were poorly resolved with fewer loci. We generate sequence data for 333 single-copy nuclear loci with ∼100% coverage (∼0% missing data) for 31 major lineages. We estimate phylogenies using neighbor joining, maximum parsimony, maximum likelihood, and three summary species-tree approaches (NJst, STAR, and MP-EST). All methods yield similar resolution and support for most nodes. However, not all methods support monophyly of Caenophidia, with Acrochordidae placed as the sister taxon to Pythonidae in some analyses. Thus, phylogenomic species-tree estimation may occasionally disagree with well-supported relationships from concatenated analyses of small numbers of nuclear or mitochondrial genes, a consideration for future studies. In contrast for at least two diverse, rapid radiations (Lamprophiidae and Colubridae), phylogenomic data and species-tree inference do little to improve resolution and support. Thus, certain nodes may lack strong signal, and larger datasets and more sophisticated analyses may still fail to resolve them. Copyright © 2014 Elsevier Inc. All rights reserved.

  17. Assessing hydrological impacts of tree-based bioenergy feedstock

    CSIR Research Space (South Africa)

    Gush, Mark B

    2010-01-01

    Full Text Available This chapter provides a methodology for assessing the hydrological impacts of tree-based bioenergy feedstock. Based on experience gained in South Africa, it discusses the tasks required to reach an understanding of the likely water resource impacts...

  18. Earthquake likelihood model testing

    Science.gov (United States)

    Schorlemmer, D.; Gerstenberger, M.C.; Wiemer, S.; Jackson, D.D.; Rhoades, D.A.

    2007-01-01

    INTRODUCTIONThe Regional Earthquake Likelihood Models (RELM) project aims to produce and evaluate alternate models of earthquake potential (probability per unit volume, magnitude, and time) for California. Based on differing assumptions, these models are produced to test the validity of their assumptions and to explore which models should be incorporated in seismic hazard and risk evaluation. Tests based on physical and geological criteria are useful but we focus on statistical methods using future earthquake catalog data only. We envision two evaluations: a test of consistency with observed data and a comparison of all pairs of models for relative consistency. Both tests are based on the likelihood method, and both are fully prospective (i.e., the models are not adjusted to fit the test data). To be tested, each model must assign a probability to any possible event within a specified region of space, time, and magnitude. For our tests the models must use a common format: earthquake rates in specified “bins” with location, magnitude, time, and focal mechanism limits.Seismology cannot yet deterministically predict individual earthquakes; however, it should seek the best possible models for forecasting earthquake occurrence. This paper describes the statistical rules of an experiment to examine and test earthquake forecasts. The primary purposes of the tests described below are to evaluate physical models for earthquakes, assure that source models used in seismic hazard and risk studies are consistent with earthquake data, and provide quantitative measures by which models can be assigned weights in a consensus model or be judged as suitable for particular regions.In this paper we develop a statistical method for testing earthquake likelihood models. A companion paper (Schorlemmer and Gerstenberger 2007, this issue) discusses the actual implementation of these tests in the framework of the RELM initiative.Statistical testing of hypotheses is a common task and a

  19. VMCast: A VM-Assisted Stability Enhancing Solution for Tree-Based Overlay Multicast.

    Directory of Open Access Journals (Sweden)

    Weidong Gu

    Full Text Available Tree-based overlay multicast is an effective group communication method for media streaming applications. However, a group member's departure causes all of its descendants to be disconnected from the multicast tree for some time, which results in poor performance. The above problem is difficult to be addressed because overlay multicast tree is intrinsically instable. In this paper, we proposed a novel stability enhancing solution, VMCast, for tree-based overlay multicast. This solution uses two types of on-demand cloud virtual machines (VMs, i.e., multicast VMs (MVMs and compensation VMs (CVMs. MVMs are used to disseminate the multicast data, whereas CVMs are used to offer streaming compensation. The used VMs in the same cloud datacenter constitute a VM cluster. Each VM cluster is responsible for a service domain (VMSD, and each group member belongs to a specific VMSD. The data source delivers the multicast data to MVMs through a reliable path, and MVMs further disseminate the data to group members along domain overlay multicast trees. The above approach structurally improves the stability of the overlay multicast tree. We further utilized CVM-based streaming compensation to enhance the stability of the data distribution in the VMSDs. VMCast can be used as an extension to existing tree-based overlay multicast solutions, to provide better services for media streaming applications. We applied VMCast to two application instances (i.e., HMTP and HCcast. The results show that it can obviously enhance the stability of the data distribution.

  20. Mapping trees outside forests using high-resolution aerial imagery: a comparison of pixel- and object based classification approaches

    Science.gov (United States)

    Dacia M. Meneguzzo; Greg C. Liknes; Mark D. Nelson

    2013-01-01

    Discrete trees and small groups of trees in nonforest settings are considered an essential resource around the world and are collectively referred to as trees outside forests (ToF). ToF provide important functions across the landscape, such as protecting soil and water resources, providing wildlife habitat, and improving farmstead energy efficiency and aesthetics....

  1. An investigation of the leaf retention capacity, efficiency and mechanism for atmospheric particulate matter of five greening tree species in Beijing, China.

    Science.gov (United States)

    Liu, Jinqiang; Cao, Zhiguo; Zou, Songyan; Liu, Huanhuan; Hai, Xiao; Wang, Shihua; Duan, Jie; Xi, Benye; Yan, Guangxuan; Zhang, Shaowei; Jia, Zhongkui

    2018-03-01

    Urban trees have the potential to reduce air pollution, but the retention capacity and efficiency of different tree species for atmospheric particulate matter (PM) accumulation and the underlying mechanism hasn't been well understood. To select tree species with high air purification abilities, the supplementing ultrasonic cleaning (UC) procedure was first introduced into the conventional leaf cleaning methods [single water cleaning (WC) or plus brush cleaning (BC)] for eluting the leaf-retained PM. Further updates to the methodology were applied to investigate the retention capacity, efficiency, and mechanism for PM of five typical greening tree species in Beijing, China. Meanwhile, the particle size distribution of PM on the leaves, the PM retention efficiencies of easily removable (ERP), difficult-to-remove (DRP) and totally removable (TRP) particles on the leaf (AE leaf ), and the individual tree scales were estimated. The experimental leaf samples were collected from trees with similar sizes 4 (SDR) and 14days (LDR) after rainfall. When the leaves were cleaned by WC+BC, there was, on average, 29%-46% of the PM remaining on the leaves of different species, which could be removed almost completely if UC was supplemented. From SDR to LDR, the mass of the leaf-retained PM increased greatly, and the particle size distribution changed markedly for all species except for Sophorajaponica. Pinus tabuliformis retains particles with the largest average diameter (34.2μm), followed by Ginkgo biloba (20.5μm), Sabina chinensis (16.4μm), Salix babylonica (16.0μm), and S. japonica (13.1μm). S. japonica and S. chinensis had the highest AE leaf to retain the TRP and ERP of both PM 1 and PM 1-2.5 , respectively. Conversely, S. babylonica and P. tabuliformis could retain both TRP and ERP of PM 2.5-5 and PM 5-10 , and PM >10 and TSP with the highest AE leaf , respectively. In conclusion, our results could be useful in selecting greening tree species with high air purification

  2. Computation of the Likelihood in Biallelic Diffusion Models Using Orthogonal Polynomials

    Directory of Open Access Journals (Sweden)

    Claus Vogl

    2014-11-01

    Full Text Available In population genetics, parameters describing forces such as mutation, migration and drift are generally inferred from molecular data. Lately, approximate methods based on simulations and summary statistics have been widely applied for such inference, even though these methods waste information. In contrast, probabilistic methods of inference can be shown to be optimal, if their assumptions are met. In genomic regions where recombination rates are high relative to mutation rates, polymorphic nucleotide sites can be assumed to evolve independently from each other. The distribution of allele frequencies at a large number of such sites has been called “allele-frequency spectrum” or “site-frequency spectrum” (SFS. Conditional on the allelic proportions, the likelihoods of such data can be modeled as binomial. A simple model representing the evolution of allelic proportions is the biallelic mutation-drift or mutation-directional selection-drift diffusion model. With series of orthogonal polynomials, specifically Jacobi and Gegenbauer polynomials, or the related spheroidal wave function, the diffusion equations can be solved efficiently. In the neutral case, the product of the binomial likelihoods with the sum of such polynomials leads to finite series of polynomials, i.e., relatively simple equations, from which the exact likelihoods can be calculated. In this article, the use of orthogonal polynomials for inferring population genetic parameters is investigated.

  3. Recruiting Conventional Tree Architecture Models into State-of-the-Art LiDAR Mapping for Investigating Tree Growth Habits in Structure.

    Science.gov (United States)

    Lin, Yi; Jiang, Miao; Pellikka, Petri; Heiskanen, Janne

    2018-01-01

    Mensuration of tree growth habits is of considerable importance for understanding forest ecosystem processes and forest biophysical responses to climate changes. However, the complexity of tree crown morphology that is typically formed after many years of growth tends to render it a non-trivial task, even for the state-of-the-art 3D forest mapping technology-light detection and ranging (LiDAR). Fortunately, botanists have deduced the large structural diversity of tree forms into only a limited number of tree architecture models, which can present a-priori knowledge about tree structure, growth, and other attributes for different species. This study attempted to recruit Hallé architecture models (HAMs) into LiDAR mapping to investigate tree growth habits in structure. First, following the HAM-characterized tree structure organization rules, we run the kernel procedure of tree species classification based on the LiDAR-collected point clouds using a support vector machine classifier in the leave-one-out-for-cross-validation mode. Then, the HAM corresponding to each of the classified tree species was identified based on expert knowledge, assisted by the comparison of the LiDAR-derived feature parameters. Next, the tree growth habits in structure for each of the tree species were derived from the determined HAM. In the case of four tree species growing in the boreal environment, the tests indicated that the classification accuracy reached 85.0%, and their growth habits could be derived by qualitative and quantitative means. Overall, the strategy of recruiting conventional HAMs into LiDAR mapping for investigating tree growth habits in structure was validated, thereby paving a new way for efficiently reflecting tree growth habits and projecting forest structure dynamics.

  4. Decision tree methods: applications for classification and prediction.

    Science.gov (United States)

    Song, Yan-Yan; Lu, Ying

    2015-04-25

    Decision tree methodology is a commonly used data mining method for establishing classification systems based on multiple covariates or for developing prediction algorithms for a target variable. This method classifies a population into branch-like segments that construct an inverted tree with a root node, internal nodes, and leaf nodes. The algorithm is non-parametric and can efficiently deal with large, complicated datasets without imposing a complicated parametric structure. When the sample size is large enough, study data can be divided into training and validation datasets. Using the training dataset to build a decision tree model and a validation dataset to decide on the appropriate tree size needed to achieve the optimal final model. This paper introduces frequently used algorithms used to develop decision trees (including CART, C4.5, CHAID, and QUEST) and describes the SPSS and SAS programs that can be used to visualize tree structure.

  5. Efficient Delaunay Tessellation through K-D Tree Decomposition

    Energy Technology Data Exchange (ETDEWEB)

    Morozov, Dmitriy; Peterka, Tom

    2017-08-21

    Delaunay tessellations are fundamental data structures in computational geometry. They are important in data analysis, where they can represent the geometry of a point set or approximate its density. The algorithms for computing these tessellations at scale perform poorly when the input data is unbalanced. We investigate the use of k-d trees to evenly distribute points among processes and compare two strategies for picking split points between domain regions. Because resulting point distributions no longer satisfy the assumptions of existing parallel Delaunay algorithms, we develop a new parallel algorithm that adapts to its input and prove its correctness. We evaluate the new algorithm using two late-stage cosmology datasets. The new running times are up to 50 times faster using k-d tree compared with regular grid decomposition. Moreover, in the unbalanced data sets, decomposing the domain into a k-d tree is up to five times faster than decomposing it into a regular grid.

  6. Maximum Likelihood, Consistency and Data Envelopment Analysis: A Statistical Foundation

    OpenAIRE

    Rajiv D. Banker

    1993-01-01

    This paper provides a formal statistical basis for the efficiency evaluation techniques of data envelopment analysis (DEA). DEA estimators of the best practice monotone increasing and concave production function are shown to be also maximum likelihood estimators if the deviation of actual output from the efficient output is regarded as a stochastic variable with a monotone decreasing probability density function. While the best practice frontier estimator is biased below the theoretical front...

  7. Screening of tomato varieties for fruit tree based Agroforestry system

    Directory of Open Access Journals (Sweden)

    J. Hossain

    2014-12-01

    Full Text Available An experiment was conducted with four tomato varieties under a six year old orchard was accomplished at the Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU research farm during October 2011 to April 2012. The experiment was laid out in a Randomized Complete Block Design with three replications. Four tomato varieties (BARI Tomato 2, BARI Tomato 8, BARI Tomato 14 and BARI Tomato 15 were grown under guava, mango, olive and control. Results showed that light availability in control plot (999.75 μ mol m-2s-1 was remarkably higher over fruit tree based agroforestry systems and it was 58.8, 43.9 and 31.5% of the control for guava, mango and olive based systems, respectively. The shortest tomato plant was observed in olive based system (54.91 cm, while the tallest plant was observed in mango based system (60.09 cm. The highest SPAD value and number of primary branches per plant was recorded in control plot. Fruit length, fruit girth was found lowest in olive based system. The highest yield (34.06 t ha-1 was recorded in control plot while the lowest yield (10.26 t ha-1 was recorded in olive based system. The economic performance of fruit tree based tomato production system showed that both the net return and BCR of mango and guava based system was higher over control and olive based system. The contents of organic carbon, nitrogen, available phosphorus, potassium and sulfur of before experimentation soil were slightly higher in fruit tree based agroforestry systems than the control. After experimentation, nutrient elements in soil were found increased slightly than initial soils. Fruit tree based agroforestry systems could be ranked based on the economic performance as mango> guava> control> olive based system with BARI Tomato 15, BARI Tomato 2, BARI Tomato 14 and BARI Tomato 8, respectively.

  8. Multicasting in Wireless Communications (Ad-Hoc Networks): Comparison against a Tree-Based Approach

    Science.gov (United States)

    Rizos, G. E.; Vasiliadis, D. C.

    2007-12-01

    We examine on-demand multicasting in ad hoc networks. The Core Assisted Mesh Protocol (CAMP) is a well-known protocol for multicast routing in ad-hoc networks, generalizing the notion of core-based trees employed for internet multicasting into multicast meshes that have much richer connectivity than trees. On the other hand, wireless tree-based multicast routing protocols use much simpler structures for determining route paths, using only parent-child relationships. In this work, we compare the performance of the CAMP protocol against the performance of wireless tree-based multicast routing protocols, in terms of two important factors, namely packet delay and ratio of dropped packets.

  9. Radiofrequency radiation injures trees around mobile phone base stations.

    Science.gov (United States)

    Waldmann-Selsam, Cornelia; Balmori-de la Puente, Alfonso; Breunig, Helmut; Balmori, Alfonso

    2016-12-01

    In the last two decades, the deployment of phone masts around the world has taken place and, for many years, there has been a discussion in the scientific community about the possible environmental impact from mobile phone base stations. Trees have several advantages over animals as experimental subjects and the aim of this study was to verify whether there is a connection between unusual (generally unilateral) tree damage and radiofrequency exposure. To achieve this, a detailed long-term (2006-2015) field monitoring study was performed in the cities of Bamberg and Hallstadt (Germany). During monitoring, observations and photographic recordings of unusual or unexplainable tree damage were taken, alongside the measurement of electromagnetic radiation. In 2015 measurements of RF-EMF (Radiofrequency Electromagnetic Fields) were carried out. A polygon spanning both cities was chosen as the study site, where 144 measurements of the radiofrequency of electromagnetic fields were taken at a height of 1.5m in streets and parks at different locations. By interpolation of the 144 measurement points, we were able to compile an electromagnetic map of the power flux density in Bamberg and Hallstadt. We selected 60 damaged trees, in addition to 30 randomly selected trees and 30 trees in low radiation areas (n=120) in this polygon. The measurements of all trees revealed significant differences between the damaged side facing a phone mast and the opposite side, as well as differences between the exposed side of damaged trees and all other groups of trees in both sides. Thus, we found that side differences in measured values of power flux density corresponded to side differences in damage. The 30 selected trees in low radiation areas (no visual contact to any phone mast and power flux density under 50μW/m 2 ) showed no damage. Statistical analysis demonstrated that electromagnetic radiation from mobile phone masts is harmful for trees. These results are consistent with the fact

  10. Wind-Induced Reconfigurations in Flexible Branched Trees

    Science.gov (United States)

    Ojo, Oluwafemi; Shoele, Kourosh

    2017-11-01

    Wind induced stresses are the major mechanical cause of failure in trees. We know that the branching mechanism has an important effect on the stress distribution and stability of a tree in the wind. Eloy in PRL 2011, showed that Leonardo da Vinci's original observation which states the total cross section of branches is conserved across branching nodes is the best configuration for resisting wind-induced fracture in rigid trees. However, prediction of the fracture risk and pattern of a tree is also a function of their reconfiguration capabilities and how they mitigate large wind-induced stresses. In this studies through developing an efficient numerical simulation of flexible branched trees, we explore the role of the tree flexibility on the optimal branching. Our results show that the probability of a tree breaking at any point depends on both the cross-section changes in the branching nodes and the level of tree flexibility. It is found that the branching mechanism based on Leonardo da Vinci's original observation leads to a uniform stress distribution over a wide range of flexibilities but the pattern changes for more flexible systems.

  11. DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments.

    Science.gov (United States)

    Kelly, Steven; Maini, Philip K

    2013-01-01

    The rapidly growing availability of genome information has created considerable demand for both fast and accurate phylogenetic inference algorithms. We present a novel method called DendroBLAST for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. This method differs from other methods by incorporating a simple model of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred tree. Using realistic simulated sequence data we demonstrate that this method produces phylogenetic trees that are more accurate than other commonly-used distance based methods though not as accurate as maximum likelihood methods from good quality multiple sequence alignments. In addition to tests on simulated data, we use DendroBLAST to generate input trees for a supertree reconstruction of the phylogeny of the Archaea. This independent analysis produces an approximate phylogeny of the Archaea that has both high precision and recall when compared to previously published analysis of the same dataset using conventional methods. Taken together these results demonstrate that approximate phylogenetic trees can be produced in the absence of multiple sequence alignments, and we propose that these trees will provide a platform for improving and informing downstream bioinformatic analysis. A web implementation of the DendroBLAST method is freely available for use at http://www.dendroblast.com/.

  12. DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments.

    Directory of Open Access Journals (Sweden)

    Steven Kelly

    Full Text Available The rapidly growing availability of genome information has created considerable demand for both fast and accurate phylogenetic inference algorithms. We present a novel method called DendroBLAST for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. This method differs from other methods by incorporating a simple model of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred tree. Using realistic simulated sequence data we demonstrate that this method produces phylogenetic trees that are more accurate than other commonly-used distance based methods though not as accurate as maximum likelihood methods from good quality multiple sequence alignments. In addition to tests on simulated data, we use DendroBLAST to generate input trees for a supertree reconstruction of the phylogeny of the Archaea. This independent analysis produces an approximate phylogeny of the Archaea that has both high precision and recall when compared to previously published analysis of the same dataset using conventional methods. Taken together these results demonstrate that approximate phylogenetic trees can be produced in the absence of multiple sequence alignments, and we propose that these trees will provide a platform for improving and informing downstream bioinformatic analysis. A web implementation of the DendroBLAST method is freely available for use at http://www.dendroblast.com/.

  13. Human Factors Reliability Analysis for Assuring Nuclear Safety Using Fuzzy Fault Tree

    International Nuclear Information System (INIS)

    Eisawy, E.A.-F. I.; Sallam, H.

    2016-01-01

    In order to ensure effective prevention of harmful events, the risk assessment process cannot ignore the role of humans in the dynamics of accidental events and thus the seriousness of the consequences that may derive from them. Human reliability analysis (HRA) involves the use of qualitative and quantitative methods to assess the human contribution to risk. HRA techniques have been developed in order to provide human error probability values associated with operators’ tasks to be included within the broader context of system risk assessment, and are aimed at reducing the probability of accidental events. Fault tree analysis (FTA) is a graphical model that displays the various combinations of equipment failures and human errors that can result in the main system failure of interest. FTA is a risk analysis technique to assess likelihood (in a probabilistic context) of an event. The objective data available to estimate the likelihood is often missing, and even if available, is subject to incompleteness and imprecision or vagueness. Without addressing incompleteness and imprecision in the available data, FTA and subsequent risk analysis give a false impression of precision and correctness that undermines the overall credibility of the process. To solve this problem, qualitative justification in the context of failure possibilities can be used as alternative for quantitative justification. In this paper, we introduce the approach of fuzzy reliability as solution for fault tree analysis drawbacks. A new fuzzy fault tree method is proposed for the analysis of human reliability based on fuzzy sets and fuzzy operations t-norms, co-norms, defuzzification, and fuzzy failure probability. (author)

  14. Exploring the relationship between sequence similarity and accurate phylogenetic trees.

    Science.gov (United States)

    Cantarel, Brandi L; Morrison, Hilary G; Pearson, William

    2006-11-01

    We have characterized the relationship between accurate phylogenetic reconstruction and sequence similarity, testing whether high levels of sequence similarity can consistently produce accurate evolutionary trees. We generated protein families with known phylogenies using a modified version of the PAML/EVOLVER program that produces insertions and deletions as well as substitutions. Protein families were evolved over a range of 100-400 point accepted mutations; at these distances 63% of the families shared significant sequence similarity. Protein families were evolved using balanced and unbalanced trees, with ancient or recent radiations. In families sharing statistically significant similarity, about 60% of multiple sequence alignments were 95% identical to true alignments. To compare recovered topologies with true topologies, we used a score that reflects the fraction of clades that were correctly clustered. As expected, the accuracy of the phylogenies was greatest in the least divergent families. About 88% of phylogenies clustered over 80% of clades in families that shared significant sequence similarity, using Bayesian, parsimony, distance, and maximum likelihood methods. However, for protein families with short ancient branches (ancient radiation), only 30% of the most divergent (but statistically significant) families produced accurate phylogenies, and only about 70% of the second most highly conserved families, with median expectation values better than 10(-60), produced accurate trees. These values represent upper bounds on expected tree accuracy for sequences with a simple divergence history; proteins from 700 Giardia families, with a similar range of sequence similarities but considerably more gaps, produced much less accurate trees. For our simulated insertions and deletions, correct multiple sequence alignments did not perform much better than those produced by T-COFFEE, and including sequences with expressed sequence tag-like sequencing errors did not

  15. Sampling strategies for efficient estimation of tree foliage biomass

    Science.gov (United States)

    Hailemariam Temesgen; Vicente Monleon; Aaron Weiskittel; Duncan Wilson

    2011-01-01

    Conifer crowns can be highly variable both within and between trees, particularly with respect to foliage biomass and leaf area. A variety of sampling schemes have been used to estimate biomass and leaf area at the individual tree and stand scales. Rarely has the effectiveness of these sampling schemes been compared across stands or even across species. In addition,...

  16. Efficient computation of hashes

    International Nuclear Information System (INIS)

    Lopes, Raul H C; Franqueira, Virginia N L; Hobson, Peter R

    2014-01-01

    The sequential computation of hashes at the core of many distributed storage systems and found, for example, in grid services can hinder efficiency in service quality and even pose security challenges that can only be addressed by the use of parallel hash tree modes. The main contributions of this paper are, first, the identification of several efficiency and security challenges posed by the use of sequential hash computation based on the Merkle-Damgard engine. In addition, alternatives for the parallel computation of hash trees are discussed, and a prototype for a new parallel implementation of the Keccak function, the SHA-3 winner, is introduced.

  17. Transpiration and water-use efficiency in mixed-species forests versus monocultures: effects of tree size, stand density and season.

    Science.gov (United States)

    Forrester, David I

    2015-03-01

    Mixtures can be more productive than monocultures and may therefore use more water, which may make them more susceptible to droughts. The species interactions that influence growth, transpiration and water-use efficiency (WUE, tree growth per unit transpiration) within a given mixture vary with intra- and inter-annual climatic variability, stand density and tree size, but these effects remain poorly quantified. These relationships were examined in mixtures and monocultures of Eucalyptus globulus Labill. and Acacia mearnsii de Wildeman. Growth and transpiration were measured between ages 14 and 15 years. All E. globulus trees in mixture that were growing faster than similar sized trees in monocultures had higher WUE, while trees with similar growth rates had similar WUE. By the age of 14 years A. mearnsii trees were beginning to senesce and there were no longer any relationships between tree size and growth or WUE. The relationship between transpiration and tree size did not differ between treatments for either species, so stand-level increases in transpiration simply reflected the larger mean tree size in mixtures. Increasing neighbourhood basal area increased the complementarity effect on E. globulus growth and transpiration. The complementarity effect also varied throughout the year, but this was not related to the climatic seasonality. This study shows that stand-level responses can be the net effect of a much wider range of individual tree-level responses, but at both levels, if growth has not increased for a given species, it appears unlikely that there will be differences in transpiration or WUE for that species. Growth data may provide a useful initial indication of whether mixtures have higher transpiration or WUE, and which species and tree sizes contribute to this effect. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  18. Estimating Uncertainty of Point-Cloud Based Single-Tree Segmentation with Ensemble Based Filtering

    Directory of Open Access Journals (Sweden)

    Matthew Parkan

    2018-02-01

    Full Text Available Individual tree crown segmentation from Airborne Laser Scanning data is a nodal problem in forest remote sensing. Focusing on single layered spruce and fir dominated coniferous forests, this article addresses the problem of directly estimating 3D segment shape uncertainty (i.e., without field/reference surveys, using a probabilistic approach. First, a coarse segmentation (marker controlled watershed is applied. Then, the 3D alpha hull and several descriptors are computed for each segment. Based on these descriptors, the alpha hulls are grouped to form ensembles (i.e., groups of similar tree shapes. By examining how frequently regions of a shape occur within an ensemble, it is possible to assign a shape probability to each point within a segment. The shape probability can subsequently be thresholded to obtain improved (filtered tree segments. Results indicate this approach can be used to produce segmentation reliability maps. A comparison to manually segmented tree crowns also indicates that the approach is able to produce more reliable tree shapes than the initial (unfiltered segmentation.

  19. A General Self-Organized Tree-Based Energy-Balance Routing Protocol for Wireless Sensor Network

    Science.gov (United States)

    Han, Zhao; Wu, Jie; Zhang, Jie; Liu, Liefeng; Tian, Kaiyun

    2014-04-01

    Wireless sensor network (WSN) is a system composed of a large number of low-cost micro-sensors. This network is used to collect and send various kinds of messages to a base station (BS). WSN consists of low-cost nodes with limited battery power, and the battery replacement is not easy for WSN with thousands of physically embedded nodes, which means energy efficient routing protocol should be employed to offer a long-life work time. To achieve the aim, we need not only to minimize total energy consumption but also to balance WSN load. Researchers have proposed many protocols such as LEACH, HEED, PEGASIS, TBC and PEDAP. In this paper, we propose a General Self-Organized Tree-Based Energy-Balance routing protocol (GSTEB) which builds a routing tree using a process where, for each round, BS assigns a root node and broadcasts this selection to all sensor nodes. Subsequently, each node selects its parent by considering only itself and its neighbors' information, thus making GSTEB a dynamic protocol. Simulation results show that GSTEB has a better performance than other protocols in balancing energy consumption, thus prolonging the lifetime of WSN.

  20. Recruiting Conventional Tree Architecture Models into State-of-the-Art LiDAR Mapping for Investigating Tree Growth Habits in Structure

    Directory of Open Access Journals (Sweden)

    Yi Lin

    2018-02-01

    Full Text Available Mensuration of tree growth habits is of considerable importance for understanding forest ecosystem processes and forest biophysical responses to climate changes. However, the complexity of tree crown morphology that is typically formed after many years of growth tends to render it a non-trivial task, even for the state-of-the-art 3D forest mapping technology—light detection and ranging (LiDAR. Fortunately, botanists have deduced the large structural diversity of tree forms into only a limited number of tree architecture models, which can present a-priori knowledge about tree structure, growth, and other attributes for different species. This study attempted to recruit Hallé architecture models (HAMs into LiDAR mapping to investigate tree growth habits in structure. First, following the HAM-characterized tree structure organization rules, we run the kernel procedure of tree species classification based on the LiDAR-collected point clouds using a support vector machine classifier in the leave-one-out-for-cross-validation mode. Then, the HAM corresponding to each of the classified tree species was identified based on expert knowledge, assisted by the comparison of the LiDAR-derived feature parameters. Next, the tree growth habits in structure for each of the tree species were derived from the determined HAM. In the case of four tree species growing in the boreal environment, the tests indicated that the classification accuracy reached 85.0%, and their growth habits could be derived by qualitative and quantitative means. Overall, the strategy of recruiting conventional HAMs into LiDAR mapping for investigating tree growth habits in structure was validated, thereby paving a new way for efficiently reflecting tree growth habits and projecting forest structure dynamics.

  1. Pylogeny: an open-source Python framework for phylogenetic tree reconstruction and search space heuristics

    Directory of Open Access Journals (Sweden)

    Alexander Safatli

    2015-06-01

    Full Text Available Summary. Pylogeny is a cross-platform library for the Python programming language that provides an object-oriented application programming interface for phylogenetic heuristic searches. Its primary function is to permit both heuristic search and analysis of the phylogenetic tree search space, as well as to enable the design of novel algorithms to search this space. To this end, the framework supports the structural manipulation of phylogenetic trees, in particular using rearrangement operators such as NNI, SPR, and TBR, the scoring of trees using parsimony and likelihood methods, the construction of a tree search space graph, and the programmatic execution of a few existing heuristic programs. The library supports a range of common phylogenetic file formats and can be used for both nucleotide and protein data. Furthermore, it is also capable of supporting GPU likelihood calculation on nucleotide character data through the BEAGLE library.Availability. Existing development and source code is available for contribution and for download by the public from GitHub (http://github.com/AlexSafatli/Pylogeny. A stable release of this framework is available for download through PyPi (Python Package Index at http://pypi.python.org/pypi/pylogeny.

  2. Decision tree and PCA-based fault diagnosis of rotating machinery

    Science.gov (United States)

    Sun, Weixiang; Chen, Jin; Li, Jiaqing

    2007-04-01

    After analysing the flaws of conventional fault diagnosis methods, data mining technology is introduced to fault diagnosis field, and a new method based on C4.5 decision tree and principal component analysis (PCA) is proposed. In this method, PCA is used to reduce features after data collection, preprocessing and feature extraction. Then, C4.5 is trained by using the samples to generate a decision tree model with diagnosis knowledge. At last the tree model is used to make diagnosis analysis. To validate the method proposed, six kinds of running states (normal or without any defect, unbalance, rotor radial rub, oil whirl, shaft crack and a simultaneous state of unbalance and radial rub), are simulated on Bently Rotor Kit RK4 to test C4.5 and PCA-based method and back-propagation neural network (BPNN). The result shows that C4.5 and PCA-based diagnosis method has higher accuracy and needs less training time than BPNN.

  3. Project CAPTURE: using forest inventory and analysis data to prioritize tree species for conservation, management, and restoration

    Science.gov (United States)

    Kevin M. Potter; Barbara S. Crane; William W. Hargrove

    2015-01-01

    A variety of threats, most importantly climate change and insect and disease infestation, will increase the likelihood that forest tree species could experience population-level extirpation or species-level extinction during the next century. Project CAPTURE (Conservation Assessment and Prioritization of Forest Trees Under Risk of Extirpation) is a cooperative effort...

  4. Detecting Difference between Process Models Based on the Refined Process Structure Tree

    Directory of Open Access Journals (Sweden)

    Jing Fan

    2017-01-01

    Full Text Available The development of mobile workflow management systems (mWfMS leads to large number of business process models. In the meantime, the location restriction embedded in mWfMS may result in different process models for a single business process. In order to help users quickly locate the difference and rebuild the process model, detecting the difference between different process models is needed. Existing detection methods either provide a dissimilarity value to represent the difference or use predefined difference template to generate the result, which cannot reflect the entire composition of the difference. Hence, in this paper, we present a new approach to solve this problem. Firstly, we parse the process models to their corresponding refined process structure trees (PSTs, that is, decomposing a process model into a hierarchy of subprocess models. Then we design a method to convert the PST to its corresponding task based process structure tree (TPST. As a consequence, the problem of detecting difference between two process models is transformed to detect difference between their corresponding TPSTs. Finally, we obtain the difference between two TPSTs based on the divide and conquer strategy, where the difference is described by an edit script and we make the cost of the edit script close to minimum. The extensive experimental evaluation shows that our method can meet the real requirements in terms of precision and efficiency.

  5. Comparing Individual Tree Segmentation Based on High Resolution Multispectral Image and Lidar Data

    Science.gov (United States)

    Xiao, P.; Kelly, M.; Guo, Q.

    2014-12-01

    This study compares the use of high-resolution multispectral WorldView images and high density Lidar data for individual tree segmentation. The application focuses on coniferous and deciduous forests in the Sierra Nevada Mountains. The tree objects are obtained in two ways: a hybrid region-merging segmentation method with multispectral images, and a top-down and bottom-up region-growing method with Lidar data. The hybrid region-merging method is used to segment individual tree from multispectral images. It integrates the advantages of global-oriented and local-oriented region-merging strategies into a unified framework. The globally most-similar pair of regions is used to determine the starting point of a growing region. The merging iterations are constrained within the local vicinity, thus the segmentation is accelerated and can reflect the local context. The top-down region-growing method is adopted in coniferous forest to delineate individual tree from Lidar data. It exploits the spacing between the tops of trees to identify and group points into a single tree based on simple rules of proximity and likely tree shape. The bottom-up region-growing method based on the intensity and 3D structure of Lidar data is applied in deciduous forest. It segments tree trunks based on the intensity and topological relationships of the points, and then allocate other points to exact tree crowns according to distance. The accuracies for each method are evaluated with field survey data in several test sites, covering dense and sparse canopy. Three types of segmentation results are produced: true positive represents a correctly segmented individual tree, false negative represents a tree that is not detected and assigned to a nearby tree, and false positive represents that a point or pixel cluster is segmented as a tree that does not in fact exist. They respectively represent correct-, under-, and over-segmentation. Three types of index are compared for segmenting individual tree

  6. On defining a unique phylogenetic tree with homoplastic characters.

    Science.gov (United States)

    Goloboff, Pablo A; Wilkinson, Mark

    2018-05-01

    This paper discusses the problem of whether creating a matrix with all the character state combinations that have a fixed number of steps (or extra steps) on a given tree T, produces the same tree T when analyzed with maximum parsimony or maximum likelihood. Exhaustive enumeration of cases up to 20 taxa for binary characters, and up to 12 taxa for 4-state characters, shows that the same tree is recovered (as unique most likely or most parsimonious tree) as long as the number of extra steps is within 1/4 of the number of taxa. This dependence, 1/4 of the number of taxa, is discussed with a general argumentation, in terms of the spread of the character changes on the tree used to select character state distributions. The present finding allows creating matrices which have as much homoplasy as possible for the most parsimonious or likely tree to be predictable, and examination of these matrices with hill-climbing search algorithms provides additional evidence on the (lack of a) necessary relationship between homoplasy and the ability of search methods to find optimal trees. Copyright © 2018 Elsevier Inc. All rights reserved.

  7. The decision tree classifier - Design and potential. [for Landsat-1 data

    Science.gov (United States)

    Hauska, H.; Swain, P. H.

    1975-01-01

    A new classifier has been developed for the computerized analysis of remote sensor data. The decision tree classifier is essentially a maximum likelihood classifier using multistage decision logic. It is characterized by the fact that an unknown sample can be classified into a class using one or several decision functions in a successive manner. The classifier is applied to the analysis of data sensed by Landsat-1 over Kenosha Pass, Colorado. The classifier is illustrated by a tree diagram which for processing purposes is encoded as a string of symbols such that there is a unique one-to-one relationship between string and decision tree.

  8. Main-Memory Operation Buffering for Efficient R-Tree Update

    DEFF Research Database (Denmark)

    Jensen, Christian Søndergaard; Saltenis, Simonas; Biveinis, Laurynas

    2007-01-01

    the buffering of update operations in main memory as well as the grouping of operations to reduce disk I/O. In particular, operations are performed in bulk so that multiple operations are able to share I/O. The paper presents an analytical cost model that is shown to be accurate by empirical studies...... the main memory that is indeed available, or do not support some of the standard index operations. Assuming a setting where the index updates need not be written to disk immediately, we propose an R-tree-based indexing technique that does not exhibit any of these drawbacks. This technique exploits...

  9. Species-Level Differences in Hyperspectral Metrics among Tropical Rainforest Trees as Determined by a Tree-Based Classifier

    Directory of Open Access Journals (Sweden)

    Dar A. Roberts

    2012-06-01

    Full Text Available This study explores a method to classify seven tropical rainforest tree species from full-range (400–2,500 nm hyperspectral data acquired at tissue (leaf and bark, pixel and crown scales using laboratory and airborne sensors. Metrics that respond to vegetation chemistry and structure were derived using narrowband indices, derivative- and absorption-based techniques, and spectral mixture analysis. We then used the Random Forests tree-based classifier to discriminate species with minimally-correlated, importance-ranked metrics. At all scales, best overall accuracies were achieved with metrics derived from all four techniques and that targeted chemical and structural properties across the visible to shortwave infrared spectrum (400–2500 nm. For tissue spectra, overall accuracies were 86.8% for leaves, 74.2% for bark, and 84.9% for leaves plus bark. Variation in tissue metrics was best explained by an axis of red absorption related to photosynthetic leaves and an axis distinguishing bark water and other chemical absorption features. Overall accuracies for individual tree crowns were 71.5% for pixel spectra, 70.6% crown-mean spectra, and 87.4% for a pixel-majority technique. At pixel and crown scales, tree structure and phenology at the time of image acquisition were important factors that determined species spectral separability.

  10. Adjustable chain trees for proteins

    DEFF Research Database (Denmark)

    Winter, Pawel; Fonseca, Rasmus

    2012-01-01

    A chain tree is a data structure for changing protein conformations. It enables very fast detection of clashes and free energy potential calculations. A modified version of chain trees that adjust themselves to the changing conformations of folding proteins is introduced. This results in much...... tighter bounding volume hierarchies and therefore fewer intersection checks. Computational results indicate that the efficiency of the adjustable chain trees is significantly improved compared to the traditional chain trees....

  11. Statistical tracking of tree-like tubular structures with efficient branching detection in 3D medical image data

    International Nuclear Information System (INIS)

    Wang, X; Heimann, T; Meinzer, H P; Wegner, I; Lo, P; Sumkauskaite, M; Puderbach, M; De Bruijne, M

    2012-01-01

    The segmentation of tree-like tubular structures such as coronary arteries and airways is an essential step for many 3D medical imaging applications. Statistical tracking techniques for the extraction of elongated structures have received considerable attention in recent years due to their robustness against image noise and pathological changes. However, most tracking methods are limited to a specific application and do not support branching structures efficiently. In this work, we present a novel statistical tracking approach for the extraction of different types of tubular structures with ringlike cross-sections. Domain-specific knowledge is learned from training data sets and integrated into the tracking process by simple adaption of parameters. In addition, an efficient branching detection algorithm is presented. This approach was evaluated by extracting coronary arteries from 32 CTA data sets and distal airways from 20 CT scans. These data sets were provided by the organizers of the workshop ‘3D Segmentation in the Clinic: A Grand Challenge II-Coronary Artery Tracking (CAT08)’ and ‘Extraction of Airways from CT 2009 (EXACT’09)’. On average, 81.5% overlap and 0.51 mm accuracy for the tracking of coronary arteries were achieved. For the extraction of airway trees, 51.3% of the total tree length, 53.6% of the total number of branches and a 4.98% false positive rate were attained. In both experiments, our approach is comparable to state-of-the-art methods. (paper)

  12. Species tree estimation for the late blight pathogen, Phytophthora infestans, and close relatives.

    Science.gov (United States)

    Blair, Jaime E; Coffey, Michael D; Martin, Frank N

    2012-01-01

    To better understand the evolutionary history of a group of organisms, an accurate estimate of the species phylogeny must be known. Traditionally, gene trees have served as a proxy for the species tree, although it was acknowledged early on that these trees represented different evolutionary processes. Discordances among gene trees and between the gene trees and the species tree are also expected in closely related species that have rapidly diverged, due to processes such as the incomplete sorting of ancestral polymorphisms. Recently, methods have been developed for the explicit estimation of species trees, using information from multilocus gene trees while accommodating heterogeneity among them. Here we have used three distinct approaches to estimate the species tree for five Phytophthora pathogens, including P. infestans, the causal agent of late blight disease in potato and tomato. Our concatenation-based "supergene" approach was unable to resolve relationships even with data from both the nuclear and mitochondrial genomes, and from multiple isolates per species. Our multispecies coalescent approach using both Bayesian and maximum likelihood methods was able to estimate a moderately supported species tree showing a close relationship among P. infestans, P. andina, and P. ipomoeae. The topology of the species tree was also identical to the dominant phylogenetic history estimated in our third approach, Bayesian concordance analysis. Our results support previous suggestions that P. andina is a hybrid species, with P. infestans representing one parental lineage. The other parental lineage is not known, but represents an independent evolutionary lineage more closely related to P. ipomoeae. While all five species likely originated in the New World, further study is needed to determine when and under what conditions this hybridization event may have occurred.

  13. Accelerated maximum likelihood parameter estimation for stochastic biochemical systems

    Directory of Open Access Journals (Sweden)

    Daigle Bernie J

    2012-05-01

    . Conclusions This work provides a novel, accelerated version of a likelihood-based parameter estimation method that can be readily applied to stochastic biochemical systems. In addition, our results suggest opportunities for added efficiency improvements that will further enhance our ability to mechanistically simulate biological processes.

  14. Tree-based indexing for real-time ConvNet landmark-based visual place recognition

    Directory of Open Access Journals (Sweden)

    Yi Hou

    2017-01-01

    Full Text Available Recent impressive studies on using ConvNet landmarks for visual place recognition take an approach that involves three steps: (a detection of landmarks, (b description of the landmarks by ConvNet features using a convolutional neural network, and (c matching of the landmarks in the current view with those in the database views. Such an approach has been shown to achieve the state-of-the-art accuracy even under significant viewpoint and environmental changes. However, the computational burden in step (c significantly prevents this approach from being applied in practice, due to the complexity of linear search in high-dimensional space of the ConvNet features. In this article, we propose two simple and efficient search methods to tackle this issue. Both methods are built upon tree-based indexing. Given a set of ConvNet features of a query image, the first method directly searches the features’ approximate nearest neighbors in a tree structure that is constructed from ConvNet features of database images. The database images are voted on by features in the query image, according to a lookup table which maps each ConvNet feature to its corresponding database image. The database image with the highest vote is considered the solution. Our second method uses a coarse-to-fine procedure: the coarse step uses the first method to coarsely find the top-N database images, and the fine step performs a linear search in Hamming space of the hash codes of the ConvNet features to determine the best match. Experimental results demonstrate that our methods achieve real-time search performance on five data sets with different sizes and various conditions. Most notably, by achieving an average search time of 0.035 seconds/query, our second method improves the matching efficiency by the three orders of magnitude over a linear search baseline on a database with 20,688 images, with negligible loss in place recognition accuracy.

  15. Algorithms of maximum likelihood data clustering with applications

    Science.gov (United States)

    Giada, Lorenzo; Marsili, Matteo

    2002-12-01

    We address the problem of data clustering by introducing an unsupervised, parameter-free approach based on maximum likelihood principle. Starting from the observation that data sets belonging to the same cluster share a common information, we construct an expression for the likelihood of any possible cluster structure. The likelihood in turn depends only on the Pearson's coefficient of the data. We discuss clustering algorithms that provide a fast and reliable approximation to maximum likelihood configurations. Compared to standard clustering methods, our approach has the advantages that (i) it is parameter free, (ii) the number of clusters need not be fixed in advance and (iii) the interpretation of the results is transparent. In order to test our approach and compare it with standard clustering algorithms, we analyze two very different data sets: time series of financial market returns and gene expression data. We find that different maximization algorithms produce similar cluster structures whereas the outcome of standard algorithms has a much wider variability.

  16. A toolkit for visualizing the coherence of tree-based reordering with word-alignments

    NARCIS (Netherlands)

    Maillette de Buy Wenniger, G.; Khalilov, M.; Sima'an, K.

    2010-01-01

    Tree-based reordering constitutes an important motivation for the increasing interest in syntax-driven machine translation. It has often been argued that tree-based reordering might provide a more effective approach for bridging the word-order differences between source and target sentences. One

  17. Non-Destructive, Laser-Based Individual Tree Aboveground Biomass Estimation in a Tropical Rainforest

    Directory of Open Access Journals (Sweden)

    Muhammad Zulkarnain Abd Rahman

    2017-03-01

    Full Text Available Recent methods for detailed and accurate biomass and carbon stock estimation of forests have been driven by advances in remote sensing technology. The conventional approach to biomass estimation heavily relies on the tree species and site-specific allometric equations, which are based on destructive methods. This paper introduces a non-destructive, laser-based approach (terrestrial laser scanner for individual tree aboveground biomass estimation in the Royal Belum forest reserve, Perak, Malaysia. The study area is in the state park, and it is believed to be one of the oldest rainforests in the world. The point clouds generated for 35 forest plots, using the terrestrial laser scanner, were geo-rectified and cleaned to produce separate point clouds for individual trees. The volumes of tree trunks were estimated based on a cylinder model fitted to the point clouds. The biomasses of tree trunks were calculated by multiplying the volume and the species wood density. The biomasses of branches and leaves were also estimated based on the estimated volume and density values. Branch and leaf volumes were estimated based on the fitted point clouds using an alpha-shape approach. The estimated individual biomass and the total above ground biomass were compared with the aboveground biomass (AGB value estimated using existing allometric equations and individual tree census data collected in the field. The results show that the combination of a simple single-tree stem reconstruction and wood density can be used to estimate stem biomass comparable to the results usually obtained through existing allometric equations. However, there are several issues associated with the data and method used for branch and leaf biomass estimations, which need further improvement.

  18. AnswerTree – a hyperplace-based game for collaborative mobile learning

    OpenAIRE

    Moore, Adam; Goulding, James; Brown, Elizabeth; Swan, Jerry

    2009-01-01

    In this paper we present AnswerTree, a collaborative mobile location-based educational game designed to teach 8-12 year olds about trees and wildlife within the University of Nottingham campus. The activity is designed around collecting virtual cards (similar in nature to the popular Top TrumpsTM games) containing graphics and information about notable trees. Each player begins by collecting one card from a game location, but then he or she can only collect further cards by answering question...

  19. Accurate recapture identification for genetic mark–recapture studies with error-tolerant likelihood-based match calling and sample clustering

    Science.gov (United States)

    Sethi, Suresh; Linden, Daniel; Wenburg, John; Lewis, Cara; Lemons, Patrick R.; Fuller, Angela K.; Hare, Matthew P.

    2016-01-01

    Error-tolerant likelihood-based match calling presents a promising technique to accurately identify recapture events in genetic mark–recapture studies by combining probabilities of latent genotypes and probabilities of observed genotypes, which may contain genotyping errors. Combined with clustering algorithms to group samples into sets of recaptures based upon pairwise match calls, these tools can be used to reconstruct accurate capture histories for mark–recapture modelling. Here, we assess the performance of a recently introduced error-tolerant likelihood-based match-calling model and sample clustering algorithm for genetic mark–recapture studies. We assessed both biallelic (i.e. single nucleotide polymorphisms; SNP) and multiallelic (i.e. microsatellite; MSAT) markers using a combination of simulation analyses and case study data on Pacific walrus (Odobenus rosmarus divergens) and fishers (Pekania pennanti). A novel two-stage clustering approach is demonstrated for genetic mark–recapture applications. First, repeat captures within a sampling occasion are identified. Subsequently, recaptures across sampling occasions are identified. The likelihood-based matching protocol performed well in simulation trials, demonstrating utility for use in a wide range of genetic mark–recapture studies. Moderately sized SNP (64+) and MSAT (10–15) panels produced accurate match calls for recaptures and accurate non-match calls for samples from closely related individuals in the face of low to moderate genotyping error. Furthermore, matching performance remained stable or increased as the number of genetic markers increased, genotyping error notwithstanding.

  20. Fast Image Texture Classification Using Decision Trees

    Science.gov (United States)

    Thompson, David R.

    2011-01-01

    Texture analysis would permit improved autonomous, onboard science data interpretation for adaptive navigation, sampling, and downlink decisions. These analyses would assist with terrain analysis and instrument placement in both macroscopic and microscopic image data products. Unfortunately, most state-of-the-art texture analysis demands computationally expensive convolutions of filters involving many floating-point operations. This makes them infeasible for radiation- hardened computers and spaceflight hardware. A new method approximates traditional texture classification of each image pixel with a fast decision-tree classifier. The classifier uses image features derived from simple filtering operations involving integer arithmetic. The texture analysis method is therefore amenable to implementation on FPGA (field-programmable gate array) hardware. Image features based on the "integral image" transform produce descriptive and efficient texture descriptors. Training the decision tree on a set of training data yields a classification scheme that produces reasonable approximations of optimal "texton" analysis at a fraction of the computational cost. A decision-tree learning algorithm employing the traditional k-means criterion of inter-cluster variance is used to learn tree structure from training data. The result is an efficient and accurate summary of surface morphology in images. This work is an evolutionary advance that unites several previous algorithms (k-means clustering, integral images, decision trees) and applies them to a new problem domain (morphology analysis for autonomous science during remote exploration). Advantages include order-of-magnitude improvements in runtime, feasibility for FPGA hardware, and significant improvements in texture classification accuracy.

  1. Reset Tree-Based Optical Fault Detection

    Directory of Open Access Journals (Sweden)

    Howon Kim

    2013-05-01

    Full Text Available In this paper, we present a new reset tree-based scheme to protect cryptographic hardware against optical fault injection attacks. As one of the most powerful invasive attacks on cryptographic hardware, optical fault attacks cause semiconductors to misbehave by injecting high-energy light into a decapped integrated circuit. The contaminated result from the affected chip is then used to reveal secret information, such as a key, from the cryptographic hardware. Since the advent of such attacks, various countermeasures have been proposed. Although most of these countermeasures are strong, there is still the possibility of attack. In this paper, we present a novel optical fault detection scheme that utilizes the buffers on a circuit’s reset signal tree as a fault detection sensor. To evaluate our proposal, we model radiation-induced currents into circuit components and perform a SPICE simulation. The proposed scheme is expected to be used as a supplemental security tool.

  2. Learning in data-limited multimodal scenarios: Scandent decision forests and tree-based features.

    Science.gov (United States)

    Hor, Soheil; Moradi, Mehdi

    2016-12-01

    Incomplete and inconsistent datasets often pose difficulties in multimodal studies. We introduce the concept of scandent decision trees to tackle these difficulties. Scandent trees are decision trees that optimally mimic the partitioning of the data determined by another decision tree, and crucially, use only a subset of the feature set. We show how scandent trees can be used to enhance the performance of decision forests trained on a small number of multimodal samples when we have access to larger datasets with vastly incomplete feature sets. Additionally, we introduce the concept of tree-based feature transforms in the decision forest paradigm. When combined with scandent trees, the tree-based feature transforms enable us to train a classifier on a rich multimodal dataset, and use it to classify samples with only a subset of features of the training data. Using this methodology, we build a model trained on MRI and PET images of the ADNI dataset, and then test it on cases with only MRI data. We show that this is significantly more effective in staging of cognitive impairments compared to a similar decision forest model trained and tested on MRI only, or one that uses other kinds of feature transform applied to the MRI data. Copyright © 2016. Published by Elsevier B.V.

  3. Vegetative fallows and potential value of the neem tree (Azadirachta indica) in the tropics

    Energy Technology Data Exchange (ETDEWEB)

    Radwanski, S.A.; Wickens, G.E.

    1981-01-01

    Research into the systems of agriculture based on vegetative fallows should begin from enquiries into the shrubs and trees most efficient in restoring soil productivity and providing essential products. Azadirachta indica, of the semiarid regions is an outstanding example of a species which is not only an efficient soil ameliorant, but also provides products that are highly competitive in price and quality with petroleum-based synthetics. The launching of a research and development programme leading to the exploitation of this tree is proposed. Several projects that could be studied in such a programme are briefly outlined.

  4. Study on reliability analysis based on multilevel flow models and fault tree method

    International Nuclear Information System (INIS)

    Chen Qiang; Yang Ming

    2014-01-01

    Multilevel flow models (MFM) and fault tree method describe the system knowledge in different forms, so the two methods express an equivalent logic of the system reliability under the same boundary conditions and assumptions. Based on this and combined with the characteristics of MFM, a method mapping MFM to fault tree was put forward, thus providing a way to establish fault tree rapidly and realizing qualitative reliability analysis based on MFM. Taking the safety injection system of pressurized water reactor nuclear power plant as an example, its MFM was established and its reliability was analyzed qualitatively. The analysis result shows that the logic of mapping MFM to fault tree is correct. The MFM is easily understood, created and modified. Compared with the traditional fault tree analysis, the workload is greatly reduced and the modeling time is saved. (authors)

  5. Mineralization and N-use efficiency of tree legume prunings from ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-09-17

    Sep 17, 2008 ... There is substantial evidence that fertilizer tree systems are capable of maintaining increased and sustainable crop ... of N immobilized early in the season by the low quality organic materials is stimulated by well distributed rainfall. .... and 10 months old sesbania trees were cut and incorporated on.

  6. Anticipating cognitive effort: roles of perceived error-likelihood and time demands.

    Science.gov (United States)

    Dunn, Timothy L; Inzlicht, Michael; Risko, Evan F

    2017-11-13

    Why are some actions evaluated as effortful? In the present set of experiments we address this question by examining individuals' perception of effort when faced with a trade-off between two putative cognitive costs: how much time a task takes vs. how error-prone it is. Specifically, we were interested in whether individuals anticipate engaging in a small amount of hard work (i.e., low time requirement, but high error-likelihood) vs. a large amount of easy work (i.e., high time requirement, but low error-likelihood) as being more effortful. In between-subject designs, Experiments 1 through 3 demonstrated that individuals anticipate options that are high in perceived error-likelihood (yet less time consuming) as more effortful than options that are perceived to be more time consuming (yet low in error-likelihood). Further, when asked to evaluate which of the two tasks was (a) more effortful, (b) more error-prone, and (c) more time consuming, effort-based and error-based choices closely tracked one another, but this was not the case for time-based choices. Utilizing a within-subject design, Experiment 4 demonstrated overall similar pattern of judgments as Experiments 1 through 3. However, both judgments of error-likelihood and time demand similarly predicted effort judgments. Results are discussed within the context of extant accounts of cognitive control, with considerations of how error-likelihood and time demands may independently and conjunctively factor into judgments of cognitive effort.

  7. Investigation on electrical tree propagation in polyethylene based on etching method

    Directory of Open Access Journals (Sweden)

    Zexiang Shi

    2017-11-01

    Full Text Available To investigate the characteristic of electrical tree propagation in semi-crystalline polymers, the low-density polyethylene (LDPE samples containing electrical trees are cut into slices by using ultramicrotome. Then the slice samples are etched by potassium permanganate etchant. Finally, the crystalline structure and the electrical tree propagation path in samples are observed by polarized light microscopy (PLM. According to the observation, the LDPE spherocrystal structure model is established on the basis of crystallization kinetics and morphology of polymers. And the electrical tree growth process in LDPE is discussed based on the free volume breakdown theory, the molecular chain relaxation theory, the electromechanical force theory, the thermal expansion effect and the space charge shielding effect.

  8. YBYRÁ facilitates comparison of large phylogenetic trees.

    Science.gov (United States)

    Machado, Denis Jacob

    2015-07-01

    The number and size of tree topologies that are being compared by phylogenetic systematists is increasing due to technological advancements in high-throughput DNA sequencing. However, we still lack tools to facilitate comparison among phylogenetic trees with a large number of terminals. The "YBYRÁ" project integrates software solutions for data analysis in phylogenetics. It comprises tools for (1) topological distance calculation based on the number of shared splits or clades, (2) sensitivity analysis and automatic generation of sensitivity plots and (3) clade diagnoses based on different categories of synapomorphies. YBYRÁ also provides (4) an original framework to facilitate the search for potential rogue taxa based on how much they affect average matching split distances (using MSdist). YBYRÁ facilitates comparison of large phylogenetic trees and outperforms competing software in terms of usability and time efficiency, specially for large data sets. The programs that comprises this toolkit are written in Python, hence they do not require installation and have minimum dependencies. The entire project is available under an open-source licence at http://www.ib.usp.br/grant/anfibios/researchSoftware.html .

  9. An enhanced component connection method for conversion of fault trees to binary decision diagrams

    International Nuclear Information System (INIS)

    Remenyte-Prescott, R.; Andrews, J.D.

    2008-01-01

    Fault tree analysis (FTA) is widely applied to assess the failure probability of industrial systems. Many computer packages are available, which are based on conventional kinetic tree theory methods. When dealing with large (possibly non-coherent) fault trees, the limitations of the technique in terms of accuracy of the solutions and the efficiency of the processing time become apparent. Over recent years, the binary decision diagram (BDD) method has been developed that solves fault trees and overcomes the disadvantages of the conventional FTA approach. First of all, a fault tree for a particular system failure mode is constructed and then converted to a BDD for analysis. This paper analyses alternative methods for the fault tree to BDD conversion process. For most fault tree to BDD conversion approaches, the basic events of the fault tree are placed in an ordering. This can dramatically affect the size of the final BDD and the success of qualitative and quantitative analyses of the system. A set of rules is then applied to each gate in the fault tree to generate the BDD. An alternative approach can also be used, where BDD constructs for each of the gate types are first built and then merged to represent a parent gate. A powerful and efficient property, sub-node sharing, is also incorporated in the enhanced method proposed in this paper. Finally, a combined approach is developed taking the best features of the alternative methods. The efficiency of the techniques is analysed and discussed

  10. A Weibull-based compositional approach for hierarchical dynamic fault trees

    International Nuclear Information System (INIS)

    Chiacchio, F.; Cacioppo, M.; D'Urso, D.; Manno, G.; Trapani, N.; Compagno, L.

    2013-01-01

    The solution of a dynamic fault tree (DFT) for the reliability assessment can be achieved using a wide variety of techniques. These techniques have a strong theoretical foundation as both the analytical and the simulation methods have been extensively developed. Nevertheless, they all present the same limits that appear with the increasing of the size of the fault trees (i.e., state space explosion, time-consuming simulations), compromising the resolution. We have tested the feasibility of a composition algorithm based on a Weibull distribution, addressed to the resolution of a general class of dynamic fault trees characterized by non-repairable basic events and generally distributed failure times. The proposed composition algorithm is used to generalize the traditional hierarchical technique that, as previous literature have extensively confirmed, is able to reduce the computational effort of a large DFT through the modularization of independent parts of the tree. The results of this study are achieved both through simulation and analytical techniques, thus confirming the capability to solve a quite general class of dynamic fault trees and overcome the limits of traditional techniques.

  11. Estimation Methods for Non-Homogeneous Regression - Minimum CRPS vs Maximum Likelihood

    Science.gov (United States)

    Gebetsberger, Manuel; Messner, Jakob W.; Mayr, Georg J.; Zeileis, Achim

    2017-04-01

    Non-homogeneous regression models are widely used to statistically post-process numerical weather prediction models. Such regression models correct for errors in mean and variance and are capable to forecast a full probability distribution. In order to estimate the corresponding regression coefficients, CRPS minimization is performed in many meteorological post-processing studies since the last decade. In contrast to maximum likelihood estimation, CRPS minimization is claimed to yield more calibrated forecasts. Theoretically, both scoring rules used as an optimization score should be able to locate a similar and unknown optimum. Discrepancies might result from a wrong distributional assumption of the observed quantity. To address this theoretical concept, this study compares maximum likelihood and minimum CRPS estimation for different distributional assumptions. First, a synthetic case study shows that, for an appropriate distributional assumption, both estimation methods yield to similar regression coefficients. The log-likelihood estimator is slightly more efficient. A real world case study for surface temperature forecasts at different sites in Europe confirms these results but shows that surface temperature does not always follow the classical assumption of a Gaussian distribution. KEYWORDS: ensemble post-processing, maximum likelihood estimation, CRPS minimization, probabilistic temperature forecasting, distributional regression models

  12. Music genre classification via likelihood fusion from multiple feature models

    Science.gov (United States)

    Shiu, Yu; Kuo, C.-C. J.

    2005-01-01

    Music genre provides an efficient way to index songs in a music database, and can be used as an effective means to retrieval music of a similar type, i.e. content-based music retrieval. A new two-stage scheme for music genre classification is proposed in this work. At the first stage, we examine a couple of different features, construct their corresponding parametric models (e.g. GMM and HMM) and compute their likelihood functions to yield soft classification results. In particular, the timbre, rhythm and temporal variation features are considered. Then, at the second stage, these soft classification results are integrated to result in a hard decision for final music genre classification. Experimental results are given to demonstrate the performance of the proposed scheme.

  13. Root activity patterns of some tree crops. Results of a five-year co-ordinated research programme of the Joint FAO/IAEA Division of Atomic Energy in Food and Agriculture. [32p; injection into banana trees, orange trees, cacao trees, coffee trees, and oil palms

    Energy Technology Data Exchange (ETDEWEB)

    1975-01-01

    A coordinated research program was followed using a soil injection method which employed /sup 32/P-labelled superphosphate solution. The technique was applied for determining the root activity distribution of various crops. Field experiments were carried out in Uganda on bananas, Spain and Taiwan on citrus, Ghana on cocoa, Columbia and Kenya on coffee, and Ivory Coast and Malaysia on oil palms, to study the patterns of root activity as a function of depth and distance from the tree base, soil type, tree age and season. A few weeks after injection, leaf samples of similar age were taken from well-defined morphological positions on the tree and analyzed for /sup 32/P. The activity of the label in the sample reflects the root activity at the various positions in the soil. Some preliminary experiments were also carried out using /sup 32/P-superphosphate to evaluate the efficiency of different methods of fertilizer placement in relation to phosphate uptake by the plantation as a whole.

  14. Physician Bayesian updating from personal beliefs about the base rate and likelihood ratio.

    Science.gov (United States)

    Rottman, Benjamin Margolin

    2017-02-01

    Whether humans can accurately make decisions in line with Bayes' rule has been one of the most important yet contentious topics in cognitive psychology. Though a number of paradigms have been used for studying Bayesian updating, rarely have subjects been allowed to use their own preexisting beliefs about the prior and the likelihood. A study is reported in which physicians judged the posttest probability of a diagnosis for a patient vignette after receiving a test result, and the physicians' posttest judgments were compared to the normative posttest calculated from their own beliefs in the sensitivity and false positive rate of the test (likelihood ratio) and prior probability of the diagnosis. On the one hand, the posttest judgments were strongly related to the physicians' beliefs about both the prior probability as well as the likelihood ratio, and the priors were used considerably more strongly than in previous research. On the other hand, both the prior and the likelihoods were still not used quite as much as they should have been, and there was evidence of other nonnormative aspects to the updating, such as updating independent of the likelihood beliefs. By focusing on how physicians use their own prior beliefs for Bayesian updating, this study provides insight into how well experts perform probabilistic inference in settings in which they rely upon their own prior beliefs rather than experimenter-provided cues. It suggests that there is reason to be optimistic about experts' abilities, but that there is still considerable need for improvement.

  15. MFAULT: a computer program for analyzing fault trees

    International Nuclear Information System (INIS)

    Pelto, P.J.; Purcell, W.L.

    1977-11-01

    A description and user instructions are presented for MFAULT, a FORTRAN computer program for fault tree analysis. MFAULT identifies the cut sets of a fault tree, calculates their probabilities, and screens the cut sets on the basis of specified cut-offs on probability and/or cut set length. MFAULT is based on an efficient upward-working algorithm for cut set identification. The probability calculations are based on the assumption of small probabilities and constant hazard rates (i.e., exponential failure distributions). Cut sets consisting of repairable components (basic events) only, non-repairable components only, or mixtures of both types can be evaluated. Components can be on-line or standby. Unavailability contributions from pre-existing failures, failures on demand, and testing and maintenance down-time can be handled. MFAULT can analyze fault trees with AND gates, OR gates, inhibit gates, on switches (houses) and off switches. The code is presently capable of finding up to ten event cut sets from a fault tree with up to 512 basic events and 400 gates. It is operational on the CONTROL DATA CYBER 74 computer. 11 figures

  16. Improved phylogenetic analyses corroborate a plausible position of Martialis heureka in the ant tree of life.

    Directory of Open Access Journals (Sweden)

    Patrick Kück

    Full Text Available Martialinae are pale, eyeless and probably hypogaeic predatory ants. Morphological character sets suggest a close relationship to the ant subfamily Leptanillinae. Recent analyses based on molecular sequence data suggest that Martialinae are the sister group to all extant ants. However, by comparing molecular studies and different reconstruction methods, the position of Martialinae remains ambiguous. While this sister group relationship was well supported by Bayesian partitioned analyses, Maximum Likelihood approaches could not unequivocally resolve the position of Martialinae. By re-analysing a previous published molecular data set, we show that the Maximum Likelihood approach is highly appropriate to resolve deep ant relationships, especially between Leptanillinae, Martialinae and the remaining ant subfamilies. Based on improved alignments, alignment masking, and tree reconstructions with a sufficient number of bootstrap replicates, our results strongly reject a placement of Martialinae at the first split within the ant tree of life. Instead, we suggest that Leptanillinae are a sister group to all other extant ant subfamilies, whereas Martialinae branch off as a second lineage. This assumption is backed by approximately unbiased (AU tests, additional Bayesian analyses and split networks. Our results demonstrate clear effects of improved alignment approaches, alignment masking and data partitioning. We hope that our study illustrates the importance of thorough, comprehensible phylogenetic analyses using the example of ant relationships.

  17. Species tree estimation for the late blight pathogen, Phytophthora infestans, and close relatives.

    Directory of Open Access Journals (Sweden)

    Jaime E Blair

    Full Text Available To better understand the evolutionary history of a group of organisms, an accurate estimate of the species phylogeny must be known. Traditionally, gene trees have served as a proxy for the species tree, although it was acknowledged early on that these trees represented different evolutionary processes. Discordances among gene trees and between the gene trees and the species tree are also expected in closely related species that have rapidly diverged, due to processes such as the incomplete sorting of ancestral polymorphisms. Recently, methods have been developed for the explicit estimation of species trees, using information from multilocus gene trees while accommodating heterogeneity among them. Here we have used three distinct approaches to estimate the species tree for five Phytophthora pathogens, including P. infestans, the causal agent of late blight disease in potato and tomato. Our concatenation-based "supergene" approach was unable to resolve relationships even with data from both the nuclear and mitochondrial genomes, and from multiple isolates per species. Our multispecies coalescent approach using both Bayesian and maximum likelihood methods was able to estimate a moderately supported species tree showing a close relationship among P. infestans, P. andina, and P. ipomoeae. The topology of the species tree was also identical to the dominant phylogenetic history estimated in our third approach, Bayesian concordance analysis. Our results support previous suggestions that P. andina is a hybrid species, with P. infestans representing one parental lineage. The other parental lineage is not known, but represents an independent evolutionary lineage more closely related to P. ipomoeae. While all five species likely originated in the New World, further study is needed to determine when and under what conditions this hybridization event may have occurred.

  18. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.

    Science.gov (United States)

    Letunic, Ivica; Bork, Peer

    2016-07-08

    Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. The current version was completely redesigned and rewritten, utilizing current web technologies for speedy and streamlined processing. Numerous new features were introduced and several new data types are now supported. Trees with up to 100,000 leaves can now be efficiently displayed. Full interactive control over precise positioning of various annotation features and an unlimited number of datasets allow the easy creation of complex tree visualizations. iTOL 3 is the first tool which supports direct visualization of the recently proposed phylogenetic placements format. Finally, iTOL's account system has been redesigned to simplify the management of trees in user-defined workspaces and projects, as it is heavily used and currently handles already more than 500,000 trees from more than 10,000 individual users. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. New flux based dose–response relationships for ozone for European forest tree species

    International Nuclear Information System (INIS)

    Büker, P.; Feng, Z.; Uddling, J.; Briolat, A.; Alonso, R.; Braun, S.; Elvira, S.; Gerosa, G.; Karlsson, P.E.; Le Thiec, D.

    2015-01-01

    To derive O 3 dose–response relationships (DRR) for five European forest trees species and broadleaf deciduous and needleleaf tree plant functional types (PFTs), phytotoxic O 3 doses (PODy) were related to biomass reductions. PODy was calculated using a stomatal flux model with a range of cut-off thresholds (y) indicative of varying detoxification capacities. Linear regression analysis showed that DRR for PFT and individual tree species differed in their robustness. A simplified parameterisation of the flux model was tested and showed that for most non-Mediterranean tree species, this simplified model led to similarly robust DRR as compared to a species- and climate region-specific parameterisation. Experimentally induced soil water stress was not found to substantially reduce PODy, mainly due to the short duration of soil water stress periods. This study validates the stomatal O 3 flux concept and represents a step forward in predicting O 3 damage to forests in a spatially and temporally varying climate. - Highlights: • We present new ozone flux based dose–response relationships for European trees. • The model-based study accounted for the soil water effect on stomatal flux. • Different statistically derived ozone flux thresholds were applied. • Climate region specific parameterisation often outperformed simplified parameterisation. • Findings could help redefining critical levels for ozone effects on trees. - New stomatal flux based ozone dose–response relationships for tree species are derived for the regional risk assessment of ozone effects on European forest ecosystems.

  20. Explicit area-based accuracy assessment for mangrove tree crown delineation using Geographic Object-Based Image Analysis (GEOBIA)

    Science.gov (United States)

    Kamal, Muhammad; Johansen, Kasper

    2017-10-01

    Effective mangrove management requires spatially explicit information of mangrove tree crown map as a basis for ecosystem diversity study and health assessment. Accuracy assessment is an integral part of any mapping activities to measure the effectiveness of the classification approach. In geographic object-based image analysis (GEOBIA) the assessment of the geometric accuracy (shape, symmetry and location) of the created image objects from image segmentation is required. In this study we used an explicit area-based accuracy assessment to measure the degree of similarity between the results of the classification and reference data from different aspects, including overall quality (OQ), user's accuracy (UA), producer's accuracy (PA) and overall accuracy (OA). We developed a rule set to delineate the mangrove tree crown using WorldView-2 pan-sharpened image. The reference map was obtained by visual delineation of the mangrove tree crowns boundaries form a very high-spatial resolution aerial photograph (7.5cm pixel size). Ten random points with a 10 m radius circular buffer were created to calculate the area-based accuracy assessment. The resulting circular polygons were used to clip both the classified image objects and reference map for area comparisons. In this case, the area-based accuracy assessment resulted 64% and 68% for the OQ and OA, respectively. The overall quality of the calculation results shows the class-related area accuracy; which is the area of correctly classified as tree crowns was 64% out of the total area of tree crowns. On the other hand, the overall accuracy of 68% was calculated as the percentage of all correctly classified classes (tree crowns and canopy gaps) in comparison to the total class area (an entire image). Overall, the area-based accuracy assessment was simple to implement and easy to interpret. It also shows explicitly the omission and commission error variations of object boundary delineation with colour coded polygons.

  1. A theory of timing in scintillation counters based on maximum likelihood estimation

    International Nuclear Information System (INIS)

    Tomitani, Takehiro

    1982-01-01

    A theory of timing in scintillation counters based on the maximum likelihood estimation is presented. An optimum filter that minimizes the variance of timing is described. A simple formula to estimate the variance of timing is presented as a function of photoelectron number, scintillation decay constant and the single electron transit time spread in the photomultiplier. The present method was compared with the theory by E. Gatti and V. Svelto. The proposed method was applied to two simple models and rough estimations of potential time resolution of several scintillators are given. The proposed method is applicable to the timing in Cerenkov counters and semiconductor detectors as well. (author)

  2. Evaluation of hedgerow trees in alley cropping for phosphorus use efficiency and N{sub 2} fixation in low P soils in moist savanna in Nigeria

    Energy Technology Data Exchange (ETDEWEB)

    Sanginga, N [International Inst. of Tropical Agriculture, Ibadan (Nigeria); Danso, S K.A. [Joint FAO/IAEA Div. of Nuclear Techniques in Food and Agriculture, Vienna (Austria). Soil Fertility and Crop Production Section; Zapata, F [FAO/IAEA Agriculture and Biotechnology Lab., Seibersdorf (Austria). Soils Science Unit; Bowen, G D [Commonwealth Scientific and Industrial Research Organization, Glen Osmond (Australia). Div. of Soils

    1996-07-01

    Soils low in P and N are common in the moist savanna climatic zones and consequently growth of hedgerow trees in alley cropping systems might require addition of N and P fertilizers. This is difficult for small scale farmers who have limited access to fertilizers and therefore depend only on limited input cropping systems. Exploiting genetic differences in P use efficiency and using hedgerow trees selected for high N{sub 2} fixation ability can improve tree establishment and growth on N and P-poor soils, restore soil fertility and preserve soil from degradation. Field experiments carried out at Fashola (moist savanna) have shown that large differences in growth and P use efficiency occurred between N{sub 2} fixing trees such as Gliricidia sepium, and non N{sub 2}-fixing trees such as Senna siamea and Senna spectabilis. Provenances or isoline differences in P use efficiency also occurred within species and was also influenced by level of P and period of growth. Differences between species and provenances in P uptake and growth were largely related to differences in physiological P-use efficiency (PPUE), root length and VAM infection rate, especially at low P. In general, nodulation was improved by P application, but varied among provenances. Gliricidia Sepium fixed about 61% of its N from atmospheric N{sub 2} in the pot experiment and 40% in the field. The percentage of N fixed was not affected by rate of P application. Differences in P and N accumulation and use efficiency were also influenced by management practices such as pruning. The distribution of total P followed the same trend as that of dry matter yield, while no significant correlations were found between partitioning of dry matter and total N. Uncut and cut G. Sepium derived 35 and 54% respectively of their N from atmospheric N{sub 2}. About 54% of the fixed N{sub 2} was partitioned to shoots and roots and this was not proportional to the size of these organs relative the whole plant. 17refs,2figs,2tabs.

  3. Evaluating score- and feature-based likelihood ratio models for multivariate continuous data: applied to forensic MDMA comparison

    NARCIS (Netherlands)

    Bolck, A.; Ni, H.; Lopatka, M.

    2015-01-01

    Likelihood ratio (LR) models are moving into the forefront of forensic evidence evaluation as these methods are adopted by a diverse range of application areas in forensic science. We examine the fundamentally different results that can be achieved when feature- and score-based methodologies are

  4. H.264 SVC Complexity Reduction Based on Likelihood Mode Decision.

    Science.gov (United States)

    Balaji, L; Thyagharajan, K K

    2015-01-01

    H.264 Advanced Video Coding (AVC) was prolonged to Scalable Video Coding (SVC). SVC executes in different electronics gadgets such as personal computer, HDTV, SDTV, IPTV, and full-HDTV in which user demands various scaling of the same content. The various scaling is resolution, frame rate, quality, heterogeneous networks, bandwidth, and so forth. Scaling consumes more encoding time and computational complexity during mode selection. In this paper, to reduce encoding time and computational complexity, a fast mode decision algorithm based on likelihood mode decision (LMD) is proposed. LMD is evaluated in both temporal and spatial scaling. From the results, we conclude that LMD performs well, when compared to the previous fast mode decision algorithms. The comparison parameters are time, PSNR, and bit rate. LMD achieve time saving of 66.65% with 0.05% detriment in PSNR and 0.17% increment in bit rate compared with the full search method.

  5. Efficient Computation of Popular Phylogenetic Tree Measures

    DEFF Research Database (Denmark)

    Tsirogiannis, Constantinos; Sandel, Brody Steven; Cheliotis, Dimitris

    2012-01-01

    Given a phylogenetic tree $\\mathcal{T}$ of n nodes, and a sample R of its tips (leaf nodes) a very common problem in ecological and evolutionary research is to evaluate a distance measure for the elements in R. Two of the most common measures of this kind are the Mean Pairwise Distance ($\\ensurem...

  6. Efficiency of nuclear and mitochondrial markers recovering and supporting known amniote groups.

    Science.gov (United States)

    Lambret-Frotté, Julia; Perini, Fernando Araújo; de Moraes Russo, Claudia Augusta

    2012-01-01

    We have analysed the efficiency of all mitochondrial protein coding genes and six nuclear markers (Adora3, Adrb2, Bdnf, Irbp, Rag2 and Vwf) in reconstructing and statistically supporting known amniote groups (murines, rodents, primates, eutherians, metatherians, therians). The efficiencies of maximum likelihood, Bayesian inference, maximum parsimony, neighbor-joining and UPGMA were also evaluated, by assessing the number of correct and incorrect recovered groupings. In addition, we have compared support values using the conservative bootstrap test and the Bayesian posterior probabilities. First, no correlation was observed between gene size and marker efficiency in recovering or supporting correct nodes. As expected, tree-building methods performed similarly, even UPGMA that, in some cases, outperformed other most extensively used methods. Bayesian posterior probabilities tend to show much higher support values than the conservative bootstrap test, for correct and incorrect nodes. Our results also suggest that nuclear markers do not necessarily show a better performance than mitochondrial genes. The so-called dependency among mitochondrial markers was not observed comparing genome performances. Finally, the amniote groups with lowest recovery rates were therians and rodents, despite the morphological support for their monophyletic status. We suggest that, regardless of the tree-building method, a few carefully selected genes are able to unfold a detailed and robust scenario of phylogenetic hypotheses, particularly if taxon sampling is increased.

  7. Safety validation of decision trees for hepatocellular carcinoma.

    Science.gov (United States)

    Wang, Xian-Qiang; Liu, Zhe; Lv, Wen-Ping; Luo, Ying; Yang, Guang-Yun; Li, Chong-Hui; Meng, Xiang-Fei; Liu, Yang; Xu, Ke-Sen; Dong, Jia-Hong

    2015-08-21

    To evaluate a different decision tree for safe liver resection and verify its efficiency. A total of 2457 patients underwent hepatic resection between January 2004 and December 2010 at the Chinese PLA General Hospital, and 634 hepatocellular carcinoma (HCC) patients were eligible for the final analyses. Post-hepatectomy liver failure (PHLF) was identified by the association of prothrombin time 50 μmol/L (the "50-50" criteria), which were assessed at day 5 postoperatively or later. The Swiss-Clavien decision tree, Tokyo University-Makuuchi decision tree, and Chinese consensus decision tree were adopted to divide patients into two groups based on those decision trees in sequence, and the PHLF rates were recorded. The overall mortality and PHLF rate were 0.16% and 3.0%. A total of 19 patients experienced PHLF. The numbers of patients to whom the Swiss-Clavien, Tokyo University-Makuuchi, and Chinese consensus decision trees were applied were 581, 573, and 622, and the PHLF rates were 2.75%, 2.62%, and 2.73%, respectively. Significantly more cases satisfied the Chinese consensus decision tree than the Swiss-Clavien decision tree and Tokyo University-Makuuchi decision tree (P decision trees. The Chinese consensus decision tree expands the indications for hepatic resection for HCC patients and does not increase the PHLF rate compared to the Swiss-Clavien and Tokyo University-Makuuchi decision trees. It would be a safe and effective algorithm for hepatectomy in patients with hepatocellular carcinoma.

  8. Extended likelihood inference in reliability

    International Nuclear Information System (INIS)

    Martz, H.F. Jr.; Beckman, R.J.; Waller, R.A.

    1978-10-01

    Extended likelihood methods of inference are developed in which subjective information in the form of a prior distribution is combined with sampling results by means of an extended likelihood function. The extended likelihood function is standardized for use in obtaining extended likelihood intervals. Extended likelihood intervals are derived for the mean of a normal distribution with known variance, the failure-rate of an exponential distribution, and the parameter of a binomial distribution. Extended second-order likelihood methods are developed and used to solve several prediction problems associated with the exponential and binomial distributions. In particular, such quantities as the next failure-time, the number of failures in a given time period, and the time required to observe a given number of failures are predicted for the exponential model with a gamma prior distribution on the failure-rate. In addition, six types of life testing experiments are considered. For the binomial model with a beta prior distribution on the probability of nonsurvival, methods are obtained for predicting the number of nonsurvivors in a given sample size and for predicting the required sample size for observing a specified number of nonsurvivors. Examples illustrate each of the methods developed. Finally, comparisons are made with Bayesian intervals in those cases where these are known to exist

  9. Reversible polymorphism-aware phylogenetic models and their application to tree inference.

    Science.gov (United States)

    Schrempf, Dominik; Minh, Bui Quang; De Maio, Nicola; von Haeseler, Arndt; Kosiol, Carolin

    2016-10-21

    We present a reversible Polymorphism-Aware Phylogenetic Model (revPoMo) for species tree estimation from genome-wide data. revPoMo enables the reconstruction of large scale species trees for many within-species samples. It expands the alphabet of DNA substitution models to include polymorphic states, thereby, naturally accounting for incomplete lineage sorting. We implemented revPoMo in the maximum likelihood software IQ-TREE. A simulation study and an application to great apes data show that the runtimes of our approach and standard substitution models are comparable but that revPoMo has much better accuracy in estimating trees, divergence times and mutation rates. The advantage of revPoMo is that an increase of sample size per species improves estimations but does not increase runtime. Therefore, revPoMo is a valuable tool with several applications, from speciation dating to species tree reconstruction. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  10. Runtime Optimizations for Tree-Based Machine Learning Models

    NARCIS (Netherlands)

    N. Asadi; J.J.P. Lin (Jimmy); A.P. de Vries (Arjen)

    2014-01-01

    htmlabstractTree-based models have proven to be an effective solution for web ranking as well as other machine learning problems in diverse domains. This paper focuses on optimizing the runtime performance of applying such models to make predictions, specifically using gradient-boosted regression

  11. A Penalized Likelihood Framework For High-Dimensional Phylogenetic Comparative Methods And An Application To New-World Monkeys Brain Evolution.

    Science.gov (United States)

    Julien, Clavel; Leandro, Aristide; Hélène, Morlon

    2018-06-19

    Working with high-dimensional phylogenetic comparative datasets is challenging because likelihood-based multivariate methods suffer from low statistical performances as the number of traits p approaches the number of species n and because some computational complications occur when p exceeds n. Alternative phylogenetic comparative methods have recently been proposed to deal with the large p small n scenario but their use and performances are limited. Here we develop a penalized likelihood framework to deal with high-dimensional comparative datasets. We propose various penalizations and methods for selecting the intensity of the penalties. We apply this general framework to the estimation of parameters (the evolutionary trait covariance matrix and parameters of the evolutionary model) and model comparison for the high-dimensional multivariate Brownian (BM), Early-burst (EB), Ornstein-Uhlenbeck (OU) and Pagel's lambda models. We show using simulations that our penalized likelihood approach dramatically improves the estimation of evolutionary trait covariance matrices and model parameters when p approaches n, and allows for their accurate estimation when p equals or exceeds n. In addition, we show that penalized likelihood models can be efficiently compared using Generalized Information Criterion (GIC). We implement these methods, as well as the related estimation of ancestral states and the computation of phylogenetic PCA in the R package RPANDA and mvMORPH. Finally, we illustrate the utility of the new proposed framework by evaluating evolutionary models fit, analyzing integration patterns, and reconstructing evolutionary trajectories for a high-dimensional 3-D dataset of brain shape in the New World monkeys. We find a clear support for an Early-burst model suggesting an early diversification of brain morphology during the ecological radiation of the clade. Penalized likelihood offers an efficient way to deal with high-dimensional multivariate comparative data.

  12. Understanding the Roles of Forests and Tree-based Systems in Food Provision

    NARCIS (Netherlands)

    Jamnadass, R.; McMullin, S.; Dawson, M.I.I.K.; Powell, B.; Termote, C.; Lckowitz, A.; Kehlenbeck, K.; Vinceti, B.; Vliet, van N.; Keding, G.; Stadlmayr, B.; Damme, van P.; Carsan, S.; Sunderland, T.; Njenga, M.; Gyau, A.; Cerutti, P.; Schure, J.M.; Kouame, C.; Obiri, B.D.; Ofori, D.; Agarwal, B.; Neufeldt, H.; Degrande, A.; Serban, A.

    2015-01-01

    Forests and other tree-based systems such as agroforestry contribute to food and nutritional security in myriad ways. Directly, trees provide a variety of healthy foods including fruits, leafy vegetables, nuts, seeds and edible oils that can diversify diets and address seasonal food and nutritional

  13. A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analysis of 606 Sequences

    Directory of Open Access Journals (Sweden)

    Guido W. Grimm

    2006-01-01

    Full Text Available The multi-copy internal transcribed spacer (ITS region of nuclear ribosomal DNA is widely used to infer phylogenetic relationships among closely related taxa. Here we use maximum likelihood (ML and splits graph analyses to extract phylogenetic information from ~ 600 mostly cloned ITS sequences, representing 81 species and subspecies of Acer, and both species of its sister Dipteronia. Additional analyses compared sequence motifs in Acer and several hundred Anacardiaceae, Burseraceae, Meliaceae, Rutaceae, and Sapindaceae ITS sequences in GenBank. We also assessed the effects of using smaller data sets of consensus sequences with ambiguity coding (accounting for within-species variation instead of the full (partly redundant original sequences. Neighbor-nets and bipartition networks were used to visualize conflict among character state patterns. Species clusters observed in the trees and networks largely agree with morphology-based classifications; of de Jong’s (1994 16 sections, nine are supported in neighbor-net and bipartition networks, and ten by sequence motifs and the ML tree; of his 19 series, 14 are supported in networks, motifs, and the ML tree. Most nodes had higher bootstrap support with matrices of 105 or 40 consensus sequences than with the original matrix. Within-taxon ITS divergence did not differ between diploid and polyploid Acer, and there was little evidence of differentiated parental ITS haplotypes, suggesting that concerted evolution in Acer acts rapidly.

  14. A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analysis of 606 Sequences

    Science.gov (United States)

    Grimm, Guido W.; Renner, Susanne S.; Stamatakis, Alexandros; Hemleben, Vera

    2007-01-01

    The multi-copy internal transcribed spacer (ITS) region of nuclear ribosomal DNA is widely used to infer phylogenetic relationships among closely related taxa. Here we use maximum likelihood (ML) and splits graph analyses to extract phylogenetic information from ~ 600 mostly cloned ITS sequences, representing 81 species and subspecies of Acer, and both species of its sister Dipteronia. Additional analyses compared sequence motifs in Acer and several hundred Anacardiaceae, Burseraceae, Meliaceae, Rutaceae, and Sapindaceae ITS sequences in GenBank. We also assessed the effects of using smaller data sets of consensus sequences with ambiguity coding (accounting for within-species variation) instead of the full (partly redundant) original sequences. Neighbor-nets and bipartition networks were used to visualize conflict among character state patterns. Species clusters observed in the trees and networks largely agree with morphology-based classifications; of de Jong’s (1994) 16 sections, nine are supported in neighbor-net and bipartition networks, and ten by sequence motifs and the ML tree; of his 19 series, 14 are supported in networks, motifs, and the ML tree. Most nodes had higher bootstrap support with matrices of 105 or 40 consensus sequences than with the original matrix. Within-taxon ITS divergence did not differ between diploid and polyploid Acer, and there was little evidence of differentiated parental ITS haplotypes, suggesting that concerted evolution in Acer acts rapidly. PMID:19455198

  15. FTAP, Minimal Cut Sets of Arbitrary Fault Trees. FRTPLT, Fault Tree Structure and Logical Gates Plot for Program FTAP. FRTGEN, Fault Trees by Sub-tree Generator from Parent Tree for Program FTAP

    International Nuclear Information System (INIS)

    Willie, Randall R.; Rabien, U.

    1997-01-01

    1 - Description of problem or function: FTAP is a general-purpose program for deriving minimal reliability cut and path set families from the fault tree for a complex system. The program has a number of useful features that make it well-suited to nearly all fault tree applications. An input fault tree may specify the system state as any logical function of subsystem or component state variables or complements of these variables; thus, for instance, 'exclusive-or' type relations may be formed. When fault tree logical relations involve complements of state variables, the analyst may instruct FTAP to produce a family of prime implicants, a generalization of the minimal cut set concept. The program offers the flexibility of several distinct methods of generating cut set families. FTAP can also identify certain subsystems as system modules and provide a collection of minimal cut set families that essentially expresses the system state as a function of these module state variables. Another feature allows a useful subfamily to be obtained when the family of minimal cut sets or prime implicants is too large to be found in its entirety; this subfamily may consist of only those sets not containing more than some fixed number of elements or only those sets 'interesting' to the analyst in some special sense. Finally, the analyst can modify the input fault tree in various ways by declaring state variables identically true or false. 2 - Method of solution: Fault tree methods are based on the observation that the system state, either working or failed, can usually be expressed as a Boolean relation between states of several large, readily identifiable subsystems. The state of each subsystem in turn depends on states of simpler subsystems and components which compose it, so that the state of the system itself is determined by a hierarchy of logical relationships between states of subsystems. A fault tree is a graphical representation of these relationships. 3 - Restrictions on the

  16. Individual tree detection based on densities of high points of high resolution airborne lidar

    NARCIS (Netherlands)

    Abd Rahman, M.Z.; Gorte, B.G.H.

    2008-01-01

    The retrieval of individual tree location from Airborne LiDAR has focused largely on utilizing canopy height. However, high resolution Airborne LiDAR offers another source of information for tree detection. This paper presents a new method for tree detection based on high points’ densities from a

  17. An alternative empirical likelihood method in missing response problems and causal inference.

    Science.gov (United States)

    Ren, Kaili; Drummond, Christopher A; Brewster, Pamela S; Haller, Steven T; Tian, Jiang; Cooper, Christopher J; Zhang, Biao

    2016-11-30

    Missing responses are common problems in medical, social, and economic studies. When responses are missing at random, a complete case data analysis may result in biases. A popular debias method is inverse probability weighting proposed by Horvitz and Thompson. To improve efficiency, Robins et al. proposed an augmented inverse probability weighting method. The augmented inverse probability weighting estimator has a double-robustness property and achieves the semiparametric efficiency lower bound when the regression model and propensity score model are both correctly specified. In this paper, we introduce an empirical likelihood-based estimator as an alternative to Qin and Zhang (2007). Our proposed estimator is also doubly robust and locally efficient. Simulation results show that the proposed estimator has better performance when the propensity score is correctly modeled. Moreover, the proposed method can be applied in the estimation of average treatment effect in observational causal inferences. Finally, we apply our method to an observational study of smoking, using data from the Cardiovascular Outcomes in Renal Atherosclerotic Lesions clinical trial. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  18. Likelihood inference for unions of interacting discs

    DEFF Research Database (Denmark)

    Møller, Jesper; Helisova, K.

    2010-01-01

    This is probably the first paper which discusses likelihood inference for a random set using a germ-grain model, where the individual grains are unobservable, edge effects occur and other complications appear. We consider the case where the grains form a disc process modelled by a marked point...... process, where the germs are the centres and the marks are the associated radii of the discs. We propose to use a recent parametric class of interacting disc process models, where the minimal sufficient statistic depends on various geometric properties of the random set, and the density is specified......-based maximum likelihood inference and the effect of specifying different reference Poisson models....

  19. Estimation of Model's Marginal likelihood Using Adaptive Sparse Grid Surrogates in Bayesian Model Averaging

    Science.gov (United States)

    Zeng, X.

    2015-12-01

    A large number of model executions are required to obtain alternative conceptual models' predictions and their posterior probabilities in Bayesian model averaging (BMA). The posterior model probability is estimated through models' marginal likelihood and prior probability. The heavy computation burden hinders the implementation of BMA prediction, especially for the elaborated marginal likelihood estimator. For overcoming the computation burden of BMA, an adaptive sparse grid (SG) stochastic collocation method is used to build surrogates for alternative conceptual models through the numerical experiment of a synthetical groundwater model. BMA predictions depend on model posterior weights (or marginal likelihoods), and this study also evaluated four marginal likelihood estimators, including arithmetic mean estimator (AME), harmonic mean estimator (HME), stabilized harmonic mean estimator (SHME), and thermodynamic integration estimator (TIE). The results demonstrate that TIE is accurate in estimating conceptual models' marginal likelihoods. The BMA-TIE has better predictive performance than other BMA predictions. TIE has high stability for estimating conceptual model's marginal likelihood. The repeated estimated conceptual model's marginal likelihoods by TIE have significant less variability than that estimated by other estimators. In addition, the SG surrogates are efficient to facilitate BMA predictions, especially for BMA-TIE. The number of model executions needed for building surrogates is 4.13%, 6.89%, 3.44%, and 0.43% of the required model executions of BMA-AME, BMA-HME, BMA-SHME, and BMA-TIE, respectively.

  20. Planck 2013 results. XV. CMB power spectra and likelihood

    CERN Document Server

    Ade, P.A.R.; Armitage-Caplan, C.; Arnaud, M.; Ashdown, M.; Atrio-Barandela, F.; Aumont, J.; Baccigalupi, C.; Banday, A.J.; Barreiro, R.B.; Bartlett, J.G.; Battaner, E.; Benabed, K.; Benoit, A.; Benoit-Levy, A.; Bernard, J.P.; Bersanelli, M.; Bielewicz, P.; Bobin, J.; Bock, J.J.; Bonaldi, A.; Bonavera, L.; Bond, J.R.; Borrill, J.; Bouchet, F.R.; Boulanger, F.; Bridges, M.; Bucher, M.; Burigana, C.; Butler, R.C.; Calabrese, E.; Cardoso, J.F.; Catalano, A.; Challinor, A.; Chamballu, A.; Chiang, L.Y.; Chiang, H.C.; Christensen, P.R.; Church, S.; Clements, D.L.; Colombi, S.; Colombo, L.P.L.; Combet, C.; Couchot, F.; Coulais, A.; Crill, B.P.; Curto, A.; Cuttaia, F.; Danese, L.; Davies, R.D.; Davis, R.J.; de Bernardis, P.; de Rosa, A.; de Zotti, G.; Delabrouille, J.; Delouis, J.M.; Desert, F.X.; Dickinson, C.; Diego, J.M.; Dole, H.; Donzelli, S.; Dore, O.; Douspis, M.; Dunkley, J.; Dupac, X.; Efstathiou, G.; Elsner, F.; Ensslin, T.A.; Eriksen, H.K.; Finelli, F.; Forni, O.; Frailis, M.; Fraisse, A.A.; Franceschi, E.; Gaier, T.C.; Galeotta, S.; Galli, S.; Ganga, K.; Giard, M.; Giardino, G.; Giraud-Heraud, Y.; Gjerlow, E.; Gonzalez-Nuevo, J.; Gorski, K.M.; Gratton, S.; Gregorio, A.; Gruppuso, A.; Gudmundsson, J.E.; Hansen, F.K.; Hanson, D.; Harrison, D.; Helou, G.; Henrot-Versille, S.; Hernandez-Monteagudo, C.; Herranz, D.; Hildebrandt, S.R.; Hivon, E.; Hobson, M.; Holmes, W.A.; Hornstrup, A.; Hovest, W.; Huffenberger, K.M.; Hurier, G.; Jaffe, T.R.; Jaffe, A.H.; Jewell, J.; Jones, W.C.; Juvela, M.; Keihanen, E.; Keskitalo, R.; Kiiveri, K.; Kisner, T.S.; Kneissl, R.; Knoche, J.; Knox, L.; Kunz, M.; Kurki-Suonio, H.; Lagache, G.; Lahteenmaki, A.; Lamarre, J.M.; Lasenby, A.; Lattanzi, M.; Laureijs, R.J.; Lawrence, C.R.; Le Jeune, M.; Leach, S.; Leahy, J.P.; Leonardi, R.; Leon-Tavares, J.; Lesgourgues, J.; Liguori, M.; Lilje, P.B.; Lindholm, V.; Linden-Vornle, M.; Lopez-Caniego, M.; Lubin, P.M.; Macias-Perez, J.F.; Maffei, B.; Maino, D.; Mandolesi, N.; Marinucci, D.; Maris, M.; Marshall, D.J.; Martin, P.G.; Martinez-Gonzalez, E.; Masi, S.; Matarrese, S.; Matthai, F.; Mazzotta, P.; Meinhold, P.R.; Melchiorri, A.; Mendes, L.; Menegoni, E.; Mennella, A.; Migliaccio, M.; Millea, M.; Mitra, S.; Miville-Deschenes, M.A.; Molinari, D.; Moneti, A.; Montier, L.; Morgante, G.; Mortlock, D.; Moss, A.; Munshi, D.; Naselsky, P.; Nati, F.; Natoli, P.; Netterfield, C.B.; Norgaard-Nielsen, H.U.; Noviello, F.; Novikov, D.; Novikov, I.; O'Dwyer, I.J.; Orieux, F.; Osborne, S.; Oxborrow, C.A.; Paci, F.; Pagano, L.; Pajot, F.; Paladini, R.; Paoletti, D.; Partridge, B.; Pasian, F.; Patanchon, G.; Paykari, P.; Perdereau, O.; Perotto, L.; Perrotta, F.; Piacentini, F.; Piat, M.; Pierpaoli, E.; Pietrobon, D.; Plaszczynski, S.; Pointecouteau, E.; Polenta, G.; Ponthieu, N.; Popa, L.; Poutanen, T.; Pratt, G.W.; Prezeau, G.; Prunet, S.; Puget, J.L.; Rachen, J.P.; Rahlin, A.; Rebolo, R.; Reinecke, M.; Remazeilles, M.; Renault, C.; Ricciardi, S.; Riller, T.; Ringeval, C.; Ristorcelli, I.; Rocha, G.; Rosset, C.; Roudier, G.; Rowan-Robinson, M.; Rubino-Martin, J.A.; Rusholme, B.; Sandri, M.; Sanselme, L.; Santos, D.; Savini, G.; Scott, D.; Seiffert, M.D.; Shellard, E.P.S.; Spencer, L.D.; Starck, J.L.; Stolyarov, V.; Stompor, R.; Sudiwala, R.; Sureau, F.; Sutton, D.; Suur-Uski, A.S.; Sygnet, J.F.; Tauber, J.A.; Tavagnacco, D.; Terenzi, L.; Toffolatti, L.; Tomasi, M.; Tristram, M.; Tucci, M.; Tuovinen, J.; Turler, M.; Valenziano, L.; Valiviita, J.; Van Tent, B.; Varis, J.; Vielva, P.; Villa, F.; Vittorio, N.; Wade, L.A.; Wandelt, B.D.; Wehus, I.K.; White, M.; White, S.D.M.; Yvon, D.; Zacchei, A.; Zonca, A.

    2014-01-01

    We present the Planck likelihood, a complete statistical description of the two-point correlation function of the CMB temperature fluctuations. We use this likelihood to derive the Planck CMB power spectrum over three decades in l, covering 2 = 50, we employ a correlated Gaussian likelihood approximation based on angular cross-spectra derived from the 100, 143 and 217 GHz channels. We validate our likelihood through an extensive suite of consistency tests, and assess the impact of residual foreground and instrumental uncertainties on cosmological parameters. We find good internal agreement among the high-l cross-spectra with residuals of a few uK^2 at l <= 1000. We compare our results with foreground-cleaned CMB maps, and with cross-spectra derived from the 70 GHz Planck map, and find broad agreement in terms of spectrum residuals and cosmological parameters. The best-fit LCDM cosmology is in excellent agreement with preliminary Planck polarisation spectra. The standard LCDM cosmology is well constrained b...

  1. A tree based method for the rapid screening of chemical fingerprints

    DEFF Research Database (Denmark)

    Kristensen, Thomas Greve; Nielsen, Jesper; Pedersen, Christian Nørgaard Storm

    2009-01-01

    The fingerprint of a molecule is a bitstring based on its structure, constructed such that structurally similar molecules will have similar fingerprints. Molecular fingerprints can be used in an initial phase for identifying novel drug candidates by screening large databases for molecules......: the kD grid and the Multibit tree. The kD grid is based on splitting the fingerprints into k shorter bitstrings and utilising these to compute bounds on the similarity of the complete bitstrings. The Multibit tree uses hierarchical clustering and similarity within each cluster to compute similar bounds...

  2. H.264 SVC Complexity Reduction Based on Likelihood Mode Decision

    Directory of Open Access Journals (Sweden)

    L. Balaji

    2015-01-01

    Full Text Available H.264 Advanced Video Coding (AVC was prolonged to Scalable Video Coding (SVC. SVC executes in different electronics gadgets such as personal computer, HDTV, SDTV, IPTV, and full-HDTV in which user demands various scaling of the same content. The various scaling is resolution, frame rate, quality, heterogeneous networks, bandwidth, and so forth. Scaling consumes more encoding time and computational complexity during mode selection. In this paper, to reduce encoding time and computational complexity, a fast mode decision algorithm based on likelihood mode decision (LMD is proposed. LMD is evaluated in both temporal and spatial scaling. From the results, we conclude that LMD performs well, when compared to the previous fast mode decision algorithms. The comparison parameters are time, PSNR, and bit rate. LMD achieve time saving of 66.65% with 0.05% detriment in PSNR and 0.17% increment in bit rate compared with the full search method.

  3. On Chinese and Western Family Trees: Mechanism and Performance

    Directory of Open Access Journals (Sweden)

    Elton S SIQUEIRA

    2016-10-01

    Full Text Available Family tree is an efficient data structure to store the kinship information in a family. There are basically two kinds of trees: Western Family Tree (WFT and Oriental Family Tree such as Chinese Family Tree (CFT. To get an insight of their efficiency in the context of family kinship presentation and information extraction, in this paper we develop WFT and CFT presentation models and search algorithms, comparing their search performance and inherent mechanism. The study reveals that the computational cost is higher in CFT model, but it provides a greater gain in information retrieval and produces more details of the kinship between individuals in the family.

  4. Maximum likelihood estimation for Cox's regression model under nested case-control sampling

    DEFF Research Database (Denmark)

    Scheike, Thomas; Juul, Anders

    2004-01-01

    Nested case-control sampling is designed to reduce the costs of large cohort studies. It is important to estimate the parameters of interest as efficiently as possible. We present a new maximum likelihood estimator (MLE) for nested case-control sampling in the context of Cox's proportional hazard...

  5. The likelihood principle and its proof – a never-ending story…

    DEFF Research Database (Denmark)

    Jørgensen, Thomas Martini

    2015-01-01

    An ongoing controversy in philosophy of statistics is the so-called “likelihood principle” essentially stating that all evidence which is obtained from an experiment about an unknown quantity θ is contained in the likelihood function of θ. Common classical statistical methodology, such as the use...... of significance tests, and confidence intervals, depends on the experimental procedure and unrealized events and thus violates the likelihood principle. The likelihood principle was identified by that name and proved in a famous paper by Allan Birnbaum in 1962. However, ever since both the principle itself...... as well as the proof has been highly debated. This presentation will illustrate the debate of both the principle and its proof, from 1962 and up to today. An often-used experiment to illustrate the controversy between classical interpretation and evidential confirmation based on the likelihood principle...

  6. Algorithms for MDC-based multi-locus phylogeny inference: beyond rooted binary gene trees on single alleles.

    Science.gov (United States)

    Yu, Yun; Warnow, Tandy; Nakhleh, Luay

    2011-11-01

    One of the criteria for inferring a species tree from a collection of gene trees, when gene tree incongruence is assumed to be due to incomplete lineage sorting (ILS), is Minimize Deep Coalescence (MDC). Exact algorithms for inferring the species tree from rooted, binary trees under MDC were recently introduced. Nevertheless, in phylogenetic analyses of biological data sets, estimated gene trees may differ from true gene trees, be incompletely resolved, and not necessarily rooted. In this article, we propose new MDC formulations for the cases where the gene trees are unrooted/binary, rooted/non-binary, and unrooted/non-binary. Further, we prove structural theorems that allow us to extend the algorithms for the rooted/binary gene tree case to these cases in a straightforward manner. In addition, we devise MDC-based algorithms for cases when multiple alleles per species may be sampled. We study the performance of these methods in coalescent-based computer simulations.

  7. RBT—A Tool for Building Refined Buneman Trees

    DEFF Research Database (Denmark)

    Besenbacher, Søren; Mailund; Westh-Nielsen, Lasse

    2005-01-01

    We have developed a tool implementing an efficient algorithm for refined Buneman tree reconstruction. The algorithm—which has the same complexity as the neighbour-joining method and the (plain) Buneman tree construction—enables refined Buneman tree reconstruction on large taxa sets....

  8. Identification and characterization of toll-like receptors (TLRs) in the Chinese tree shrew (Tupaia belangeri chinensis).

    Science.gov (United States)

    Yu, Dandan; Wu, Yong; Xu, Ling; Fan, Yu; Peng, Li; Xu, Min; Yao, Yong-Gang

    2016-07-01

    In mammals, the toll-like receptors (TLRs) play a major role in initiating innate immune responses against pathogens. Comparison of the TLRs in different mammals may help in understanding the TLR-mediated responses and developing of animal models and efficient therapeutic measures for infectious diseases. The Chinese tree shrew (Tupaia belangeri chinensis), a small mammal with a close relationship to primates, is a viable experimental animal for studying viral and bacterial infections. In this study, we characterized the TLRs genes (tTLRs) in the Chinese tree shrew and identified 13 putative TLRs, which are orthologs of mammalian TLR1-TLR9 and TLR11-TLR13, and TLR10 was a pseudogene in tree shrew. Positive selection analyses using the Maximum likelihood (ML) method showed that tTLR8 and tTLR9 were under positive selection, which might be associated with the adaptation to the pathogen challenge. The mRNA expression levels of tTLRs presented an overall low and tissue-specific pattern, and were significantly upregulated upon Hepatitis C virus (HCV) infection. tTLR4 and tTLR9 underwent alternative splicing, which leads to different transcripts. Phylogenetic analysis and TLR structure prediction indicated that tTLRs were evolutionarily conserved, which might reflect an ancient mechanism and structure in the innate immune response system. Taken together, TLRs had both conserved and unique features in the Chinese tree shrew. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. NDE of logs and standing trees using new acoustic tools : technical application and results

    Science.gov (United States)

    Peter Carter; Xiping Wang; Robert J. Ross; David Briggs

    2005-01-01

    The new Director ST300 provides a means to efficiently assess stands for stiffness and related wood properties based on standing tree acoustic velocily measures, and can be easily integrated with pre-harvest and earlier stand assessments. This provides for effective valuation for forest sale, stumpage purchase, harvest planning, and ranking of progeny or clones in tree...

  10. Neandertal admixture in Eurasia confirmed by maximum-likelihood analysis of three genomes.

    Science.gov (United States)

    Lohse, Konrad; Frantz, Laurent A F

    2014-04-01

    Although there has been much interest in estimating histories of divergence and admixture from genomic data, it has proved difficult to distinguish recent admixture from long-term structure in the ancestral population. Thus, recent genome-wide analyses based on summary statistics have sparked controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. Here we derive the probability of full mutational configurations in nonrecombining sequence blocks under both admixture and ancestral structure scenarios. Dividing the genome into short blocks gives an efficient way to compute maximum-likelihood estimates of parameters. We apply this likelihood scheme to triplets of human and Neandertal genomes and compare the relative support for a model of admixture from Neandertals into Eurasian populations after their expansion out of Africa against a history of persistent structure in their common ancestral population in Africa. Our analysis allows us to conclusively reject a model of ancestral structure in Africa and instead reveals strong support for Neandertal admixture in Eurasia at a higher rate (3.4-7.3%) than suggested previously. Using analysis and simulations we show that our inference is more powerful than previous summary statistics and robust to realistic levels of recombination.

  11. Approximate maximum likelihood estimation for population genetic inference.

    Science.gov (United States)

    Bertl, Johanna; Ewing, Gregory; Kosiol, Carolin; Futschik, Andreas

    2017-11-27

    In many population genetic problems, parameter estimation is obstructed by an intractable likelihood function. Therefore, approximate estimation methods have been developed, and with growing computational power, sampling-based methods became popular. However, these methods such as Approximate Bayesian Computation (ABC) can be inefficient in high-dimensional problems. This led to the development of more sophisticated iterative estimation methods like particle filters. Here, we propose an alternative approach that is based on stochastic approximation. By moving along a simulated gradient or ascent direction, the algorithm produces a sequence of estimates that eventually converges to the maximum likelihood estimate, given a set of observed summary statistics. This strategy does not sample much from low-likelihood regions of the parameter space, and is fast, even when many summary statistics are involved. We put considerable efforts into providing tuning guidelines that improve the robustness and lead to good performance on problems with high-dimensional summary statistics and a low signal-to-noise ratio. We then investigate the performance of our resulting approach and study its properties in simulations. Finally, we re-estimate parameters describing the demographic history of Bornean and Sumatran orang-utans.

  12. A biclustering algorithm for binary matrices based on penalized Bernoulli likelihood

    KAUST Repository

    Lee, Seokho; Huang, Jianhua Z.

    2013-01-01

    We propose a new biclustering method for binary data matrices using the maximum penalized Bernoulli likelihood estimation. Our method applies a multi-layer model defined on the logits of the success probabilities, where each layer represents a

  13. a Gross Error Elimination Method for Point Cloud Data Based on Kd-Tree

    Science.gov (United States)

    Kang, Q.; Huang, G.; Yang, S.

    2018-04-01

    Point cloud data has been one type of widely used data sources in the field of remote sensing. Key steps of point cloud data's pro-processing focus on gross error elimination and quality control. Owing to the volume feature of point could data, existed gross error elimination methods need spend massive memory both in space and time. This paper employed a new method which based on Kd-tree algorithm to construct, k-nearest neighbor algorithm to search, settled appropriate threshold to determine with result turns out a judgement that whether target point is or not an outlier. Experimental results show that, our proposed algorithm will help to delete gross error in point cloud data and facilitate to decrease memory consumption, improve efficiency.

  14. A GROSS ERROR ELIMINATION METHOD FOR POINT CLOUD DATA BASED ON KD-TREE

    Directory of Open Access Journals (Sweden)

    Q. Kang

    2018-04-01

    Full Text Available Point cloud data has been one type of widely used data sources in the field of remote sensing. Key steps of point cloud data’s pro-processing focus on gross error elimination and quality control. Owing to the volume feature of point could data, existed gross error elimination methods need spend massive memory both in space and time. This paper employed a new method which based on Kd-tree algorithm to construct, k-nearest neighbor algorithm to search, settled appropriate threshold to determine with result turns out a judgement that whether target point is or not an outlier. Experimental results show that, our proposed algorithm will help to delete gross error in point cloud data and facilitate to decrease memory consumption, improve efficiency.

  15. Performances of the likelihood-ratio classifier based on different data modelings

    NARCIS (Netherlands)

    Chen, C.; Veldhuis, Raymond N.J.

    2008-01-01

    The classical likelihood ratio classifier easily collapses in many biometric applications especially with independent training-test subjects. The reason lies in the inaccurate estimation of the underlying user-specific feature density. Firstly, the feature density estimation suffers from

  16. Bayesian Inference using Neural Net Likelihood Models for Protein Secondary Structure Prediction

    Directory of Open Access Journals (Sweden)

    Seong-Gon Kim

    2011-06-01

    Full Text Available Several techniques such as Neural Networks, Genetic Algorithms, Decision Trees and other statistical or heuristic methods have been used to approach the complex non-linear task of predicting Alpha-helicies, Beta-sheets and Turns of a proteins secondary structure in the past. This project introduces a new machine learning method by using an offline trained Multilayered Perceptrons (MLP as the likelihood models within a Bayesian Inference framework to predict secondary structures proteins. Varying window sizes are used to extract neighboring amino acid information and passed back and forth between the Neural Net models and the Bayesian Inference process until there is a convergence of the posterior secondary structure probability.

  17. Thematic and spatial resolutions affect model-based predictions of tree species distribution.

    Science.gov (United States)

    Liang, Yu; He, Hong S; Fraser, Jacob S; Wu, ZhiWei

    2013-01-01

    Subjective decisions of thematic and spatial resolutions in characterizing environmental heterogeneity may affect the characterizations of spatial pattern and the simulation of occurrence and rate of ecological processes, and in turn, model-based tree species distribution. Thus, this study quantified the importance of thematic and spatial resolutions, and their interaction in predictions of tree species distribution (quantified by species abundance). We investigated how model-predicted species abundances changed and whether tree species with different ecological traits (e.g., seed dispersal distance, competitive capacity) had different responses to varying thematic and spatial resolutions. We used the LANDIS forest landscape model to predict tree species distribution at the landscape scale and designed a series of scenarios with different thematic (different numbers of land types) and spatial resolutions combinations, and then statistically examined the differences of species abundance among these scenarios. Results showed that both thematic and spatial resolutions affected model-based predictions of species distribution, but thematic resolution had a greater effect. Species ecological traits affected the predictions. For species with moderate dispersal distance and relatively abundant seed sources, predicted abundance increased as thematic resolution increased. However, for species with long seeding distance or high shade tolerance, thematic resolution had an inverse effect on predicted abundance. When seed sources and dispersal distance were not limiting, the predicted species abundance increased with spatial resolution and vice versa. Results from this study may provide insights into the choice of thematic and spatial resolutions for model-based predictions of tree species distribution.

  18. Using decision trees and their ensembles for analysis of NIR spectroscopic data

    DEFF Research Database (Denmark)

    Kucheryavskiy, Sergey V.

    and interpretation of the models. In this presentation, we are going to discuss an applicability of decision trees based methods (including gradient boosting) for solving classification and regression tasks with NIR spectra as predictors. We will cover such aspects as evaluation, optimization and validation......Advanced machine learning methods, like convolutional neural networks and decision trees, became extremely popular in the last decade. This, first of all, is directly related to the current boom in Big data analysis, where traditional statistical methods are not efficient. According to the kaggle.......com — the most popular online resource for Big data problems and solutions — methods based on decision trees and their ensembles are most widely used for solving the problems. It can be noted that the decision trees and convolutional neural networks are not very popular in Chemometrics. One of the reasons...

  19. Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference.

    Science.gov (United States)

    Chernomor, Olga; Minh, Bui Quang; von Haeseler, Arndt

    2015-12-01

    In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged. Here, we provide the conditions under which the three most widely used topological rearrangements (nearest neighbor interchange, subtree pruning and regrafting, and tree bisection and reconnection) change the topologies of induced partition trees. During the tree search, these conditions allow us to quickly identify whether we can save computation time on the evaluation of newly encountered trees. We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original "full" terrace. Hence, partial terrace is the more important factor of timesaving compared to full terrace. Therefore, taking into account the above conditions and the partial terrace concept will help to speed up the tree search in phylogenomic inference.

  20. Plant delta 15N correlates with the transpiration efficiency of nitrogen acquisition in tropical trees.

    Science.gov (United States)

    Cernusak, Lucas A; Winter, Klaus; Turner, Benjamin L

    2009-11-01

    Based upon considerations of a theoretical model of (15)N/(14)N fractionation during steady-state nitrate uptake from soil, we hypothesized that, for plants grown in a common soil environment, whole-plant delta(15)N (deltaP) should vary as a function of the transpiration efficiency of nitrogen acquisition (F(N)/v) and the difference between deltaP and root delta(15)N (deltaP - deltaR). We tested these hypotheses with measurements of several tropical tree and liana species. Consistent with theoretical expectations, both F(N)/v and deltaP - deltaR were significant sources of variation in deltaP, and the relationship between deltaP and F(N)/v differed between non-N(2)-fixing and N(2)-fixing species. We interpret the correlation between deltaP and F(N)/v as resulting from variation in mineral nitrogen efflux-to-influx ratios across plasma membranes of root cells. These results provide a simple explanation of variation in delta(15)N of terrestrial plants and have implications for understanding nitrogen cycling in ecosystems.

  1. Improved Frame Mode Selection for AMR-WB+ Based on Decision Tree

    Science.gov (United States)

    Kim, Jong Kyu; Kim, Nam Soo

    In this letter, we propose a coding mode selection method for the AMR-WB+ audio coder based on a decision tree. In order to reduce computation while maintaining good performance, decision tree classifier is adopted with the closed loop mode selection results as the target classification labels. The size of the decision tree is controlled by pruning, so the proposed method does not increase the memory requirement significantly. Through an evaluation test on a database covering both speech and music materials, the proposed method is found to achieve a much better mode selection accuracy compared with the open loop mode selection module in the AMR-WB+.

  2. Fruit tree model for uptake of organic compounds from soil

    DEFF Research Database (Denmark)

    Trapp, Stefan; Rasmussen, D.; Samsoe-Petersen, L.

    2003-01-01

    -state, and an example calculation is given. The Fruit Tree Model is compared to the empirical equation of Travis and Arms (T&A), and to results from fruits, collected in contaminated areas. For polar compounds, both T&A and the Fruit Tree Model predict bioconcentration factors fruit to soil (BCF, wet weight based......) of > 1. No empirical data are available to support this prediction. For very lipophilic compounds (log K-OW > 5), T&A overestimates the uptake. The conclusion from the Fruit Tree Model is that the transfer of lipophilic compounds into fruits is not relevant. This was also found by an empirical study...... with PCDD/F. According to the Fruit Tree Model, polar chemicals are transferred efficiently into fruits, but empirical data to verify these predictions are lacking....

  3. Energy Analysis of Contention Tree-Based Access Protocols in Dense Machine-to-Machine Area Networks

    Directory of Open Access Journals (Sweden)

    Francisco Vázquez-Gallego

    2015-01-01

    Full Text Available Machine-to-Machine (M2M area networks aim at connecting an M2M gateway with a large number of energy-constrained devices that must operate autonomously for years. Therefore, attaining high energy efficiency is essential in the deployment of M2M networks. In this paper, we consider a dense M2M area network composed of hundreds or thousands of devices that periodically transmit data upon request from a gateway or coordinator. We theoretically analyse the devices’ energy consumption using two Medium Access Control (MAC protocols which are based on a tree-splitting algorithm to resolve collisions among devices: the Contention Tree Algorithm (CTA and the Distributed Queuing (DQ access. We have carried out computer-based simulations to validate the accuracy of the theoretical models and to compare the energy performance using DQ, CTA, and Frame Slotted-ALOHA (FSA in M2M area networks with devices in compliance with the IEEE 802.15.4 physical layer. Results show that the performance of DQ is totally independent of the number of contending devices, and it can reduce the energy consumed per device in more than 35% with respect to CTA and in more than 80% with respect to FSA.

  4. α-Cut method based importance measure for criticality analysis in fuzzy probability – Based fault tree analysis

    International Nuclear Information System (INIS)

    Purba, Julwan Hendry; Sony Tjahyani, D.T.; Widodo, Surip; Tjahjono, Hendro

    2017-01-01

    Highlights: •FPFTA deals with epistemic uncertainty using fuzzy probability. •Criticality analysis is important for reliability improvement. •An α-cut method based importance measure is proposed for criticality analysis in FPFTA. •The α-cut method based importance measure utilises α-cut multiplication, α-cut subtraction, and area defuzzification technique. •Benchmarking confirm that the proposed method is feasible for criticality analysis in FPFTA. -- Abstract: Fuzzy probability – based fault tree analysis (FPFTA) has been recently developed and proposed to deal with the limitations of conventional fault tree analysis. In FPFTA, reliabilities of basic events, intermediate events and top event are characterized by fuzzy probabilities. Furthermore, the quantification of the FPFTA is based on fuzzy multiplication rule and fuzzy complementation rule to propagate uncertainties from basic event to the top event. Since the objective of the fault tree analysis is to improve the reliability of the system being evaluated, it is necessary to find the weakest path in the system. For this purpose, criticality analysis can be implemented. Various importance measures, which are based on conventional probabilities, have been developed and proposed for criticality analysis in fault tree analysis. However, not one of those importance measures can be applied for criticality analysis in FPFTA, which is based on fuzzy probability. To be fully applied in nuclear power plant probabilistic safety assessment, FPFTA needs to have its corresponding importance measure. The objective of this study is to develop an α-cut method based importance measure to evaluate and rank the importance of basic events for criticality analysis in FPFTA. To demonstrate the applicability of the proposed measure, a case study is performed and its results are then benchmarked to the results generated by the four well known importance measures in conventional fault tree analysis. The results

  5. MXLKID: a maximum likelihood parameter identifier

    International Nuclear Information System (INIS)

    Gavel, D.T.

    1980-07-01

    MXLKID (MaXimum LiKelihood IDentifier) is a computer program designed to identify unknown parameters in a nonlinear dynamic system. Using noisy measurement data from the system, the maximum likelihood identifier computes a likelihood function (LF). Identification of system parameters is accomplished by maximizing the LF with respect to the parameters. The main body of this report briefly summarizes the maximum likelihood technique and gives instructions and examples for running the MXLKID program. MXLKID is implemented LRLTRAN on the CDC7600 computer at LLNL. A detailed mathematical description of the algorithm is given in the appendices. 24 figures, 6 tables

  6. Maintenance cost, toppling risk and size of trees in a self-thinning stand.

    Science.gov (United States)

    Larjavaara, Markku

    2010-07-07

    Wind routinely topples trees during storms, and the likelihood that a tree is toppled depends critically on its allometry. Yet none of the existing theories to explain tree allometry consider wind drag on tree canopies. Since leaf area index in crowded, self-thinning stands is independent of stand density, the drag force per unit land can also be assumed to be independent of stand density, with only canopy height influencing the total toppling moment. Tree stem dimensions and the self-thinning biomass can then be computed by further assuming that the risk of toppling over and stem maintenance per unit land area are independent of stand density, and that stem maintenance cost is a linear function of stem surface area and sapwood volume. These assumptions provide a novel way to understand tree allometry and lead to a self-thinning line relating tree biomass and stand density with a power between -3/2 and -2/3 depending on the ratio of maintenance of sapwood and stem surface. (c) 2010 Elsevier Ltd. All rights reserved.

  7. Tree Identification. Competency Based Teaching Materials in Horticulture.

    Science.gov (United States)

    Legacy, Jim; And Others

    This competency-based curriculum unit on tree identification is one of five developed for classroom use in teaching the landscape/nursery area of horticulture. The three sections are each divided into teaching content (in a question-and-answer format) and student skills that outline steps and factors for consideration. Topics covered include…

  8. Not seeing the forest for the trees: size of the minimum spanning trees (MSTs) forest and branch significance in MST-based phylogenetic analysis.

    Science.gov (United States)

    Teixeira, Andreia Sofia; Monteiro, Pedro T; Carriço, João A; Ramirez, Mário; Francisco, Alexandre P

    2015-01-01

    Trees, including minimum spanning trees (MSTs), are commonly used in phylogenetic studies. But, for the research community, it may be unclear that the presented tree is just a hypothesis, chosen from among many possible alternatives. In this scenario, it is important to quantify our confidence in both the trees and the branches/edges included in such trees. In this paper, we address this problem for MSTs by introducing a new edge betweenness metric for undirected and weighted graphs. This spanning edge betweenness metric is defined as the fraction of equivalent MSTs where a given edge is present. The metric provides a per edge statistic that is similar to that of the bootstrap approach frequently used in phylogenetics to support the grouping of taxa. We provide methods for the exact computation of this metric based on the well known Kirchhoff's matrix tree theorem. Moreover, we implement and make available a module for the PHYLOViZ software and evaluate the proposed metric concerning both effectiveness and computational performance. Analysis of trees generated using multilocus sequence typing data (MLST) and the goeBURST algorithm revealed that the space of possible MSTs in real data sets is extremely large. Selection of the edge to be represented using bootstrap could lead to unreliable results since alternative edges are present in the same fraction of equivalent MSTs. The choice of the MST to be presented, results from criteria implemented in the algorithm that must be based in biologically plausible models.

  9. Applying and Individual-Based Model to Simultaneously Evaluate Net Ecosystem Production and Tree Diameter Increment

    Science.gov (United States)

    Fang, F. J.

    2017-12-01

    Reconciling observations at fundamentally different scales is central in understanding the global carbon cycle. This study investigates a model-based melding of forest inventory data, remote-sensing data and micrometeorological-station data ("flux towers" estimating forest heat, CO2 and H2O fluxes). The individual tree-based model FORCCHN was used to evaluate the tree DBH increment and forest carbon fluxes. These are the first simultaneous simulations of the forest carbon budgets from flux towers and individual-tree growth estimates of forest carbon budgets using the continuous forest inventory data — under circumstances in which both predictions can be tested. Along with the global implications of such findings, this also improves the capacity for forest sustainable management and the comprehensive understanding of forest ecosystems. In forest ecology, diameter at breast height (DBH) of a tree significantly determines an individual tree's cross-sectional sapwood area, its biomass and carbon storage. Evaluation the annual DBH increment (ΔDBH) of an individual tree is central to understanding tree growth and forest ecology. Ecosystem Carbon flux is a consequence of key ecosystem processes in the forest-ecosystem carbon cycle, Gross and Net Primary Production (GPP and NPP, respectively) and Net Ecosystem Respiration (NEP). All of these closely relate with tree DBH changes and tree death. Despite advances in evaluating forest carbon fluxes with flux towers and forest inventories for individual tree ΔDBH, few current ecological models can simultaneously quantify and predict the tree ΔDBH and forest carbon flux.

  10. Detection of Citrus Trees from Uav Dsms

    Science.gov (United States)

    Ok, A. O.; Ozdarici-Ok, A.

    2017-05-01

    This paper presents an automated approach to detect citrus trees from digitals surface models (DSMs) as a single source. The DSMs in this study are generated from Unmanned Aerial Vehicles (UAVs), and the proposed approach first considers the symmetric nature of the citrus trees, and it computes the orientation-based radial symmetry in an efficient way. The approach also takes into account the local maxima (LM) information to verify the output of the radial symmetry. Our contributions in this study are twofold: (i) Such an integrated approach (symmetry + LM) has not been tested to detect (citrus) trees (in orchards), and (ii) the validity of such an integrated approach has not been experienced for an input, e.g. a single DSM. Experiments are performed on five test patches. The results reveal that our approach is capable of counting most of the citrus trees without manual intervention. Comparison to the state-of-the-art reveals that the proposed approach provides notable detection performance by providing the best balance between precision and recall measures.

  11. T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life.

    Science.gov (United States)

    Carbone, Ignazio; White, James B; Miadlikowska, Jolanta; Arnold, A Elizabeth; Miller, Mark A; Kauff, Frank; U'Ren, Jana M; May, Georgiana; Lutzoni, François

    2017-04-15

    High-quality phylogenetic placement of sequence data has the potential to greatly accelerate studies of the diversity, systematics, ecology and functional biology of diverse groups. We developed the Tree-Based Alignment Selector (T-BAS) toolkit to allow evolutionary placement and visualization of diverse DNA sequences representing unknown taxa within a robust phylogenetic context, and to permit the downloading of highly curated, single- and multi-locus alignments for specific clades. In its initial form, T-BAS v1.0 uses a core phylogeny of 979 taxa (including 23 outgroup taxa, as well as 61 orders, 175 families and 496 genera) representing all 13 classes of largest subphylum of Fungi-Pezizomycotina (Ascomycota)-based on sequence alignments for six loci (nr5.8S, nrLSU, nrSSU, mtSSU, RPB1, RPB2 ). T-BAS v1.0 has three main uses: (i) Users may download alignments and voucher tables for members of the Pezizomycotina directly from the reference tree, facilitating systematics studies of focal clades. (ii) Users may upload sequence files with reads representing unknown taxa and place these on the phylogeny using either BLAST or phylogeny-based approaches, and then use the displayed tree to select reference taxa to include when downloading alignments. The placement of unknowns can be performed for large numbers of Sanger sequences obtained from fungal cultures and for alignable, short reads of environmental amplicons. (iii) User-customizable metadata can be visualized on the tree. T-BAS Version 1.0 is available online at http://tbas.hpc.ncsu.edu . Registration is required to access the CIPRES Science Gateway and NSF XSEDE's large computational resources. icarbon@ncsu.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  12. Detecting Structural Metadata with Decision Trees and Transformation-Based Learning

    National Research Council Canada - National Science Library

    Kim, Joungbum; Schwarm, Sarah E; Ostendorf, Mari

    2004-01-01

    .... Specifically, combinations of decision trees and language models are used to predict sentence ends and interruption points and given these events transformation based learning is used to detect edit...

  13. Use of empirical likelihood to calibrate auxiliary information in partly linear monotone regression models.

    Science.gov (United States)

    Chen, Baojiang; Qin, Jing

    2014-05-10

    In statistical analysis, a regression model is needed if one is interested in finding the relationship between a response variable and covariates. When the response depends on the covariate, then it may also depend on the function of this covariate. If one has no knowledge of this functional form but expect for monotonic increasing or decreasing, then the isotonic regression model is preferable. Estimation of parameters for isotonic regression models is based on the pool-adjacent-violators algorithm (PAVA), where the monotonicity constraints are built in. With missing data, people often employ the augmented estimating method to improve estimation efficiency by incorporating auxiliary information through a working regression model. However, under the framework of the isotonic regression model, the PAVA does not work as the monotonicity constraints are violated. In this paper, we develop an empirical likelihood-based method for isotonic regression model to incorporate the auxiliary information. Because the monotonicity constraints still hold, the PAVA can be used for parameter estimation. Simulation studies demonstrate that the proposed method can yield more efficient estimates, and in some situations, the efficiency improvement is substantial. We apply this method to a dementia study. Copyright © 2013 John Wiley & Sons, Ltd.

  14. Identifying Different Transportation Modes from Trajectory Data Using Tree-Based Ensemble Classifiers

    Directory of Open Access Journals (Sweden)

    Zhibin Xiao

    2017-02-01

    Full Text Available Recognition of transportation modes can be used in different applications including human behavior research, transport management and traffic control. Previous work on transportation mode recognition has often relied on using multiple sensors or matching Geographic Information System (GIS information, which is not possible in many cases. In this paper, an approach based on ensemble learning is proposed to infer hybrid transportation modes using only Global Position System (GPS data. First, in order to distinguish between different transportation modes, we used a statistical method to generate global features and extract several local features from sub-trajectories after trajectory segmentation, before these features were combined in the classification stage. Second, to obtain a better performance, we used tree-based ensemble models (Random Forest, Gradient Boosting Decision Tree, and XGBoost instead of traditional methods (K-Nearest Neighbor, Decision Tree, and Support Vector Machines to classify the different transportation modes. The experiment results on the later have shown the efficacy of our proposed approach. Among them, the XGBoost model produced the best performance with a classification accuracy of 90.77% obtained on the GEOLIFE dataset, and we used a tree-based ensemble method to ensure accurate feature selection to reduce the model complexity.

  15. Estimation of Financial Agent-Based Models with Simulated Maximum Likelihood

    Czech Academy of Sciences Publication Activity Database

    Kukačka, Jiří; Baruník, Jozef

    2017-01-01

    Roč. 85, č. 1 (2017), s. 21-45 ISSN 0165-1889 R&D Projects: GA ČR(CZ) GBP402/12/G097 Institutional support: RVO:67985556 Keywords : heterogeneous agent model, * simulated maximum likelihood * switching Subject RIV: AH - Economics OBOR OECD: Finance Impact factor: 1.000, year: 2016 http://library.utia.cas.cz/separaty/2017/E/kukacka-0478481.pdf

  16. Likelihood devices in spatial statistics

    NARCIS (Netherlands)

    Zwet, E.W. van

    1999-01-01

    One of the main themes of this thesis is the application to spatial data of modern semi- and nonparametric methods. Another, closely related theme is maximum likelihood estimation from spatial data. Maximum likelihood estimation is not common practice in spatial statistics. The method of moments

  17. Statistical modelling of survival data with random effects h-likelihood approach

    CERN Document Server

    Ha, Il Do; Lee, Youngjo

    2017-01-01

    This book provides a groundbreaking introduction to the likelihood inference for correlated survival data via the hierarchical (or h-) likelihood in order to obtain the (marginal) likelihood and to address the computational difficulties in inferences and extensions. The approach presented in the book overcomes shortcomings in the traditional likelihood-based methods for clustered survival data such as intractable integration. The text includes technical materials such as derivations and proofs in each chapter, as well as recently developed software programs in R (“frailtyHL”), while the real-world data examples together with an R package, “frailtyHL” in CRAN, provide readers with useful hands-on tools. Reviewing new developments since the introduction of the h-likelihood to survival analysis (methods for interval estimation of the individual frailty and for variable selection of the fixed effects in the general class of frailty models) and guiding future directions, the book is of interest to research...

  18. Study on Cloud Security Based on Trust Spanning Tree Protocol

    Science.gov (United States)

    Lai, Yingxu; Liu, Zenghui; Pan, Qiuyue; Liu, Jing

    2015-09-01

    Attacks executed on Spanning Tree Protocol (STP) expose the weakness of link layer protocols and put the higher layers in jeopardy. Although the problems have been studied for many years and various solutions have been proposed, many security issues remain. To enhance the security and credibility of layer-2 network, we propose a trust-based spanning tree protocol aiming at achieving a higher credibility of LAN switch with a simple and lightweight authentication mechanism. If correctly implemented in each trusted switch, the authentication of trust-based STP can guarantee the credibility of topology information that is announced to other switch in the LAN. To verify the enforcement of the trusted protocol, we present a new trust evaluation method of the STP using a specification-based state model. We implement a prototype of trust-based STP to investigate its practicality. Experiment shows that the trusted protocol can achieve security goals and effectively avoid STP attacks with a lower computation overhead and good convergence performance.

  19. An IPv6 routing lookup algorithm using weight-balanced tree based on prefix value for virtual router

    Science.gov (United States)

    Chen, Lingjiang; Zhou, Shuguang; Zhang, Qiaoduo; Li, Fenghua

    2016-10-01

    Virtual router enables the coexistence of different networks on the same physical facility and has lately attracted a great deal of attention from researchers. As the number of IPv6 addresses is rapidly increasing in virtual routers, designing an efficient IPv6 routing lookup algorithm is of great importance. In this paper, we present an IPv6 lookup algorithm called weight-balanced tree (WBT). WBT merges Forwarding Information Bases (FIBs) of virtual routers into one spanning tree, and compresses the space cost. WBT's average time complexity and the worst case time complexity of lookup and update process are both O(logN) and space complexity is O(cN) where N is the size of routing table and c is a constant. Experiments show that WBT helps reduce more than 80% Static Random Access Memory (SRAM) cost in comparison to those separation schemes. WBT also achieves the least average search depth comparing with other homogeneous algorithms.

  20. Surface-based geometric modelling using teaching trees for advanced robots

    International Nuclear Information System (INIS)

    Nakamura, Akira; Ogasawara, Tsukasa; Tsukune, Hideo; Oshima, Masaki

    2000-01-01

    Geometric modelling of the environment is important in robot motion planning. Generally, shapes can be stored in a data base, so the elements that need to be decided are positions and orientations. In this paper, surface-based geometric modelling using a teaching tree is proposed. In this modelling, combinations of surfaces are considered in order to decide positions and orientations of objects. The combinations are represented by a depth-first tree, which makes it easy for the operator to select one combination out of several. This method is effective not only in the case when perfect data can be obtained, but also when conditions for measurement of three-dimensional data are unfavorable, which often occur in the environment of a working robot. (author)

  1. Long-term tree growth rate, water use efficiency, and tree ring nitrogen isotope composition of Pinus massoniana L. in response to global climate change and local nitrogen deposition in Southern China

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Fangfang [Chinese Academy of Sciences, Guangzhou (China). South China Botanical Garden; Graduate Univ. of Chinese Academy of Sciences, Beijing (China); Griffith Univ., Nathan, QLD (Australia). Environmental Future Centre; Kuang, Yuanwen; Wen, Dazhi [Chinese Academy of Sciences, Guangzhou (China). South China Botanical Garden; Chinese Academy of Sciences, Guangzhou (China). Pearl River Delta Research Centre of Environmental Pollution and Control; Xu, Zhihong [Griffith Univ., Nathan, QLD (Australia). Environmental Future Centre; Li, Jianli; Zuo, Weidong [Agriculture and Forestry Technology Extension Centre, Nanhai District, Guangdong (China); Hou, Enqing [Chinese Academy of Sciences, Guangzhou (China). South China Botanical Garden; Graduate Univ. of Chinese Academy of Sciences, Beijing (China)

    2010-12-15

    We aimed to investigate long-term tree growth rates, water use efficiencies (WUE), and tree ring nitrogen (N) isotope compositions ({delta}{sup 15}N) of Masson pine (Pinus massoniana L.) in response to global climate change and local N deposition in Southern China. Tree annual growth rings of Masson pine were collected from four forest sites, viz. South China Botanical Garden (SBG), Xi Qiao Shan (XQS) Forest Park, Ding Hu Shan (DHS) Natural Reserve, and Nan Kun Shan (NKS) Natural Reserve in Southern China. The mean annual basal area increment (BAI), WUE, and {delta}{sup 15}N at every 5-year intervals of Masson pine during the last 50 years were determined. Regression analyses were used to quantify the relationships of BAI and WUE with atmospheric carbon dioxide concentration ([CO{sub 2}]), temperature, rainfall, and tree ring elemental concentrations at the four study sites. Tree BAI showed a quadratic relationship with rising [CO{sub 2}]. The tipping points of [CO{sub 2}] for BAI, the peaks of BAI when the critical [CO{sub 2}] was reached, occurred earlier at the sites of SBG, XQS, and DHS which were exposed to higher temperature, N deposition, and lower mineral nutrient availability, as compared with the tipping points of [CO{sub 2}] for BAI at the site of NKS which had higher rainfall, lower temperature, and better nutritional status. The average tipping point of [CO{sub 2}] at the four sites for the BAI response curves was 356 ppm, after which, the BAI would be expected to decrease quadratically with rising [CO{sub 2}]. The multiple regressions of BAI confirmed the relationships of long-term tree growth rate with rainfall, tree WUE, and nutrients and {delta}{sup 15}N in tree rings. Nonlinear relationships between BAI and tree ring {delta}{sup 15}N at DHS and negatively linear one at NKS reflected the fertilization effect of N deposition on tree growth rate initially, but this effect peaked or became negative once the forest approached or passed the N saturation

  2. Computer aided construction of fault tree

    International Nuclear Information System (INIS)

    Kovacs, Z.

    1982-01-01

    Computer code CAT for the automatic construction of the fault tree is briefly described. Code CAT makes possible simple modelling of components using decision tables, it accelerates the fault tree construction process, constructs fault trees of different complexity, and is capable of harmonized co-operation with programs PREPandKITT 1,2 for fault tree analysis. The efficiency of program CAT and thus the accuracy and completeness of fault trees constructed significantly depends on the compilation and sophistication of decision tables. Currently, program CAT is used in co-operation with programs PREPandKITT 1,2 in reliability analyses of nuclear power plant systems. (B.S.)

  3. Responses of Tree Growths to Tree Size, Competition, and Topographic Conditions in Sierra Nevada Forests Using Bi-temporal Airborne LiDAR Data

    Science.gov (United States)

    Ma, Q.; Su, Y.; Tao, S.; Guo, Q.

    2016-12-01

    Trees in the Sierra Nevada (SN) forests are experiencing rapid changes due to human disturbances and climatic changes. An improved monitoring of tree growth and understanding of how tree growth responses to different impact factors, such as tree competition, forest density, topographic and hydrologic conditions, are urgently needed in tree growth modeling. Traditional tree growth modeling mainly relied on field survey, which was highly time-consuming and labor-intensive. Airborne Light detection and ranging System (ALS) is increasingly used in forest survey, due to its high efficiency and accuracy in three-dimensional tree structure delineation and terrain characterization. This study successfully detected individual tree growth in height (ΔH), crown area (ΔA), and crown volume (ΔV) over a five-year period (2007-2012) using bi-temporal ALS data in two conifer forest areas in SN. We further analyzed their responses to original tree size, competition indices, forest structure indices, and topographic environmental parameters at individual tree and forest stand scales. Our results indicated ΔH was strongly sensitive to topographic wetness index; whereas ΔA and ΔV were highly responsive to forest density and original tree sizes. These ALS based findings in ΔH were consistent with field measurements. Our study demonstrated the promising potential of using bi-temporal ALS data in forest growth measurements and analysis. A more comprehensive study over a longer temporal period and a wider range of forest stands would give better insights into tree growth in the SN, and provide useful guides for forest growth monitoring, modeling, and management.

  4. Multi-focus image fusion based on area-based standard deviation in dual tree contourlet transform domain

    Science.gov (United States)

    Dong, Min; Dong, Chenghui; Guo, Miao; Wang, Zhe; Mu, Xiaomin

    2018-04-01

    Multiresolution-based methods, such as wavelet and Contourlet are usually used to image fusion. This work presents a new image fusion frame-work by utilizing area-based standard deviation in dual tree Contourlet trans-form domain. Firstly, the pre-registered source images are decomposed with dual tree Contourlet transform; low-pass and high-pass coefficients are obtained. Then, the low-pass bands are fused with weighted average based on area standard deviation rather than the simple "averaging" rule. While the high-pass bands are merged with the "max-absolute' fusion rule. Finally, the modified low-pass and high-pass coefficients are used to reconstruct the final fused image. The major advantage of the proposed fusion method over conventional fusion is the approximately shift invariance and multidirectional selectivity of dual tree Contourlet transform. The proposed method is compared with wavelet- , Contourletbased methods and other the state-of-the art methods on common used multi focus images. Experiments demonstrate that the proposed fusion framework is feasible and effective, and it performs better in both subjective and objective evaluation.

  5. Market-based approaches to tree valuation

    Science.gov (United States)

    Geoffrey H. Donovan; David T. Butry

    2008-01-01

    A recent four-part series in Arborist News outlined different appraisal processes used to value urban trees. The final article in the series described the three generally accepted approaches to tree valuation: the sales comparison approach, the cost approach, and the income capitalization approach. The author, D. Logan Nelson, noted that the sales comparison approach...

  6. Live phylogeny with polytomies: Finding the most compact parsimonious trees.

    Science.gov (United States)

    Papamichail, D; Huang, A; Kennedy, E; Ott, J-L; Miller, A; Papamichail, G

    2017-08-01

    Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral evolution and transmission, paleontology, linguistics, and phylogenetic stemmatics, often require phylogeny inference that involves placing input species on ancestral tree nodes (live phylogeny), and polytomies. These requirements, despite their prevalence, lead to computationally harder algorithmic solutions and have been sparsely examined in the literature to date. In this article we prove some unique properties of most parsimonious live phylogenetic trees with polytomies, and their mapping to traditional binary phylogenetic trees. We show that our problem reduces to finding the most compact parsimonious tree for n species, and describe a novel efficient algorithm to find such trees without resorting to exhaustive enumeration of all possible tree topologies. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Fault tree synthesis for software design analysis of PLC based safety-critical systems

    International Nuclear Information System (INIS)

    Koo, S. R.; Cho, C. H.; Seong, P. H.

    2006-01-01

    As a software verification and validation should be performed for the development of PLC based safety-critical systems, a software safety analysis is also considered in line with entire software life cycle. In this paper, we propose a technique of software safety analysis in the design phase. Among various software hazard analysis techniques, fault tree analysis is most widely used for the safety analysis of nuclear power plant systems. Fault tree analysis also has the most intuitive notation and makes both qualitative and quantitative analyses possible. To analyze the design phase more effectively, we propose a technique of fault tree synthesis, along with a universal fault tree template for the architecture modules of nuclear software. Consequently, we can analyze the safety of software on the basis of fault tree synthesis. (authors)

  8. Parallelization of maximum likelihood fits with OpenMP and CUDA

    CERN Document Server

    Jarp, S; Leduc, J; Nowak, A; Pantaleo, F

    2011-01-01

    Data analyses based on maximum likelihood fits are commonly used in the high energy physics community for fitting statistical models to data samples. This technique requires the numerical minimization of the negative log-likelihood function. MINUIT is the most common package used for this purpose in the high energy physics community. The main algorithm in this package, MIGRAD, searches the minimum by using the gradient information. The procedure requires several evaluations of the function, depending on the number of free parameters and their initial values. The whole procedure can be very CPU-time consuming in case of complex functions, with several free parameters, many independent variables and large data samples. Therefore, it becomes particularly important to speed-up the evaluation of the negative log-likelihood function. In this paper we present an algorithm and its implementation which benefits from data vectorization and parallelization (based on OpenMP) and which was also ported to Graphics Processi...

  9. A scaling transformation for classifier output based on likelihood ratio: Applications to a CAD workstation for diagnosis of breast cancer

    International Nuclear Information System (INIS)

    Horsch, Karla; Pesce, Lorenzo L.; Giger, Maryellen L.; Metz, Charles E.; Jiang Yulei

    2012-01-01

    Purpose: The authors developed scaling methods that monotonically transform the output of one classifier to the ''scale'' of another. Such transformations affect the distribution of classifier output while leaving the ROC curve unchanged. In particular, they investigated transformations between radiologists and computer classifiers, with the goal of addressing the problem of comparing and interpreting case-specific values of output from two classifiers. Methods: Using both simulated and radiologists' rating data of breast imaging cases, the authors investigated a likelihood-ratio-scaling transformation, based on ''matching'' classifier likelihood ratios. For comparison, three other scaling transformations were investigated that were based on matching classifier true positive fraction, false positive fraction, or cumulative distribution function, respectively. The authors explored modifying the computer output to reflect the scale of the radiologist, as well as modifying the radiologist's ratings to reflect the scale of the computer. They also evaluated how dataset size affects the transformations. Results: When ROC curves of two classifiers differed substantially, the four transformations were found to be quite different. The likelihood-ratio scaling transformation was found to vary widely from radiologist to radiologist. Similar results were found for the other transformations. Our simulations explored the effect of database sizes on the accuracy of the estimation of our scaling transformations. Conclusions: The likelihood-ratio-scaling transformation that the authors have developed and evaluated was shown to be capable of transforming computer and radiologist outputs to a common scale reliably, thereby allowing the comparison of the computer and radiologist outputs on the basis of a clinically relevant statistic.

  10. Maximum Likelihood Joint Tracking and Association in Strong Clutter

    Directory of Open Access Journals (Sweden)

    Leonid I. Perlovsky

    2013-01-01

    Full Text Available We have developed a maximum likelihood formulation for a joint detection, tracking and association problem. An efficient non-combinatorial algorithm for this problem is developed in case of strong clutter for radar data. By using an iterative procedure of the dynamic logic process “from vague-to-crisp” explained in the paper, the new tracker overcomes the combinatorial complexity of tracking in highly-cluttered scenarios and results in an orders-of-magnitude improvement in signal-to-clutter ratio.

  11. Frequentist and Bayesian inference for Gaussian-log-Gaussian wavelet trees and statistical signal processing applications

    DEFF Research Database (Denmark)

    Jacobsen, Christian Robert Dahl; Møller, Jesper

    2017-01-01

    We introduce new estimation methods for a subclass of the Gaussian scale mixture models for wavelet trees by Wainwright, Simoncelli and Willsky that rely on modern results for composite likelihoods and approximate Bayesian inference. Our methodology is illustrated for denoising and edge detection...

  12. Horn clause verification with convex polyhedral abstraction and tree automata-based refinement

    DEFF Research Database (Denmark)

    Kafle, Bishoksan; Gallagher, John Patrick

    2017-01-01

    In this paper we apply tree-automata techniques to refinement of abstract interpretation in Horn clause verification. We go beyond previous work on refining trace abstractions; firstly we handle tree automata rather than string automata and thereby can capture traces in any Horn clause derivations...... underlying the Horn clauses. Experiments using linear constraint problems and the abstract domain of convex polyhedra show that the refinement technique is practical and that iteration of abstract interpretation with tree automata-based refinement solves many challenging Horn clause verification problems. We...... compare the results with other state-of-the-art Horn clause verification tools....

  13. An FMM based on dual tree traversal for many-core architectures

    KAUST Repository

    Yokota, Rio

    2013-09-01

    The present work attempts to integrate the independent efforts in the fast N-body community to create the fastest N-body library for many-core and heterogenous architectures. Focus is placed on low accuracy optimizations, in response to the recent interest to use FMM as a preconditioner for sparse linear solvers. A direct comparison with other state-of-the-art fast N-body codes demonstrates that orders of magnitude increase in performance can be achieved by careful selection of the optimal algorithm and low-level optimization of the code. The current N-body solver uses a fast multipole method with an efficient strategy for finding the list of cell-cell interactions by a dual tree traversal. A task-based threading model is used to maximize thread-level parallelism and intra-node load-balancing. In order to extract the full potential of the SIMD units on the latest CPUs, the inner kernels are optimized using AVX instructions.

  14. Maximum-likelihood methods for array processing based on time-frequency distributions

    Science.gov (United States)

    Zhang, Yimin; Mu, Weifeng; Amin, Moeness G.

    1999-11-01

    This paper proposes a novel time-frequency maximum likelihood (t-f ML) method for direction-of-arrival (DOA) estimation for non- stationary signals, and compares this method with conventional maximum likelihood DOA estimation techniques. Time-frequency distributions localize the signal power in the time-frequency domain, and as such enhance the effective SNR, leading to improved DOA estimation. The localization of signals with different t-f signatures permits the division of the time-frequency domain into smaller regions, each contains fewer signals than those incident on the array. The reduction of the number of signals within different time-frequency regions not only reduces the required number of sensors, but also decreases the computational load in multi- dimensional optimizations. Compared to the recently proposed time- frequency MUSIC (t-f MUSIC), the proposed t-f ML method can be applied in coherent environments, without the need to perform any type of preprocessing that is subject to both array geometry and array aperture.

  15. Efficiency of a new strategy involving a new class of natural hetero-ligand iron(III) chelates (Fe(III)-NHL) to improve fruit tree growth in alkaline/calcareous soils.

    Science.gov (United States)

    Fuentes, Marta; Ortuño, María F; Pérez-Sarmiento, Francisco; Bacaicoa, Eva; Baigorri, Roberto; Conejero, Wenceslao; Torrecillas, Arturo; García-Mina, José M

    2012-12-01

    Iron (Fe) chlorosis is a serious problem affecting the yield and quality of numerous crops and fruit trees cultivated in alkaline/calcareous soils. This paper describes the efficiency of a new class of natural hetero-ligand Fe(III) chelates (Fe-NHL) to provide available Fe for chlorotic lemon trees grown in alkaline/calcareous soils. These chelates involve the participation in the reaction system of a partially humified lignin-based natural polymer and citric acid. First results showed that Fe-NHL was adsorbed on the soil matrix while maintaining available Fe for plants in alkaline/calcareous solution. The effects of using three different sources as Fe fertilisers were also compared: two Fe-NHL formulations (NHL1, containing 100% of Fe as Fe-NHL, and NHL2, containing 80% of Fe as Fe-NHL and 20% of Fe as Fe-ethylenediamine-N,N'-bis-(o-hydroxyphenylacetic) acid (Fe-EDDHA)) and Fe-EDDHA. Both Fe-NHL formulations increased fruit yield without negative effects on fruit quality in comparison with Fe-EDDHA. In the absence of the Fe-starter fraction (NHL1), trees seemed to optimise Fe assimilation and translocation from Fe-NHL, directing it to those parts of the plant more involved in development. The field assays confirmed that Fe-NHL-based fertilisers are able to provide Fe to chlorotic trees, with results comparable to Fe-EDDHA. Besides, this would imply a more sustainable and less expensive remediation than synthetic chelates. Copyright © 2012 Society of Chemical Industry.

  16. Investigation on the efficiency of treated Palm Tree waste for removal of organic pollutants

    Science.gov (United States)

    Azoulay, Karima; El HajjajiI, Souad; Dahchour, Abdelmalek

    2017-04-01

    Development of the industrial sector generates several problems of environmental pollution. This issue rises concern among scientific community and decision makers, in this work; we e interested in water resources polluted by the chemical substances, which can cause various problems of health. As an example, dyes generated by different industrial activities such as textile, cosmetic, metal plating, leather, paper and plastic sectors, constitute an important source of pollution. In this work, we aim at investigating the efficiency of palm tree waste for removal of dyes from polluted solution. Our work presents a double environmental aspect, on one hand it constitutes an attempt for valorization of Palm Tree waste, and on the other hand it provides natural adsorbent. The study focuses on the effectiveness of the waste in removing Methylene Bleu and Methyl Orange taken as models of pollutants from aqueous solution. Kinetics and isotherm experiments were conducted in order to determine the sorption behavior of the examined dye. The effects of initial dye and adsorbent concentrations are considered. The results indicate that the correlation coefficient calculated from pseudo-second order equation was higher than the other kinetic equations, indicating that equilibrium data fitted well with pseudo-second order model where adsorption process was chemisorption. The adsorption equilibrium was well described by Langmuir isotherm model.

  17. On Maximum Likelihood Estimation for Left Censored Burr Type III Distribution

    Directory of Open Access Journals (Sweden)

    Navid Feroze

    2015-12-01

    Full Text Available Burr type III is an important distribution used to model the failure time data. The paper addresses the problem of estimation of parameters of the Burr type III distribution based on maximum likelihood estimation (MLE when the samples are left censored. As the closed form expression for the MLEs of the parameters cannot be derived, the approximate solutions have been obtained through iterative procedures. An extensive simulation study has been carried out to investigate the performance of the estimators with respect to sample size, censoring rate and true parametric values. A real life example has also been presented. The study revealed that the proposed estimators are consistent and capable of providing efficient results under small to moderate samples.

  18. A Gossip-based Energy Efficient Protocol for Robust In-network Aggregation in Wireless Sensor Networks

    Science.gov (United States)

    Fauji, Shantanu

    We consider the problem of energy efficient and fault tolerant in--network aggregation for wireless sensor networks (WSNs). In-network aggregation is the process of aggregation while collecting data from sensors to the base station. This process should be energy efficient due to the limited energy at the sensors and tolerant to the high failure rates common in sensor networks. Tree based in--network aggregation protocols, although energy efficient, are not robust to network failures. Multipath routing protocols are robust to failures to a certain degree but are not energy efficient due to the overhead in the maintenance of multiple paths. We propose a new protocol for in-network aggregation in WSNs, which is energy efficient, achieves high lifetime, and is robust to the changes in the network topology. Our protocol, gossip--based protocol for in-network aggregation (GPIA) is based on the spreading of information via gossip. GPIA is not only adaptive to failures and changes in the network topology, but is also energy efficient. Energy efficiency of GPIA comes from all the nodes being capable of selective message reception and detecting convergence of the aggregation early. We experimentally show that GPIA provides significant improvement over some other competitors like the Ridesharing, Synopsis Diffusion and the pure version of gossip. GPIA shows ten fold, five fold and two fold improvement over the pure gossip, the synopsis diffusion and Ridesharing protocols in terms of network lifetime, respectively. Further, GPIA retains gossip's robustness to failures and improves upon the accuracy of synopsis diffusion and Ridesharing.

  19. TreeBASIS Feature Descriptor and Its Hardware Implementation

    Directory of Open Access Journals (Sweden)

    Spencer Fowers

    2014-01-01

    Full Text Available This paper presents a novel feature descriptor called TreeBASIS that provides improvements in descriptor size, computation time, matching speed, and accuracy. This new descriptor uses a binary vocabulary tree that is computed using basis dictionary images and a test set of feature region images. To facilitate real-time implementation, a feature region image is binary quantized and the resulting quantized vector is passed into the BASIS vocabulary tree. A Hamming distance is then computed between the feature region image and the effectively descriptive basis dictionary image at a node to determine the branch taken and the path the feature region image takes is saved as a descriptor. The TreeBASIS feature descriptor is an excellent candidate for hardware implementation because of its reduced descriptor size and the fact that descriptors can be created and features matched without the use of floating point operations. The TreeBASIS descriptor is more computationally and space efficient than other descriptors such as BASIS, SIFT, and SURF. Moreover, it can be computed entirely in hardware without the support of a CPU for additional software-based computations. Experimental results and a hardware implementation show that the TreeBASIS descriptor compares well with other descriptors for frame-to-frame homography computation while requiring fewer hardware resources.

  20. Improved Likelihood Function in Particle-based IR Eye Tracking

    DEFF Research Database (Denmark)

    Satria, R.; Sorensen, J.; Hammoud, R.

    2005-01-01

    In this paper we propose a log likelihood-ratio function of foreground and background models used in a particle filter to track the eye region in dark-bright pupil image sequences. This model fuses information from both dark and bright pupil images and their difference image into one model. Our...... enhanced tracker overcomes the issues of prior selection of static thresholds during the detection of feature observations in the bright-dark difference images. The auto-initialization process is performed using cascaded classifier trained using adaboost and adapted to IR eye images. Experiments show good...

  1. Temperature Effect on Electrical Treeing and Partial Discharge Characteristics of Silicone Rubber-Based Nanocomposites

    Directory of Open Access Journals (Sweden)

    Mohd Hafizi Ahmad

    2015-01-01

    Full Text Available This study investigated electrical treeing and its associated phase-resolved partial discharge (PD activities in room-temperature, vulcanized silicone rubber/organomontmorillonite nanocomposite sample materials over a range of temperatures in order to assess the effect of temperature on different filler concentrations under AC voltage. The samples were prepared with three levels of nanofiller content: 0% by weight (wt, 1% by wt, and 3% by wt. The electrical treeing and PD activities of these samples were investigated at temperatures of 20°C, 40°C, and 60°C. The results show that the characteristics of the electrical tree changed with increasing temperature. The tree inception times decreased at 20°C due to space charge dynamics, and the tree growth time increased at 40°C due to the increase in the number of cross-link network structures caused by the vulcanization process. At 60°C, more enhanced and reinforced properties of the silicone rubber-based nanocomposite samples occurred. This led to an increase in electrical tree inception time and electrical tree growth time. However, the PD characteristics, particularly the mean phase angle of occurrence of the positive and negative discharge distributions, were insensitive to variations in temperature. This reflects an enhanced stability in the nanocomposite electrical properties compared with the base polymer.

  2. ARMA-Based SEM When the Number of Time Points T Exceeds the Number of Cases N: Raw Data Maximum Likelihood.

    Science.gov (United States)

    Hamaker, Ellen L.; Dolan, Conor V.; Molenaar, Peter C. M.

    2003-01-01

    Demonstrated, through simulation, that stationary autoregressive moving average (ARMA) models may be fitted readily when T>N, using normal theory raw maximum likelihood structural equation modeling. Also provides some illustrations based on real data. (SLD)

  3. Evidence Based Medicine; Positive and Negative Likelihood Ratios of Diagnostic Tests

    Directory of Open Access Journals (Sweden)

    Alireza Baratloo

    2015-10-01

    Full Text Available In the previous two parts of educational manuscript series in Emergency, we explained some screening characteristics of diagnostic tests including accuracy, sensitivity, specificity, and positive and negative predictive values. In the 3rd  part we aimed to explain positive and negative likelihood ratio (LR as one of the most reliable performance measures of a diagnostic test. To better understand this characteristic of a test, it is first necessary to fully understand the concept of sensitivity and specificity. So we strongly advise you to review the 1st part of this series again. In short, the likelihood ratios are about the percentage of people with and without a disease but having the same test result. The prevalence of a disease can directly influence screening characteristics of a diagnostic test, especially its sensitivity and specificity. Trying to eliminate this effect, LR was developed. Pre-test probability of a disease multiplied by positive or negative LR can estimate post-test probability. Therefore, LR is the most important characteristic of a test to rule out or rule in a diagnosis. A positive likelihood ratio > 1 means higher probability of the disease to be present in a patient with a positive test. The further from 1, either higher or lower, the stronger the evidence to rule in or rule out the disease, respectively. It is obvious that tests with LR close to one are less practical. On the other hand, LR further from one will have more value for application in medicine. Usually tests with 0.1 < LR > 10 are considered suitable for implication in routine practice.

  4. A New Tree-Type Fracturing Method for Stimulating Coal Seam Gas Reservoirs

    Directory of Open Access Journals (Sweden)

    Qian Li

    2017-09-01

    Full Text Available Hydraulic fracturing is used widely to stimulate coalbed methane production in coal mines. However, some factors associated with conventional hydraulic fracturing, such as the simple morphology of the fractures it generates and inhomogeneous stress relief, limit its scope of application in coal mines. These problems mean that gas extraction efficiency is low. Conventional fracturing may leave hidden pockets of gas, which will be safety hazards for subsequent coal mining operations. Based on a new drilling technique applicable to drilling boreholes in coal seams, this paper proposes a tree-type fracturing technique for stimulating reservoir volumes. Tree-type fracturing simulation experiments using a large-scale triaxial testing apparatus were conducted in the laboratory. In contrast to the single hole drilled for conventional hydraulic fracturing, the tree-type sub-boreholes induce radial and tangential fractures that form complex fracture networks. These fracture networks can eliminate the “blank area” that may host dangerous gas pockets. Gas seepage in tree-type fractures was analyzed, and gas seepage tests after tree-type fracturing showed that permeability was greatly enhanced. The equipment developed for tree-type fracturing was tested in the Fengchun underground coal mine in China. After implementing tree-type fracturing, the gas extraction rate was around 2.3 times greater than that for traditional fracturing, and the extraction rate remained high for a long time during a 30-day test. This shortened the gas drainage time and improved gas extraction efficiency.

  5. Improved anomaly detection using multi-scale PLS and generalized likelihood ratio test

    KAUST Repository

    Madakyaru, Muddu

    2017-02-16

    Process monitoring has a central role in the process industry to enhance productivity, efficiency, and safety, and to avoid expensive maintenance. In this paper, a statistical approach that exploit the advantages of multiscale PLS models (MSPLS) and those of a generalized likelihood ratio (GLR) test to better detect anomalies is proposed. Specifically, to consider the multivariate and multi-scale nature of process dynamics, a MSPLS algorithm combining PLS and wavelet analysis is used as modeling framework. Then, GLR hypothesis testing is applied using the uncorrelated residuals obtained from MSPLS model to improve the anomaly detection abilities of these latent variable based fault detection methods even further. Applications to a simulated distillation column data are used to evaluate the proposed MSPLS-GLR algorithm.

  6. Improved anomaly detection using multi-scale PLS and generalized likelihood ratio test

    KAUST Repository

    Madakyaru, Muddu; Harrou, Fouzi; Sun, Ying

    2017-01-01

    Process monitoring has a central role in the process industry to enhance productivity, efficiency, and safety, and to avoid expensive maintenance. In this paper, a statistical approach that exploit the advantages of multiscale PLS models (MSPLS) and those of a generalized likelihood ratio (GLR) test to better detect anomalies is proposed. Specifically, to consider the multivariate and multi-scale nature of process dynamics, a MSPLS algorithm combining PLS and wavelet analysis is used as modeling framework. Then, GLR hypothesis testing is applied using the uncorrelated residuals obtained from MSPLS model to improve the anomaly detection abilities of these latent variable based fault detection methods even further. Applications to a simulated distillation column data are used to evaluate the proposed MSPLS-GLR algorithm.

  7. MADmap: A Massively Parallel Maximum-Likelihood Cosmic Microwave Background Map-Maker

    Energy Technology Data Exchange (ETDEWEB)

    Cantalupo, Christopher; Borrill, Julian; Jaffe, Andrew; Kisner, Theodore; Stompor, Radoslaw

    2009-06-09

    MADmap is a software application used to produce maximum-likelihood images of the sky from time-ordered data which include correlated noise, such as those gathered by Cosmic Microwave Background (CMB) experiments. It works efficiently on platforms ranging from small workstations to the most massively parallel supercomputers. Map-making is a critical step in the analysis of all CMB data sets, and the maximum-likelihood approach is the most accurate and widely applicable algorithm; however, it is a computationally challenging task. This challenge will only increase with the next generation of ground-based, balloon-borne and satellite CMB polarization experiments. The faintness of the B-mode signal that these experiments seek to measure requires them to gather enormous data sets. MADmap is already being run on up to O(1011) time samples, O(108) pixels and O(104) cores, with ongoing work to scale to the next generation of data sets and supercomputers. We describe MADmap's algorithm based around a preconditioned conjugate gradient solver, fast Fourier transforms and sparse matrix operations. We highlight MADmap's ability to address problems typically encountered in the analysis of realistic CMB data sets and describe its application to simulations of the Planck and EBEX experiments. The massively parallel and distributed implementation is detailed and scaling complexities are given for the resources required. MADmap is capable of analysing the largest data sets now being collected on computing resources currently available, and we argue that, given Moore's Law, MADmap will be capable of reducing the most massive projected data sets.

  8. Image-Based Multi-Target Tracking through Multi-Bernoulli Filtering with Interactive Likelihoods.

    Science.gov (United States)

    Hoak, Anthony; Medeiros, Henry; Povinelli, Richard J

    2017-03-03

    We develop an interactive likelihood (ILH) for sequential Monte Carlo (SMC) methods for image-based multiple target tracking applications. The purpose of the ILH is to improve tracking accuracy by reducing the need for data association. In addition, we integrate a recently developed deep neural network for pedestrian detection along with the ILH with a multi-Bernoulli filter. We evaluate the performance of the multi-Bernoulli filter with the ILH and the pedestrian detector in a number of publicly available datasets (2003 PETS INMOVE, Australian Rules Football League (AFL) and TUD-Stadtmitte) using standard, well-known multi-target tracking metrics (optimal sub-pattern assignment (OSPA) and classification of events, activities and relationships for multi-object trackers (CLEAR MOT)). In all datasets, the ILH term increases the tracking accuracy of the multi-Bernoulli filter.

  9. Statistically and Computationally Efficient Estimating Equations for Large Spatial Datasets

    KAUST Repository

    Sun, Ying; Stein, Michael L.

    2014-01-01

    For Gaussian process models, likelihood based methods are often difficult to use with large irregularly spaced spatial datasets, because exact calculations of the likelihood for n observations require O(n3) operations and O(n2) memory. Various approximation methods have been developed to address the computational difficulties. In this paper, we propose new unbiased estimating equations based on score equation approximations that are both computationally and statistically efficient. We replace the inverse covariance matrix that appears in the score equations by a sparse matrix to approximate the quadratic forms, then set the resulting quadratic forms equal to their expected values to obtain unbiased estimating equations. The sparse matrix is constructed by a sparse inverse Cholesky approach to approximate the inverse covariance matrix. The statistical efficiency of the resulting unbiased estimating equations are evaluated both in theory and by numerical studies. Our methods are applied to nearly 90,000 satellite-based measurements of water vapor levels over a region in the Southeast Pacific Ocean.

  10. Statistically and Computationally Efficient Estimating Equations for Large Spatial Datasets

    KAUST Repository

    Sun, Ying

    2014-11-07

    For Gaussian process models, likelihood based methods are often difficult to use with large irregularly spaced spatial datasets, because exact calculations of the likelihood for n observations require O(n3) operations and O(n2) memory. Various approximation methods have been developed to address the computational difficulties. In this paper, we propose new unbiased estimating equations based on score equation approximations that are both computationally and statistically efficient. We replace the inverse covariance matrix that appears in the score equations by a sparse matrix to approximate the quadratic forms, then set the resulting quadratic forms equal to their expected values to obtain unbiased estimating equations. The sparse matrix is constructed by a sparse inverse Cholesky approach to approximate the inverse covariance matrix. The statistical efficiency of the resulting unbiased estimating equations are evaluated both in theory and by numerical studies. Our methods are applied to nearly 90,000 satellite-based measurements of water vapor levels over a region in the Southeast Pacific Ocean.

  11. Comparison of tree types of models for the prediction of final academic achievement

    Directory of Open Access Journals (Sweden)

    Silvana Gasar

    2002-12-01

    Full Text Available For efficient prevention of inappropriate secondary school choices and by that academic failure, school counselors need a tool for the prediction of individual pupil's final academic achievements. Using data mining techniques on pupils' data base and expert modeling, we developed several models for the prediction of final academic achievement in an individual high school educational program. For data mining, we used statistical analyses, clustering and two machine learning methods: developing classification decision trees and hierarchical decision models. Using an expert system shell DEX, an expert system, based on a hierarchical multi-attribute decision model, was developed manually. All the models were validated and evaluated from the viewpoint of their applicability. The predictive accuracy of DEX models and decision trees was equal and very satisfying, as it reached the predictive accuracy of an experienced counselor. With respect on the efficiency and difficulties in developing models, and relatively rapid changing of our education system, we propose that decision trees are used in further development of predictive models.

  12. Maximum likelihood versus likelihood-free quantum system identification in the atom maser

    International Nuclear Information System (INIS)

    Catana, Catalin; Kypraios, Theodore; Guţă, Mădălin

    2014-01-01

    We consider the problem of estimating a dynamical parameter of a Markovian quantum open system (the atom maser), by performing continuous time measurements in the system's output (outgoing atoms). Two estimation methods are investigated and compared. Firstly, the maximum likelihood estimator (MLE) takes into account the full measurement data and is asymptotically optimal in terms of its mean square error. Secondly, the ‘likelihood-free’ method of approximate Bayesian computation (ABC) produces an approximation of the posterior distribution for a given set of summary statistics, by sampling trajectories at different parameter values and comparing them with the measurement data via chosen statistics. Building on previous results which showed that atom counts are poor statistics for certain values of the Rabi angle, we apply MLE to the full measurement data and estimate its Fisher information. We then select several correlation statistics such as waiting times, distribution of successive identical detections, and use them as input of the ABC algorithm. The resulting posterior distribution follows closely the data likelihood, showing that the selected statistics capture ‘most’ statistical information about the Rabi angle. (paper)

  13. Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo.

    Science.gov (United States)

    Kapli, P; Lutteropp, S; Zhang, J; Kobert, K; Pavlidis, P; Stamatakis, A; Flouri, T

    2017-06-01

    In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds. Yet, two weaknesses of PTP impact its accuracy and practicality when applied to large datasets; it does not account for divergent intraspecific variation and is slow for a large number of sequences. We introduce the multi-rate PTP (mPTP), an improved method that alleviates the theoretical and technical shortcomings of PTP. It incorporates different levels of intraspecific genetic diversity deriving from differences in either the evolutionary history or sampling of each species. Results on empirical data suggest that mPTP is superior to PTP and popular distance-based methods as it, consistently yields more accurate delimitations with respect to the taxonomy (i.e., identifies more taxonomic species, infers species numbers closer to the taxonomy). Moreover, mPTP does not require any similarity threshold as input. The novel dynamic programming algorithm attains a speedup of at least five orders of magnitude compared to PTP, allowing it to delimit species in large (meta-) barcoding data. In addition, Markov Chain Monte Carlo sampling provides a comprehensive evaluation of the inferred delimitation in just a few seconds for millions of steps, independently of tree size. mPTP is implemented in C and is available for download at http://github.com/Pas-Kapli/mptp under the GNU Affero 3 license. A web-service is available at http://mptp.h-its.org . : paschalia.kapli@h-its.org or

  14. Nonparametric decision tree: The impact of ISO 9000 on certified and non certified companies Nonparametric decision tree: The impact of ISO 9000 on certified and non certified companies Nonparametric decision tree: The impact of ISO 9000 on certified and non certified companies

    Directory of Open Access Journals (Sweden)

    Joaquín Texeira Quirós

    2013-09-01

    Full Text Available Purpose: This empirical study analyzes a questionnaire answered by a sample of ISO 9000 certified companies and a control sample of companies which have not been certified, using a multivariate predictive model. With this approach, we assess which quality practices are associated to the likelihood of the firm being certified. Design/methodology/approach: We implemented nonparametric decision trees, in order to see which variables influence more the fact that the company be certified or not, i.e., the motivations that lead companies to make sure. Findings: The results show that only four questionnaire items are sufficient to predict if a firm is certified or not. It is shown that companies in which the respondent manifests greater concern with respect to customers relations; motivations of the employees and strategic planning have higher likelihood of being certified. Research implications: the reader should note that this study is based on data from a single country and, of course, these results capture many idiosyncrasies if its economic and corporate environment. It would be of interest to understand if this type of analysis reveals some regularities across different countries. Practical implications: companies should look for a set of practices congruent with total quality management and ISO 9000 certified. Originality/value: This study contributes to the literature on the internal motivation of companies to achieve certification under the ISO 9000 standard, by performing a comparative analysis of questionnaires answered by a sample of certified companies and a control sample of companies which have not been certified. In particular, we assess how the manager’s perception on the intensity in which quality practices are deployed in their firms is associated to the likelihood of the firm being certified.Purpose: This empirical study analyzes a questionnaire answered by a sample of ISO 9000 certified companies and a control sample of companies

  15. An Assessment of the Effectiveness of Tree-Based Models for Multi-Variate Flood Damage Assessment in Australia

    Directory of Open Access Journals (Sweden)

    Roozbeh Hasanzadeh Nafari

    2016-07-01

    Full Text Available Flood is a frequent natural hazard that has significant financial consequences for Australia. In Australia, physical losses caused by floods are commonly estimated by stage-damage functions. These methods usually consider only the depth of the water and the type of buildings at risk. However, flood damage is a complicated process, and it is dependent on a variety of factors which are rarely taken into account. This study explores the interaction, importance, and influence of water depth, flow velocity, water contamination, precautionary measures, emergency measures, flood experience, floor area, building value, building quality, and socioeconomic status. The study uses tree-based models (regression trees and bagging decision trees and a dataset collected from 2012 to 2013 flood events in Queensland, which includes information on structural damages, impact parameters, and resistance variables. The tree-based approaches show water depth, floor area, precautionary measures, building value, and building quality to be important damage-influencing parameters. Furthermore, the performance of the tree-based models is validated and contrasted with the outcomes of a multi-parameter loss function (FLFArs from Australia. The tree-based models are shown to be more accurate than the stage-damage function. Consequently, considering more parameters and taking advantage of tree-based models is recommended. The outcome is important for improving established Australian flood loss models and assisting decision-makers and insurance companies dealing with flood risk assessment.

  16. Root activity patterns of some tree crops

    International Nuclear Information System (INIS)

    1975-01-01

    A coordinated research programme was followed using a soil injection method which employed 32 P-labelled superphosphate solution. The technique was applied for determining the root activity distribution of various crops. Field experiments were carried out in Uganda on bananas, Spain and Taiwan on citrus, Ghana on cocoa, Columbia and Kenya on coffee, and Ivory Coast and Malaysia on oil palms, to study the patterns of root activity as a function of depth and distance from the tree base, soil type, tree age and season. A few weeks after injection, leaf samples of similar age were taken from well-defined morphological positions on the tree and analyzed for 32 P. The activity of the label in the sample reflects the root activity at the various positions in the soil. Some preliminary experiments were also carried out using 32 P-superphosphate to evaluate the efficiency of different methods of fertilizer placement in relation to phosphate uptake by the plantation as a whole

  17. Generalized Likelihood Uncertainty Estimation (GLUE) Using Multi-Optimization Algorithm as Sampling Method

    Science.gov (United States)

    Wang, Z.

    2015-12-01

    For decades, distributed and lumped hydrological models have furthered our understanding of hydrological system. The development of hydrological simulation in large scale and high precision elaborated the spatial descriptions and hydrological behaviors. Meanwhile, the new trend is also followed by the increment of model complexity and number of parameters, which brings new challenges of uncertainty quantification. Generalized Likelihood Uncertainty Estimation (GLUE) has been widely used in uncertainty analysis for hydrological models referring to Monte Carlo method coupled with Bayesian estimation. However, the stochastic sampling method of prior parameters adopted by GLUE appears inefficient, especially in high dimensional parameter space. The heuristic optimization algorithms utilizing iterative evolution show better convergence speed and optimality-searching performance. In light of the features of heuristic optimization algorithms, this study adopted genetic algorithm, differential evolution, shuffled complex evolving algorithm to search the parameter space and obtain the parameter sets of large likelihoods. Based on the multi-algorithm sampling, hydrological model uncertainty analysis is conducted by the typical GLUE framework. To demonstrate the superiority of the new method, two hydrological models of different complexity are examined. The results shows the adaptive method tends to be efficient in sampling and effective in uncertainty analysis, providing an alternative path for uncertainty quantilization.

  18. Computer aided fault tree synthesis

    International Nuclear Information System (INIS)

    Poucet, A.

    1983-01-01

    Nuclear as well as non-nuclear organisations are showing during the past few years a growing interest in the field of reliability analysis. This urges for the development of powerful, state of the art methods and computer codes for performing such analysis on complex systems. In this report an interactive, computer aided approach is discussed, based on the well known fault tree technique. The time consuming and difficut task of manually constructing a system model (one or more fault trees) is replaced by an efficient interactive procedure in which the flexibility and the learning process inherent to the manual approach are combined with the accuracy in the modelling and the speed of the fully automatical approach. The method presented is based upon the use of a library containing component models. The possibility of setting up a standard library of models of general use and the link with a data collection system are discussed. The method has been implemented in the CAFTS-SALP software package which is described shortly in the report

  19. ERA: Efficient serial and parallel suffix tree construction for very long strings

    KAUST Repository

    Mansour, Essam; Allam, Amin; Skiadopoulos, Spiros G.; Kalnis, Panos

    2011-01-01

    The suffix tree is a data structure for indexing strings. It is used in a variety of applications such as bioinformatics, time series analysis, clustering, text editing and data compression. However, when the string and the resulting suffix tree

  20. An object-based approach for tree species extraction from digital orthophoto maps

    Science.gov (United States)

    Jamil, Akhtar; Bayram, Bulent

    2018-05-01

    Tree segmentation is an active and ongoing research area in the field of photogrammetry and remote sensing. It is more challenging due to both intra-class and inter-class similarities among various tree species. In this study, we exploited various statistical features for extraction of hazelnut trees from 1 : 5000 scaled digital orthophoto maps. Initially, the non-vegetation areas were eliminated using traditional normalized difference vegetation index (NDVI) followed by application of mean shift segmentation for transforming the pixels into meaningful homogeneous objects. In order to eliminate false positives, morphological opening and closing was employed on candidate objects. A number of heuristics were also derived to eliminate unwanted effects such as shadow and bounding box aspect ratios, before passing them into the classification stage. Finally, a knowledge based decision tree was constructed to distinguish the hazelnut trees from rest of objects which include manmade objects and other type of vegetation. We evaluated the proposed methodology on 10 sample orthophoto maps obtained from Giresun province in Turkey. The manually digitized hazelnut tree boundaries were taken as reference data for accuracy assessment. Both manually digitized and segmented tree borders were converted into binary images and the differences were calculated. According to the obtained results, the proposed methodology obtained an overall accuracy of more than 85 % for all sample images.

  1. Predicting volume of distribution with decision tree-based regression methods using predicted tissue:plasma partition coefficients.

    Science.gov (United States)

    Freitas, Alex A; Limbu, Kriti; Ghafourian, Taravat

    2015-01-01

    Volume of distribution is an important pharmacokinetic property that indicates the extent of a drug's distribution in the body tissues. This paper addresses the problem of how to estimate the apparent volume of distribution at steady state (Vss) of chemical compounds in the human body using decision tree-based regression methods from the area of data mining (or machine learning). Hence, the pros and cons of several different types of decision tree-based regression methods have been discussed. The regression methods predict Vss using, as predictive features, both the compounds' molecular descriptors and the compounds' tissue:plasma partition coefficients (Kt:p) - often used in physiologically-based pharmacokinetics. Therefore, this work has assessed whether the data mining-based prediction of Vss can be made more accurate by using as input not only the compounds' molecular descriptors but also (a subset of) their predicted Kt:p values. Comparison of the models that used only molecular descriptors, in particular, the Bagging decision tree (mean fold error of 2.33), with those employing predicted Kt:p values in addition to the molecular descriptors, such as the Bagging decision tree using adipose Kt:p (mean fold error of 2.29), indicated that the use of predicted Kt:p values as descriptors may be beneficial for accurate prediction of Vss using decision trees if prior feature selection is applied. Decision tree based models presented in this work have an accuracy that is reasonable and similar to the accuracy of reported Vss inter-species extrapolations in the literature. The estimation of Vss for new compounds in drug discovery will benefit from methods that are able to integrate large and varied sources of data and flexible non-linear data mining methods such as decision trees, which can produce interpretable models. Graphical AbstractDecision trees for the prediction of tissue partition coefficient and volume of distribution of drugs.

  2. Applied Swarm-based medicine: collecting decision trees for patterns of algorithms analysis.

    Science.gov (United States)

    Panje, Cédric M; Glatzer, Markus; von Rappard, Joscha; Rothermundt, Christian; Hundsberger, Thomas; Zumstein, Valentin; Plasswilm, Ludwig; Putora, Paul Martin

    2017-08-16

    The objective consensus methodology has recently been applied in consensus finding in several studies on medical decision-making among clinical experts or guidelines. The main advantages of this method are an automated analysis and comparison of treatment algorithms of the participating centers which can be performed anonymously. Based on the experience from completed consensus analyses, the main steps for the successful implementation of the objective consensus methodology were identified and discussed among the main investigators. The following steps for the successful collection and conversion of decision trees were identified and defined in detail: problem definition, population selection, draft input collection, tree conversion, criteria adaptation, problem re-evaluation, results distribution and refinement, tree finalisation, and analysis. This manuscript provides information on the main steps for successful collection of decision trees and summarizes important aspects at each point of the analysis.

  3. Efficient crop type mapping based on remote sensing in the Central Valley, California

    Science.gov (United States)

    Zhong, Liheng

    Most agricultural systems in California's Central Valley are purposely flexible and intentionally designed to meet the demands of dynamic markets. Agricultural land use is also impacted by climate change and urban development. As a result, crops change annually and semiannually, which makes estimating agricultural water use difficult, especially given the existing method by which agricultural land use is identified and mapped. A minor portion of agricultural land is surveyed annually for land-use type, and every 5 to 8 years the entire valley is completely evaluated. So far no effort has been made to effectively and efficiently identify specific crop types on an annual basis in this area. The potential of satellite imagery to map agricultural land cover and estimate water usage in the Central Valley is explored. Efforts are made to minimize the cost and reduce the time of production during the mapping process. The land use change analysis shows that a remote sensing based mapping method is the only means to map the frequent change of major crop types. The traditional maximum likelihood classification approach is first utilized to map crop types to test the classification capacity of existing algorithms. High accuracy is achieved with sufficient ground truth data for training, and crop maps of moderate quality can be timely produced to facilitate a near-real-time water use estimate. However, the large set of ground truth data required by this method results in high costs in data collection. It is difficult to reduce the cost because a trained classification algorithm is not transferable between different years or different regions. A phenology based classification (PBC) approach is developed which extracts phenological metrics from annual vegetation index profiles and identifies crop types based on these metrics using decision trees. According to the comparison with traditional maximum likelihood classification, this phenology-based approach shows great advantages

  4. Accuracy of maximum likelihood estimates of a two-state model in single-molecule FRET

    Energy Technology Data Exchange (ETDEWEB)

    Gopich, Irina V. [Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 (United States)

    2015-01-21

    Photon sequences from single-molecule Förster resonance energy transfer (FRET) experiments can be analyzed using a maximum likelihood method. Parameters of the underlying kinetic model (FRET efficiencies of the states and transition rates between conformational states) are obtained by maximizing the appropriate likelihood function. In addition, the errors (uncertainties) of the extracted parameters can be obtained from the curvature of the likelihood function at the maximum. We study the standard deviations of the parameters of a two-state model obtained from photon sequences with recorded colors and arrival times. The standard deviations can be obtained analytically in a special case when the FRET efficiencies of the states are 0 and 1 and in the limiting cases of fast and slow conformational dynamics. These results are compared with the results of numerical simulations. The accuracy and, therefore, the ability to predict model parameters depend on how fast the transition rates are compared to the photon count rate. In the limit of slow transitions, the key parameters that determine the accuracy are the number of transitions between the states and the number of independent photon sequences. In the fast transition limit, the accuracy is determined by the small fraction of photons that are correlated with their neighbors. The relative standard deviation of the relaxation rate has a “chevron” shape as a function of the transition rate in the log-log scale. The location of the minimum of this function dramatically depends on how well the FRET efficiencies of the states are separated.

  5. Determination of point of maximum likelihood in failure domain using genetic algorithms

    International Nuclear Information System (INIS)

    Obadage, A.S.; Harnpornchai, N.

    2006-01-01

    The point of maximum likelihood in a failure domain yields the highest value of the probability density function in the failure domain. The maximum-likelihood point thus represents the worst combination of random variables that contribute in the failure event. In this work Genetic Algorithms (GAs) with an adaptive penalty scheme have been proposed as a tool for the determination of the maximum likelihood point. The utilization of only numerical values in the GAs operation makes the algorithms applicable to cases of non-linear and implicit single and multiple limit state function(s). The algorithmic simplicity readily extends its application to higher dimensional problems. When combined with Monte Carlo Simulation, the proposed methodology will reduce the computational complexity and at the same time will enhance the possibility in rare-event analysis under limited computational resources. Since, there is no approximation done in the procedure, the solution obtained is considered accurate. Consequently, GAs can be used as a tool for increasing the computational efficiency in the element and system reliability analyses

  6. Computer aided process planning system based on workflow technology and integrated bill of material tree

    Institute of Scientific and Technical Information of China (English)

    LU Chun-guang; MENG Li-li

    2006-01-01

    It is extremely important for procedure of process design and management of process data for product life cycle in Computer Aided Process Planning (CAPP) system,but there are many shortcomings with traditional CAPP system in these respects.To solve these questions,application of workflow technology in CAPP system based on web-integrated Bill of Material (BOM) tree is discussed,and a concept of integrated BOM tree was brought forward.Taking integrated BOM as the thread,CAPP systematic technological process is analyzed.The function,system architecture,and implementation mechanism of CAPP system based on Browser/Server and Customer/Server model are expatiated.Based on it,the key technologies of workflow management device were analyzed.Eventually,the implementation mechanism of integrated BOM tree was analyzed from viewpoints of material information encoding,organization node design of integrated BOM tree,transformation from Engineering BOM (EBOM)to Process BOM (PBOM),and the programming implementation technology.

  7. Effects of tree-to-tree variations on sap flux-based transpiration estimates in a forested watershed

    Science.gov (United States)

    Kume, Tomonori; Tsuruta, Kenji; Komatsu, Hikaru; Kumagai, Tomo'omi; Higashi, Naoko; Shinohara, Yoshinori; Otsuki, Kyoichi

    2010-05-01

    To estimate forest stand-scale water use, we assessed how sample sizes affect confidence of stand-scale transpiration (E) estimates calculated from sap flux (Fd) and sapwood area (AS_tree) measurements of individual trees. In a Japanese cypress plantation, we measured Fd and AS_tree in all trees (n = 58) within a 20 × 20 m study plot, which was divided into four 10 × 10 subplots. We calculated E from stand AS_tree (AS_stand) and mean stand Fd (JS) values. Using Monte Carlo analyses, we examined potential errors associated with sample sizes in E, AS_stand, and JS by using the original AS_tree and Fd data sets. Consequently, we defined optimal sample sizes of 10 and 15 for AS_stand and JS estimates, respectively, in the 20 × 20 m plot. Sample sizes greater than the optimal sample sizes did not decrease potential errors. The optimal sample sizes for JS changed according to plot size (e.g., 10 × 10 m and 10 × 20 m), while the optimal sample sizes for AS_stand did not. As well, the optimal sample sizes for JS did not change in different vapor pressure deficit conditions. In terms of E estimates, these results suggest that the tree-to-tree variations in Fd vary among different plots, and that plot size to capture tree-to-tree variations in Fd is an important factor. This study also discusses planning balanced sampling designs to extrapolate stand-scale estimates to catchment-scale estimates.

  8. Efficient Spatial Data Structure for Multiversion Management of Engineering Drawings

    Directory of Open Access Journals (Sweden)

    Yasuaki Nakamura

    2004-08-01

    Full Text Available In the engineering database system, multiple versions of a design including engineering drawings should be managed efficiently. The paper proposes an extended spatial data structure for efficient management of multiversion engineering drawings. The R-tree is adapted as a basic data structure. The efficient mechanism to manage the difference between drawings is introduced to the R-tree to eliminate redundant duplications and to reduce the amount of storage required for the data structure. The extended data structures of the R-tree, MVR and MVR* trees, are developed and the performances of these trees are evaluated. A series of simulation tests shows that, compared with the basic R-tree, the amounts of storage required for the MVR and MVR* trees are reduced to 50% and 30%, respectively. The search efficiencies of the R, MVR, and MVR* trees are almost the same.

  9. A Voronoi interior adjacency-based approach for generating a contour tree

    Science.gov (United States)

    Chen, Jun; Qiao, Chaofei; Zhao, Renliang

    2004-05-01

    A contour tree is a good graphical tool for representing the spatial relations of contour lines and has found many applications in map generalization, map annotation, terrain analysis, etc. A new approach for generating contour trees by introducing a Voronoi-based interior adjacency set concept is proposed in this paper. The immediate interior adjacency set is employed to identify all of the children contours of each contour without contour elevations. It has advantages over existing methods such as the point-in-polygon method and the region growing-based method. This new approach can be used for spatial data mining and knowledge discovering, such as the automatic extraction of terrain features and construction of multi-resolution digital elevation model.

  10. Effects of liana load, tree diameter and distances between conspecifics on seed production in tropical timber trees

    DEFF Research Database (Denmark)

    Nabe-Nielsen, Jacob; Kollmann, Johannes Christian; Peña-Claros, Marielos

    2009-01-01

    Seed production in tropical timber trees is limited by abiotic resources, pollination and pre-dispersal seed predation. Resource availability is influenced by the number of competing trees and by lianas that often reach high densities in disturbed parts of tropical forests. The distance between...... conspecific trees affects pollination efficiency and seed predation intensity, and may therefore indirectly affect the long-term sustainability of selective logging. Here we investigate how reproductive status and the number of seeds dispersed per tree are affected by liana load, distance to the nearest...... and positively with tree diameter. In C. ianeirensis the most liana-infested trees dispersed fewer seeds. In T. oblonga the intensity of pre-dispersal seed predation decreased with distance to the nearest conspecifics. There was no evidence that seed viability or seed production decreased with distance...

  11. Detecting tree-like multicellular life on extrasolar planets.

    Science.gov (United States)

    Doughty, Christopher E; Wolf, Adam

    2010-11-01

    Over the next two decades, NASA and ESA are planning a series of space-based observatories to find Earth-like planets and determine whether life exists on these planets. Previous studies have assessed the likelihood of detecting life through signs of biogenic gases in the atmosphere or a red edge. Biogenic gases and the red edge could be signs of either single-celled or multicellular life. In this study, we propose a technique with which to determine whether tree-like multicellular life exists on extrasolar planets. For multicellular photosynthetic organisms on Earth, competition for light and the need to transport water and nutrients has led to a tree-like body plan characterized by hierarchical branching networks. This design results in a distinct bidirectional reflectance distribution function (BRDF) that causes differing reflectance at different sun/view geometries. BRDF arises from the changing visibility of the shadows cast by objects, and the presence of tree-like structures is clearly distinguishable from flat ground with the same reflectance spectrum. We examined whether the BRDF could detect the existence of tree-like structures on an extrasolar planet by using changes in planetary albedo as a planet orbits its star. We used a semi-empirical BRDF model to simulate vegetation reflectance at different planetary phase angles and both simulated and real cloud cover to calculate disk and rotation-averaged planetary albedo for a vegetated and non-vegetated planet with abundant liquid water. We found that even if the entire planetary albedo were rendered to a single pixel, the rate of increase of albedo as a planet approaches full illumination would be comparatively greater on a vegetated planet than on a non-vegetated planet. Depending on how accurately planetary cloud cover can be resolved and the capabilities of the coronagraph to resolve exoplanets, this technique could theoretically detect tree-like multicellular life on exoplanets in 50 stellar systems.

  12. A voting-based statistical cylinder detection framework applied to fallen tree mapping in terrestrial laser scanning point clouds

    Science.gov (United States)

    Polewski, Przemyslaw; Yao, Wei; Heurich, Marco; Krzystek, Peter; Stilla, Uwe

    2017-07-01

    This paper introduces a statistical framework for detecting cylindrical shapes in dense point clouds. We target the application of mapping fallen trees in datasets obtained through terrestrial laser scanning. This is a challenging task due to the presence of ground vegetation, standing trees, DTM artifacts, as well as the fragmentation of dead trees into non-collinear segments. Our method shares the concept of voting in parameter space with the generalized Hough transform, however two of its significant drawbacks are improved upon. First, the need to generate samples on the shape's surface is eliminated. Instead, pairs of nearby input points lying on the surface cast a vote for the cylinder's parameters based on the intrinsic geometric properties of cylindrical shapes. Second, no discretization of the parameter space is required: the voting is carried out in continuous space by means of constructing a kernel density estimator and obtaining its local maxima, using automatic, data-driven kernel bandwidth selection. Furthermore, we show how the detected cylindrical primitives can be efficiently merged to obtain object-level (entire tree) semantic information using graph-cut segmentation and a tailored dynamic algorithm for eliminating cylinder redundancy. Experiments were performed on 3 plots from the Bavarian Forest National Park, with ground truth obtained through visual inspection of the point clouds. It was found that relative to sample consensus (SAC) cylinder fitting, the proposed voting framework can improve the detection completeness by up to 10 percentage points while maintaining the correctness rate.

  13. Profile-likelihood Confidence Intervals in Item Response Theory Models.

    Science.gov (United States)

    Chalmers, R Philip; Pek, Jolynn; Liu, Yang

    2017-01-01

    Confidence intervals (CIs) are fundamental inferential devices which quantify the sampling variability of parameter estimates. In item response theory, CIs have been primarily obtained from large-sample Wald-type approaches based on standard error estimates, derived from the observed or expected information matrix, after parameters have been estimated via maximum likelihood. An alternative approach to constructing CIs is to quantify sampling variability directly from the likelihood function with a technique known as profile-likelihood confidence intervals (PL CIs). In this article, we introduce PL CIs for item response theory models, compare PL CIs to classical large-sample Wald-type CIs, and demonstrate important distinctions among these CIs. CIs are then constructed for parameters directly estimated in the specified model and for transformed parameters which are often obtained post-estimation. Monte Carlo simulation results suggest that PL CIs perform consistently better than Wald-type CIs for both non-transformed and transformed parameters.

  14. COSMIC MICROWAVE BACKGROUND LIKELIHOOD APPROXIMATION BY A GAUSSIANIZED BLACKWELL-RAO ESTIMATOR

    International Nuclear Information System (INIS)

    Rudjord, Oe.; Groeneboom, N. E.; Eriksen, H. K.; Huey, Greg; Gorski, K. M.; Jewell, J. B.

    2009-01-01

    We introduce a new cosmic microwave background (CMB) temperature likelihood approximation called the Gaussianized Blackwell-Rao estimator. This estimator is derived by transforming the observed marginal power spectrum distributions obtained by the CMB Gibbs sampler into standard univariate Gaussians, and then approximating their joint transformed distribution by a multivariate Gaussian. The method is exact for full-sky coverage and uniform noise and an excellent approximation for sky cuts and scanning patterns relevant for modern satellite experiments such as the Wilkinson Microwave Anisotropy Probe (WMAP) and Planck. The result is a stable, accurate, and computationally very efficient CMB temperature likelihood representation that allows the user to exploit the unique error propagation capabilities of the Gibbs sampler to high ls. A single evaluation of this estimator between l = 2 and 200 takes ∼0.2 CPU milliseconds, while for comparison, a singe pixel space likelihood evaluation between l = 2 and 30 for a map with ∼2500 pixels requires ∼20 s. We apply this tool to the five-year WMAP temperature data, and re-estimate the angular temperature power spectrum, C l , and likelihood, L(C l ), for l ≤ 200, and derive new cosmological parameters for the standard six-parameter ΛCDM model. Our spectrum is in excellent agreement with the official WMAP spectrum, but we find slight differences in the derived cosmological parameters. Most importantly, the spectral index of scalar perturbations is n s = 0.973 ± 0.014, 1.9σ away from unity and 0.6σ higher than the official WMAP result, n s = 0.965 ± 0.014. This suggests that an exact likelihood treatment is required to higher ls than previously believed, reinforcing and extending our conclusions from the three-year WMAP analysis. In that case, we found that the suboptimal likelihood approximation adopted between l = 12 and 30 by the WMAP team biased n s low by 0.4σ, while here we find that the same approximation

  15. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

    Science.gov (United States)

    De Oliveira Martins, Leonardo; Mallo, Diego; Posada, David

    2016-01-01

    Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models. PMID:25281847

  16. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction.

    Science.gov (United States)

    De Oliveira Martins, Leonardo; Mallo, Diego; Posada, David

    2016-05-01

    Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

  17. Construction of a phylogenetic tree of photosynthetic prokaryotes based on average similarities of whole genome sequences.

    Directory of Open Access Journals (Sweden)

    Soichirou Satoh

    Full Text Available Phylogenetic trees have been constructed for a wide range of organisms using gene sequence information, especially through the identification of orthologous genes that have been vertically inherited. The number of available complete genome sequences is rapidly increasing, and many tools for construction of genome trees based on whole genome sequences have been proposed. However, development of a reasonable method of using complete genome sequences for construction of phylogenetic trees has not been established. We have developed a method for construction of phylogenetic trees based on the average sequence similarities of whole genome sequences. We used this method to examine the phylogeny of 115 photosynthetic prokaryotes, i.e., cyanobacteria, Chlorobi, proteobacteria, Chloroflexi, Firmicutes and nonphotosynthetic organisms including Archaea. Although the bootstrap values for the branching order of phyla were low, probably due to lateral gene transfer and saturated mutation, the obtained tree was largely consistent with the previously reported phylogenetic trees, indicating that this method is a robust alternative to traditional phylogenetic methods.

  18. Rare itemsets mining algorithm based on RP-Tree and spark framework

    Science.gov (United States)

    Liu, Sainan; Pan, Haoan

    2018-05-01

    For the issues of the rare itemsets mining in big data, this paper proposed a rare itemsets mining algorithm based on RP-Tree and Spark framework. Firstly, it arranged the data vertically according to the transaction identifier, in order to solve the defects of scan the entire data set, the vertical datasets are divided into frequent vertical datasets and rare vertical datasets. Then, it adopted the RP-Tree algorithm to construct the frequent pattern tree that contains rare items and generate rare 1-itemsets. After that, it calculated the support of the itemsets by scanning the two vertical data sets, finally, it used the iterative process to generate rare itemsets. The experimental show that the algorithm can effectively excavate rare itemsets and have great superiority in execution time.

  19. Deformation of log-likelihood loss function for multiclass boosting.

    Science.gov (United States)

    Kanamori, Takafumi

    2010-09-01

    The purpose of this paper is to study loss functions in multiclass classification. In classification problems, the decision function is estimated by minimizing an empirical loss function, and then, the output label is predicted by using the estimated decision function. We propose a class of loss functions which is obtained by a deformation of the log-likelihood loss function. There are four main reasons why we focus on the deformed log-likelihood loss function: (1) this is a class of loss functions which has not been deeply investigated so far, (2) in terms of computation, a boosting algorithm with a pseudo-loss is available to minimize the proposed loss function, (3) the proposed loss functions provide a clear correspondence between the decision functions and conditional probabilities of output labels, (4) the proposed loss functions satisfy the statistical consistency of the classification error rate which is a desirable property in classification problems. Based on (3), we show that the deformed log-likelihood loss provides a model of mislabeling which is useful as a statistical model of medical diagnostics. We also propose a robust loss function against outliers in multiclass classification based on our approach. The robust loss function is a natural extension of the existing robust loss function for binary classification. A model of mislabeling and a robust loss function are useful to cope with noisy data. Some numerical studies are presented to show the robustness of the proposed loss function. A mathematical characterization of the deformed log-likelihood loss function is also presented. Copyright 2010 Elsevier Ltd. All rights reserved.

  20. Deterministic Automata for Unordered Trees

    Directory of Open Access Journals (Sweden)

    Adrien Boiret

    2014-08-01

    Full Text Available Automata for unordered unranked trees are relevant for defining schemas and queries for data trees in Json or Xml format. While the existing notions are well-investigated concerning expressiveness, they all lack a proper notion of determinism, which makes it difficult to distinguish subclasses of automata for which problems such as inclusion, equivalence, and minimization can be solved efficiently. In this paper, we propose and investigate different notions of "horizontal determinism", starting from automata for unranked trees in which the horizontal evaluation is performed by finite state automata. We show that a restriction to confluent horizontal evaluation leads to polynomial-time emptiness and universality, but still suffers from coNP-completeness of the emptiness of binary intersections. Finally, efficient algorithms can be obtained by imposing an order of horizontal evaluation globally for all automata in the class. Depending on the choice of the order, we obtain different classes of automata, each of which has the same expressiveness as CMso.

  1. Likelihood ratio-based integrated personal risk assessment of type 2 diabetes.

    Science.gov (United States)

    Sato, Noriko; Htun, Nay Chi; Daimon, Makoto; Tamiya, Gen; Kato, Takeo; Kubota, Isao; Ueno, Yoshiyuki; Yamashita, Hidetoshi; Fukao, Akira; Kayama, Takamasa; Muramatsu, Masaaki

    2014-01-01

    To facilitate personalized health care for multifactorial diseases, risks of genetic and clinical/environmental factors should be assessed together for each individual in an integrated fashion. This approach is possible with the likelihood ratio (LR)-based risk assessment system, as this system can incorporate manifold tests. We examined the usefulness of this system for assessing type 2 diabetes (T2D). Our system employed 29 genetic susceptibility variants, body mass index (BMI), and hypertension as risk factors whose LRs can be estimated from openly available T2D association data for the Japanese population. The pretest probability was set at a sex- and age-appropriate population average of diabetes prevalence. The classification performance of our LR-based risk assessment was compared to that of a non-invasive screening test for diabetes called TOPICS (with score based on age, sex, family history, smoking, BMI, and hypertension) using receiver operating characteristic analysis with a community cohort (n = 1263). The area under the receiver operating characteristic curve (AUC) for the LR-based assessment and TOPICS was 0.707 (95% CI 0.665-0.750) and 0.719 (0.675-0.762), respectively. These AUCs were much higher than that of a genetic risk score constructed using the same genetic susceptibility variants, 0.624 (0.574-0.674). The use of ethnically matched LRs is necessary for proper personal risk assessment. In conclusion, although LR-based integrated risk assessment for T2D still requires additional tests that evaluate other factors, such as risks involved in missing heritability, our results indicate the potential usability of LR-based assessment system and stress the importance of stratified epidemiological investigations in personalized medicine.

  2. Examining the influences of tree-to-tree competition and climate on size-growth relationships in hydric, multi-aged Fraxinus nigra stands

    Science.gov (United States)

    Christopher E. Looney; Anthony W. D' Amato; Shawn Fraver; Brian J. Palik; Michael R. Reinikainen

    2016-01-01

    Most research on tree-tree competition and size-growth relationship (SGR – a stand-level metric that infers the relative efficiency with which different sized trees utilize available resources) has focused on upland systems. It is unclear if inferences from these studies extend to wetland forests. Moreover, no study to date has thoroughly investigated the relationship...

  3. Gaussian copula as a likelihood function for environmental models

    Science.gov (United States)

    Wani, O.; Espadas, G.; Cecinati, F.; Rieckermann, J.

    2017-12-01

    Parameter estimation of environmental models always comes with uncertainty. To formally quantify this parametric uncertainty, a likelihood function needs to be formulated, which is defined as the probability of observations given fixed values of the parameter set. A likelihood function allows us to infer parameter values from observations using Bayes' theorem. The challenge is to formulate a likelihood function that reliably describes the error generating processes which lead to the observed monitoring data, such as rainfall and runoff. If the likelihood function is not representative of the error statistics, the parameter inference will give biased parameter values. Several uncertainty estimation methods that are currently being used employ Gaussian processes as a likelihood function, because of their favourable analytical properties. Box-Cox transformation is suggested to deal with non-symmetric and heteroscedastic errors e.g. for flow data which are typically more uncertain in high flows than in periods with low flows. Problem with transformations is that the results are conditional on hyper-parameters, for which it is difficult to formulate the analyst's belief a priori. In an attempt to address this problem, in this research work we suggest learning the nature of the error distribution from the errors made by the model in the "past" forecasts. We use a Gaussian copula to generate semiparametric error distributions . 1) We show that this copula can be then used as a likelihood function to infer parameters, breaking away from the practice of using multivariate normal distributions. Based on the results from a didactical example of predicting rainfall runoff, 2) we demonstrate that the copula captures the predictive uncertainty of the model. 3) Finally, we find that the properties of autocorrelation and heteroscedasticity of errors are captured well by the copula, eliminating the need to use transforms. In summary, our findings suggest that copulas are an

  4. Linking and Cutting Spanning Trees

    Directory of Open Access Journals (Sweden)

    Luís M. S. Russo

    2018-04-01

    Full Text Available We consider the problem of uniformly generating a spanning tree for an undirected connected graph. This process is useful for computing statistics, namely for phylogenetic trees. We describe a Markov chain for producing these trees. For cycle graphs, we prove that this approach significantly outperforms existing algorithms. For general graphs, experimental results show that the chain converges quickly. This yields an efficient algorithm due to the use of proper fast data structures. To obtain the mixing time of the chain we describe a coupling, which we analyze for cycle graphs and simulate for other graphs.

  5. Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks.

    Science.gov (United States)

    Oh, S June; Joung, Je-Gun; Chang, Jeong-Ho; Zhang, Byoung-Tak

    2006-06-06

    To infer the tree of life requires knowledge of the common characteristics of each species descended from a common ancestor as the measuring criteria and a method to calculate the distance between the resulting values of each measure. Conventional phylogenetic analysis based on genomic sequences provides information about the genetic relationships between different organisms. In contrast, comparative analysis of metabolic pathways in different organisms can yield insights into their functional relationships under different physiological conditions. However, evaluating the similarities or differences between metabolic networks is a computationally challenging problem, and systematic methods of doing this are desirable. Here we introduce a graph-kernel method for computing the similarity between metabolic networks in polynomial time, and use it to profile metabolic pathways and to construct phylogenetic trees. To compare the structures of metabolic networks in organisms, we adopted the exponential graph kernel, which is a kernel-based approach with a labeled graph that includes a label matrix and an adjacency matrix. To construct the phylogenetic trees, we used an unweighted pair-group method with arithmetic mean, i.e., a hierarchical clustering algorithm. We applied the kernel-based network profiling method in a comparative analysis of nine carbohydrate metabolic networks from 81 biological species encompassing Archaea, Eukaryota, and Eubacteria. The resulting phylogenetic hierarchies generally support the tripartite scheme of three domains rather than the two domains of prokaryotes and eukaryotes. By combining the kernel machines with metabolic information, the method infers the context of biosphere development that covers physiological events required for adaptation by genetic reconstruction. The results show that one may obtain a global view of the tree of life by comparing the metabolic pathway structures using meta-level information rather than sequence

  6. Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks

    Directory of Open Access Journals (Sweden)

    Chang Jeong-Ho

    2006-06-01

    Full Text Available Abstract Background To infer the tree of life requires knowledge of the common characteristics of each species descended from a common ancestor as the measuring criteria and a method to calculate the distance between the resulting values of each measure. Conventional phylogenetic analysis based on genomic sequences provides information about the genetic relationships between different organisms. In contrast, comparative analysis of metabolic pathways in different organisms can yield insights into their functional relationships under different physiological conditions. However, evaluating the similarities or differences between metabolic networks is a computationally challenging problem, and systematic methods of doing this are desirable. Here we introduce a graph-kernel method for computing the similarity between metabolic networks in polynomial time, and use it to profile metabolic pathways and to construct phylogenetic trees. Results To compare the structures of metabolic networks in organisms, we adopted the exponential graph kernel, which is a kernel-based approach with a labeled graph that includes a label matrix and an adjacency matrix. To construct the phylogenetic trees, we used an unweighted pair-group method with arithmetic mean, i.e., a hierarchical clustering algorithm. We applied the kernel-based network profiling method in a comparative analysis of nine carbohydrate metabolic networks from 81 biological species encompassing Archaea, Eukaryota, and Eubacteria. The resulting phylogenetic hierarchies generally support the tripartite scheme of three domains rather than the two domains of prokaryotes and eukaryotes. Conclusion By combining the kernel machines with metabolic information, the method infers the context of biosphere development that covers physiological events required for adaptation by genetic reconstruction. The results show that one may obtain a global view of the tree of life by comparing the metabolic pathway

  7. Image-Based Multi-Target Tracking through Multi-Bernoulli Filtering with Interactive Likelihoods

    Directory of Open Access Journals (Sweden)

    Anthony Hoak

    2017-03-01

    Full Text Available We develop an interactive likelihood (ILH for sequential Monte Carlo (SMC methods for image-based multiple target tracking applications. The purpose of the ILH is to improve tracking accuracy by reducing the need for data association. In addition, we integrate a recently developed deep neural network for pedestrian detection along with the ILH with a multi-Bernoulli filter. We evaluate the performance of the multi-Bernoulli filter with the ILH and the pedestrian detector in a number of publicly available datasets (2003 PETS INMOVE, Australian Rules Football League (AFL and TUD-Stadtmitte using standard, well-known multi-target tracking metrics (optimal sub-pattern assignment (OSPA and classification of events, activities and relationships for multi-object trackers (CLEAR MOT. In all datasets, the ILH term increases the tracking accuracy of the multi-Bernoulli filter.

  8. SWPhylo - A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees.

    Science.gov (United States)

    Yu, Xiaoyu; Reva, Oleg N

    2018-01-01

    Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities. For example, the super-matrix and super-tree approaches of phylogenomics use multiple integrated genomic loci or individual gene-based trees to infer an overall consensus tree. However, these approaches potentially multiply errors of gene annotation and sequence alignment not mentioning the computational complexity and laboriousness of the methods. In this article, we demonstrate that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees. These were congruent to the corresponding whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16S ribosomal RNA and GyrA protein sequence comparison, complete genome-based MAUVE, and CVTree methods. A Web-based program to perform the alignment-free OUP-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. Applicability of the tool was tested on different taxa from subspecies to intergeneric levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, eg, GyrA.

  9. A stable RNA virus-based vector for citrus trees

    International Nuclear Information System (INIS)

    Folimonov, Alexey S.; Folimonova, Svetlana Y.; Bar-Joseph, Moshe; Dawson, William O.

    2007-01-01

    Virus-based vectors are important tools in plant molecular biology and plant genomics. A number of vectors based on viruses that infect herbaceous plants are in use for expression or silencing of genes in plants as well as screening unknown sequences for function. Yet there is a need for useful virus-based vectors for woody plants, which demand much greater stability because of the longer time required for systemic infection and analysis. We examined several strategies to develop a Citrus tristeza virus (CTV)-based vector for transient expression of foreign genes in citrus trees using a green fluorescent protein (GFP) as a reporter. These strategies included substitution of the p13 open reading frame (ORF) by the ORF of GFP, construction of a self-processing fusion of GFP in-frame with the major coat protein (CP), or expression of the GFP ORF as an extra gene from a subgenomic (sg) mRNA controlled either by a duplicated CTV CP sgRNA controller element (CE) or an introduced heterologous CE of Beet yellows virus. Engineered vector constructs were examined for replication, encapsidation, GFP expression during multiple passages in protoplasts, and for their ability to infect, move, express GFP, and be maintained in citrus plants. The most successful vectors based on the 'add-a-gene' strategy have been unusually stable, continuing to produce GFP fluorescence after more than 4 years in citrus trees

  10. A MongoDB-Based Management of Planar Spatial Data with a Flattened R-Tree

    Directory of Open Access Journals (Sweden)

    Longgang Xiang

    2016-07-01

    Full Text Available This paper addresses how to manage planar spatial data using MongoDB, a popular NoSQL database characterized as a document-oriented, rich query language and high availability. The core idea is to flatten a hierarchical R-tree structure into a tabular MongoDB collection, during which R-tree nodes are represented as collection documents and R-tree pointers are expressed as document identifiers. By following this strategy, a storage schema to support R-tree-based create, read, update, and delete (CRUD operations is designed and a module to manage planar spatial data by consuming and maintaining flattened R-tree structure is developed. The R-tree module is then seamlessly integrated into MongoDB, so that users could manipulate planar spatial data with existing command interfaces oriented to geodetic spatial data. The experimental evaluation, using real-world datasets with diverse coverage, types, and sizes, shows that planar spatial data can be effectively managed by MongoDB with our flattened R-tree and, therefore, the application extent of MongoDB will be greatly enlarged. Our work resulted in a MongoDB branch with R-tree support, which has been released on GitHub for open access.

  11. A classification model of Hyperion image base on SAM combined decision tree

    Science.gov (United States)

    Wang, Zhenghai; Hu, Guangdao; Zhou, YongZhang; Liu, Xin

    2009-10-01

    Monitoring the Earth using imaging spectrometers has necessitated more accurate analyses and new applications to remote sensing. A very high dimensional input space requires an exponentially large amount of data to adequately and reliably represent the classes in that space. On the other hand, with increase in the input dimensionality the hypothesis space grows exponentially, which makes the classification performance highly unreliable. Traditional classification algorithms Classification of hyperspectral images is challenging. New algorithms have to be developed for hyperspectral data classification. The Spectral Angle Mapper (SAM) is a physically-based spectral classification that uses an ndimensional angle to match pixels to reference spectra. The algorithm determines the spectral similarity between two spectra by calculating the angle between the spectra, treating them as vectors in a space with dimensionality equal to the number of bands. The key and difficulty is that we should artificial defining the threshold of SAM. The classification precision depends on the rationality of the threshold of SAM. In order to resolve this problem, this paper proposes a new automatic classification model of remote sensing image using SAM combined with decision tree. It can automatic choose the appropriate threshold of SAM and improve the classify precision of SAM base on the analyze of field spectrum. The test area located in Heqing Yunnan was imaged by EO_1 Hyperion imaging spectrometer using 224 bands in visual and near infrared. The area included limestone areas, rock fields, soil and forests. The area was classified into four different vegetation and soil types. The results show that this method choose the appropriate threshold of SAM and eliminates the disturbance and influence of unwanted objects effectively, so as to improve the classification precision. Compared with the likelihood classification by field survey data, the classification precision of this model

  12. Monte-Carlo Tree Search for Simulated Car Racing

    DEFF Research Database (Denmark)

    Fischer, Jacob; Falsted, Nikolaj; Vielwerth, Mathias

    2015-01-01

    Monte Carlo Tree Search (MCTS) has recently seen considerable success in playing certain types of games, most of which are discrete, fully observable zero-sum games. Consequently there is currently considerable interest within the research community in investigating what other games this algorithm...... might play well, and how it can be modified to achieve this. In this paper, we investigate the application of MCTS to simulated car racing, in particular the open-source racing game TORCS. The presented approach is based on the development of an efficient forward model and the discretization...... of the action space. This combination allows the controller to effectively search the tree of potential future states. Results show that it is indeed possible to implement a competent MCTS-based racing controller. The controller generalizes to most road tracks as long as a warm-up period is provided....

  13. Attitude determination and calibration using a recursive maximum likelihood-based adaptive Kalman filter

    Science.gov (United States)

    Kelly, D. A.; Fermelia, A.; Lee, G. K. F.

    1990-01-01

    An adaptive Kalman filter design that utilizes recursive maximum likelihood parameter identification is discussed. At the center of this design is the Kalman filter itself, which has the responsibility for attitude determination. At the same time, the identification algorithm is continually identifying the system parameters. The approach is applicable to nonlinear, as well as linear systems. This adaptive Kalman filter design has much potential for real time implementation, especially considering the fast clock speeds, cache memory and internal RAM available today. The recursive maximum likelihood algorithm is discussed in detail, with special attention directed towards its unique matrix formulation. The procedure for using the algorithm is described along with comments on how this algorithm interacts with the Kalman filter.

  14. Data Clustering and Evolving Fuzzy Decision Tree for Data Base Classification Problems

    Science.gov (United States)

    Chang, Pei-Chann; Fan, Chin-Yuan; Wang, Yen-Wen

    Data base classification suffers from two well known difficulties, i.e., the high dimensionality and non-stationary variations within the large historic data. This paper presents a hybrid classification model by integrating a case based reasoning technique, a Fuzzy Decision Tree (FDT), and Genetic Algorithms (GA) to construct a decision-making system for data classification in various data base applications. The model is major based on the idea that the historic data base can be transformed into a smaller case-base together with a group of fuzzy decision rules. As a result, the model can be more accurately respond to the current data under classifying from the inductions by these smaller cases based fuzzy decision trees. Hit rate is applied as a performance measure and the effectiveness of our proposed model is demonstrated by experimentally compared with other approaches on different data base classification applications. The average hit rate of our proposed model is the highest among others.

  15. Ozone uptake by adult urban trees based on sap flow measurement

    International Nuclear Information System (INIS)

    Wang Hua; Zhou Weiqi; Wang Xiaoke; Gao Fuyuan; Zheng Hua; Tong Lei; Ouyang Zhiyun

    2012-01-01

    The O 3 uptake in 17 adult trees of six urban species was evaluated by the sap flow-based approach under free atmospheric conditions. The results showed very large species differences in ground area scaled whole-tree ozone uptake (F O 3 ), with estimates ranging from 0.61 ± 0.07 nmol m −2 s −1 in Robinia pseudoacacia to 4.80 ± 1.04 nmol m −2 s −1 in Magnolia liliiflora. However, average F O 3 by deciduous foliages was not significantly higher than that by evergreen ones (3.13 vs 2.21 nmol m −2 s −1 , p = 0.160). Species of high canopy conductance for O 3 (G O 3 ) took up more O 3 than those of low G O 3 , but that their sensitivity to vapour pressure deficit (D) were also higher, and their F O 3 decreased faster with increasing D, regardless of species. The responses of F O 3 to D and total radiation led to the relative high flux of O 3 uptake, indicating high ozone risk for urban tree species. - Highlights: ► O 3 uptake by urban trees varied considering contrasting species and study period. ►The responses of G O 3 to microclimate lead to relative high O 3 uptake by urban trees. ►Many urban species are susceptible to O 3 damage. ►The annual O 3 uptake in our study is greatly less than that from modeling approaches. ►The difference suggests considering the species-specific flux in O 3 risk assessment. - Sap flow-based O 3 uptake among urban species suggests high capacity and variation of ozone uptake, as well as potentially detrimental effects to urban species.

  16. Users' manual for the FTDRAW (Fault Tree Draw) code

    International Nuclear Information System (INIS)

    Oikawa, Tetsukuni; Hikawa, Michihiro; Tanabe, Syuichi; Nakamura, Norihiro

    1985-02-01

    This report provides the information needed to use the FTDRAW (Fault Tree Draw) code, which is designed for drawing a fault tree. The FTDRAW code has several optional functions, such as the overview of a fault tree output, fault tree output in English description, fault tree output in Japanese description and summary tree output. Inputs for the FTDRAW code are component failure rate information and gate information which are filed out by a execution of the FTA-J (Fault Tree Analysis-JAERI) code system and option control data. Using the FTDRAW code, we can get drawings of fault trees which is easy to see, efficiently. (author)

  17. Forest FIRE and FIRE wood : tools for tree automata and tree algorithms

    NARCIS (Netherlands)

    Cleophas, L.G.W.A.; Piskorski, J.; Watson, B.W.; Yli-Jyrä, A.

    2009-01-01

    Pattern matching, acceptance, and parsing algorithms on node-labeled, ordered, ranked trees ('tree algorithms') are important for applications such as instruction selection and tree transformation/term rewriting. Many such algorithms have been developed. They often are based on results from such

  18. Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta

    Directory of Open Access Journals (Sweden)

    Rahmann Sven

    2004-06-01

    Full Text Available Abstract Background In phylogenetic analysis we face the problem that several subclade topologies are known or easily inferred and well supported by bootstrap analysis, but basal branching patterns cannot be unambiguously estimated by the usual methods (maximum parsimony (MP, neighbor-joining (NJ, or maximum likelihood (ML, nor are they well supported. We represent each subclade by a sequence profile and estimate evolutionary distances between profiles to obtain a matrix of distances between subclades. Results Our estimator of profile distances generalizes the maximum likelihood estimator of sequence distances. The basal branching pattern can be estimated by any distance-based method, such as neighbor-joining. Our method (profile neighbor-joining, PNJ then inherits the accuracy and robustness of profiles and the time efficiency of neighbor-joining. Conclusions Phylogenetic analysis of Chlorophyceae with traditional methods (MP, NJ, ML and MrBayes reveals seven well supported subclades, but the methods disagree on the basal branching pattern. The tree reconstructed by our method is better supported and can be confirmed by known morphological characters. Moreover the accuracy is significantly improved as shown by parametric bootstrap.

  19. The decision tree approach to classification

    Science.gov (United States)

    Wu, C.; Landgrebe, D. A.; Swain, P. H.

    1975-01-01

    A class of multistage decision tree classifiers is proposed and studied relative to the classification of multispectral remotely sensed data. The decision tree classifiers are shown to have the potential for improving both the classification accuracy and the computation efficiency. Dimensionality in pattern recognition is discussed and two theorems on the lower bound of logic computation for multiclass classification are derived. The automatic or optimization approach is emphasized. Experimental results on real data are reported, which clearly demonstrate the usefulness of decision tree classifiers.

  20. Observation Likelihood Model Design and Failure Recovery Scheme toward Reliable Localization of Mobile Robots

    Directory of Open Access Journals (Sweden)

    Chang-bae Moon

    2011-01-01

    Full Text Available Although there have been many researches on mobile robot localization, it is still difficult to obtain reliable localization performance in a human co-existing real environment. Reliability of localization is highly dependent upon developer's experiences because uncertainty is caused by a variety of reasons. We have developed a range sensor based integrated localization scheme for various indoor service robots. Through the experience, we found out that there are several significant experimental issues. In this paper, we provide useful solutions for following questions which are frequently faced with in practical applications: 1 How to design an observation likelihood model? 2 How to detect the localization failure? 3 How to recover from the localization failure? We present design guidelines of observation likelihood model. Localization failure detection and recovery schemes are presented by focusing on abrupt wheel slippage. Experiments were carried out in a typical office building environment. The proposed scheme to identify the localizer status is useful in practical environments. Moreover, the semi-global localization is a computationally efficient recovery scheme from localization failure. The results of experiments and analysis clearly present the usefulness of proposed solutions.