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Sample records for bayesian partition method

  1. Basics of Bayesian methods.

    Science.gov (United States)

    Ghosh, Sujit K

    2010-01-01

    Bayesian methods are rapidly becoming popular tools for making statistical inference in various fields of science including biology, engineering, finance, and genetics. One of the key aspects of Bayesian inferential method is its logical foundation that provides a coherent framework to utilize not only empirical but also scientific information available to a researcher. Prior knowledge arising from scientific background, expert judgment, or previously collected data is used to build a prior distribution which is then combined with current data via the likelihood function to characterize the current state of knowledge using the so-called posterior distribution. Bayesian methods allow the use of models of complex physical phenomena that were previously too difficult to estimate (e.g., using asymptotic approximations). Bayesian methods offer a means of more fully understanding issues that are central to many practical problems by allowing researchers to build integrated models based on hierarchical conditional distributions that can be estimated even with limited amounts of data. Furthermore, advances in numerical integration methods, particularly those based on Monte Carlo methods, have made it possible to compute the optimal Bayes estimators. However, there is a reasonably wide gap between the background of the empirically trained scientists and the full weight of Bayesian statistical inference. Hence, one of the goals of this chapter is to bridge the gap by offering elementary to advanced concepts that emphasize linkages between standard approaches and full probability modeling via Bayesian methods.

  2. Bayesian methods for data analysis

    CERN Document Server

    Carlin, Bradley P.

    2009-01-01

    Approaches for statistical inference Introduction Motivating Vignettes Defining the Approaches The Bayes-Frequentist Controversy Some Basic Bayesian Models The Bayes approach Introduction Prior Distributions Bayesian Inference Hierarchical Modeling Model Assessment Nonparametric Methods Bayesian computation Introduction Asymptotic Methods Noniterative Monte Carlo Methods Markov Chain Monte Carlo Methods Model criticism and selection Bayesian Modeling Bayesian Robustness Model Assessment Bayes Factors via Marginal Density Estimation Bayes Factors

  3. Bayesian methods in reliability

    Science.gov (United States)

    Sander, P.; Badoux, R.

    1991-11-01

    The present proceedings from a course on Bayesian methods in reliability encompasses Bayesian statistical methods and their computational implementation, models for analyzing censored data from nonrepairable systems, the traits of repairable systems and growth models, the use of expert judgment, and a review of the problem of forecasting software reliability. Specific issues addressed include the use of Bayesian methods to estimate the leak rate of a gas pipeline, approximate analyses under great prior uncertainty, reliability estimation techniques, and a nonhomogeneous Poisson process. Also addressed are the calibration sets and seed variables of expert judgment systems for risk assessment, experimental illustrations of the use of expert judgment for reliability testing, and analyses of the predictive quality of software-reliability growth models such as the Weibull order statistics.

  4. Bayesian Monte Carlo method

    International Nuclear Information System (INIS)

    Rajabalinejad, M.

    2010-01-01

    To reduce cost of Monte Carlo (MC) simulations for time-consuming processes, Bayesian Monte Carlo (BMC) is introduced in this paper. The BMC method reduces number of realizations in MC according to the desired accuracy level. BMC also provides a possibility of considering more priors. In other words, different priors can be integrated into one model by using BMC to further reduce cost of simulations. This study suggests speeding up the simulation process by considering the logical dependence of neighboring points as prior information. This information is used in the BMC method to produce a predictive tool through the simulation process. The general methodology and algorithm of BMC method are presented in this paper. The BMC method is applied to the simplified break water model as well as the finite element model of 17th Street Canal in New Orleans, and the results are compared with the MC and Dynamic Bounds methods.

  5. Development of partitioning method

    International Nuclear Information System (INIS)

    Kubota, Kazuo; Dojiri, Shigeru; Kubota, Masumitsu

    1988-10-01

    The literature survey was carried out on the amount of natural resources, behaviors in reprocessing process and in separation and recovery methods of the platinum group elements and technetium which are contained in spent fuel. The essential results are described below. (1) The platinum group elements, which are contained in spent fuel, are quantitatively limited, compared with total demand for them in Japan. And estimated separation and recovery cost is rather high. In spite of that, development of these techniques is considered to be very important because the supply of these elements is almost from foreign resources in Japan. (2) For recovery of these elements, studies of recovery from undisolved residue and from high level liquid waste (HLLW) also seem to be required. (3) As separation and recovery methods, following techniques are considered to be effective; lead extraction, liquid metal extraction, solvent extraction, ion-exchange, adsorption, precipitation, distillation, electrolysis or their combination. (4) But each of these methods has both advantages and disadvantages. So development of such processes largely depends on future works. (author) 94 refs

  6. Development of partitioning method

    International Nuclear Information System (INIS)

    Kobayashi, Tsutomu; Shirahashi, Koichi; Kubota, Masumitsu

    1989-11-01

    Precipitation behavior of elements in a high-level liquid waste (HLW) was studied by using the simulated liquid waste, when the transuranic elements group was precipitated and separated as oxalate from HLW generated from the reprocessing of spent nuclear fuel. The results showed that over 90 % of strontium and barium were precipitated when oxalic acid was directly added to HLW to precipitate the transuranic elements group, and the percentages of these elements precipitated were affected by molybdenum and or zirconium. Therefore, a method of adding oxalic acid into the filtrate was studied after removing previously molybdenum and zirconium as precipitate by denitrating HLW, and it was found that precipitated fractions of strontium and barium could be suppressed about 10 %. Adding oxalic acid under the co-existance of ascorbic acid is effective for quantitative precipitation of neptunium in HLW. In this case, it was found that adding ascorbic acid had little influence on precipitation behavior of the other elements except palladium. (author)

  7. Bayesian methods for hackers probabilistic programming and Bayesian inference

    CERN Document Server

    Davidson-Pilon, Cameron

    2016-01-01

    Bayesian methods of inference are deeply natural and extremely powerful. However, most discussions of Bayesian inference rely on intensely complex mathematical analyses and artificial examples, making it inaccessible to anyone without a strong mathematical background. Now, though, Cameron Davidson-Pilon introduces Bayesian inference from a computational perspective, bridging theory to practice–freeing you to get results using computing power. Bayesian Methods for Hackers illuminates Bayesian inference through probabilistic programming with the powerful PyMC language and the closely related Python tools NumPy, SciPy, and Matplotlib. Using this approach, you can reach effective solutions in small increments, without extensive mathematical intervention. Davidson-Pilon begins by introducing the concepts underlying Bayesian inference, comparing it with other techniques and guiding you through building and training your first Bayesian model. Next, he introduces PyMC through a series of detailed examples a...

  8. Applied Bayesian hierarchical methods

    National Research Council Canada - National Science Library

    Congdon, P

    2010-01-01

    ... . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.2 Posterior Inference from Bayes Formula . . . . . . . . . . . . 1.3 Markov Chain Monte Carlo Sampling in Relation to Monte Carlo Methods: Obtaining Posterior...

  9. Deep Learning and Bayesian Methods

    Directory of Open Access Journals (Sweden)

    Prosper Harrison B.

    2017-01-01

    Full Text Available A revolution is underway in which deep neural networks are routinely used to solve diffcult problems such as face recognition and natural language understanding. Particle physicists have taken notice and have started to deploy these methods, achieving results that suggest a potentially significant shift in how data might be analyzed in the not too distant future. We discuss a few recent developments in the application of deep neural networks and then indulge in speculation about how such methods might be used to automate certain aspects of data analysis in particle physics. Next, the connection to Bayesian methods is discussed and the paper ends with thoughts on a significant practical issue, namely, how, from a Bayesian perspective, one might optimize the construction of deep neural networks.

  10. Bayesian approach to estimate AUC, partition coefficient and drug targeting index for studies with serial sacrifice design.

    Science.gov (United States)

    Wang, Tianli; Baron, Kyle; Zhong, Wei; Brundage, Richard; Elmquist, William

    2014-03-01

    The current study presents a Bayesian approach to non-compartmental analysis (NCA), which provides the accurate and precise estimate of AUC 0 (∞) and any AUC 0 (∞) -based NCA parameter or derivation. In order to assess the performance of the proposed method, 1,000 simulated datasets were generated in different scenarios. A Bayesian method was used to estimate the tissue and plasma AUC 0 (∞) s and the tissue-to-plasma AUC 0 (∞) ratio. The posterior medians and the coverage of 95% credible intervals for the true parameter values were examined. The method was applied to laboratory data from a mice brain distribution study with serial sacrifice design for illustration. Bayesian NCA approach is accurate and precise in point estimation of the AUC 0 (∞) and the partition coefficient under a serial sacrifice design. It also provides a consistently good variance estimate, even considering the variability of the data and the physiological structure of the pharmacokinetic model. The application in the case study obtained a physiologically reasonable posterior distribution of AUC, with a posterior median close to the value estimated by classic Bailer-type methods. This Bayesian NCA approach for sparse data analysis provides statistical inference on the variability of AUC 0 (∞) -based parameters such as partition coefficient and drug targeting index, so that the comparison of these parameters following destructive sampling becomes statistically feasible.

  11. Bayesian methods for proteomic biomarker development

    Directory of Open Access Journals (Sweden)

    Belinda Hernández

    2015-12-01

    In this review we provide an introduction to Bayesian inference and demonstrate some of the advantages of using a Bayesian framework. We summarize how Bayesian methods have been used previously in proteomics and other areas of bioinformatics. Finally, we describe some popular and emerging Bayesian models from the statistical literature and provide a worked tutorial including code snippets to show how these methods may be applied for the evaluation of proteomic biomarkers.

  12. Bayesian estimation methods in metrology

    International Nuclear Information System (INIS)

    Cox, M.G.; Forbes, A.B.; Harris, P.M.

    2004-01-01

    In metrology -- the science of measurement -- a measurement result must be accompanied by a statement of its associated uncertainty. The degree of validity of a measurement result is determined by the validity of the uncertainty statement. In recognition of the importance of uncertainty evaluation, the International Standardization Organization in 1995 published the Guide to the Expression of Uncertainty in Measurement and the Guide has been widely adopted. The validity of uncertainty statements is tested in interlaboratory comparisons in which an artefact is measured by a number of laboratories and their measurement results compared. Since the introduction of the Mutual Recognition Arrangement, key comparisons are being undertaken to determine the degree of equivalence of laboratories for particular measurement tasks. In this paper, we discuss the possible development of the Guide to reflect Bayesian approaches and the evaluation of key comparison data using Bayesian estimation methods

  13. Bayesian Methods and Universal Darwinism

    Science.gov (United States)

    Campbell, John

    2009-12-01

    Bayesian methods since the time of Laplace have been understood by their practitioners as closely aligned to the scientific method. Indeed a recent Champion of Bayesian methods, E. T. Jaynes, titled his textbook on the subject Probability Theory: the Logic of Science. Many philosophers of science including Karl Popper and Donald Campbell have interpreted the evolution of Science as a Darwinian process consisting of a `copy with selective retention' algorithm abstracted from Darwin's theory of Natural Selection. Arguments are presented for an isomorphism between Bayesian Methods and Darwinian processes. Universal Darwinism, as the term has been developed by Richard Dawkins, Daniel Dennett and Susan Blackmore, is the collection of scientific theories which explain the creation and evolution of their subject matter as due to the Operation of Darwinian processes. These subject matters span the fields of atomic physics, chemistry, biology and the social sciences. The principle of Maximum Entropy states that Systems will evolve to states of highest entropy subject to the constraints of scientific law. This principle may be inverted to provide illumination as to the nature of scientific law. Our best cosmological theories suggest the universe contained much less complexity during the period shortly after the Big Bang than it does at present. The scientific subject matter of atomic physics, chemistry, biology and the social sciences has been created since that time. An explanation is proposed for the existence of this subject matter as due to the evolution of constraints in the form of adaptations imposed on Maximum Entropy. It is argued these adaptations were discovered and instantiated through the Operations of a succession of Darwinian processes.

  14. Maximum entropy and Bayesian methods

    International Nuclear Information System (INIS)

    Smith, C.R.; Erickson, G.J.; Neudorfer, P.O.

    1992-01-01

    Bayesian probability theory and Maximum Entropy methods are at the core of a new view of scientific inference. These 'new' ideas, along with the revolution in computational methods afforded by modern computers allow astronomers, electrical engineers, image processors of any type, NMR chemists and physicists, and anyone at all who has to deal with incomplete and noisy data, to take advantage of methods that, in the past, have been applied only in some areas of theoretical physics. The title workshops have been the focus of a group of researchers from many different fields, and this diversity is evident in this book. There are tutorial and theoretical papers, and applications in a very wide variety of fields. Almost any instance of dealing with incomplete and noisy data can be usefully treated by these methods, and many areas of theoretical research are being enhanced by the thoughtful application of Bayes' theorem. Contributions contained in this volume present a state-of-the-art overview that will be influential and useful for many years to come

  15. Bayesian flood forecasting methods: A review

    Science.gov (United States)

    Han, Shasha; Coulibaly, Paulin

    2017-08-01

    Over the past few decades, floods have been seen as one of the most common and largely distributed natural disasters in the world. If floods could be accurately forecasted in advance, then their negative impacts could be greatly minimized. It is widely recognized that quantification and reduction of uncertainty associated with the hydrologic forecast is of great importance for flood estimation and rational decision making. Bayesian forecasting system (BFS) offers an ideal theoretic framework for uncertainty quantification that can be developed for probabilistic flood forecasting via any deterministic hydrologic model. It provides suitable theoretical structure, empirically validated models and reasonable analytic-numerical computation method, and can be developed into various Bayesian forecasting approaches. This paper presents a comprehensive review on Bayesian forecasting approaches applied in flood forecasting from 1999 till now. The review starts with an overview of fundamentals of BFS and recent advances in BFS, followed with BFS application in river stage forecasting and real-time flood forecasting, then move to a critical analysis by evaluating advantages and limitations of Bayesian forecasting methods and other predictive uncertainty assessment approaches in flood forecasting, and finally discusses the future research direction in Bayesian flood forecasting. Results show that the Bayesian flood forecasting approach is an effective and advanced way for flood estimation, it considers all sources of uncertainties and produces a predictive distribution of the river stage, river discharge or runoff, thus gives more accurate and reliable flood forecasts. Some emerging Bayesian forecasting methods (e.g. ensemble Bayesian forecasting system, Bayesian multi-model combination) were shown to overcome limitations of single model or fixed model weight and effectively reduce predictive uncertainty. In recent years, various Bayesian flood forecasting approaches have been

  16. Innovative Bayesian and Parsimony Phylogeny of Dung Beetles (Coleoptera, Scarabaeidae, Scarabaeinae) Enhanced by Ontology-Based Partitioning of Morphological Characters

    Science.gov (United States)

    Tarasov, Sergei; Génier, François

    2015-01-01

    Scarabaeine dung beetles are the dominant dung feeding group of insects and are widely used as model organisms in conservation, ecology and developmental biology. Due to the conflicts among 13 recently published phylogenies dealing with the higher-level relationships of dung beetles, the phylogeny of this lineage remains largely unresolved. In this study, we conduct rigorous phylogenetic analyses of dung beetles, based on an unprecedented taxon sample (110 taxa) and detailed investigation of morphology (205 characters). We provide the description of morphology and thoroughly illustrate the used characters. Along with parsimony, traditionally used in the analysis of morphological data, we also apply the Bayesian method with a novel approach that uses anatomy ontology for matrix partitioning. This approach allows for heterogeneity in evolutionary rates among characters from different anatomical regions. Anatomy ontology generates a number of parameter-partition schemes which we compare using Bayes factor. We also test the effect of inclusion of autapomorphies in the morphological analysis, which hitherto has not been examined. Generally, schemes with more parameters were favored in the Bayesian comparison suggesting that characters located on different body regions evolve at different rates and that partitioning of the data matrix using anatomy ontology is reasonable; however, trees from the parsimony and all the Bayesian analyses were quite consistent. The hypothesized phylogeny reveals many novel clades and provides additional support for some clades recovered in previous analyses. Our results provide a solid basis for a new classification of dung beetles, in which the taxonomic limits of the tribes Dichotomiini, Deltochilini and Coprini are restricted and many new tribes must be described. Based on the consistency of the phylogeny with biogeography, we speculate that dung beetles may have originated in the Mesozoic contrary to the traditional view pointing to a

  17. Spatially Partitioned Embedded Runge--Kutta Methods

    KAUST Repository

    Ketcheson, David I.; MacDonald, Colin B.; Ruuth, Steven J.

    2013-01-01

    We study spatially partitioned embedded Runge--Kutta (SPERK) schemes for partial differential equations (PDEs), in which each of the component schemes is applied over a different part of the spatial domain. Such methods may be convenient for problems in which the smoothness of the solution or the magnitudes of the PDE coefficients vary strongly in space. We focus on embedded partitioned methods as they offer greater efficiency and avoid the order reduction that may occur in nonembedded schemes. We demonstrate that the lack of conservation in partitioned schemes can lead to nonphysical effects and propose conservative additive schemes based on partitioning the fluxes rather than the ordinary differential equations. A variety of SPERK schemes are presented, including an embedded pair suitable for the time evolution of fifth-order weighted nonoscillatory spatial discretizations. Numerical experiments are provided to support the theory.

  18. Spatially Partitioned Embedded Runge--Kutta Methods

    KAUST Repository

    Ketcheson, David I.

    2013-10-30

    We study spatially partitioned embedded Runge--Kutta (SPERK) schemes for partial differential equations (PDEs), in which each of the component schemes is applied over a different part of the spatial domain. Such methods may be convenient for problems in which the smoothness of the solution or the magnitudes of the PDE coefficients vary strongly in space. We focus on embedded partitioned methods as they offer greater efficiency and avoid the order reduction that may occur in nonembedded schemes. We demonstrate that the lack of conservation in partitioned schemes can lead to nonphysical effects and propose conservative additive schemes based on partitioning the fluxes rather than the ordinary differential equations. A variety of SPERK schemes are presented, including an embedded pair suitable for the time evolution of fifth-order weighted nonoscillatory spatial discretizations. Numerical experiments are provided to support the theory.

  19. Bayesian simultaneous equation models for the analysis of energy intake and partitioning in growing pigs

    DEFF Research Database (Denmark)

    Strathe, Anders Bjerring; Jørgensen, Henry; Kebreab, E

    2012-01-01

    ABSTRACT SUMMARY The objective of the current study was to develop Bayesian simultaneous equation models for modelling energy intake and partitioning in growing pigs. A key feature of the Bayesian approach is that parameters are assigned prior distributions, which may reflect the current state...... of nature. In the models, rates of metabolizable energy (ME) intake, protein deposition (PD) and lipid deposition (LD) were treated as dependent variables accounting for residuals being correlated. Two complementary equation systems were used to model ME intake (MEI), PD and LD. Informative priors were...... developed, reflecting current knowledge about metabolic scaling and partial efficiencies of PD and LD rates, whereas flat non-informative priors were used for the reminder of the parameters. The experimental data analysed originate from a balance and respiration trial with 17 cross-bred pigs of three...

  20. Conceptual methods for actinide partitioning

    International Nuclear Information System (INIS)

    Leuze, R.E.; Bond, W.D.; Tedder, D.W.

    1978-01-01

    The conceptual processing sequence under consideration is based on a combination of modified Purex processing and secondary processing of the high-level waste. In this concept, iodine will be removed from dissolver solution prior to extraction, and the Purex processing will be modified so that low- and intermediate-level wastes, all the way through final product purification, are recycled. A supplementary extraction is assumed to ensure adequate recovery of uranium, neptunium and possibly plutonium. Technetium may be removed from the high-level waste if a satisfactory method can be developed. Extraction into a quaternary amine is being evaluated for this removal. Methods that have been used in the past to recover americium and curium have some rather serious deficiencies, including inadequate recovery, solids formation and generation of large volumes of low- and intermediate-level wastes containing significant quantities of chemical reagents

  1. Phylogenetic systematics and biogeography of hummingbirds: Bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy.

    Science.gov (United States)

    McGuire, Jimmy A; Witt, Christopher C; Altshuler, Douglas L; Remsen, J V

    2007-10-01

    Hummingbirds are an important model system in avian biology, but to date the group has been the subject of remarkably few phylogenetic investigations. Here we present partitioned Bayesian and maximum likelihood phylogenetic analyses for 151 of approximately 330 species of hummingbirds and 12 outgroup taxa based on two protein-coding mitochondrial genes (ND2 and ND4), flanking tRNAs, and two nuclear introns (AK1 and BFib). We analyzed these data under several partitioning strategies ranging between unpartitioned and a maximum of nine partitions. In order to select a statistically justified partitioning strategy following partitioned Bayesian analysis, we considered four alternative criteria including Bayes factors, modified versions of the Akaike information criterion for small sample sizes (AIC(c)), Bayesian information criterion (BIC), and a decision-theoretic methodology (DT). Following partitioned maximum likelihood analyses, we selected a best-fitting strategy using hierarchical likelihood ratio tests (hLRTS), the conventional AICc, BIC, and DT, concluding that the most stringent criterion, the performance-based DT, was the most appropriate methodology for selecting amongst partitioning strategies. In the context of our well-resolved and well-supported phylogenetic estimate, we consider the historical biogeography of hummingbirds using ancestral state reconstructions of (1) primary geographic region of occurrence (i.e., South America, Central America, North America, Greater Antilles, Lesser Antilles), (2) Andean or non-Andean geographic distribution, and (3) minimum elevational occurrence. These analyses indicate that the basal hummingbird assemblages originated in the lowlands of South America, that most of the principle clades of hummingbirds (all but Mountain Gems and possibly Bees) originated on this continent, and that there have been many (at least 30) independent invasions of other primary landmasses, especially Central America.

  2. Bayesian Methods for Radiation Detection and Dosimetry

    CERN Document Server

    Groer, Peter G

    2002-01-01

    We performed work in three areas: radiation detection, external and internal radiation dosimetry. In radiation detection we developed Bayesian techniques to estimate the net activity of high and low activity radioactive samples. These techniques have the advantage that the remaining uncertainty about the net activity is described by probability densities. Graphs of the densities show the uncertainty in pictorial form. Figure 1 below demonstrates this point. We applied stochastic processes for a method to obtain Bayesian estimates of 222Rn-daughter products from observed counting rates. In external radiation dosimetry we studied and developed Bayesian methods to estimate radiation doses to an individual with radiation induced chromosome aberrations. We analyzed chromosome aberrations after exposure to gammas and neutrons and developed a method for dose-estimation after criticality accidents. The research in internal radiation dosimetry focused on parameter estimation for compartmental models from observed comp...

  3. Bayesian Inference Methods for Sparse Channel Estimation

    DEFF Research Database (Denmark)

    Pedersen, Niels Lovmand

    2013-01-01

    This thesis deals with sparse Bayesian learning (SBL) with application to radio channel estimation. As opposed to the classical approach for sparse signal representation, we focus on the problem of inferring complex signals. Our investigations within SBL constitute the basis for the development...... of Bayesian inference algorithms for sparse channel estimation. Sparse inference methods aim at finding the sparse representation of a signal given in some overcomplete dictionary of basis vectors. Within this context, one of our main contributions to the field of SBL is a hierarchical representation...... analysis of the complex prior representation, where we show that the ability to induce sparse estimates of a given prior heavily depends on the inference method used and, interestingly, whether real or complex variables are inferred. We also show that the Bayesian estimators derived from the proposed...

  4. Nested partitions method, theory and applications

    CERN Document Server

    Shi, Leyuan

    2009-01-01

    There is increasing need to solve large-scale complex optimization problems in a wide variety of science and engineering applications, including designing telecommunication networks for multimedia transmission, planning and scheduling problems in manufacturing and military operations, or designing nanoscale devices and systems. Advances in technology and information systems have made such optimization problems more and more complicated in terms of size and uncertainty. Nested Partitions Method, Theory and Applications provides a cutting-edge research tool to use for large-scale, complex systems optimization. The Nested Partitions (NP) framework is an innovative mix of traditional optimization methodology and probabilistic assumptions. An important feature of the NP framework is that it combines many well-known optimization techniques, including dynamic programming, mixed integer programming, genetic algorithms and tabu search, while also integrating many problem-specific local search heuristics. The book uses...

  5. Assessing Local Model Adequacy in Bayesian Hierarchical Models Using the Partitioned Deviance Information Criterion

    Science.gov (United States)

    Wheeler, David C.; Hickson, DeMarc A.; Waller, Lance A.

    2010-01-01

    Many diagnostic tools and goodness-of-fit measures, such as the Akaike information criterion (AIC) and the Bayesian deviance information criterion (DIC), are available to evaluate the overall adequacy of linear regression models. In addition, visually assessing adequacy in models has become an essential part of any regression analysis. In this paper, we focus on a spatial consideration of the local DIC measure for model selection and goodness-of-fit evaluation. We use a partitioning of the DIC into the local DIC, leverage, and deviance residuals to assess local model fit and influence for both individual observations and groups of observations in a Bayesian framework. We use visualization of the local DIC and differences in local DIC between models to assist in model selection and to visualize the global and local impacts of adding covariates or model parameters. We demonstrate the utility of the local DIC in assessing model adequacy using HIV prevalence data from pregnant women in the Butare province of Rwanda during 1989-1993 using a range of linear model specifications, from global effects only to spatially varying coefficient models, and a set of covariates related to sexual behavior. Results of applying the diagnostic visualization approach include more refined model selection and greater understanding of the models as applied to the data. PMID:21243121

  6. New parallel SOR method by domain partitioning

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Dexuan [Courant Inst. of Mathematical Sciences New York Univ., NY (United States)

    1996-12-31

    In this paper, we propose and analyze a new parallel SOR method, the PSOR method, formulated by using domain partitioning together with an interprocessor data-communication technique. For the 5-point approximation to the Poisson equation on a square, we show that the ordering of the PSOR based on the strip partition leads to a consistently ordered matrix, and hence the PSOR and the SOR using the row-wise ordering have the same convergence rate. However, in general, the ordering used in PSOR may not be {open_quote}consistently ordered{close_quotes}. So, there is a need to analyze the convergence of PSOR directly. In this paper, we present a PSOR theory, and show that the PSOR method can have the same asymptotic rate of convergence as the corresponding sequential SOR method for a wide class of linear systems in which the matrix is {open_quotes}consistently ordered{close_quotes}. Finally, we demonstrate the parallel performance of the PSOR method on four different message passing multiprocessors (a KSR1, the Intel Delta, an Intel Paragon and an IBM SP2), along with a comparison with the point Red-Black and four-color SOR methods.

  7. Deep Learning and Bayesian Methods

    OpenAIRE

    Prosper Harrison B.

    2017-01-01

    A revolution is underway in which deep neural networks are routinely used to solve diffcult problems such as face recognition and natural language understanding. Particle physicists have taken notice and have started to deploy these methods, achieving results that suggest a potentially significant shift in how data might be analyzed in the not too distant future. We discuss a few recent developments in the application of deep neural networks and then indulge in speculation about how such meth...

  8. Essays on portfolio choice with Bayesian methods

    OpenAIRE

    Kebabci, Deniz

    2007-01-01

    How investors should allocate assets to their portfolios in the presence of predictable components in asset returns is a question of great importance in finance. While early studies took the return generating process as given, recent studies have addressed issues such as parameter estimation and model uncertainty. My dissertation develops Bayesian methods for portfolio choice - and industry allocation in particular - under parameter and model uncertainty. The first chapter of my dissertation,...

  9. Bayesian Methods for Radiation Detection and Dosimetry

    International Nuclear Information System (INIS)

    Peter G. Groer

    2002-01-01

    We performed work in three areas: radiation detection, external and internal radiation dosimetry. In radiation detection we developed Bayesian techniques to estimate the net activity of high and low activity radioactive samples. These techniques have the advantage that the remaining uncertainty about the net activity is described by probability densities. Graphs of the densities show the uncertainty in pictorial form. Figure 1 below demonstrates this point. We applied stochastic processes for a method to obtain Bayesian estimates of 222Rn-daughter products from observed counting rates. In external radiation dosimetry we studied and developed Bayesian methods to estimate radiation doses to an individual with radiation induced chromosome aberrations. We analyzed chromosome aberrations after exposure to gammas and neutrons and developed a method for dose-estimation after criticality accidents. The research in internal radiation dosimetry focused on parameter estimation for compartmental models from observed compartmental activities. From the estimated probability densities of the model parameters we were able to derive the densities for compartmental activities for a two compartment catenary model at different times. We also calculated the average activities and their standard deviation for a simple two compartment model

  10. Prior approval: the growth of Bayesian methods in psychology.

    Science.gov (United States)

    Andrews, Mark; Baguley, Thom

    2013-02-01

    Within the last few years, Bayesian methods of data analysis in psychology have proliferated. In this paper, we briefly review the history or the Bayesian approach to statistics, and consider the implications that Bayesian methods have for the theory and practice of data analysis in psychology.

  11. Bayesian clustering of DNA sequences using Markov chains and a stochastic partition model.

    Science.gov (United States)

    Jääskinen, Väinö; Parkkinen, Ville; Cheng, Lu; Corander, Jukka

    2014-02-01

    In many biological applications it is necessary to cluster DNA sequences into groups that represent underlying organismal units, such as named species or genera. In metagenomics this grouping needs typically to be achieved on the basis of relatively short sequences which contain different types of errors, making the use of a statistical modeling approach desirable. Here we introduce a novel method for this purpose by developing a stochastic partition model that clusters Markov chains of a given order. The model is based on a Dirichlet process prior and we use conjugate priors for the Markov chain parameters which enables an analytical expression for comparing the marginal likelihoods of any two partitions. To find a good candidate for the posterior mode in the partition space, we use a hybrid computational approach which combines the EM-algorithm with a greedy search. This is demonstrated to be faster and yield highly accurate results compared to earlier suggested clustering methods for the metagenomics application. Our model is fairly generic and could also be used for clustering of other types of sequence data for which Markov chains provide a reasonable way to compress information, as illustrated by experiments on shotgun sequence type data from an Escherichia coli strain.

  12. Internal Dosimetry Intake Estimation using Bayesian Methods

    International Nuclear Information System (INIS)

    Miller, G.; Inkret, W.C.; Martz, H.F.

    1999-01-01

    New methods for the inverse problem of internal dosimetry are proposed based on evaluating expectations of the Bayesian posterior probability distribution of intake amounts, given bioassay measurements. These expectation integrals are normally of very high dimension and hence impractical to use. However, the expectations can be algebraically transformed into a sum of terms representing different numbers of intakes, with a Poisson distribution of the number of intakes. This sum often rapidly converges, when the average number of intakes for a population is small. A simplified algorithm using data unfolding is described (UF code). (author)

  13. Diet reconstruction and resource partitioning of a Caribbean marine mesopredator using stable isotope bayesian modelling.

    Science.gov (United States)

    Tilley, Alexander; López-Angarita, Juliana; Turner, John R

    2013-01-01

    The trophic ecology of epibenthic mesopredators is not well understood in terms of prey partitioning with sympatric elasmobranchs or their effects on prey communities, yet the importance of omnivores in community trophic dynamics is being increasingly realised. This study used stable isotope analysis of (15)N and (13)C to model diet composition of wild southern stingrays Dasyatis americana and compare trophic niche space to nurse sharks Ginglymostoma cirratum and Caribbean reef sharks Carcharhinus perezi on Glovers Reef Atoll, Belize. Bayesian stable isotope mixing models were used to investigate prey choice as well as viable Diet-Tissue Discrimination Factors for use with stingrays. Stingray δ(15)N values showed the greatest variation and a positive relationship with size, with an isotopic niche width approximately twice that of sympatric species. Shark species exhibited comparatively restricted δ(15)N values and greater δ(13)C variation, with very little overlap of stingray niche space. Mixing models suggest bivalves and annelids are proportionally more important prey in the stingray diet than crustaceans and teleosts at Glovers Reef, in contrast to all but one published diet study using stomach contents from other locations. Incorporating gut contents information from the literature, we suggest diet-tissue discrimination factors values of Δ(15)N ≈ 2.7‰ and Δ(13)C ≈ 0.9‰ for stingrays in the absence of validation experiments. The wide trophic niche and lower trophic level exhibited by stingrays compared to sympatric sharks supports their putative role as important base stabilisers in benthic systems, with the potential to absorb trophic perturbations through numerous opportunistic prey interactions.

  14. Diet reconstruction and resource partitioning of a Caribbean marine mesopredator using stable isotope bayesian modelling.

    Directory of Open Access Journals (Sweden)

    Alexander Tilley

    Full Text Available The trophic ecology of epibenthic mesopredators is not well understood in terms of prey partitioning with sympatric elasmobranchs or their effects on prey communities, yet the importance of omnivores in community trophic dynamics is being increasingly realised. This study used stable isotope analysis of (15N and (13C to model diet composition of wild southern stingrays Dasyatis americana and compare trophic niche space to nurse sharks Ginglymostoma cirratum and Caribbean reef sharks Carcharhinus perezi on Glovers Reef Atoll, Belize. Bayesian stable isotope mixing models were used to investigate prey choice as well as viable Diet-Tissue Discrimination Factors for use with stingrays. Stingray δ(15N values showed the greatest variation and a positive relationship with size, with an isotopic niche width approximately twice that of sympatric species. Shark species exhibited comparatively restricted δ(15N values and greater δ(13C variation, with very little overlap of stingray niche space. Mixing models suggest bivalves and annelids are proportionally more important prey in the stingray diet than crustaceans and teleosts at Glovers Reef, in contrast to all but one published diet study using stomach contents from other locations. Incorporating gut contents information from the literature, we suggest diet-tissue discrimination factors values of Δ(15N ≈ 2.7‰ and Δ(13C ≈ 0.9‰ for stingrays in the absence of validation experiments. The wide trophic niche and lower trophic level exhibited by stingrays compared to sympatric sharks supports their putative role as important base stabilisers in benthic systems, with the potential to absorb trophic perturbations through numerous opportunistic prey interactions.

  15. A conjugate gradient method for the spectral partitioning of graphs

    NARCIS (Netherlands)

    Kruyt, Nicolaas P.

    1997-01-01

    The partitioning of graphs is a frequently occurring problem in science and engineering. The spectral graph partitioning method is a promising heuristic method for this class of problems. Its main disadvantage is the large computing time required to solve a special eigenproblem. Here a simple and

  16. Bayesian non- and semi-parametric methods and applications

    CERN Document Server

    Rossi, Peter

    2014-01-01

    This book reviews and develops Bayesian non-parametric and semi-parametric methods for applications in microeconometrics and quantitative marketing. Most econometric models used in microeconomics and marketing applications involve arbitrary distributional assumptions. As more data becomes available, a natural desire to provide methods that relax these assumptions arises. Peter Rossi advocates a Bayesian approach in which specific distributional assumptions are replaced with more flexible distributions based on mixtures of normals. The Bayesian approach can use either a large but fixed number

  17. A Bayesian method for detecting stellar flares

    Science.gov (United States)

    Pitkin, M.; Williams, D.; Fletcher, L.; Grant, S. D. T.

    2014-12-01

    We present a Bayesian-odds-ratio-based algorithm for detecting stellar flares in light-curve data. We assume flares are described by a model in which there is a rapid rise with a half-Gaussian profile, followed by an exponential decay. Our signal model also contains a polynomial background model required to fit underlying light-curve variations in the data, which could otherwise partially mimic a flare. We characterize the false alarm probability and efficiency of this method under the assumption that any unmodelled noise in the data is Gaussian, and compare it with a simpler thresholding method based on that used in Walkowicz et al. We find our method has a significant increase in detection efficiency for low signal-to-noise ratio (S/N) flares. For a conservative false alarm probability our method can detect 95 per cent of flares with S/N less than 20, as compared to S/N of 25 for the simpler method. We also test how well the assumption of Gaussian noise holds by applying the method to a selection of `quiet' Kepler stars. As an example we have applied our method to a selection of stars in Kepler Quarter 1 data. The method finds 687 flaring stars with a total of 1873 flares after vetos have been applied. For these flares we have made preliminary characterizations of their durations and and S/N.

  18. Numerical Methods for Bayesian Inverse Problems

    KAUST Repository

    Ernst, Oliver

    2014-01-06

    We present recent results on Bayesian inversion for a groundwater flow problem with an uncertain conductivity field. In particular, we show how direct and indirect measurements can be used to obtain a stochastic model for the unknown. The main tool here is Bayes’ theorem which merges the indirect data with the stochastic prior model for the conductivity field obtained by the direct measurements. Further, we demonstrate how the resulting posterior distribution of the quantity of interest, in this case travel times of radionuclide contaminants, can be obtained by Markov Chain Monte Carlo (MCMC) simulations. Moreover, we investigate new, promising MCMC methods which exploit geometrical features of the posterior and which are suited to infinite dimensions.

  19. Numerical Methods for Bayesian Inverse Problems

    KAUST Repository

    Ernst, Oliver; Sprungk, Bjorn; Cliffe, K. Andrew; Starkloff, Hans-Jorg

    2014-01-01

    We present recent results on Bayesian inversion for a groundwater flow problem with an uncertain conductivity field. In particular, we show how direct and indirect measurements can be used to obtain a stochastic model for the unknown. The main tool here is Bayes’ theorem which merges the indirect data with the stochastic prior model for the conductivity field obtained by the direct measurements. Further, we demonstrate how the resulting posterior distribution of the quantity of interest, in this case travel times of radionuclide contaminants, can be obtained by Markov Chain Monte Carlo (MCMC) simulations. Moreover, we investigate new, promising MCMC methods which exploit geometrical features of the posterior and which are suited to infinite dimensions.

  20. Sparse Event Modeling with Hierarchical Bayesian Kernel Methods

    Science.gov (United States)

    2016-01-05

    SECURITY CLASSIFICATION OF: The research objective of this proposal was to develop a predictive Bayesian kernel approach to model count data based on...several predictive variables. Such an approach, which we refer to as the Poisson Bayesian kernel model, is able to model the rate of occurrence of... kernel methods made use of: (i) the Bayesian property of improving predictive accuracy as data are dynamically obtained, and (ii) the kernel function

  1. Dominant partition method. [based on a wave function formalism

    Science.gov (United States)

    Dixon, R. M.; Redish, E. F.

    1979-01-01

    By use of the L'Huillier, Redish, and Tandy (LRT) wave function formalism, a partially connected method, the dominant partition method (DPM) is developed for obtaining few body reductions of the many body problem in the LRT and Bencze, Redish, and Sloan (BRS) formalisms. The DPM maps the many body problem to a fewer body one by using the criterion that the truncated formalism must be such that consistency with the full Schroedinger equation is preserved. The DPM is based on a class of new forms for the irreducible cluster potential, which is introduced in the LRT formalism. Connectivity is maintained with respect to all partitions containing a given partition, which is referred to as the dominant partition. Degrees of freedom corresponding to the breakup of one or more of the clusters of the dominant partition are treated in a disconnected manner. This approach for simplifying the complicated BRS equations is appropriate for physical problems where a few body reaction mechanism prevails.

  2. Comparative Study of Inference Methods for Bayesian Nonnegative Matrix Factorisation

    DEFF Research Database (Denmark)

    Brouwer, Thomas; Frellsen, Jes; Liò, Pietro

    2017-01-01

    In this paper, we study the trade-offs of different inference approaches for Bayesian matrix factorisation methods, which are commonly used for predicting missing values, and for finding patterns in the data. In particular, we consider Bayesian nonnegative variants of matrix factorisation and tri......-factorisation, and compare non-probabilistic inference, Gibbs sampling, variational Bayesian inference, and a maximum-a-posteriori approach. The variational approach is new for the Bayesian nonnegative models. We compare their convergence, and robustness to noise and sparsity of the data, on both synthetic and real...

  3. Bayesian adaptive methods for clinical trials

    National Research Council Canada - National Science Library

    Berry, Scott M

    2011-01-01

    .... One is that Bayesian approaches implemented with the majority of their informative content coming from the current data, and not any external prior informa- tion, typically have good frequentist properties (e.g...

  4. A Bayesian Method for Weighted Sampling

    OpenAIRE

    Lo, Albert Y.

    1993-01-01

    Bayesian statistical inference for sampling from weighted distribution models is studied. Small-sample Bayesian bootstrap clone (BBC) approximations to the posterior distribution are discussed. A second-order property for the BBC in unweighted i.i.d. sampling is given. A consequence is that BBC approximations to a posterior distribution of the mean and to the sampling distribution of the sample average, can be made asymptotically accurate by a proper choice of the random variables that genera...

  5. Bayesian data analysis in population ecology: motivations, methods, and benefits

    Science.gov (United States)

    Dorazio, Robert

    2016-01-01

    During the 20th century ecologists largely relied on the frequentist system of inference for the analysis of their data. However, in the past few decades ecologists have become increasingly interested in the use of Bayesian methods of data analysis. In this article I provide guidance to ecologists who would like to decide whether Bayesian methods can be used to improve their conclusions and predictions. I begin by providing a concise summary of Bayesian methods of analysis, including a comparison of differences between Bayesian and frequentist approaches to inference when using hierarchical models. Next I provide a list of problems where Bayesian methods of analysis may arguably be preferred over frequentist methods. These problems are usually encountered in analyses based on hierarchical models of data. I describe the essentials required for applying modern methods of Bayesian computation, and I use real-world examples to illustrate these methods. I conclude by summarizing what I perceive to be the main strengths and weaknesses of using Bayesian methods to solve ecological inference problems.

  6. Approximation methods for efficient learning of Bayesian networks

    CERN Document Server

    Riggelsen, C

    2008-01-01

    This publication offers and investigates efficient Monte Carlo simulation methods in order to realize a Bayesian approach to approximate learning of Bayesian networks from both complete and incomplete data. For large amounts of incomplete data when Monte Carlo methods are inefficient, approximations are implemented, such that learning remains feasible, albeit non-Bayesian. The topics discussed are: basic concepts about probabilities, graph theory and conditional independence; Bayesian network learning from data; Monte Carlo simulation techniques; and, the concept of incomplete data. In order to provide a coherent treatment of matters, thereby helping the reader to gain a thorough understanding of the whole concept of learning Bayesian networks from (in)complete data, this publication combines in a clarifying way all the issues presented in the papers with previously unpublished work.

  7. Gait Partitioning Methods: A Systematic Review

    Science.gov (United States)

    Taborri, Juri; Palermo, Eduardo; Rossi, Stefano; Cappa, Paolo

    2016-01-01

    In the last years, gait phase partitioning has come to be a challenging research topic due to its impact on several applications related to gait technologies. A variety of sensors can be used to feed algorithms for gait phase partitioning, mainly classifiable as wearable or non-wearable. Among wearable sensors, footswitches or foot pressure insoles are generally considered as the gold standard; however, to overcome some inherent limitations of the former, inertial measurement units have become popular in recent decades. Valuable results have been achieved also though electromyography, electroneurography, and ultrasonic sensors. Non-wearable sensors, such as opto-electronic systems along with force platforms, remain the most accurate system to perform gait analysis in an indoor environment. In the present paper we identify, select, and categorize the available methodologies for gait phase detection, analyzing advantages and disadvantages of each solution. Finally, we comparatively examine the obtainable gait phase granularities, the usable computational methodologies and the optimal sensor placements on the targeted body segments. PMID:26751449

  8. Gait Partitioning Methods: A Systematic Review

    Directory of Open Access Journals (Sweden)

    Juri Taborri

    2016-01-01

    Full Text Available In the last years, gait phase partitioning has come to be a challenging research topic due to its impact on several applications related to gait technologies. A variety of sensors can be used to feed algorithms for gait phase partitioning, mainly classifiable as wearable or non-wearable. Among wearable sensors, footswitches or foot pressure insoles are generally considered as the gold standard; however, to overcome some inherent limitations of the former, inertial measurement units have become popular in recent decades. Valuable results have been achieved also though electromyography, electroneurography, and ultrasonic sensors. Non-wearable sensors, such as opto-electronic systems along with force platforms, remain the most accurate system to perform gait analysis in an indoor environment. In the present paper we identify, select, and categorize the available methodologies for gait phase detection, analyzing advantages and disadvantages of each solution. Finally, we comparatively examine the obtainable gait phase granularities, the usable computational methodologies and the optimal sensor placements on the targeted body segments.

  9. Development of partitioning method : cold experiment with partitioning test facility in NUCEF (I)

    International Nuclear Information System (INIS)

    Yamaguchi, Isoo; Morita, Yasuji; Kondo, Yasuo

    1996-03-01

    A test facility in which about 1.85 x 10 14 Bq of high-level liquid waste can be treated has been completed in 1994 at Nuclear Fuel Cycle Safety Engineering Research Facility (NUCEF) for research and development of Partitioning Method. The outline of the partitioning test facility and support equipments for it which were design terms, constructions, arrangements, functions and inspections were given in JAERI-Tech 94-030. The present report describes the results of the water transfer test and partitioning tests, which are methods of precipitation by denitration, oxalate precipitation, solvent extraction, and adsorption with inorganic ion exchanger, using nitric acid to master operation method of the test facility. As often as issues related to equipments occurred during the tests, they were improved. As to issues related to processes such as being stopped up of columns, their measures of solution were found by testing in laboratories. They were reflected in operation of the Partitioning Test Facility. Their particulars and improving points were described in this report. (author)

  10. Radiation Source Mapping with Bayesian Inverse Methods

    Science.gov (United States)

    Hykes, Joshua Michael

    We present a method to map the spectral and spatial distributions of radioactive sources using a small number of detectors. Locating and identifying radioactive materials is important for border monitoring, accounting for special nuclear material in processing facilities, and in clean-up operations. Most methods to analyze these problems make restrictive assumptions about the distribution of the source. In contrast, the source-mapping method presented here allows an arbitrary three-dimensional distribution in space and a flexible group and gamma peak distribution in energy. To apply the method, the system's geometry and materials must be known. A probabilistic Bayesian approach is used to solve the resulting inverse problem (IP) since the system of equations is ill-posed. The probabilistic approach also provides estimates of the confidence in the final source map prediction. A set of adjoint flux, discrete ordinates solutions, obtained in this work by the Denovo code, are required to efficiently compute detector responses from a candidate source distribution. These adjoint fluxes are then used to form the linear model to map the state space to the response space. The test for the method is simultaneously locating a set of 137Cs and 60Co gamma sources in an empty room. This test problem is solved using synthetic measurements generated by a Monte Carlo (MCNP) model and using experimental measurements that we collected for this purpose. With the synthetic data, the predicted source distributions identified the locations of the sources to within tens of centimeters, in a room with an approximately four-by-four meter floor plan. Most of the predicted source intensities were within a factor of ten of their true value. The chi-square value of the predicted source was within a factor of five from the expected value based on the number of measurements employed. With a favorable uniform initial guess, the predicted source map was nearly identical to the true distribution

  11. A novel partitioning method for block-structured adaptive meshes

    Science.gov (United States)

    Fu, Lin; Litvinov, Sergej; Hu, Xiangyu Y.; Adams, Nikolaus A.

    2017-07-01

    We propose a novel partitioning method for block-structured adaptive meshes utilizing the meshless Lagrangian particle concept. With the observation that an optimum partitioning has high analogy to the relaxation of a multi-phase fluid to steady state, physically motivated model equations are developed to characterize the background mesh topology and are solved by multi-phase smoothed-particle hydrodynamics. In contrast to well established partitioning approaches, all optimization objectives are implicitly incorporated and achieved during the particle relaxation to stationary state. Distinct partitioning sub-domains are represented by colored particles and separated by a sharp interface with a surface tension model. In order to obtain the particle relaxation, special viscous and skin friction models, coupled with a tailored time integration algorithm are proposed. Numerical experiments show that the present method has several important properties: generation of approximately equal-sized partitions without dependence on the mesh-element type, optimized interface communication between distinct partitioning sub-domains, continuous domain decomposition which is physically localized and implicitly incremental. Therefore it is particularly suitable for load-balancing of high-performance CFD simulations.

  12. A novel partitioning method for block-structured adaptive meshes

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Lin, E-mail: lin.fu@tum.de; Litvinov, Sergej, E-mail: sergej.litvinov@aer.mw.tum.de; Hu, Xiangyu Y., E-mail: xiangyu.hu@tum.de; Adams, Nikolaus A., E-mail: nikolaus.adams@tum.de

    2017-07-15

    We propose a novel partitioning method for block-structured adaptive meshes utilizing the meshless Lagrangian particle concept. With the observation that an optimum partitioning has high analogy to the relaxation of a multi-phase fluid to steady state, physically motivated model equations are developed to characterize the background mesh topology and are solved by multi-phase smoothed-particle hydrodynamics. In contrast to well established partitioning approaches, all optimization objectives are implicitly incorporated and achieved during the particle relaxation to stationary state. Distinct partitioning sub-domains are represented by colored particles and separated by a sharp interface with a surface tension model. In order to obtain the particle relaxation, special viscous and skin friction models, coupled with a tailored time integration algorithm are proposed. Numerical experiments show that the present method has several important properties: generation of approximately equal-sized partitions without dependence on the mesh-element type, optimized interface communication between distinct partitioning sub-domains, continuous domain decomposition which is physically localized and implicitly incremental. Therefore it is particularly suitable for load-balancing of high-performance CFD simulations.

  13. Covariance Partition Priors: A Bayesian Approach to Simultaneous Covariance Estimation for Longitudinal Data.

    Science.gov (United States)

    Gaskins, J T; Daniels, M J

    2016-01-02

    The estimation of the covariance matrix is a key concern in the analysis of longitudinal data. When data consists of multiple groups, it is often assumed the covariance matrices are either equal across groups or are completely distinct. We seek methodology to allow borrowing of strength across potentially similar groups to improve estimation. To that end, we introduce a covariance partition prior which proposes a partition of the groups at each measurement time. Groups in the same set of the partition share dependence parameters for the distribution of the current measurement given the preceding ones, and the sequence of partitions is modeled as a Markov chain to encourage similar structure at nearby measurement times. This approach additionally encourages a lower-dimensional structure of the covariance matrices by shrinking the parameters of the Cholesky decomposition toward zero. We demonstrate the performance of our model through two simulation studies and the analysis of data from a depression study. This article includes Supplementary Material available online.

  14. Approximation methods for the partition functions of anharmonic systems

    International Nuclear Information System (INIS)

    Lew, P.; Ishida, T.

    1979-07-01

    The analytical approximations for the classical, quantum mechanical and reduced partition functions of the diatomic molecule oscillating internally under the influence of the Morse potential have been derived and their convergences have been tested numerically. This successful analytical method is used in the treatment of anharmonic systems. Using Schwinger perturbation method in the framework of second quantization formulism, the reduced partition function of polyatomic systems can be put into an expression which consists separately of contributions from the harmonic terms, Morse potential correction terms and interaction terms due to the off-diagonal potential coefficients. The calculated results of the reduced partition function from the approximation method on the 2-D and 3-D model systems agree well with the numerical exact calculations

  15. The bootstrap and Bayesian bootstrap method in assessing bioequivalence

    International Nuclear Information System (INIS)

    Wan Jianping; Zhang Kongsheng; Chen Hui

    2009-01-01

    Parametric method for assessing individual bioequivalence (IBE) may concentrate on the hypothesis that the PK responses are normal. Nonparametric method for evaluating IBE would be bootstrap method. In 2001, the United States Food and Drug Administration (FDA) proposed a draft guidance. The purpose of this article is to evaluate the IBE between test drug and reference drug by bootstrap and Bayesian bootstrap method. We study the power of bootstrap test procedures and the parametric test procedures in FDA (2001). We find that the Bayesian bootstrap method is the most excellent.

  16. Further Stable methods for the calculation of partition functions

    International Nuclear Information System (INIS)

    Wilson, B G; Gilleron, F; Pain, J

    2007-01-01

    The extension to recursion over holes of the Gilleron and Pain method for calculating partition functions of a canonical ensemble of non-interacting bound electrons is presented as well as a generalization for the efficient computation of collisional line broadening

  17. Rationalizing method of replacement intervals by using Bayesian statistics

    International Nuclear Information System (INIS)

    Kasai, Masao; Notoya, Junichi; Kusakari, Yoshiyuki

    2007-01-01

    This study represents the formulations for rationalizing the replacement intervals of equipments and/or parts taking into account the probability density functions (PDF) of the parameters of failure distribution functions (FDF) and compares the optimized intervals by our formulations with those by conventional formulations which uses only representative values of the parameters of FDF instead of using these PDFs. The failure data are generated by Monte Carlo simulations since the real failure data can not be available for us. The PDF of PDF parameters are obtained by Bayesian method and the representative values are obtained by likelihood estimation and Bayesian method. We found that the method using PDF by Bayesian method brings longer replacement intervals than one using the representative of the parameters. (author)

  18. Numerical methods for Bayesian inference in the face of aging

    International Nuclear Information System (INIS)

    Clarotti, C.A.; Villain, B.; Procaccia, H.

    1996-01-01

    In recent years, much attention has been paid to Bayesian methods for Risk Assessment. Until now, these methods have been studied from a theoretical point of view. Researchers have been mainly interested in: studying the effectiveness of Bayesian methods in handling rare events; debating about the problem of priors and other philosophical issues. An aspect central to the Bayesian approach is numerical computation because any safety/reliability problem, in a Bayesian frame, ends with a problem of numerical integration. This aspect has been neglected until now because most Risk studies assumed the Exponential model as the basic probabilistic model. The existence of conjugate priors makes numerical integration unnecessary in this case. If aging is to be taken into account, no conjugate family is available and the use of numerical integration becomes compulsory. EDF (National Board of Electricity, of France) and ENEA (National Committee for Energy, New Technologies and Environment, of Italy) jointly carried out a research program aimed at developing quadrature methods suitable for Bayesian Interference with underlying Weibull or gamma distributions. The paper will illustrate the main results achieved during the above research program and will discuss, via some sample cases, the performances of the numerical algorithms which on the appearance of stress corrosion cracking in the tubes of Steam Generators of PWR French power plants. (authors)

  19. A Bayesian method for construction of Markov models to describe dynamics on various time-scales.

    Science.gov (United States)

    Rains, Emily K; Andersen, Hans C

    2010-10-14

    The dynamics of many biological processes of interest, such as the folding of a protein, are slow and complicated enough that a single molecular dynamics simulation trajectory of the entire process is difficult to obtain in any reasonable amount of time. Moreover, one such simulation may not be sufficient to develop an understanding of the mechanism of the process, and multiple simulations may be necessary. One approach to circumvent this computational barrier is the use of Markov state models. These models are useful because they can be constructed using data from a large number of shorter simulations instead of a single long simulation. This paper presents a new Bayesian method for the construction of Markov models from simulation data. A Markov model is specified by (τ,P,T), where τ is the mesoscopic time step, P is a partition of configuration space into mesostates, and T is an N(P)×N(P) transition rate matrix for transitions between the mesostates in one mesoscopic time step, where N(P) is the number of mesostates in P. The method presented here is different from previous Bayesian methods in several ways. (1) The method uses Bayesian analysis to determine the partition as well as the transition probabilities. (2) The method allows the construction of a Markov model for any chosen mesoscopic time-scale τ. (3) It constructs Markov models for which the diagonal elements of T are all equal to or greater than 0.5. Such a model will be called a "consistent mesoscopic Markov model" (CMMM). Such models have important advantages for providing an understanding of the dynamics on a mesoscopic time-scale. The Bayesian method uses simulation data to find a posterior probability distribution for (P,T) for any chosen τ. This distribution can be regarded as the Bayesian probability that the kinetics observed in the atomistic simulation data on the mesoscopic time-scale τ was generated by the CMMM specified by (P,T). An optimization algorithm is used to find the most

  20. Bayesian methods to estimate urban growth potential

    Science.gov (United States)

    Smith, Jordan W.; Smart, Lindsey S.; Dorning, Monica; Dupéy, Lauren Nicole; Méley, Andréanne; Meentemeyer, Ross K.

    2017-01-01

    Urban growth often influences the production of ecosystem services. The impacts of urbanization on landscapes can subsequently affect landowners’ perceptions, values and decisions regarding their land. Within land-use and land-change research, very few models of dynamic landscape-scale processes like urbanization incorporate empirically-grounded landowner decision-making processes. Very little attention has focused on the heterogeneous decision-making processes that aggregate to influence broader-scale patterns of urbanization. We examine the land-use tradeoffs faced by individual landowners in one of the United States’ most rapidly urbanizing regions − the urban area surrounding Charlotte, North Carolina. We focus on the land-use decisions of non-industrial private forest owners located across the region’s development gradient. A discrete choice experiment is used to determine the critical factors influencing individual forest owners’ intent to sell their undeveloped properties across a series of experimentally varied scenarios of urban growth. Data are analyzed using a hierarchical Bayesian approach. The estimates derived from the survey data are used to modify a spatially-explicit trend-based urban development potential model, derived from remotely-sensed imagery and observed changes in the region’s socioeconomic and infrastructural characteristics between 2000 and 2011. This modeling approach combines the theoretical underpinnings of behavioral economics with spatiotemporal data describing a region’s historical development patterns. By integrating empirical social preference data into spatially-explicit urban growth models, we begin to more realistically capture processes as well as patterns that drive the location, magnitude and rates of urban growth.

  1. A variational Bayesian method to inverse problems with impulsive noise

    KAUST Repository

    Jin, Bangti

    2012-01-01

    We propose a novel numerical method for solving inverse problems subject to impulsive noises which possibly contain a large number of outliers. The approach is of Bayesian type, and it exploits a heavy-tailed t distribution for data noise to achieve

  2. Application of Bayesian Methods for Detecting Fraudulent Behavior on Tests

    Science.gov (United States)

    Sinharay, Sandip

    2018-01-01

    Producers and consumers of test scores are increasingly concerned about fraudulent behavior before and during the test. There exist several statistical or psychometric methods for detecting fraudulent behavior on tests. This paper provides a review of the Bayesian approaches among them. Four hitherto-unpublished real data examples are provided to…

  3. Optimisation-Based Solution Methods for Set Partitioning Models

    DEFF Research Database (Denmark)

    Rasmussen, Matias Sevel

    The scheduling of crew, i.e. the construction of work schedules for crew members, is often not a trivial task, but a complex puzzle. The task is complicated by rules, restrictions, and preferences. Therefore, manual solutions as well as solutions from standard software packages are not always su......_cient with respect to solution quality and solution time. Enhancement of the overall solution quality as well as the solution time can be of vital importance to many organisations. The _elds of operations research and mathematical optimisation deal with mathematical modelling of di_cult scheduling problems (among...... other topics). The _elds also deal with the development of sophisticated solution methods for these mathematical models. This thesis describes the set partitioning model which has been widely used for modelling crew scheduling problems. Integer properties for the set partitioning model are shown...

  4. Space-partition method for the variance-based sensitivity analysis: Optimal partition scheme and comparative study

    International Nuclear Information System (INIS)

    Zhai, Qingqing; Yang, Jun; Zhao, Yu

    2014-01-01

    Variance-based sensitivity analysis has been widely studied and asserted itself among practitioners. Monte Carlo simulation methods are well developed in the calculation of variance-based sensitivity indices but they do not make full use of each model run. Recently, several works mentioned a scatter-plot partitioning method to estimate the variance-based sensitivity indices from given data, where a single bunch of samples is sufficient to estimate all the sensitivity indices. This paper focuses on the space-partition method in the estimation of variance-based sensitivity indices, and its convergence and other performances are investigated. Since the method heavily depends on the partition scheme, the influence of the partition scheme is discussed and the optimal partition scheme is proposed based on the minimized estimator's variance. A decomposition and integration procedure is proposed to improve the estimation quality for higher order sensitivity indices. The proposed space-partition method is compared with the more traditional method and test cases show that it outperforms the traditional one

  5. Complexity analysis of accelerated MCMC methods for Bayesian inversion

    International Nuclear Information System (INIS)

    Hoang, Viet Ha; Schwab, Christoph; Stuart, Andrew M

    2013-01-01

    The Bayesian approach to inverse problems, in which the posterior probability distribution on an unknown field is sampled for the purposes of computing posterior expectations of quantities of interest, is starting to become computationally feasible for partial differential equation (PDE) inverse problems. Balancing the sources of error arising from finite-dimensional approximation of the unknown field, the PDE forward solution map and the sampling of the probability space under the posterior distribution are essential for the design of efficient computational Bayesian methods for PDE inverse problems. We study Bayesian inversion for a model elliptic PDE with an unknown diffusion coefficient. We provide complexity analyses of several Markov chain Monte Carlo (MCMC) methods for the efficient numerical evaluation of expectations under the Bayesian posterior distribution, given data δ. Particular attention is given to bounds on the overall work required to achieve a prescribed error level ε. Specifically, we first bound the computational complexity of ‘plain’ MCMC, based on combining MCMC sampling with linear complexity multi-level solvers for elliptic PDE. Our (new) work versus accuracy bounds show that the complexity of this approach can be quite prohibitive. Two strategies for reducing the computational complexity are then proposed and analyzed: first, a sparse, parametric and deterministic generalized polynomial chaos (gpc) ‘surrogate’ representation of the forward response map of the PDE over the entire parameter space, and, second, a novel multi-level Markov chain Monte Carlo strategy which utilizes sampling from a multi-level discretization of the posterior and the forward PDE. For both of these strategies, we derive asymptotic bounds on work versus accuracy, and hence asymptotic bounds on the computational complexity of the algorithms. In particular, we provide sufficient conditions on the regularity of the unknown coefficients of the PDE and on the

  6. Application of an efficient Bayesian discretization method to biomedical data

    Directory of Open Access Journals (Sweden)

    Gopalakrishnan Vanathi

    2011-07-01

    Full Text Available Abstract Background Several data mining methods require data that are discrete, and other methods often perform better with discrete data. We introduce an efficient Bayesian discretization (EBD method for optimal discretization of variables that runs efficiently on high-dimensional biomedical datasets. The EBD method consists of two components, namely, a Bayesian score to evaluate discretizations and a dynamic programming search procedure to efficiently search the space of possible discretizations. We compared the performance of EBD to Fayyad and Irani's (FI discretization method, which is commonly used for discretization. Results On 24 biomedical datasets obtained from high-throughput transcriptomic and proteomic studies, the classification performances of the C4.5 classifier and the naïve Bayes classifier were statistically significantly better when the predictor variables were discretized using EBD over FI. EBD was statistically significantly more stable to the variability of the datasets than FI. However, EBD was less robust, though not statistically significantly so, than FI and produced slightly more complex discretizations than FI. Conclusions On a range of biomedical datasets, a Bayesian discretization method (EBD yielded better classification performance and stability but was less robust than the widely used FI discretization method. The EBD discretization method is easy to implement, permits the incorporation of prior knowledge and belief, and is sufficiently fast for application to high-dimensional data.

  7. Quantifying Uncertainty in Near Surface Electromagnetic Imaging Using Bayesian Methods

    Science.gov (United States)

    Blatter, D. B.; Ray, A.; Key, K.

    2017-12-01

    Geoscientists commonly use electromagnetic methods to image the Earth's near surface. Field measurements of EM fields are made (often with the aid an artificial EM source) and then used to infer near surface electrical conductivity via a process known as inversion. In geophysics, the standard inversion tool kit is robust and can provide an estimate of the Earth's near surface conductivity that is both geologically reasonable and compatible with the measured field data. However, standard inverse methods struggle to provide a sense of the uncertainty in the estimate they provide. This is because the task of finding an Earth model that explains the data to within measurement error is non-unique - that is, there are many, many such models; but the standard methods provide only one "answer." An alternative method, known as Bayesian inversion, seeks to explore the full range of Earth model parameters that can adequately explain the measured data, rather than attempting to find a single, "ideal" model. Bayesian inverse methods can therefore provide a quantitative assessment of the uncertainty inherent in trying to infer near surface conductivity from noisy, measured field data. This study applies a Bayesian inverse method (called trans-dimensional Markov chain Monte Carlo) to transient airborne EM data previously collected over Taylor Valley - one of the McMurdo Dry Valleys in Antarctica. Our results confirm the reasonableness of previous estimates (made using standard methods) of near surface conductivity beneath Taylor Valley. In addition, we demonstrate quantitatively the uncertainty associated with those estimates. We demonstrate that Bayesian inverse methods can provide quantitative uncertainty to estimates of near surface conductivity.

  8. A Bayesian statistical method for particle identification in shower counters

    International Nuclear Information System (INIS)

    Takashimizu, N.; Kimura, A.; Shibata, A.; Sasaki, T.

    2004-01-01

    We report an attempt on identifying particles using a Bayesian statistical method. We have developed the mathematical model and software for this purpose. We tried to identify electrons and charged pions in shower counters using this method. We designed an ideal shower counter and studied the efficiency of identification using Monte Carlo simulation based on Geant4. Without having any other information, e.g. charges of particles which are given by tracking detectors, we have achieved 95% identifications of both particles

  9. Bayesian methods for interpreting plutonium urinalysis data

    International Nuclear Information System (INIS)

    Miller, G.; Inkret, W.C.

    1995-01-01

    The authors discuss an internal dosimetry problem, where measurements of plutonium in urine are used to calculate radiation doses. The authors have developed an algorithm using the MAXENT method. The method gives reasonable results, however the role of the entropy prior distribution is to effectively fit the urine data using intakes occurring close in time to each measured urine result, which is unrealistic. A better approximation for the actual prior is the log-normal distribution; however, with the log-normal distribution another calculational approach must be used. Instead of calculating the most probable values, they turn to calculating expectation values directly from the posterior probability, which is feasible for a small number of intakes

  10. Bayesian maximum posterior probability method for interpreting plutonium urinalysis data

    International Nuclear Information System (INIS)

    Miller, G.; Inkret, W.C.

    1996-01-01

    A new internal dosimetry code for interpreting urinalysis data in terms of radionuclide intakes is described for the case of plutonium. The mathematical method is to maximise the Bayesian posterior probability using an entropy function as the prior probability distribution. A software package (MEMSYS) developed for image reconstruction is used. Some advantages of the new code are that it ensures positive calculated dose, it smooths out fluctuating data, and it provides an estimate of the propagated uncertainty in the calculated doses. (author)

  11. Binary recursive partitioning: background, methods, and application to psychology.

    Science.gov (United States)

    Merkle, Edgar C; Shaffer, Victoria A

    2011-02-01

    Binary recursive partitioning (BRP) is a computationally intensive statistical method that can be used in situations where linear models are often used. Instead of imposing many assumptions to arrive at a tractable statistical model, BRP simply seeks to accurately predict a response variable based on values of predictor variables. The method outputs a decision tree depicting the predictor variables that were related to the response variable, along with the nature of the variables' relationships. No significance tests are involved, and the tree's 'goodness' is judged based on its predictive accuracy. In this paper, we describe BRP methods in a detailed manner and illustrate their use in psychological research. We also provide R code for carrying out the methods.

  12. An Overview of Bayesian Methods for Neural Spike Train Analysis

    Directory of Open Access Journals (Sweden)

    Zhe Chen

    2013-01-01

    Full Text Available Neural spike train analysis is an important task in computational neuroscience which aims to understand neural mechanisms and gain insights into neural circuits. With the advancement of multielectrode recording and imaging technologies, it has become increasingly demanding to develop statistical tools for analyzing large neuronal ensemble spike activity. Here we present a tutorial overview of Bayesian methods and their representative applications in neural spike train analysis, at both single neuron and population levels. On the theoretical side, we focus on various approximate Bayesian inference techniques as applied to latent state and parameter estimation. On the application side, the topics include spike sorting, tuning curve estimation, neural encoding and decoding, deconvolution of spike trains from calcium imaging signals, and inference of neuronal functional connectivity and synchrony. Some research challenges and opportunities for neural spike train analysis are discussed.

  13. A physically based catchment partitioning method for hydrological analysis

    Science.gov (United States)

    Menduni, Giovanni; Riboni, Vittoria

    2000-07-01

    We propose a partitioning method for the topographic surface, which is particularly suitable for hydrological distributed modelling and shallow-landslide distributed modelling. The model provides variable mesh size and appears to be a natural evolution of contour-based digital terrain models. The proposed method allows the drainage network to be derived from the contour lines. The single channels are calculated via a search for the steepest downslope lines. Then, for each network node, the contributing area is determined by means of a search for both steepest upslope and downslope lines. This leads to the basin being partitioned into physically based finite elements delimited by irregular polygons. In particular, the distributed computation of local geomorphological parameters (i.e. aspect, average slope and elevation, main stream length, concentration time, etc.) can be performed easily for each single element. The contributing area system, together with the information on the distribution of geomorphological parameters provide a useful tool for distributed hydrological modelling and simulation of environmental processes such as erosion, sediment transport and shallow landslides.

  14. A Bayesian method for assessing multiscalespecies-habitat relationships

    Science.gov (United States)

    Stuber, Erica F.; Gruber, Lutz F.; Fontaine, Joseph J.

    2017-01-01

    ContextScientists face several theoretical and methodological challenges in appropriately describing fundamental wildlife-habitat relationships in models. The spatial scales of habitat relationships are often unknown, and are expected to follow a multi-scale hierarchy. Typical frequentist or information theoretic approaches often suffer under collinearity in multi-scale studies, fail to converge when models are complex or represent an intractable computational burden when candidate model sets are large.ObjectivesOur objective was to implement an automated, Bayesian method for inference on the spatial scales of habitat variables that best predict animal abundance.MethodsWe introduce Bayesian latent indicator scale selection (BLISS), a Bayesian method to select spatial scales of predictors using latent scale indicator variables that are estimated with reversible-jump Markov chain Monte Carlo sampling. BLISS does not suffer from collinearity, and substantially reduces computation time of studies. We present a simulation study to validate our method and apply our method to a case-study of land cover predictors for ring-necked pheasant (Phasianus colchicus) abundance in Nebraska, USA.ResultsOur method returns accurate descriptions of the explanatory power of multiple spatial scales, and unbiased and precise parameter estimates under commonly encountered data limitations including spatial scale autocorrelation, effect size, and sample size. BLISS outperforms commonly used model selection methods including stepwise and AIC, and reduces runtime by 90%.ConclusionsGiven the pervasiveness of scale-dependency in ecology, and the implications of mismatches between the scales of analyses and ecological processes, identifying the spatial scales over which species are integrating habitat information is an important step in understanding species-habitat relationships. BLISS is a widely applicable method for identifying important spatial scales, propagating scale uncertainty, and

  15. An Adaptively Accelerated Bayesian Deblurring Method with Entropy Prior

    Directory of Open Access Journals (Sweden)

    Yong-Hoon Kim

    2008-05-01

    Full Text Available The development of an efficient adaptively accelerated iterative deblurring algorithm based on Bayesian statistical concept has been reported. Entropy of an image has been used as a “prior” distribution and instead of additive form, used in conventional acceleration methods an exponent form of relaxation constant has been used for acceleration. Thus the proposed method is called hereafter as adaptively accelerated maximum a posteriori with entropy prior (AAMAPE. Based on empirical observations in different experiments, the exponent is computed adaptively using first-order derivatives of the deblurred image from previous two iterations. This exponent improves speed of the AAMAPE method in early stages and ensures stability at later stages of iteration. In AAMAPE method, we also consider the constraint of the nonnegativity and flux conservation. The paper discusses the fundamental idea of the Bayesian image deblurring with the use of entropy as prior, and the analytical analysis of superresolution and the noise amplification characteristics of the proposed method. The experimental results show that the proposed AAMAPE method gives lower RMSE and higher SNR in 44% lesser iterations as compared to nonaccelerated maximum a posteriori with entropy prior (MAPE method. Moreover, AAMAPE followed by wavelet wiener filtering gives better result than the state-of-the-art methods.

  16. Partition wall structure in spent fuel storage pool and construction method for the partition wall

    International Nuclear Information System (INIS)

    Izawa, Masaaki

    1998-01-01

    A partitioning wall for forming cask pits as radiation shielding regions by partitioning inside of a spent fuel storage pool is prepared by covering both surface of a concrete body by shielding metal plates. The metal plate comprises opposed plate units integrated by welding while sandwiching a metal frame as a reinforcing material for the concrete body, the lower end of the units is connected to a floor of a pool by fastening members, and concrete is set while using the metal plate of the units as a frame to form the concrete body. The shielding metal plate has a double walled structure formed by welding a lining plate disposed on the outer surface of the partition wall and a shield plate disposed to the inner side. Then the term for construction can be shortened, and the capacity for storing spent fuels can be increased. (N.H.)

  17. Statistical Bayesian method for reliability evaluation based on ADT data

    Science.gov (United States)

    Lu, Dawei; Wang, Lizhi; Sun, Yusheng; Wang, Xiaohong

    2018-05-01

    Accelerated degradation testing (ADT) is frequently conducted in the laboratory to predict the products’ reliability under normal operating conditions. Two kinds of methods, degradation path models and stochastic process models, are utilized to analyze degradation data and the latter one is the most popular method. However, some limitations like imprecise solution process and estimation result of degradation ratio still exist, which may affect the accuracy of the acceleration model and the extrapolation value. Moreover, the conducted solution of this problem, Bayesian method, lose key information when unifying the degradation data. In this paper, a new data processing and parameter inference method based on Bayesian method is proposed to handle degradation data and solve the problems above. First, Wiener process and acceleration model is chosen; Second, the initial values of degradation model and parameters of prior and posterior distribution under each level is calculated with updating and iteration of estimation values; Third, the lifetime and reliability values are estimated on the basis of the estimation parameters; Finally, a case study is provided to demonstrate the validity of the proposed method. The results illustrate that the proposed method is quite effective and accuracy in estimating the lifetime and reliability of a product.

  18. Advances in Applications of Hierarchical Bayesian Methods with Hydrological Models

    Science.gov (United States)

    Alexander, R. B.; Schwarz, G. E.; Boyer, E. W.

    2017-12-01

    Mechanistic and empirical watershed models are increasingly used to inform water resource decisions. Growing access to historical stream measurements and data from in-situ sensor technologies has increased the need for improved techniques for coupling models with hydrological measurements. Techniques that account for the intrinsic uncertainties of both models and measurements are especially needed. Hierarchical Bayesian methods provide an efficient modeling tool for quantifying model and prediction uncertainties, including those associated with measurements. Hierarchical methods can also be used to explore spatial and temporal variations in model parameters and uncertainties that are informed by hydrological measurements. We used hierarchical Bayesian methods to develop a hybrid (statistical-mechanistic) SPARROW (SPAtially Referenced Regression On Watershed attributes) model of long-term mean annual streamflow across diverse environmental and climatic drainages in 18 U.S. hydrological regions. Our application illustrates the use of a new generation of Bayesian methods that offer more advanced computational efficiencies than the prior generation. Evaluations of the effects of hierarchical (regional) variations in model coefficients and uncertainties on model accuracy indicates improved prediction accuracies (median of 10-50%) but primarily in humid eastern regions, where model uncertainties are one-third of those in arid western regions. Generally moderate regional variability is observed for most hierarchical coefficients. Accounting for measurement and structural uncertainties, using hierarchical state-space techniques, revealed the effects of spatially-heterogeneous, latent hydrological processes in the "localized" drainages between calibration sites; this improved model precision, with only minor changes in regional coefficients. Our study can inform advances in the use of hierarchical methods with hydrological models to improve their integration with stream

  19. Quantum mechanical fragment methods based on partitioning atoms or partitioning coordinates.

    Science.gov (United States)

    Wang, Bo; Yang, Ke R; Xu, Xuefei; Isegawa, Miho; Leverentz, Hannah R; Truhlar, Donald G

    2014-09-16

    atoms for capping dangling bonds, and we have shown that they can greatly improve the accuracy. Finally we present a new approach that goes beyond QM/MM by combining the convenience of molecular mechanics with the accuracy of fitting a potential function to electronic structure calculations on a specific system. To make the latter practical for systems with a large number of degrees of freedom, we developed a method to interpolate between local internal-coordinate fits to the potential energy. A key issue for the application to large systems is that rather than assigning the atoms or monomers to fragments, we assign the internal coordinates to reaction, secondary, and tertiary sets. Thus, we make a partition in coordinate space rather than atom space. Fits to the local dependence of the potential energy on tertiary coordinates are arrayed along a preselected reaction coordinate at a sequence of geometries called anchor points; the potential energy function is called an anchor points reactive potential. Electrostatically embedded fragment methods and the anchor points reactive potential, because they are based on treating an entire system by quantum mechanical electronic structure methods but are affordable for large and complex systems, have the potential to open new areas for accurate simulations where combined QM/MM methods are inadequate.

  20. OCL-BASED TEST CASE GENERATION USING CATEGORY PARTITIONING METHOD

    Directory of Open Access Journals (Sweden)

    A. Jalila

    2015-10-01

    Full Text Available The adoption of fault detection techniques during initial stages of software development life cycle urges to improve reliability of a software product. Specification-based testing is one of the major criterions to detect faults in the requirement specification or design of a software system. However, due to the non-availability of implementation details, test case generation from formal specifications become a challenging task. As a novel approach, the proposed work presents a methodology to generate test cases from OCL (Object constraint Language formal specification using Category Partitioning Method (CPM. The experiment results indicate that the proposed methodology is more effective in revealing specification based faults. Furthermore, it has been observed that OCL and CPM form an excellent combination for performing functional testing at the earliest to improve software quality with reduced cost.

  1. Bayesian methods for chromosome dosimetry following a criticality accident

    International Nuclear Information System (INIS)

    Brame, R.S.; Groer, P.G.

    2003-01-01

    Radiation doses received during a criticality accident will be from a combination of fission spectrum neutrons and gamma rays. It is desirable to estimate the total dose, as well as the neutron and gamma doses. Present methods for dose estimation with chromosome aberrations after a criticality accident use point estimates of the neutron to gamma dose ratio obtained from personnel dosemeters and/or accident reconstruction calculations. In this paper a Bayesian approach to dose estimation with chromosome aberrations is developed that allows the uncertainty of the dose ratio to be considered. Posterior probability densities for the total and the neutron and gamma doses were derived. (author)

  2. Dynamic model based on Bayesian method for energy security assessment

    International Nuclear Information System (INIS)

    Augutis, Juozas; Krikštolaitis, Ričardas; Pečiulytė, Sigita; Žutautaitė, Inga

    2015-01-01

    Highlights: • Methodology for dynamic indicator model construction and forecasting of indicators. • Application of dynamic indicator model for energy system development scenarios. • Expert judgement involvement using Bayesian method. - Abstract: The methodology for the dynamic indicator model construction and forecasting of indicators for the assessment of energy security level is presented in this article. An indicator is a special index, which provides numerical values to important factors for the investigated area. In real life, models of different processes take into account various factors that are time-dependent and dependent on each other. Thus, it is advisable to construct a dynamic model in order to describe these dependences. The energy security indicators are used as factors in the dynamic model. Usually, the values of indicators are obtained from statistical data. The developed dynamic model enables to forecast indicators’ variation taking into account changes in system configuration. The energy system development is usually based on a new object construction. Since the parameters of changes of the new system are not exactly known, information about their influences on indicators could not be involved in the model by deterministic methods. Thus, dynamic indicators’ model based on historical data is adjusted by probabilistic model with the influence of new factors on indicators using the Bayesian method

  3. ObStruct: a method to objectively analyse factors driving population structure using Bayesian ancestry profiles.

    Directory of Open Access Journals (Sweden)

    Velimir Gayevskiy

    Full Text Available Bayesian inference methods are extensively used to detect the presence of population structure given genetic data. The primary output of software implementing these methods are ancestry profiles of sampled individuals. While these profiles robustly partition the data into subgroups, currently there is no objective method to determine whether the fixed factor of interest (e.g. geographic origin correlates with inferred subgroups or not, and if so, which populations are driving this correlation. We present ObStruct, a novel tool to objectively analyse the nature of structure revealed in Bayesian ancestry profiles using established statistical methods. ObStruct evaluates the extent of structural similarity between sampled and inferred populations, tests the significance of population differentiation, provides information on the contribution of sampled and inferred populations to the observed structure and crucially determines whether the predetermined factor of interest correlates with inferred population structure. Analyses of simulated and experimental data highlight ObStruct's ability to objectively assess the nature of structure in populations. We show the method is capable of capturing an increase in the level of structure with increasing time since divergence between simulated populations. Further, we applied the method to a highly structured dataset of 1,484 humans from seven continents and a less structured dataset of 179 Saccharomyces cerevisiae from three regions in New Zealand. Our results show that ObStruct provides an objective metric to classify the degree, drivers and significance of inferred structure, as well as providing novel insights into the relationships between sampled populations, and adds a final step to the pipeline for population structure analyses.

  4. Constructive Epistemic Modeling: A Hierarchical Bayesian Model Averaging Method

    Science.gov (United States)

    Tsai, F. T. C.; Elshall, A. S.

    2014-12-01

    Constructive epistemic modeling is the idea that our understanding of a natural system through a scientific model is a mental construct that continually develops through learning about and from the model. Using the hierarchical Bayesian model averaging (HBMA) method [1], this study shows that segregating different uncertain model components through a BMA tree of posterior model probabilities, model prediction, within-model variance, between-model variance and total model variance serves as a learning tool [2]. First, the BMA tree of posterior model probabilities permits the comparative evaluation of the candidate propositions of each uncertain model component. Second, systemic model dissection is imperative for understanding the individual contribution of each uncertain model component to the model prediction and variance. Third, the hierarchical representation of the between-model variance facilitates the prioritization of the contribution of each uncertain model component to the overall model uncertainty. We illustrate these concepts using the groundwater modeling of a siliciclastic aquifer-fault system. The sources of uncertainty considered are from geological architecture, formation dip, boundary conditions and model parameters. The study shows that the HBMA analysis helps in advancing knowledge about the model rather than forcing the model to fit a particularly understanding or merely averaging several candidate models. [1] Tsai, F. T.-C., and A. S. Elshall (2013), Hierarchical Bayesian model averaging for hydrostratigraphic modeling: Uncertainty segregation and comparative evaluation. Water Resources Research, 49, 5520-5536, doi:10.1002/wrcr.20428. [2] Elshall, A.S., and F. T.-C. Tsai (2014). Constructive epistemic modeling of groundwater flow with geological architecture and boundary condition uncertainty under Bayesian paradigm, Journal of Hydrology, 517, 105-119, doi: 10.1016/j.jhydrol.2014.05.027.

  5. Development and comparison of Bayesian modularization method in uncertainty assessment of hydrological models

    Science.gov (United States)

    Li, L.; Xu, C.-Y.; Engeland, K.

    2012-04-01

    With respect to model calibration, parameter estimation and analysis of uncertainty sources, different approaches have been used in hydrological models. Bayesian method is one of the most widely used methods for uncertainty assessment of hydrological models, which incorporates different sources of information into a single analysis through Bayesian theorem. However, none of these applications can well treat the uncertainty in extreme flows of hydrological models' simulations. This study proposes a Bayesian modularization method approach in uncertainty assessment of conceptual hydrological models by considering the extreme flows. It includes a comprehensive comparison and evaluation of uncertainty assessments by a new Bayesian modularization method approach and traditional Bayesian models using the Metropolis Hasting (MH) algorithm with the daily hydrological model WASMOD. Three likelihood functions are used in combination with traditional Bayesian: the AR (1) plus Normal and time period independent model (Model 1), the AR (1) plus Normal and time period dependent model (Model 2) and the AR (1) plus multi-normal model (Model 3). The results reveal that (1) the simulations derived from Bayesian modularization method are more accurate with the highest Nash-Sutcliffe efficiency value, and (2) the Bayesian modularization method performs best in uncertainty estimates of entire flows and in terms of the application and computational efficiency. The study thus introduces a new approach for reducing the extreme flow's effect on the discharge uncertainty assessment of hydrological models via Bayesian. Keywords: extreme flow, uncertainty assessment, Bayesian modularization, hydrological model, WASMOD

  6. A Bayesian-probability-based method for assigning protein backbone dihedral angles based on chemical shifts and local sequences

    Energy Technology Data Exchange (ETDEWEB)

    Wang Jun; Liu Haiyan [University of Science and Technology of China, Hefei National Laboratory for Physical Sciences at the Microscale, and Key Laboratory of Structural Biology, School of Life Sciences (China)], E-mail: hyliu@ustc.edu.cn

    2007-01-15

    Chemical shifts contain substantial information about protein local conformations. We present a method to assign individual protein backbone dihedral angles into specific regions on the Ramachandran map based on the amino acid sequences and the chemical shifts of backbone atoms of tripeptide segments. The method uses a scoring function derived from the Bayesian probability for the central residue of a query tripeptide segment to have a particular conformation. The Ramachandran map is partitioned into representative regions at two levels of resolution. The lower resolution partitioning is equivalent to the conventional definitions of different secondary structure regions on the map. At the higher resolution level, the {alpha} and {beta} regions are further divided into subregions. Predictions are attempted at both levels of resolution. We compared our method with TALOS using the original TALOS database, and obtained comparable results. Although TALOS may produce the best results with currently available databases which are much enlarged, the Bayesian-probability-based approach can provide a quantitative measure for the reliability of predictions.

  7. A dynamic discretization method for reliability inference in Dynamic Bayesian Networks

    International Nuclear Information System (INIS)

    Zhu, Jiandao; Collette, Matthew

    2015-01-01

    The material and modeling parameters that drive structural reliability analysis for marine structures are subject to a significant uncertainty. This is especially true when time-dependent degradation mechanisms such as structural fatigue cracking are considered. Through inspection and monitoring, information such as crack location and size can be obtained to improve these parameters and the corresponding reliability estimates. Dynamic Bayesian Networks (DBNs) are a powerful and flexible tool to model dynamic system behavior and update reliability and uncertainty analysis with life cycle data for problems such as fatigue cracking. However, a central challenge in using DBNs is the need to discretize certain types of continuous random variables to perform network inference while still accurately tracking low-probability failure events. Most existing discretization methods focus on getting the overall shape of the distribution correct, with less emphasis on the tail region. Therefore, a novel scheme is presented specifically to estimate the likelihood of low-probability failure events. The scheme is an iterative algorithm which dynamically partitions the discretization intervals at each iteration. Through applications to two stochastic crack-growth example problems, the algorithm is shown to be robust and accurate. Comparisons are presented between the proposed approach and existing methods for the discretization problem. - Highlights: • A dynamic discretization method is developed for low-probability events in DBNs. • The method is compared to existing approaches on two crack growth problems. • The method is shown to improve on existing methods for low-probability events

  8. A Bayesian method for detecting pairwise associations in compositional data.

    Directory of Open Access Journals (Sweden)

    Emma Schwager

    2017-11-01

    Full Text Available Compositional data consist of vectors of proportions normalized to a constant sum from a basis of unobserved counts. The sum constraint makes inference on correlations between unconstrained features challenging due to the information loss from normalization. However, such correlations are of long-standing interest in fields including ecology. We propose a novel Bayesian framework (BAnOCC: Bayesian Analysis of Compositional Covariance to estimate a sparse precision matrix through a LASSO prior. The resulting posterior, generated by MCMC sampling, allows uncertainty quantification of any function of the precision matrix, including the correlation matrix. We also use a first-order Taylor expansion to approximate the transformation from the unobserved counts to the composition in order to investigate what characteristics of the unobserved counts can make the correlations more or less difficult to infer. On simulated datasets, we show that BAnOCC infers the true network as well as previous methods while offering the advantage of posterior inference. Larger and more realistic simulated datasets further showed that BAnOCC performs well as measured by type I and type II error rates. Finally, we apply BAnOCC to a microbial ecology dataset from the Human Microbiome Project, which in addition to reproducing established ecological results revealed unique, competition-based roles for Proteobacteria in multiple distinct habitats.

  9. Bayesian statistic methods and theri application in probabilistic simulation models

    Directory of Open Access Journals (Sweden)

    Sergio Iannazzo

    2007-03-01

    Full Text Available Bayesian statistic methods are facing a rapidly growing level of interest and acceptance in the field of health economics. The reasons of this success are probably to be found on the theoretical fundaments of the discipline that make these techniques more appealing to decision analysis. To this point should be added the modern IT progress that has developed different flexible and powerful statistical software framework. Among them probably one of the most noticeably is the BUGS language project and its standalone application for MS Windows WinBUGS. Scope of this paper is to introduce the subject and to show some interesting applications of WinBUGS in developing complex economical models based on Markov chains. The advantages of this approach reside on the elegance of the code produced and in its capability to easily develop probabilistic simulations. Moreover an example of the integration of bayesian inference models in a Markov model is shown. This last feature let the analyst conduce statistical analyses on the available sources of evidence and exploit them directly as inputs in the economic model.

  10. Analyzing bioassay data using Bayesian methods -- A primer

    Energy Technology Data Exchange (ETDEWEB)

    Miller, G.; Inkret, W.C.; Schillaci, M.E.; Martz, H.F.; Little, T.T.

    2000-06-01

    The classical statistics approach used in health physics for the interpretation of measurements is deficient in that it does not take into account needle in a haystack effects, that is, correct identification of events that are rare in a population. This is often the case in health physics measurements, and the false positive fraction (the fraction of results measuring positive that are actually zero) is often very large using the prescriptions of classical statistics. Bayesian statistics provides a methodology to minimize the number of incorrect decisions (wrong calls): false positives and false negatives. The authors present the basic method and a heuristic discussion. Examples are given using numerically generated and real bioassay data for tritium. Various analytical models are used to fit the prior probability distribution in order to test the sensitivity to choice of model. Parametric studies show that for typical situations involving rare events the normalized Bayesian decision level k{sub {alpha}} = L{sub c}/{sigma}{sub 0}, where {sigma}{sub 0} is the measurement uncertainty for zero true amount, is in the range of 3 to 5 depending on the true positive rate. Four times {sigma}{sub 0} rather than approximately two times {sigma}{sub 0}, as in classical statistics, would seem a better choice for the decision level in these situations.

  11. Axiomatic method of partitions in the theory of Noebeling spaces. I. Improvement of partition connectivity

    International Nuclear Information System (INIS)

    Ageev, S M

    2007-01-01

    The Noebeling space N k 2k+1 , a k-dimensional analogue of the Hilbert space, is considered; this is a topologically complete separable (that is, Polish) k-dimensional absolute extensor in dimension k (that is, AE(k)) and a strongly k-universal space. The conjecture that the above-listed properties characterize the Noebeling space N k 2k+1 in an arbitrary finite dimension k is proved. In the first part of the paper a full axiom system of the Noebeling spaces is presented and the problem of the improvement of a partition connectivity is solved on its basis. Bibliography: 29 titles.

  12. THz-SAR Vibrating Target Imaging via the Bayesian Method

    Directory of Open Access Journals (Sweden)

    Bin Deng

    2017-01-01

    Full Text Available Target vibration bears important information for target recognition, and terahertz, due to significant micro-Doppler effects, has strong advantages for remotely sensing vibrations. In this paper, the imaging characteristics of vibrating targets with THz-SAR are at first analyzed. An improved algorithm based on an excellent Bayesian approach, that is, the expansion-compression variance-component (ExCoV method, has been proposed for reconstructing scattering coefficients of vibrating targets, which provides more robust and efficient initialization and overcomes the deficiencies of sidelobes as well as artifacts arising from the traditional correlation method. A real vibration measurement experiment of idle cars was performed to validate the range model. Simulated SAR data of vibrating targets and a tank model in a real background in 220 GHz show good performance at low SNR. Rapidly evolving high-power terahertz devices will offer viable THz-SAR application at a distance of several kilometers.

  13. Bayesian methods in the search for MH370

    CERN Document Server

    Davey, Sam; Holland, Ian; Rutten, Mark; Williams, Jason

    2016-01-01

    This book demonstrates how nonlinear/non-Gaussian Bayesian time series estimation methods were used to produce a probability distribution of potential MH370 flight paths. It provides details of how the probabilistic models of aircraft flight dynamics, satellite communication system measurements, environmental effects and radar data were constructed and calibrated. The probability distribution was used to define the search zone in the southern Indian Ocean. The book describes particle-filter based numerical calculation of the aircraft flight-path probability distribution and validates the method using data from several of the involved aircraft’s previous flights. Finally it is shown how the Reunion Island flaperon debris find affects the search probability distribution.

  14. A variational Bayesian method to inverse problems with impulsive noise

    KAUST Repository

    Jin, Bangti

    2012-01-01

    We propose a novel numerical method for solving inverse problems subject to impulsive noises which possibly contain a large number of outliers. The approach is of Bayesian type, and it exploits a heavy-tailed t distribution for data noise to achieve robustness with respect to outliers. A hierarchical model with all hyper-parameters automatically determined from the given data is described. An algorithm of variational type by minimizing the Kullback-Leibler divergence between the true posteriori distribution and a separable approximation is developed. The numerical method is illustrated on several one- and two-dimensional linear and nonlinear inverse problems arising from heat conduction, including estimating boundary temperature, heat flux and heat transfer coefficient. The results show its robustness to outliers and the fast and steady convergence of the algorithm. © 2011 Elsevier Inc.

  15. The maximum entropy method of moments and Bayesian probability theory

    Science.gov (United States)

    Bretthorst, G. Larry

    2013-08-01

    The problem of density estimation occurs in many disciplines. For example, in MRI it is often necessary to classify the types of tissues in an image. To perform this classification one must first identify the characteristics of the tissues to be classified. These characteristics might be the intensity of a T1 weighted image and in MRI many other types of characteristic weightings (classifiers) may be generated. In a given tissue type there is no single intensity that characterizes the tissue, rather there is a distribution of intensities. Often this distributions can be characterized by a Gaussian, but just as often it is much more complicated. Either way, estimating the distribution of intensities is an inference problem. In the case of a Gaussian distribution, one must estimate the mean and standard deviation. However, in the Non-Gaussian case the shape of the density function itself must be inferred. Three common techniques for estimating density functions are binned histograms [1, 2], kernel density estimation [3, 4], and the maximum entropy method of moments [5, 6]. In the introduction, the maximum entropy method of moments will be reviewed. Some of its problems and conditions under which it fails will be discussed. Then in later sections, the functional form of the maximum entropy method of moments probability distribution will be incorporated into Bayesian probability theory. It will be shown that Bayesian probability theory solves all of the problems with the maximum entropy method of moments. One gets posterior probabilities for the Lagrange multipliers, and, finally, one can put error bars on the resulting estimated density function.

  16. Modeling error distributions of growth curve models through Bayesian methods.

    Science.gov (United States)

    Zhang, Zhiyong

    2016-06-01

    Growth curve models are widely used in social and behavioral sciences. However, typical growth curve models often assume that the errors are normally distributed although non-normal data may be even more common than normal data. In order to avoid possible statistical inference problems in blindly assuming normality, a general Bayesian framework is proposed to flexibly model normal and non-normal data through the explicit specification of the error distributions. A simulation study shows when the distribution of the error is correctly specified, one can avoid the loss in the efficiency of standard error estimates. A real example on the analysis of mathematical ability growth data from the Early Childhood Longitudinal Study, Kindergarten Class of 1998-99 is used to show the application of the proposed methods. Instructions and code on how to conduct growth curve analysis with both normal and non-normal error distributions using the the MCMC procedure of SAS are provided.

  17. Bayesian signal processing classical, modern, and particle filtering methods

    CERN Document Server

    Candy, James V

    2016-01-01

    This book aims to give readers a unified Bayesian treatment starting from the basics (Baye's rule) to the more advanced (Monte Carlo sampling), evolving to the next-generation model-based techniques (sequential Monte Carlo sampling). This next edition incorporates a new chapter on "Sequential Bayesian Detection," a new section on "Ensemble Kalman Filters" as well as an expansion of Case Studies that detail Bayesian solutions for a variety of applications. These studies illustrate Bayesian approaches to real-world problems incorporating detailed particle filter designs, adaptive particle filters and sequential Bayesian detectors. In addition to these major developments a variety of sections are expanded to "fill-in-the gaps" of the first edition. Here metrics for particle filter (PF) designs with emphasis on classical "sanity testing" lead to ensemble techniques as a basic requirement for performance analysis. The expansion of information theory metrics and their application to PF designs is fully developed an...

  18. Development and comparison in uncertainty assessment based Bayesian modularization method in hydrological modeling

    Science.gov (United States)

    Li, Lu; Xu, Chong-Yu; Engeland, Kolbjørn

    2013-04-01

    SummaryWith respect to model calibration, parameter estimation and analysis of uncertainty sources, various regression and probabilistic approaches are used in hydrological modeling. A family of Bayesian methods, which incorporates different sources of information into a single analysis through Bayes' theorem, is widely used for uncertainty assessment. However, none of these approaches can well treat the impact of high flows in hydrological modeling. This study proposes a Bayesian modularization uncertainty assessment approach in which the highest streamflow observations are treated as suspect information that should not influence the inference of the main bulk of the model parameters. This study includes a comprehensive comparison and evaluation of uncertainty assessments by our new Bayesian modularization method and standard Bayesian methods using the Metropolis-Hastings (MH) algorithm with the daily hydrological model WASMOD. Three likelihood functions were used in combination with standard Bayesian method: the AR(1) plus Normal model independent of time (Model 1), the AR(1) plus Normal model dependent on time (Model 2) and the AR(1) plus Multi-normal model (Model 3). The results reveal that the Bayesian modularization method provides the most accurate streamflow estimates measured by the Nash-Sutcliffe efficiency and provide the best in uncertainty estimates for low, medium and entire flows compared to standard Bayesian methods. The study thus provides a new approach for reducing the impact of high flows on the discharge uncertainty assessment of hydrological models via Bayesian method.

  19. Applying the partitioned multiobjective risk method (PMRM) to portfolio selection.

    Science.gov (United States)

    Reyes Santos, Joost; Haimes, Yacov Y

    2004-06-01

    The analysis of risk-return tradeoffs and their practical applications to portfolio analysis paved the way for Modern Portfolio Theory (MPT), which won Harry Markowitz a 1992 Nobel Prize in Economics. A typical approach in measuring a portfolio's expected return is based on the historical returns of the assets included in a portfolio. On the other hand, portfolio risk is usually measured using volatility, which is derived from the historical variance-covariance relationships among the portfolio assets. This article focuses on assessing portfolio risk, with emphasis on extreme risks. To date, volatility is a major measure of risk owing to its simplicity and validity for relatively small asset price fluctuations. Volatility is a justified measure for stable market performance, but it is weak in addressing portfolio risk under aberrant market fluctuations. Extreme market crashes such as that on October 19, 1987 ("Black Monday") and catastrophic events such as the terrorist attack of September 11, 2001 that led to a four-day suspension of trading on the New York Stock Exchange (NYSE) are a few examples where measuring risk via volatility can lead to inaccurate predictions. Thus, there is a need for a more robust metric of risk. By invoking the principles of the extreme-risk-analysis method through the partitioned multiobjective risk method (PMRM), this article contributes to the modeling of extreme risks in portfolio performance. A measure of an extreme portfolio risk, denoted by f(4), is defined as the conditional expectation for a lower-tail region of the distribution of the possible portfolio returns. This article presents a multiobjective problem formulation consisting of optimizing expected return and f(4), whose solution is determined using Evolver-a software that implements a genetic algorithm. Under business-as-usual market scenarios, the results of the proposed PMRM portfolio selection model are found to be compatible with those of the volatility-based model

  20. The current state of Bayesian methods in medical product development: survey results and recommendations from the DIA Bayesian Scientific Working Group.

    Science.gov (United States)

    Natanegara, Fanni; Neuenschwander, Beat; Seaman, John W; Kinnersley, Nelson; Heilmann, Cory R; Ohlssen, David; Rochester, George

    2014-01-01

    Bayesian applications in medical product development have recently gained popularity. Despite many advances in Bayesian methodology and computations, increase in application across the various areas of medical product development has been modest. The DIA Bayesian Scientific Working Group (BSWG), which includes representatives from industry, regulatory agencies, and academia, has adopted the vision to ensure Bayesian methods are well understood, accepted more broadly, and appropriately utilized to improve decision making and enhance patient outcomes. As Bayesian applications in medical product development are wide ranging, several sub-teams were formed to focus on various topics such as patient safety, non-inferiority, prior specification, comparative effectiveness, joint modeling, program-wide decision making, analytical tools, and education. The focus of this paper is on the recent effort of the BSWG Education sub-team to administer a Bayesian survey to statisticians across 17 organizations involved in medical product development. We summarize results of this survey, from which we provide recommendations on how to accelerate progress in Bayesian applications throughout medical product development. The survey results support findings from the literature and provide additional insight on regulatory acceptance of Bayesian methods and information on the need for a Bayesian infrastructure within an organization. The survey findings support the claim that only modest progress in areas of education and implementation has been made recently, despite substantial progress in Bayesian statistical research and software availability. Copyright © 2013 John Wiley & Sons, Ltd.

  1. Data partitions, Bayesian analysis and phylogeny of the zygomycetous fungal family Mortierellaceae, inferred from nuclear ribosomal DNA sequences.

    Directory of Open Access Journals (Sweden)

    Tamás Petkovits

    Full Text Available Although the fungal order Mortierellales constitutes one of the largest classical groups of Zygomycota, its phylogeny is poorly understood and no modern taxonomic revision is currently available. In the present study, 90 type and reference strains were used to infer a comprehensive phylogeny of Mortierellales from the sequence data of the complete ITS region and the LSU and SSU genes with a special attention to the monophyly of the genus Mortierella. Out of 15 alternative partitioning strategies compared on the basis of Bayes factors, the one with the highest number of partitions was found optimal (with mixture models yielding the best likelihood and tree length values, implying a higher complexity of evolutionary patterns in the ribosomal genes than generally recognized. Modeling the ITS1, 5.8S, and ITS2, loci separately improved model fit significantly as compared to treating all as one and the same partition. Further, within-partition mixture models suggests that not only the SSU, LSU and ITS regions evolve under qualitatively and/or quantitatively different constraints, but that significant heterogeneity can be found within these loci also. The phylogenetic analysis indicated that the genus Mortierella is paraphyletic with respect to the genera Dissophora, Gamsiella and Lobosporangium and the resulting phylogeny contradict previous, morphology-based sectional classification of Mortierella. Based on tree structure and phenotypic traits, we recognize 12 major clades, for which we attempt to summarize phenotypic similarities. M. longicollis is closely related to the outgroup taxon Rhizopus oryzae, suggesting that it belongs to the Mucorales. Our results demonstrate that traits used in previous classifications of the Mortierellales are highly homoplastic and that the Mortierellales is in a need of a reclassification, where new, phylogenetically informative phenotypic traits should be identified, with molecular phylogenies playing a decisive role.

  2. Metainference: A Bayesian inference method for heterogeneous systems.

    Science.gov (United States)

    Bonomi, Massimiliano; Camilloni, Carlo; Cavalli, Andrea; Vendruscolo, Michele

    2016-01-01

    Modeling a complex system is almost invariably a challenging task. The incorporation of experimental observations can be used to improve the quality of a model and thus to obtain better predictions about the behavior of the corresponding system. This approach, however, is affected by a variety of different errors, especially when a system simultaneously populates an ensemble of different states and experimental data are measured as averages over such states. To address this problem, we present a Bayesian inference method, called "metainference," that is able to deal with errors in experimental measurements and with experimental measurements averaged over multiple states. To achieve this goal, metainference models a finite sample of the distribution of models using a replica approach, in the spirit of the replica-averaging modeling based on the maximum entropy principle. To illustrate the method, we present its application to a heterogeneous model system and to the determination of an ensemble of structures corresponding to the thermal fluctuations of a protein molecule. Metainference thus provides an approach to modeling complex systems with heterogeneous components and interconverting between different states by taking into account all possible sources of errors.

  3. CEO emotional bias and investment decision, Bayesian network method

    Directory of Open Access Journals (Sweden)

    Jarboui Anis

    2012-08-01

    Full Text Available This research examines the determinants of firms’ investment introducing a behavioral perspective that has received little attention in corporate finance literature. The following central hypothesis emerges from a set of recently developed theories: Investment decisions are influenced not only by their fundamentals but also depend on some other factors. One factor is the biasness of any CEO to their investment, biasness depends on the cognition and emotions, because some leaders use them as heuristic for the investment decision instead of fundamentals. This paper shows how CEO emotional bias (optimism, loss aversion and overconfidence affects the investment decisions. The proposed model of this paper uses Bayesian Network Method to examine this relationship. Emotional bias has been measured by means of a questionnaire comprising several items. As for the selected sample, it has been composed of some 100 Tunisian executives. Our results have revealed that the behavioral analysis of investment decision implies leader affected by behavioral biases (optimism, loss aversion, and overconfidence adjusts its investment choices based on their ability to assess alternatives (optimism and overconfidence and risk perception (loss aversion to create of shareholder value and ensure its place at the head of the management team.

  4. A generic method for estimating system reliability using Bayesian networks

    International Nuclear Information System (INIS)

    Doguc, Ozge; Ramirez-Marquez, Jose Emmanuel

    2009-01-01

    This study presents a holistic method for constructing a Bayesian network (BN) model for estimating system reliability. BN is a probabilistic approach that is used to model and predict the behavior of a system based on observed stochastic events. The BN model is a directed acyclic graph (DAG) where the nodes represent system components and arcs represent relationships among them. Although recent studies on using BN for estimating system reliability have been proposed, they are based on the assumption that a pre-built BN has been designed to represent the system. In these studies, the task of building the BN is typically left to a group of specialists who are BN and domain experts. The BN experts should learn about the domain before building the BN, which is generally very time consuming and may lead to incorrect deductions. As there are no existing studies to eliminate the need for a human expert in the process of system reliability estimation, this paper introduces a method that uses historical data about the system to be modeled as a BN and provides efficient techniques for automated construction of the BN model, and hence estimation of the system reliability. In this respect K2, a data mining algorithm, is used for finding associations between system components, and thus building the BN model. This algorithm uses a heuristic to provide efficient and accurate results while searching for associations. Moreover, no human intervention is necessary during the process of BN construction and reliability estimation. The paper provides a step-by-step illustration of the method and evaluation of the approach with literature case examples

  5. A generic method for estimating system reliability using Bayesian networks

    Energy Technology Data Exchange (ETDEWEB)

    Doguc, Ozge [Stevens Institute of Technology, Hoboken, NJ 07030 (United States); Ramirez-Marquez, Jose Emmanuel [Stevens Institute of Technology, Hoboken, NJ 07030 (United States)], E-mail: jmarquez@stevens.edu

    2009-02-15

    This study presents a holistic method for constructing a Bayesian network (BN) model for estimating system reliability. BN is a probabilistic approach that is used to model and predict the behavior of a system based on observed stochastic events. The BN model is a directed acyclic graph (DAG) where the nodes represent system components and arcs represent relationships among them. Although recent studies on using BN for estimating system reliability have been proposed, they are based on the assumption that a pre-built BN has been designed to represent the system. In these studies, the task of building the BN is typically left to a group of specialists who are BN and domain experts. The BN experts should learn about the domain before building the BN, which is generally very time consuming and may lead to incorrect deductions. As there are no existing studies to eliminate the need for a human expert in the process of system reliability estimation, this paper introduces a method that uses historical data about the system to be modeled as a BN and provides efficient techniques for automated construction of the BN model, and hence estimation of the system reliability. In this respect K2, a data mining algorithm, is used for finding associations between system components, and thus building the BN model. This algorithm uses a heuristic to provide efficient and accurate results while searching for associations. Moreover, no human intervention is necessary during the process of BN construction and reliability estimation. The paper provides a step-by-step illustration of the method and evaluation of the approach with literature case examples.

  6. Wavelet-Based Bayesian Methods for Image Analysis and Automatic Target Recognition

    National Research Council Canada - National Science Library

    Nowak, Robert

    2001-01-01

    .... We have developed two new techniques. First, we have develop a wavelet-based approach to image restoration and deconvolution problems using Bayesian image models and an alternating-maximation method...

  7. Involving stakeholders in building integrated fisheries models using Bayesian methods

    DEFF Research Database (Denmark)

    Haapasaari, Päivi Elisabet; Mäntyniemi, Samu; Kuikka, Sakari

    2013-01-01

    the potential of the study to contribute to the development of participatory modeling practices. It is concluded that the subjective perspective to knowledge, that is fundamental in Bayesian theory, suits participatory modeling better than a positivist paradigm that seeks the objective truth. The methodology...

  8. An Importance Sampling Simulation Method for Bayesian Decision Feedback Equalizers

    OpenAIRE

    Chen, S.; Hanzo, L.

    2000-01-01

    An importance sampling (IS) simulation technique is presented for evaluating the lower-bound bit error rate (BER) of the Bayesian decision feedback equalizer (DFE) under the assumption of correct decisions being fed back. A design procedure is developed, which chooses appropriate bias vectors for the simulation density to ensure asymptotic efficiency of the IS simulation.

  9. Markov Chain Monte Carlo Methods for Bayesian Data Analysis in Astronomy

    Science.gov (United States)

    Sharma, Sanjib

    2017-08-01

    Markov Chain Monte Carlo based Bayesian data analysis has now become the method of choice for analyzing and interpreting data in almost all disciplines of science. In astronomy, over the last decade, we have also seen a steady increase in the number of papers that employ Monte Carlo based Bayesian analysis. New, efficient Monte Carlo based methods are continuously being developed and explored. In this review, we first explain the basics of Bayesian theory and discuss how to set up data analysis problems within this framework. Next, we provide an overview of various Monte Carlo based methods for performing Bayesian data analysis. Finally, we discuss advanced ideas that enable us to tackle complex problems and thus hold great promise for the future. We also distribute downloadable computer software (available at https://github.com/sanjibs/bmcmc/ ) that implements some of the algorithms and examples discussed here.

  10. Bayesian Methods for Predicting the Shape of Chinese Yam in Terms of Key Diameters

    Directory of Open Access Journals (Sweden)

    Mitsunori Kayano

    2017-01-01

    Full Text Available This paper proposes Bayesian methods for the shape estimation of Chinese yam (Dioscorea opposita using a few key diameters of yam. Shape prediction of yam is applicable to determining optimal cutoff positions of a yam for producing seed yams. Our Bayesian method, which is a combination of Bayesian estimation model and predictive model, enables automatic, rapid, and low-cost processing of yam. After the construction of the proposed models using a sample data set in Japan, the models provide whole shape prediction of yam based on only a few key diameters. The Bayesian method performed well on the shape prediction in terms of minimizing the mean squared error between measured shape and the prediction. In particular, a multiple regression method with key diameters at two fixed positions attained the highest performance for shape prediction. We have developed automatic, rapid, and low-cost yam-processing machines based on the Bayesian estimation model and predictive model. Development of such shape prediction approaches, including our Bayesian method, can be a valuable aid in reducing the cost and time in food processing.

  11. Review of bayesian statistical analysis methods for cytogenetic radiation biodosimetry, with a practical example

    International Nuclear Information System (INIS)

    Ainsbury, Elizabeth A.; Lloyd, David C.; Rothkamm, Kai; Vinnikov, Volodymyr A.; Maznyk, Nataliya A.; Puig, Pedro; Higueras, Manuel

    2014-01-01

    Classical methods of assessing the uncertainty associated with radiation doses estimated using cytogenetic techniques are now extremely well defined. However, several authors have suggested that a Bayesian approach to uncertainty estimation may be more suitable for cytogenetic data, which are inherently stochastic in nature. The Bayesian analysis framework focuses on identification of probability distributions (for yield of aberrations or estimated dose), which also means that uncertainty is an intrinsic part of the analysis, rather than an 'afterthought'. In this paper Bayesian, as well as some more advanced classical, data analysis methods for radiation cytogenetics are reviewed that have been proposed in the literature. A practical overview of Bayesian cytogenetic dose estimation is also presented, with worked examples from the literature. (authors)

  12. Evidence reasoning method for constructing conditional probability tables in a Bayesian network of multimorbidity.

    Science.gov (United States)

    Du, Yuanwei; Guo, Yubin

    2015-01-01

    The intrinsic mechanism of multimorbidity is difficult to recognize and prediction and diagnosis are difficult to carry out accordingly. Bayesian networks can help to diagnose multimorbidity in health care, but it is difficult to obtain the conditional probability table (CPT) because of the lack of clinically statistical data. Today, expert knowledge and experience are increasingly used in training Bayesian networks in order to help predict or diagnose diseases, but the CPT in Bayesian networks is usually irrational or ineffective for ignoring realistic constraints especially in multimorbidity. In order to solve these problems, an evidence reasoning (ER) approach is employed to extract and fuse inference data from experts using a belief distribution and recursive ER algorithm, based on which evidence reasoning method for constructing conditional probability tables in Bayesian network of multimorbidity is presented step by step. A multimorbidity numerical example is used to demonstrate the method and prove its feasibility and application. Bayesian network can be determined as long as the inference assessment is inferred by each expert according to his/her knowledge or experience. Our method is more effective than existing methods for extracting expert inference data accurately and is fused effectively for constructing CPTs in a Bayesian network of multimorbidity.

  13. Bayesian inference method for stochastic damage accumulation modeling

    International Nuclear Information System (INIS)

    Jiang, Xiaomo; Yuan, Yong; Liu, Xian

    2013-01-01

    Damage accumulation based reliability model plays an increasingly important role in successful realization of condition based maintenance for complicated engineering systems. This paper developed a Bayesian framework to establish stochastic damage accumulation model from historical inspection data, considering data uncertainty. Proportional hazards modeling technique is developed to model the nonlinear effect of multiple influencing factors on system reliability. Different from other hazard modeling techniques such as normal linear regression model, the approach does not require any distribution assumption for the hazard model, and can be applied for a wide variety of distribution models. A Bayesian network is created to represent the nonlinear proportional hazards models and to estimate model parameters by Bayesian inference with Markov Chain Monte Carlo simulation. Both qualitative and quantitative approaches are developed to assess the validity of the established damage accumulation model. Anderson–Darling goodness-of-fit test is employed to perform the normality test, and Box–Cox transformation approach is utilized to convert the non-normality data into normal distribution for hypothesis testing in quantitative model validation. The methodology is illustrated with the seepage data collected from real-world subway tunnels.

  14. Analyzing bioassay data using Bayesian methods-A primer

    International Nuclear Information System (INIS)

    Miller, G.; Inkret, W.C.; Schillaci, M.E.

    1997-01-01

    The classical statistics approach used in health physics for the interpretation of measurements is deficient in that it does not allow for the consideration of needle in a haystack effects, where events that are rare in a population are being detected. In fact, this is often the case in health physics measurements, and the false positive fraction is often very large using the prescriptions of classical statistics. Bayesian statistics provides an objective methodology to ensure acceptably small false positive fractions. The authors present the basic methodology and a heuristic discussion. Examples are given using numerically generated and real bioassay data (Tritium). Various analytical models are used to fit the prior probability distribution, in order to test the sensitivity to choice of model. Parametric studies show that the normalized Bayesian decision level k α -L c /σ 0 , where σ 0 is the measurement uncertainty for zero true amount, is usually in the range from 3 to 5 depending on the true positive rate. Four times σ 0 rather than approximately two times σ 0 , as in classical statistics, would often seem a better choice for the decision level

  15. Coupling of partitioned physics codes with quasi-Newton methods

    CSIR Research Space (South Africa)

    Haelterman, R

    2017-03-01

    Full Text Available , A class of methods for solving nonlinear simultaneous equations. Math. Comp. 19, pp. 577–593 (1965) [3] C.G. Broyden, Quasi-Newton methods and their applications to function minimization. Math. Comp. 21, pp. 368–381 (1967) [4] J.E. Dennis, J.J. More...´, Quasi-Newton methods: motivation and theory. SIAM Rev. 19, pp. 46–89 (1977) [5] J.E. Dennis, R.B. Schnabel, Least Change Secant Updates for quasi- Newton methods. SIAM Rev. 21, pp. 443–459 (1979) [6] G. Dhondt, CalculiX CrunchiX USER’S MANUAL Version 2...

  16. A Family of Trigonometrically-fitted Partitioned Runge-Kutta Symplectic Methods

    International Nuclear Information System (INIS)

    Monovasilis, Th.; Kalogiratou, Z.; Simos, T. E.

    2007-01-01

    We are presenting a family of trigonometrically fitted partitioned Runge-Kutta symplectic methods of fourth order with six stages. The solution of the one dimensional time independent Schroedinger equation is considered by trigonometrically fitted symplectic integrators. The Schroedinger equation is first transformed into a Hamiltonian canonical equation. Numerical results are obtained for the one-dimensional harmonic oscillator and the exponential potential

  17. Review of Reliability-Based Design Optimization Approach and Its Integration with Bayesian Method

    Science.gov (United States)

    Zhang, Xiangnan

    2018-03-01

    A lot of uncertain factors lie in practical engineering, such as external load environment, material property, geometrical shape, initial condition, boundary condition, etc. Reliability method measures the structural safety condition and determine the optimal design parameter combination based on the probabilistic theory. Reliability-based design optimization (RBDO) is the most commonly used approach to minimize the structural cost or other performance under uncertainty variables which combines the reliability theory and optimization. However, it cannot handle the various incomplete information. The Bayesian approach is utilized to incorporate this kind of incomplete information in its uncertainty quantification. In this paper, the RBDO approach and its integration with Bayesian method are introduced.

  18. Safety assessment of infrastructures using a new Bayesian Monte Carlo method

    NARCIS (Netherlands)

    Rajabali Nejad, Mohammadreza; Demirbilek, Z.

    2011-01-01

    A recently developed Bayesian Monte Carlo (BMC) method and its application to safety assessment of structures are described in this paper. We use a one-dimensional BMC method that was proposed in 2009 by Rajabalinejad in order to develop a weighted logical dependence between successive Monte Carlo

  19. A Multi-Objective Partition Method for Marine Sensor Networks Based on Degree of Event Correlation

    Directory of Open Access Journals (Sweden)

    Dongmei Huang

    2017-09-01

    Full Text Available Existing marine sensor networks acquire data from sea areas that are geographically divided, and store the data independently in their affiliated sea area data centers. In the case of marine events across multiple sea areas, the current network structure needs to retrieve data from multiple data centers, and thus severely affects real-time decision making. In this study, in order to provide a fast data retrieval service for a marine sensor network, we use all the marine sensors as the vertices, establish the edge based on marine events, and abstract the marine sensor network as a graph. Then, we construct a multi-objective balanced partition method to partition the abstract graph into multiple regions and store them in the cloud computing platform. This method effectively increases the correlation of the sensors and decreases the retrieval cost. On this basis, an incremental optimization strategy is designed to dynamically optimize existing partitions when new sensors are added into the network. Experimental results show that the proposed method can achieve the optimal layout for distributed storage in the process of disaster data retrieval in the China Sea area, and effectively optimize the result of partitions when new buoys are deployed, which eventually will provide efficient data access service for marine events.

  20. A Multi-Objective Partition Method for Marine Sensor Networks Based on Degree of Event Correlation.

    Science.gov (United States)

    Huang, Dongmei; Xu, Chenyixuan; Zhao, Danfeng; Song, Wei; He, Qi

    2017-09-21

    Existing marine sensor networks acquire data from sea areas that are geographically divided, and store the data independently in their affiliated sea area data centers. In the case of marine events across multiple sea areas, the current network structure needs to retrieve data from multiple data centers, and thus severely affects real-time decision making. In this study, in order to provide a fast data retrieval service for a marine sensor network, we use all the marine sensors as the vertices, establish the edge based on marine events, and abstract the marine sensor network as a graph. Then, we construct a multi-objective balanced partition method to partition the abstract graph into multiple regions and store them in the cloud computing platform. This method effectively increases the correlation of the sensors and decreases the retrieval cost. On this basis, an incremental optimization strategy is designed to dynamically optimize existing partitions when new sensors are added into the network. Experimental results show that the proposed method can achieve the optimal layout for distributed storage in the process of disaster data retrieval in the China Sea area, and effectively optimize the result of partitions when new buoys are deployed, which eventually will provide efficient data access service for marine events.

  1. The evaluation of the equilibrium partitioning method using sensitivity distributions of species in water and soil or sediment

    NARCIS (Netherlands)

    Beelen P van; Verbruggen EMJ; Peijnenburg WJGM; ECO

    2002-01-01

    The equilibrium partitioning method (EqP-method) can be used to derive environmental quality standards (like the Maximum Permissible Concentration or the intervention value) for soil or sediment, from aquatic toxicity data and a soil/water or sediment/water partitioning coefficient. The validity of

  2. Application of a data-mining method based on Bayesian networks to lesion-deficit analysis

    Science.gov (United States)

    Herskovits, Edward H.; Gerring, Joan P.

    2003-01-01

    Although lesion-deficit analysis (LDA) has provided extensive information about structure-function associations in the human brain, LDA has suffered from the difficulties inherent to the analysis of spatial data, i.e., there are many more variables than subjects, and data may be difficult to model using standard distributions, such as the normal distribution. We herein describe a Bayesian method for LDA; this method is based on data-mining techniques that employ Bayesian networks to represent structure-function associations. These methods are computationally tractable, and can represent complex, nonlinear structure-function associations. When applied to the evaluation of data obtained from a study of the psychiatric sequelae of traumatic brain injury in children, this method generates a Bayesian network that demonstrates complex, nonlinear associations among lesions in the left caudate, right globus pallidus, right side of the corpus callosum, right caudate, and left thalamus, and subsequent development of attention-deficit hyperactivity disorder, confirming and extending our previous statistical analysis of these data. Furthermore, analysis of simulated data indicates that methods based on Bayesian networks may be more sensitive and specific for detecting associations among categorical variables than methods based on chi-square and Fisher exact statistics.

  3. The Relevance Voxel Machine (RVoxM): A Bayesian Method for Image-Based Prediction

    DEFF Research Database (Denmark)

    Sabuncu, Mert R.; Van Leemput, Koen

    2011-01-01

    This paper presents the Relevance VoxelMachine (RVoxM), a Bayesian multivariate pattern analysis (MVPA) algorithm that is specifically designed for making predictions based on image data. In contrast to generic MVPA algorithms that have often been used for this purpose, the method is designed to ...

  4. A novel Bayesian learning method for information aggregation in modular neural networks

    DEFF Research Database (Denmark)

    Wang, Pan; Xu, Lida; Zhou, Shang-Ming

    2010-01-01

    Modular neural network is a popular neural network model which has many successful applications. In this paper, a sequential Bayesian learning (SBL) is proposed for modular neural networks aiming at efficiently aggregating the outputs of members of the ensemble. The experimental results on eight...... benchmark problems have demonstrated that the proposed method can perform information aggregation efficiently in data modeling....

  5. A Bayesian MCMC method for point process models with intractable normalising constants

    DEFF Research Database (Denmark)

    Berthelsen, Kasper Klitgaard; Møller, Jesper

    2004-01-01

    to simulate from the "unknown distribution", perfect simulation algorithms become useful. We illustrate the method in cases whre the likelihood is given by a Markov point process model. Particularly, we consider semi-parametric Bayesian inference in connection to both inhomogeneous Markov point process models...... and pairwise interaction point processes....

  6. An efficient Bayesian inference approach to inverse problems based on an adaptive sparse grid collocation method

    International Nuclear Information System (INIS)

    Ma Xiang; Zabaras, Nicholas

    2009-01-01

    A new approach to modeling inverse problems using a Bayesian inference method is introduced. The Bayesian approach considers the unknown parameters as random variables and seeks the probabilistic distribution of the unknowns. By introducing the concept of the stochastic prior state space to the Bayesian formulation, we reformulate the deterministic forward problem as a stochastic one. The adaptive hierarchical sparse grid collocation (ASGC) method is used for constructing an interpolant to the solution of the forward model in this prior space which is large enough to capture all the variability/uncertainty in the posterior distribution of the unknown parameters. This solution can be considered as a function of the random unknowns and serves as a stochastic surrogate model for the likelihood calculation. Hierarchical Bayesian formulation is used to derive the posterior probability density function (PPDF). The spatial model is represented as a convolution of a smooth kernel and a Markov random field. The state space of the PPDF is explored using Markov chain Monte Carlo algorithms to obtain statistics of the unknowns. The likelihood calculation is performed by directly sampling the approximate stochastic solution obtained through the ASGC method. The technique is assessed on two nonlinear inverse problems: source inversion and permeability estimation in flow through porous media

  7. A novel method to augment extraction of mangiferin by application of microwave on three phase partitioning.

    Science.gov (United States)

    Kulkarni, Vrushali M; Rathod, Virendra K

    2015-06-01

    This work reports a novel approach where three phase partitioning (TPP) was combined with microwave for extraction of mangiferin from leaves of Mangifera indica . Soxhlet extraction was used as reference method, which yielded 57 mg/g in 5 h. Under optimal conditions such as microwave irradiation time 5 min, ammonium sulphate concentration 40% w/v, power 272 W, solute to solvent ratio 1:20, slurry to t -butanol ratio 1:1, soaking time 5 min and duty cycle 50%, the mangiferin yield obtained was 54 mg/g by microwave assisted three phase partitioning extraction (MTPP). Thus extraction method developed resulted into higher extraction yield in a shorter span, thereby making it an interesting alternative prior to down-stream processing.

  8. A novel method to augment extraction of mangiferin by application of microwave on three phase partitioning

    Directory of Open Access Journals (Sweden)

    Vrushali M. Kulkarni

    2015-06-01

    Full Text Available This work reports a novel approach where three phase partitioning (TPP was combined with microwave for extraction of mangiferin from leaves of Mangifera indica. Soxhlet extraction was used as reference method, which yielded 57 mg/g in 5 h. Under optimal conditions such as microwave irradiation time 5 min, ammonium sulphate concentration 40% w/v, power 272 W, solute to solvent ratio 1:20, slurry to t-butanol ratio 1:1, soaking time 5 min and duty cycle 50%, the mangiferin yield obtained was 54 mg/g by microwave assisted three phase partitioning extraction (MTPP. Thus extraction method developed resulted into higher extraction yield in a shorter span, thereby making it an interesting alternative prior to down-stream processing.

  9. Separation of soil respiration: a site-specific comparison of partition methods

    Science.gov (United States)

    Comeau, Louis-Pierre; Lai, Derrick Y. F.; Jinglan Cui, Jane; Farmer, Jenny

    2018-06-01

    Without accurate data on soil heterotrophic respiration (Rh), assessments of soil carbon (C) sequestration rate and C balance are challenging to produce. Accordingly, it is essential to determine the contribution of the different sources of the total soil CO2 efflux (Rs) in different ecosystems, but to date, there are still many uncertainties and unknowns regarding the soil respiration partitioning procedures currently available. This study compared the suitability and relative accuracy of five different Rs partitioning methods in a subtropical forest: (1) regression between root biomass and CO2 efflux, (2) lab incubations with minimally disturbed soil microcosm cores, (3) root exclusion bags with hand-sorted roots, (4) root exclusion bags with intact soil blocks and (5) soil δ13C-CO2 natural abundance. The relationship between Rh and soil moisture and temperature was also investigated. A qualitative evaluation table of the partition methods with five performance parameters was produced. The Rs was measured weekly from 3 February to 19 April 2017 and found to average 6.1 ± 0.3 Mg C ha-1 yr-1. During this period, the Rh measured with the in situ mesh bags with intact soil blocks and hand-sorted roots was estimated to contribute 49 ± 7 and 79 ± 3 % of Rs, respectively. The Rh percentages estimated with the root biomass regression, microcosm incubation and δ13C-CO2 natural abundance were 54 ± 41, 8-17 and 61 ± 39 %, respectively. Overall, no systematically superior or inferior Rs partition method was found. The paper discusses the strengths and weaknesses of each technique with the conclusion that combining two or more methods optimizes Rh assessment reliability.

  10. A Bayesian method to estimate the neutron response matrix of a single crystal CVD diamond detector

    International Nuclear Information System (INIS)

    Reginatto, Marcel; Araque, Jorge Guerrero; Nolte, Ralf; Zbořil, Miroslav; Zimbal, Andreas; Gagnon-Moisan, Francis

    2015-01-01

    Detectors made from artificial chemical vapor deposition (CVD) single crystal diamond are very promising candidates for applications where high resolution neutron spectrometry in very high neutron fluxes is required, for example in fusion research. We propose a Bayesian method to estimate the neutron response function of the detector for a continuous range of neutron energies (in our case, 10 MeV ≤ E n ≤ 16 MeV) based on a few measurements with quasi-monoenergetic neutrons. This method is needed because a complete set of measurements is not available and the alternative approach of using responses based on Monte Carlo calculations is not feasible. Our approach uses Bayesian signal-background separation techniques and radial basis function interpolation methods. We present the analysis of data measured at the PTB accelerator facility PIAF. The method is quite general and it can be applied to other particle detectors with similar characteristics

  11. Partition functions with spin in AdS2 via quasinormal mode methods

    International Nuclear Information System (INIS)

    Keeler, Cynthia; Lisbão, Pedro; Ng, Gim Seng

    2016-01-01

    We extend the results of http://dx.doi.org/10.1007/JHEP06(2014)099, computing one loop partition functions for massive fields with spin half in AdS 2 using the quasinormal mode method proposed by Denef, Hartnoll, and Sachdev http://dx.doi.org/10.1088/0264-9381/27/12/125001. We find the finite representations of SO(2,1) for spin zero and spin half, consisting of a highest weight state |h〉 and descendants with non-unitary values of h. These finite representations capture the poles and zeroes of the one loop determinants. Together with the asymptotic behavior of the partition functions (which can be easily computed using a large mass heat kernel expansion), these are sufficient to determine the full answer for the one loop determinants. We also discuss extensions to higher dimensional AdS 2n and higher spins.

  12. Partition functions with spin in AdS{sub 2} via quasinormal mode methods

    Energy Technology Data Exchange (ETDEWEB)

    Keeler, Cynthia [Niels Bohr International Academy, Niels Bohr Institute,University of Copenhagen, Blegdamsvej 17, DK 2100, Copenhagen (Denmark); Lisbão, Pedro [Department of Physics, University of Michigan,Ann Arbor, MI-48109 (United States); Ng, Gim Seng [Department of Physics, McGill University,Montréal, QC H3A 2T8 (Canada)

    2016-10-12

    We extend the results of http://dx.doi.org/10.1007/JHEP06(2014)099, computing one loop partition functions for massive fields with spin half in AdS{sub 2} using the quasinormal mode method proposed by Denef, Hartnoll, and Sachdev http://dx.doi.org/10.1088/0264-9381/27/12/125001. We find the finite representations of SO(2,1) for spin zero and spin half, consisting of a highest weight state |h〉 and descendants with non-unitary values of h. These finite representations capture the poles and zeroes of the one loop determinants. Together with the asymptotic behavior of the partition functions (which can be easily computed using a large mass heat kernel expansion), these are sufficient to determine the full answer for the one loop determinants. We also discuss extensions to higher dimensional AdS{sub 2n} and higher spins.

  13. Development of partitioning method: confirmation of behavior of technetium in 4-Group Partitioning Process by a small scale experiment

    International Nuclear Information System (INIS)

    Morita, Yasuji; Yamaguchi, Isoo; Fujiwara, Takeshi; Kubota, Masumitsu; Mizoguchi, Kenichi

    1998-08-01

    The separation behavior of Tc in the whole of 4-Group Partitioning Process was examined by a flask-scale experiment using simulated high-level liquid waste containing a macro amount of Tc, in order to confirm the reproducibility of the results obtained in previous studies on the Tc behavior at each step of the process. The 4-Group Partitioning Process consists of pre-treatment step, extraction step with diisodecylphosphoric acid (DIDPA), adsorption step with active carbon or precipitation step by denitration for the separation of Tc and platinum group metals (PGM), and adsorption step with inorganic ion exchangers. The present study deals with the behavior of Tc and other elements at all the above steps and additional step for Tc dissolution from the precipitate formed by the denitration. At the pre-treatment step, the ratio of Tc precipitated was very low (about 0.2%) at both operations of heating-denitration and colloid removal. Tc was not extracted with DIDPA and was contained quantitatively in the raffinate from the extraction step. Batch adsorption with active carbon directly from the raffinate showed that distribution coefficient of Tc was more than 100ml/g, which is high enough for the separation. It also revealed much effect of coexisting Mo on the Tc adsorption. At the precipitation step by denitration, 98.2% of Tc were precipitated. At the Tc dissolution from the precipitate with H 2 O 2 , 84.2% of Tc were selectively dissolved in a single operation. Tc was not adsorbed with inorganic ion exchangers. From these results, composition of Tc product from the partitioning process was estimated. The weight ratio of Tc in the Tc product can be increased to about 50% at least. Main contaminating elements are Cr, Ni, Sr, Ba, Mo and Pd. Process optimization to decrease their contamination should be performed in a next study. (J.P.N.)

  14. Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): a proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses.

    Science.gov (United States)

    Tao, Wenjing; Mayden, Richard L; He, Shunping

    2013-03-01

    Despite many efforts to resolve evolutionary relationships among major clades of Cyprinidae, some nodes have been especially problematic and remain unresolved. In this study, we employ four nuclear gene fragments (3.3kb) to infer interrelationships of the Cyprinidae. A reconstruction of the phylogenetic relationships within the family using maximum parsimony, maximum likelihood, and Bayesian analyses is presented. Among the taxa within the monophyletic Cyprinidae, Rasborinae is the basal-most lineage; Cyprinine is sister to Leuciscine. The monophyly for the subfamilies Gobioninae, Leuciscinae and Acheilognathinae were resolved with high nodal support. Although our results do not completely resolve relationships within Cyprinidae, this study presents novel and significant findings having major implications for a highly diverse and enigmatic clade of East-Asian cyprinids. Within this monophyletic group five closely-related subgroups are identified. Tinca tinca, one of the most phylogenetically enigmatic genera in the family, is strongly supported as having evolutionary affinities with this East-Asian clade; an established yet remarkable association because of the natural variation in phenotypes and generalized ecological niches occupied by these taxa. Our results clearly argue that the choice of partitioning strategies has significant impacts on the phylogenetic reconstructions, especially when multiple genes are being considered. The most highly partitioned model (partitioned by codon positions within genes) extracts the strongest phylogenetic signals and performs better than any other partitioning schemes supported by the strongest 2Δln Bayes factor. Future studies should include higher levels of taxon sampling and partitioned, model-based analyses. Copyright © 2012 Elsevier Inc. All rights reserved.

  15. A fully Bayesian method for jointly fitting instrumental calibration and X-ray spectral models

    International Nuclear Information System (INIS)

    Xu, Jin; Yu, Yaming; Van Dyk, David A.; Kashyap, Vinay L.; Siemiginowska, Aneta; Drake, Jeremy; Ratzlaff, Pete; Connors, Alanna; Meng, Xiao-Li

    2014-01-01

    Owing to a lack of robust principled methods, systematic instrumental uncertainties have generally been ignored in astrophysical data analysis despite wide recognition of the importance of including them. Ignoring calibration uncertainty can cause bias in the estimation of source model parameters and can lead to underestimation of the variance of these estimates. We previously introduced a pragmatic Bayesian method to address this problem. The method is 'pragmatic' in that it introduced an ad hoc technique that simplified computation by neglecting the potential information in the data for narrowing the uncertainty for the calibration product. Following that work, we use a principal component analysis to efficiently represent the uncertainty of the effective area of an X-ray (or γ-ray) telescope. Here, however, we leverage this representation to enable a principled, fully Bayesian method that coherently accounts for the calibration uncertainty in high-energy spectral analysis. In this setting, the method is compared with standard analysis techniques and the pragmatic Bayesian method. The advantage of the fully Bayesian method is that it allows the data to provide information not only for estimation of the source parameters but also for the calibration product—here the effective area, conditional on the adopted spectral model. In this way, it can yield more accurate and efficient estimates of the source parameters along with valid estimates of their uncertainty. Provided that the source spectrum can be accurately described by a parameterized model, this method allows rigorous inference about the effective area by quantifying which possible curves are most consistent with the data.

  16. Estimating Steatosis Prevalence in Overweight and Obese Children: Comparison of Bayesian Small Area and Direct Methods

    Directory of Open Access Journals (Sweden)

    Hamid Reza Khalkhali

    2016-09-01

    Full Text Available Background Often, there is no access to sufficient sample size to estimate the prevalence using the method of direct estimator in all areas. The aim of this study was to compare small area’s Bayesian method and direct method in estimating the prevalence of steatosis in obese and overweight children. Materials and Methods: In this cross-sectional study, was conducted on 150 overweight and obese children aged 2 to 15 years referred to the Children's digestive clinic of Urmia University of Medical Sciences- Iran, in 2013. After Body mass index (BMI calculation, children with overweight and obese were assessed in terms of primary tests of obesity screening. Then children with steatosis confirmed by abdominal Ultrasonography, were referred to the laboratory for doing further tests. Steatosis prevalence was estimated by direct and Bayesian method and their efficiency were evaluated using mean-square error Jackknife method. The study data was analyzed using the open BUGS3.1.2 and R2.15.2 software. Results: The findings indicated that estimation of steatosis prevalence in children using Bayesian and direct methods were between 0.3098 to 0.493, and 0.355 to 0.560 respectively, in Health Districts; 0.3098 to 0.502, and 0.355 to 0.550 in Education Districts; 0.321 to 0.582, and 0.357 to 0.615 in age groups; 0.313 to 0.429, and 0.383 to 0.536 in sex groups. In general, according to the results, mean-square error of Bayesian estimation was smaller than direct estimation (P

  17. Bayesian biostatistics

    CERN Document Server

    Lesaffre, Emmanuel

    2012-01-01

    The growth of biostatistics has been phenomenal in recent years and has been marked by considerable technical innovation in both methodology and computational practicality. One area that has experienced significant growth is Bayesian methods. The growing use of Bayesian methodology has taken place partly due to an increasing number of practitioners valuing the Bayesian paradigm as matching that of scientific discovery. In addition, computational advances have allowed for more complex models to be fitted routinely to realistic data sets. Through examples, exercises and a combination of introd

  18. A Bayesian reliability evaluation method with integrated accelerated degradation testing and field information

    International Nuclear Information System (INIS)

    Wang, Lizhi; Pan, Rong; Li, Xiaoyang; Jiang, Tongmin

    2013-01-01

    Accelerated degradation testing (ADT) is a common approach in reliability prediction, especially for products with high reliability. However, oftentimes the laboratory condition of ADT is different from the field condition; thus, to predict field failure, one need to calibrate the prediction made by using ADT data. In this paper a Bayesian evaluation method is proposed to integrate the ADT data from laboratory with the failure data from field. Calibration factors are introduced to calibrate the difference between the lab and the field conditions so as to predict a product's actual field reliability more accurately. The information fusion and statistical inference procedure are carried out through a Bayesian approach and Markov chain Monte Carlo methods. The proposed method is demonstrated by two examples and the sensitivity analysis to prior distribution assumption

  19. A method for crack sizing using Bayesian inference arising in eddy current testing

    International Nuclear Information System (INIS)

    Kojima, Fumio; Kikuchi, Mitsuhiro

    2008-01-01

    This paper is concerned with a sizing methodology of crack using Bayesian inference arising in eddy current testing. There is often uncertainty about data through quantitative measurements of nondestructive testing and this can yield misleading inference of crack sizing at on-site monitoring. In this paper, we propose optimal strategies of measurements in eddy current testing using Bayesian prior-to-posteriori analysis. First our likelihood functional is given by Gaussian distribution with the measurement model based on the hybrid use of finite and boundary element methods. Secondly, given a priori distributions of crack sizing, we propose a method for estimating the region of interest for sizing cracks. Finally an optimal sensing method is demonstrated using our idea. (author)

  20. Evaluating Bayesian spatial methods for modelling species distributions with clumped and restricted occurrence data.

    Directory of Open Access Journals (Sweden)

    David W Redding

    Full Text Available Statistical approaches for inferring the spatial distribution of taxa (Species Distribution Models, SDMs commonly rely on available occurrence data, which is often clumped and geographically restricted. Although available SDM methods address some of these factors, they could be more directly and accurately modelled using a spatially-explicit approach. Software to fit models with spatial autocorrelation parameters in SDMs are now widely available, but whether such approaches for inferring SDMs aid predictions compared to other methodologies is unknown. Here, within a simulated environment using 1000 generated species' ranges, we compared the performance of two commonly used non-spatial SDM methods (Maximum Entropy Modelling, MAXENT and boosted regression trees, BRT, to a spatial Bayesian SDM method (fitted using R-INLA, when the underlying data exhibit varying combinations of clumping and geographic restriction. Finally, we tested how any recommended methodological settings designed to account for spatially non-random patterns in the data impact inference. Spatial Bayesian SDM method was the most consistently accurate method, being in the top 2 most accurate methods in 7 out of 8 data sampling scenarios. Within high-coverage sample datasets, all methods performed fairly similarly. When sampling points were randomly spread, BRT had a 1-3% greater accuracy over the other methods and when samples were clumped, the spatial Bayesian SDM method had a 4%-8% better AUC score. Alternatively, when sampling points were restricted to a small section of the true range all methods were on average 10-12% less accurate, with greater variation among the methods. Model inference under the recommended settings to account for autocorrelation was not impacted by clumping or restriction of data, except for the complexity of the spatial regression term in the spatial Bayesian model. Methods, such as those made available by R-INLA, can be successfully used to account

  1. Evaluating Bayesian spatial methods for modelling species distributions with clumped and restricted occurrence data.

    Science.gov (United States)

    Redding, David W; Lucas, Tim C D; Blackburn, Tim M; Jones, Kate E

    2017-01-01

    Statistical approaches for inferring the spatial distribution of taxa (Species Distribution Models, SDMs) commonly rely on available occurrence data, which is often clumped and geographically restricted. Although available SDM methods address some of these factors, they could be more directly and accurately modelled using a spatially-explicit approach. Software to fit models with spatial autocorrelation parameters in SDMs are now widely available, but whether such approaches for inferring SDMs aid predictions compared to other methodologies is unknown. Here, within a simulated environment using 1000 generated species' ranges, we compared the performance of two commonly used non-spatial SDM methods (Maximum Entropy Modelling, MAXENT and boosted regression trees, BRT), to a spatial Bayesian SDM method (fitted using R-INLA), when the underlying data exhibit varying combinations of clumping and geographic restriction. Finally, we tested how any recommended methodological settings designed to account for spatially non-random patterns in the data impact inference. Spatial Bayesian SDM method was the most consistently accurate method, being in the top 2 most accurate methods in 7 out of 8 data sampling scenarios. Within high-coverage sample datasets, all methods performed fairly similarly. When sampling points were randomly spread, BRT had a 1-3% greater accuracy over the other methods and when samples were clumped, the spatial Bayesian SDM method had a 4%-8% better AUC score. Alternatively, when sampling points were restricted to a small section of the true range all methods were on average 10-12% less accurate, with greater variation among the methods. Model inference under the recommended settings to account for autocorrelation was not impacted by clumping or restriction of data, except for the complexity of the spatial regression term in the spatial Bayesian model. Methods, such as those made available by R-INLA, can be successfully used to account for spatial

  2. A Bayesian statistical method for quantifying model form uncertainty and two model combination methods

    International Nuclear Information System (INIS)

    Park, Inseok; Grandhi, Ramana V.

    2014-01-01

    Apart from parametric uncertainty, model form uncertainty as well as prediction error may be involved in the analysis of engineering system. Model form uncertainty, inherently existing in selecting the best approximation from a model set cannot be ignored, especially when the predictions by competing models show significant differences. In this research, a methodology based on maximum likelihood estimation is presented to quantify model form uncertainty using the measured differences of experimental and model outcomes, and is compared with a fully Bayesian estimation to demonstrate its effectiveness. While a method called the adjustment factor approach is utilized to propagate model form uncertainty alone into the prediction of a system response, a method called model averaging is utilized to incorporate both model form uncertainty and prediction error into it. A numerical problem of concrete creep is used to demonstrate the processes for quantifying model form uncertainty and implementing the adjustment factor approach and model averaging. Finally, the presented methodology is applied to characterize the engineering benefits of a laser peening process

  3. Comparison of Bayesian clustering and edge detection methods for inferring boundaries in landscape genetics

    Science.gov (United States)

    Safner, T.; Miller, M.P.; McRae, B.H.; Fortin, M.-J.; Manel, S.

    2011-01-01

    Recently, techniques available for identifying clusters of individuals or boundaries between clusters using genetic data from natural populations have expanded rapidly. Consequently, there is a need to evaluate these different techniques. We used spatially-explicit simulation models to compare three spatial Bayesian clustering programs and two edge detection methods. Spatially-structured populations were simulated where a continuous population was subdivided by barriers. We evaluated the ability of each method to correctly identify boundary locations while varying: (i) time after divergence, (ii) strength of isolation by distance, (iii) level of genetic diversity, and (iv) amount of gene flow across barriers. To further evaluate the methods' effectiveness to detect genetic clusters in natural populations, we used previously published data on North American pumas and a European shrub. Our results show that with simulated and empirical data, the Bayesian spatial clustering algorithms outperformed direct edge detection methods. All methods incorrectly detected boundaries in the presence of strong patterns of isolation by distance. Based on this finding, we support the application of Bayesian spatial clustering algorithms for boundary detection in empirical datasets, with necessary tests for the influence of isolation by distance. ?? 2011 by the authors; licensee MDPI, Basel, Switzerland.

  4. Bayesian Method for Building Frequent Landsat-Like NDVI Datasets by Integrating MODIS and Landsat NDVI

    OpenAIRE

    Limin Liao; Jinling Song; Jindi Wang; Zhiqiang Xiao; Jian Wang

    2016-01-01

    Studies related to vegetation dynamics in heterogeneous landscapes often require Normalized Difference Vegetation Index (NDVI) datasets with both high spatial resolution and frequent coverage, which cannot be satisfied by a single sensor due to technical limitations. In this study, we propose a new method called NDVI-Bayesian Spatiotemporal Fusion Model (NDVI-BSFM) for accurately and effectively building frequent high spatial resolution Landsat-like NDVI datasets by integrating Moderate Resol...

  5. Using hierarchical Bayesian methods to examine the tools of decision-making

    OpenAIRE

    Michael D. Lee; Benjamin R. Newell

    2011-01-01

    Hierarchical Bayesian methods offer a principled and comprehensive way to relate psychological models to data. Here we use them to model the patterns of information search, stopping and deciding in a simulated binary comparison judgment task. The simulation involves 20 subjects making 100 forced choice comparisons about the relative magnitudes of two objects (which of two German cities has more inhabitants). Two worked-examples show how hierarchical models can be developed to account for and ...

  6. Introduction to Bayesian statistics

    CERN Document Server

    Bolstad, William M

    2017-01-01

    There is a strong upsurge in the use of Bayesian methods in applied statistical analysis, yet most introductory statistics texts only present frequentist methods. Bayesian statistics has many important advantages that students should learn about if they are going into fields where statistics will be used. In this Third Edition, four newly-added chapters address topics that reflect the rapid advances in the field of Bayesian staistics. The author continues to provide a Bayesian treatment of introductory statistical topics, such as scientific data gathering, discrete random variables, robust Bayesian methods, and Bayesian approaches to inferenfe cfor discrete random variables, bionomial proprotion, Poisson, normal mean, and simple linear regression. In addition, newly-developing topics in the field are presented in four new chapters: Bayesian inference with unknown mean and variance; Bayesian inference for Multivariate Normal mean vector; Bayesian inference for Multiple Linear RegressionModel; and Computati...

  7. Artificial Intelligence: Bayesian versus Heuristic Method for Diagnostic Decision Support.

    Science.gov (United States)

    Elkin, Peter L; Schlegel, Daniel R; Anderson, Michael; Komm, Jordan; Ficheur, Gregoire; Bisson, Leslie

    2018-04-01

    Evoking strength is one of the important contributions of the field of Biomedical Informatics to the discipline of Artificial Intelligence. The University at Buffalo's Orthopedics Department wanted to create an expert system to assist patients with self-diagnosis of knee problems and to thereby facilitate referral to the right orthopedic subspecialist. They had two independent sports medicine physicians review 469 cases. A board-certified orthopedic sports medicine practitioner, L.B., reviewed any disagreements until a gold standard diagnosis was reached. For each case, the patients entered 126 potential answers to 26 questions into a Web interface. These were modeled by an expert sports medicine physician and the answers were reviewed by L.B. For each finding, the clinician specified the sensitivity (term frequency) and both specificity (Sp) and the heuristic evoking strength (ES). Heuristics are methods of reasoning with only partial evidence. An expert system was constructed that reflected the posttest odds of disease-ranked list for each case. We compare the accuracy of using Sp to that of using ES (original model, p  < 0.0008; term importance * disease importance [DItimesTI] model, p  < 0.0001: Wilcoxon ranked sum test). For patient referral assignment, Sp in the DItimesTI model was superior to the use of ES. By the fifth diagnosis, the advantage was lost and so there is no difference between the techniques when serving as a reminder system. Schattauer GmbH Stuttgart.

  8. Application of partition chromatography method for separation and analysis of actinium radionuclides

    International Nuclear Information System (INIS)

    Sinitsina, G.S.; Shestakova, I.A.; Shestakov, B.I.; Plyushcheva, N.A.; Malyshev, N.A.; Belyatskij, A.F.; Tsirlin, V.A.

    1979-01-01

    The method of partition chromatography is considered with the use of different extractants for the extraction of actinium-227, actinium-225 and actinium-228. It is advisable to extract actinium-227 from the irradiated radium with the help of D2FGFK. The use of 2DEGFK allows us to separate actinium-227 from alkaline and alkaline-earth elements. Amines have a higher radiative stability. An express-method has been developed for the identification of actinium-227 with TOA by its intrinsic α-emission in nonequilibrium preparations of irradiated radium-226 of small activity. Actinium-225 is extracted from uranium-233 with due regard for the fact that U, Th, and Ac are extracted differently by TBP from HNO 3 solutions. With the help of the given procedure one can reach the purifying coefficient of 10 4 . Actinium-228 is extracted from the radiummesothorium preparations by a deposition of decay products, including polonium-210 on the iron hydroxyde. Actinium-228 extraction from the mixture of radium radionuclides is performed by the partition chromatography method on D2EGFK. All the procedures for separation of actinium isotopes by the above methods are described

  9. A new method for E-government procurement using collaborative filtering and Bayesian approach.

    Science.gov (United States)

    Zhang, Shuai; Xi, Chengyu; Wang, Yan; Zhang, Wenyu; Chen, Yanhong

    2013-01-01

    Nowadays, as the Internet services increase faster than ever before, government systems are reinvented as E-government services. Therefore, government procurement sectors have to face challenges brought by the explosion of service information. This paper presents a novel method for E-government procurement (eGP) to search for the optimal procurement scheme (OPS). Item-based collaborative filtering and Bayesian approach are used to evaluate and select the candidate services to get the top-M recommendations such that the involved computation load can be alleviated. A trapezoidal fuzzy number similarity algorithm is applied to support the item-based collaborative filtering and Bayesian approach, since some of the services' attributes can be hardly expressed as certain and static values but only be easily represented as fuzzy values. A prototype system is built and validated with an illustrative example from eGP to confirm the feasibility of our approach.

  10. A New Method for E-Government Procurement Using Collaborative Filtering and Bayesian Approach

    Directory of Open Access Journals (Sweden)

    Shuai Zhang

    2013-01-01

    Full Text Available Nowadays, as the Internet services increase faster than ever before, government systems are reinvented as E-government services. Therefore, government procurement sectors have to face challenges brought by the explosion of service information. This paper presents a novel method for E-government procurement (eGP to search for the optimal procurement scheme (OPS. Item-based collaborative filtering and Bayesian approach are used to evaluate and select the candidate services to get the top-M recommendations such that the involved computation load can be alleviated. A trapezoidal fuzzy number similarity algorithm is applied to support the item-based collaborative filtering and Bayesian approach, since some of the services’ attributes can be hardly expressed as certain and static values but only be easily represented as fuzzy values. A prototype system is built and validated with an illustrative example from eGP to confirm the feasibility of our approach.

  11. A method for calculating Bayesian uncertainties on internal doses resulting from complex occupational exposures

    International Nuclear Information System (INIS)

    Puncher, M.; Birchall, A.; Bull, R. K.

    2012-01-01

    Estimating uncertainties on doses from bioassay data is of interest in epidemiology studies that estimate cancer risk from occupational exposures to radionuclides. Bayesian methods provide a logical framework to calculate these uncertainties. However, occupational exposures often consist of many intakes, and this can make the Bayesian calculation computationally intractable. This paper describes a novel strategy for increasing the computational speed of the calculation by simplifying the intake pattern to a single composite intake, termed as complex intake regime (CIR). In order to assess whether this approximation is accurate and fast enough for practical purposes, the method is implemented by the Weighted Likelihood Monte Carlo Sampling (WeLMoS) method and evaluated by comparing its performance with a Markov Chain Monte Carlo (MCMC) method. The MCMC method gives the full solution (all intakes are independent), but is very computationally intensive to apply routinely. Posterior distributions of model parameter values, intakes and doses are calculated for a representative sample of plutonium workers from the United Kingdom Atomic Energy cohort using the WeLMoS method with the CIR and the MCMC method. The distributions are in good agreement: posterior means and Q 0.025 and Q 0.975 quantiles are typically within 20 %. Furthermore, the WeLMoS method using the CIR converges quickly: a typical case history takes around 10-20 min on a fast workstation, whereas the MCMC method took around 12-hr. The advantages and disadvantages of the method are discussed. (authors)

  12. Conditional maximum-entropy method for selecting prior distributions in Bayesian statistics

    Science.gov (United States)

    Abe, Sumiyoshi

    2014-11-01

    The conditional maximum-entropy method (abbreviated here as C-MaxEnt) is formulated for selecting prior probability distributions in Bayesian statistics for parameter estimation. This method is inspired by a statistical-mechanical approach to systems governed by dynamics with largely separated time scales and is based on three key concepts: conjugate pairs of variables, dimensionless integration measures with coarse-graining factors and partial maximization of the joint entropy. The method enables one to calculate a prior purely from a likelihood in a simple way. It is shown, in particular, how it not only yields Jeffreys's rules but also reveals new structures hidden behind them.

  13. Bayesian methods

    OpenAIRE

    BAUWENS, Luc; KOROBILIS, Dimitris

    2011-01-01

    This comprehensive Handbook presents the current state of art in the theory and methodology of macroeconomic data analysis. It is intended as a reference for graduate students and researchers interested in exploring new methodologies, but can also be employed as a graduate text. The Handbook concentrates on the most important issues, models and techniques for research in macroeconomics, and highlights the core methodologies and their empirical application in an accessible manner. Each chapter...

  14. The Approximate Bayesian Computation methods in the localization of the atmospheric contamination source

    International Nuclear Information System (INIS)

    Kopka, P; Wawrzynczak, A; Borysiewicz, M

    2015-01-01

    In many areas of application, a central problem is a solution to the inverse problem, especially estimation of the unknown model parameters to model the underlying dynamics of a physical system precisely. In this situation, the Bayesian inference is a powerful tool to combine observed data with prior knowledge to gain the probability distribution of searched parameters. We have applied the modern methodology named Sequential Approximate Bayesian Computation (S-ABC) to the problem of tracing the atmospheric contaminant source. The ABC is technique commonly used in the Bayesian analysis of complex models and dynamic system. Sequential methods can significantly increase the efficiency of the ABC. In the presented algorithm, the input data are the on-line arriving concentrations of released substance registered by distributed sensor network from OVER-LAND ATMOSPHERIC DISPERSION (OLAD) experiment. The algorithm output are the probability distributions of a contamination source parameters i.e. its particular location, release rate, speed and direction of the movement, start time and duration. The stochastic approach presented in this paper is completely general and can be used in other fields where the parameters of the model bet fitted to the observable data should be found. (paper)

  15. Robust modelling of solubility in supercritical carbon dioxide using Bayesian methods.

    Science.gov (United States)

    Tarasova, Anna; Burden, Frank; Gasteiger, Johann; Winkler, David A

    2010-04-01

    Two sparse Bayesian methods were used to derive predictive models of solubility of organic dyes and polycyclic aromatic compounds in supercritical carbon dioxide (scCO(2)), over a wide range of temperatures (285.9-423.2K) and pressures (60-1400 bar): a multiple linear regression employing an expectation maximization algorithm and a sparse prior (MLREM) method and a non-linear Bayesian Regularized Artificial Neural Network with a Laplacian Prior (BRANNLP). A randomly selected test set was used to estimate the predictive ability of the models. The MLREM method resulted in a model of similar predictivity to the less sparse MLR method, while the non-linear BRANNLP method created models of substantially better predictivity than either the MLREM or MLR based models. The BRANNLP method simultaneously generated context-relevant subsets of descriptors and a robust, non-linear quantitative structure-property relationship (QSPR) model for the compound solubility in scCO(2). The differences between linear and non-linear descriptor selection methods are discussed. (c) 2009 Elsevier Inc. All rights reserved.

  16. Uncertainty estimation of a complex water quality model: The influence of Box-Cox transformation on Bayesian approaches and comparison with a non-Bayesian method

    Science.gov (United States)

    Freni, Gabriele; Mannina, Giorgio

    In urban drainage modelling, uncertainty analysis is of undoubted necessity. However, uncertainty analysis in urban water-quality modelling is still in its infancy and only few studies have been carried out. Therefore, several methodological aspects still need to be experienced and clarified especially regarding water quality modelling. The use of the Bayesian approach for uncertainty analysis has been stimulated by its rigorous theoretical framework and by the possibility of evaluating the impact of new knowledge on the modelling predictions. Nevertheless, the Bayesian approach relies on some restrictive hypotheses that are not present in less formal methods like the Generalised Likelihood Uncertainty Estimation (GLUE). One crucial point in the application of Bayesian method is the formulation of a likelihood function that is conditioned by the hypotheses made regarding model residuals. Statistical transformations, such as the use of Box-Cox equation, are generally used to ensure the homoscedasticity of residuals. However, this practice may affect the reliability of the analysis leading to a wrong uncertainty estimation. The present paper aims to explore the influence of the Box-Cox equation for environmental water quality models. To this end, five cases were considered one of which was the “real” residuals distributions (i.e. drawn from available data). The analysis was applied to the Nocella experimental catchment (Italy) which is an agricultural and semi-urbanised basin where two sewer systems, two wastewater treatment plants and a river reach were monitored during both dry and wet weather periods. The results show that the uncertainty estimation is greatly affected by residual transformation and a wrong assumption may also affect the evaluation of model uncertainty. The use of less formal methods always provide an overestimation of modelling uncertainty with respect to Bayesian method but such effect is reduced if a wrong assumption is made regarding the

  17. Bayesian inference for data assimilation using Least-Squares Finite Element methods

    International Nuclear Information System (INIS)

    Dwight, Richard P

    2010-01-01

    It has recently been observed that Least-Squares Finite Element methods (LS-FEMs) can be used to assimilate experimental data into approximations of PDEs in a natural way, as shown by Heyes et al. in the case of incompressible Navier-Stokes flow. The approach was shown to be effective without regularization terms, and can handle substantial noise in the experimental data without filtering. Of great practical importance is that - unlike other data assimilation techniques - it is not significantly more expensive than a single physical simulation. However the method as presented so far in the literature is not set in the context of an inverse problem framework, so that for example the meaning of the final result is unclear. In this paper it is shown that the method can be interpreted as finding a maximum a posteriori (MAP) estimator in a Bayesian approach to data assimilation, with normally distributed observational noise, and a Bayesian prior based on an appropriate norm of the governing equations. In this setting the method may be seen to have several desirable properties: most importantly discretization and modelling error in the simulation code does not affect the solution in limit of complete experimental information, so these errors do not have to be modelled statistically. Also the Bayesian interpretation better justifies the choice of the method, and some useful generalizations become apparent. The technique is applied to incompressible Navier-Stokes flow in a pipe with added velocity data, where its effectiveness, robustness to noise, and application to inverse problems is demonstrated.

  18. Partition method and experimental validation for impact dynamics of flexible multibody system

    Science.gov (United States)

    Wang, J. Y.; Liu, Z. Y.; Hong, J. Z.

    2018-06-01

    The impact problem of a flexible multibody system is a non-smooth, high-transient, and strong-nonlinear dynamic process with variable boundary. How to model the contact/impact process accurately and efficiently is one of the main difficulties in many engineering applications. The numerical approaches being used widely in impact analysis are mainly from two fields: multibody system dynamics (MBS) and computational solid mechanics (CSM). Approaches based on MBS provide a more efficient yet less accurate analysis of the contact/impact problems, while approaches based on CSM are well suited for particularly high accuracy needs, yet require very high computational effort. To bridge the gap between accuracy and efficiency in the dynamic simulation of a flexible multibody system with contacts/impacts, a partition method is presented considering that the contact body is divided into two parts, an impact region and a non-impact region. The impact region is modeled using the finite element method to guarantee the local accuracy, while the non-impact region is modeled using the modal reduction approach to raise the global efficiency. A three-dimensional rod-plate impact experiment is designed and performed to validate the numerical results. The principle for how to partition the contact bodies is proposed: the maximum radius of the impact region can be estimated by an analytical method, and the modal truncation orders of the non-impact region can be estimated by the highest frequency of the signal measured. The simulation results using the presented method are in good agreement with the experimental results. It shows that this method is an effective formulation considering both accuracy and efficiency. Moreover, a more complicated multibody impact problem of a crank slider mechanism is investigated to strengthen this conclusion.

  19. Bayesian and maximum entropy methods for fusion diagnostic measurements with compact neutron spectrometers

    International Nuclear Information System (INIS)

    Reginatto, Marcel; Zimbal, Andreas

    2008-01-01

    In applications of neutron spectrometry to fusion diagnostics, it is advantageous to use methods of data analysis which can extract information from the spectrum that is directly related to the parameters of interest that describe the plasma. We present here methods of data analysis which were developed with this goal in mind, and which were applied to spectrometric measurements made with an organic liquid scintillation detector (type NE213). In our approach, we combine Bayesian parameter estimation methods and unfolding methods based on the maximum entropy principle. This two-step method allows us to optimize the analysis of the data depending on the type of information that we want to extract from the measurements. To illustrate these methods, we analyze neutron measurements made at the PTB accelerator under controlled conditions, using accelerator-produced neutron beams. Although the methods have been chosen with a specific application in mind, they are general enough to be useful for many other types of measurements

  20. Estimation of Lithological Classification in Taipei Basin: A Bayesian Maximum Entropy Method

    Science.gov (United States)

    Wu, Meng-Ting; Lin, Yuan-Chien; Yu, Hwa-Lung

    2015-04-01

    In environmental or other scientific applications, we must have a certain understanding of geological lithological composition. Because of restrictions of real conditions, only limited amount of data can be acquired. To find out the lithological distribution in the study area, many spatial statistical methods used to estimate the lithological composition on unsampled points or grids. This study applied the Bayesian Maximum Entropy (BME method), which is an emerging method of the geological spatiotemporal statistics field. The BME method can identify the spatiotemporal correlation of the data, and combine not only the hard data but the soft data to improve estimation. The data of lithological classification is discrete categorical data. Therefore, this research applied Categorical BME to establish a complete three-dimensional Lithological estimation model. Apply the limited hard data from the cores and the soft data generated from the geological dating data and the virtual wells to estimate the three-dimensional lithological classification in Taipei Basin. Keywords: Categorical Bayesian Maximum Entropy method, Lithological Classification, Hydrogeological Setting

  1. Cone Beam X-ray Luminescence Computed Tomography Based on Bayesian Method.

    Science.gov (United States)

    Zhang, Guanglei; Liu, Fei; Liu, Jie; Luo, Jianwen; Xie, Yaoqin; Bai, Jing; Xing, Lei

    2017-01-01

    X-ray luminescence computed tomography (XLCT), which aims to achieve molecular and functional imaging by X-rays, has recently been proposed as a new imaging modality. Combining the principles of X-ray excitation of luminescence-based probes and optical signal detection, XLCT naturally fuses functional and anatomical images and provides complementary information for a wide range of applications in biomedical research. In order to improve the data acquisition efficiency of previously developed narrow-beam XLCT, a cone beam XLCT (CB-XLCT) mode is adopted here to take advantage of the useful geometric features of cone beam excitation. Practically, a major hurdle in using cone beam X-ray for XLCT is that the inverse problem here is seriously ill-conditioned, hindering us to achieve good image quality. In this paper, we propose a novel Bayesian method to tackle the bottleneck in CB-XLCT reconstruction. The method utilizes a local regularization strategy based on Gaussian Markov random field to mitigate the ill-conditioness of CB-XLCT. An alternating optimization scheme is then used to automatically calculate all the unknown hyperparameters while an iterative coordinate descent algorithm is adopted to reconstruct the image with a voxel-based closed-form solution. Results of numerical simulations and mouse experiments show that the self-adaptive Bayesian method significantly improves the CB-XLCT image quality as compared with conventional methods.

  2. A New Ensemble Method with Feature Space Partitioning for High-Dimensional Data Classification

    Directory of Open Access Journals (Sweden)

    Yongjun Piao

    2015-01-01

    Full Text Available Ensemble data mining methods, also known as classifier combination, are often used to improve the performance of classification. Various classifier combination methods such as bagging, boosting, and random forest have been devised and have received considerable attention in the past. However, data dimensionality increases rapidly day by day. Such a trend poses various challenges as these methods are not suitable to directly apply to high-dimensional datasets. In this paper, we propose an ensemble method for classification of high-dimensional data, with each classifier constructed from a different set of features determined by partitioning of redundant features. In our method, the redundancy of features is considered to divide the original feature space. Then, each generated feature subset is trained by a support vector machine, and the results of each classifier are combined by majority voting. The efficiency and effectiveness of our method are demonstrated through comparisons with other ensemble techniques, and the results show that our method outperforms other methods.

  3. Inference of time-delayed gene regulatory networks based on dynamic Bayesian network hybrid learning method.

    Science.gov (United States)

    Yu, Bin; Xu, Jia-Meng; Li, Shan; Chen, Cheng; Chen, Rui-Xin; Wang, Lei; Zhang, Yan; Wang, Ming-Hui

    2017-10-06

    Gene regulatory networks (GRNs) research reveals complex life phenomena from the perspective of gene interaction, which is an important research field in systems biology. Traditional Bayesian networks have a high computational complexity, and the network structure scoring model has a single feature. Information-based approaches cannot identify the direction of regulation. In order to make up for the shortcomings of the above methods, this paper presents a novel hybrid learning method (DBNCS) based on dynamic Bayesian network (DBN) to construct the multiple time-delayed GRNs for the first time, combining the comprehensive score (CS) with the DBN model. DBNCS algorithm first uses CMI2NI (conditional mutual inclusive information-based network inference) algorithm for network structure profiles learning, namely the construction of search space. Then the redundant regulations are removed by using the recursive optimization algorithm (RO), thereby reduce the false positive rate. Secondly, the network structure profiles are decomposed into a set of cliques without loss, which can significantly reduce the computational complexity. Finally, DBN model is used to identify the direction of gene regulation within the cliques and search for the optimal network structure. The performance of DBNCS algorithm is evaluated by the benchmark GRN datasets from DREAM challenge as well as the SOS DNA repair network in Escherichia coli , and compared with other state-of-the-art methods. The experimental results show the rationality of the algorithm design and the outstanding performance of the GRNs.

  4. An Advanced Bayesian Method for Short-Term Probabilistic Forecasting of the Generation of Wind Power

    Directory of Open Access Journals (Sweden)

    Antonio Bracale

    2015-09-01

    Full Text Available Currently, among renewable distributed generation systems, wind generators are receiving a great deal of interest due to the great economic, technological, and environmental incentives they involve. However, the uncertainties due to the intermittent nature of wind energy make it difficult to operate electrical power systems optimally and make decisions that satisfy the needs of all the stakeholders of the electricity energy market. Thus, there is increasing interest determining how to forecast wind power production accurately. Most the methods that have been published in the relevant literature provided deterministic forecasts even though great interest has been focused recently on probabilistic forecast methods. In this paper, an advanced probabilistic method is proposed for short-term forecasting of wind power production. A mixture of two Weibull distributions was used as a probability function to model the uncertainties associated with wind speed. Then, a Bayesian inference approach with a particularly-effective, autoregressive, integrated, moving-average model was used to determine the parameters of the mixture Weibull distribution. Numerical applications also are presented to provide evidence of the forecasting performance of the Bayesian-based approach.

  5. Lifetime modelling with a Weibull law: comparison of three Bayesian Methods

    International Nuclear Information System (INIS)

    Billy, F.; Remy, E.; Bousquet, N.; Celeux, G.

    2006-01-01

    For a nuclear power plant, being able to estimate the lifetime of important components is strategic. But data is usually insufficient to do so. Thus, it is relevant to use expertise, together with data, in order to assess the value of lifetime on the grounds of both sources. The Bayesian frame and the choice of a Weibull law to model the random time for replacement are relevant. They have been chosen for this article. Two indicators are computed : the mean lifetime of any component and the mean residual lifetime of a given component, after it has been controlled. Three different Bayesian methods are compared on three sets of data. The article shows that the three methods lead to coherent results and that uncertainties are strongly reduced. The method developed around PMC has two main advantages: it models a conditional dependence of the two parameters of the Weibull law, which enables more coherent results on the prior; it has a parameter that weights the strength of the expertise. This last point is very important to do lifetime assessments, because then, expertise is not used to increase too small samples as much as to do a real extrapolation, far beyond what data itself say. (authors)

  6. Intelligent Condition Diagnosis Method Based on Adaptive Statistic Test Filter and Diagnostic Bayesian Network.

    Science.gov (United States)

    Li, Ke; Zhang, Qiuju; Wang, Kun; Chen, Peng; Wang, Huaqing

    2016-01-08

    A new fault diagnosis method for rotating machinery based on adaptive statistic test filter (ASTF) and Diagnostic Bayesian Network (DBN) is presented in this paper. ASTF is proposed to obtain weak fault features under background noise, ASTF is based on statistic hypothesis testing in the frequency domain to evaluate similarity between reference signal (noise signal) and original signal, and remove the component of high similarity. The optimal level of significance α is obtained using particle swarm optimization (PSO). To evaluate the performance of the ASTF, evaluation factor Ipq is also defined. In addition, a simulation experiment is designed to verify the effectiveness and robustness of ASTF. A sensitive evaluation method using principal component analysis (PCA) is proposed to evaluate the sensitiveness of symptom parameters (SPs) for condition diagnosis. By this way, the good SPs that have high sensitiveness for condition diagnosis can be selected. A three-layer DBN is developed to identify condition of rotation machinery based on the Bayesian Belief Network (BBN) theory. Condition diagnosis experiment for rolling element bearings demonstrates the effectiveness of the proposed method.

  7. Intelligent Condition Diagnosis Method Based on Adaptive Statistic Test Filter and Diagnostic Bayesian Network

    Directory of Open Access Journals (Sweden)

    Ke Li

    2016-01-01

    Full Text Available A new fault diagnosis method for rotating machinery based on adaptive statistic test filter (ASTF and Diagnostic Bayesian Network (DBN is presented in this paper. ASTF is proposed to obtain weak fault features under background noise, ASTF is based on statistic hypothesis testing in the frequency domain to evaluate similarity between reference signal (noise signal and original signal, and remove the component of high similarity. The optimal level of significance α is obtained using particle swarm optimization (PSO. To evaluate the performance of the ASTF, evaluation factor Ipq is also defined. In addition, a simulation experiment is designed to verify the effectiveness and robustness of ASTF. A sensitive evaluation method using principal component analysis (PCA is proposed to evaluate the sensitiveness of symptom parameters (SPs for condition diagnosis. By this way, the good SPs that have high sensitiveness for condition diagnosis can be selected. A three-layer DBN is developed to identify condition of rotation machinery based on the Bayesian Belief Network (BBN theory. Condition diagnosis experiment for rolling element bearings demonstrates the effectiveness of the proposed method.

  8. Intelligent Condition Diagnosis Method Based on Adaptive Statistic Test Filter and Diagnostic Bayesian Network

    Science.gov (United States)

    Li, Ke; Zhang, Qiuju; Wang, Kun; Chen, Peng; Wang, Huaqing

    2016-01-01

    A new fault diagnosis method for rotating machinery based on adaptive statistic test filter (ASTF) and Diagnostic Bayesian Network (DBN) is presented in this paper. ASTF is proposed to obtain weak fault features under background noise, ASTF is based on statistic hypothesis testing in the frequency domain to evaluate similarity between reference signal (noise signal) and original signal, and remove the component of high similarity. The optimal level of significance α is obtained using particle swarm optimization (PSO). To evaluate the performance of the ASTF, evaluation factor Ipq is also defined. In addition, a simulation experiment is designed to verify the effectiveness and robustness of ASTF. A sensitive evaluation method using principal component analysis (PCA) is proposed to evaluate the sensitiveness of symptom parameters (SPs) for condition diagnosis. By this way, the good SPs that have high sensitiveness for condition diagnosis can be selected. A three-layer DBN is developed to identify condition of rotation machinery based on the Bayesian Belief Network (BBN) theory. Condition diagnosis experiment for rolling element bearings demonstrates the effectiveness of the proposed method. PMID:26761006

  9. A passive dosing method to determine fugacity capacities and partitioning properties of leaves

    DEFF Research Database (Denmark)

    Bolinius, Damien Johann; Macleod, Matthew; McLachlan, Michael S.

    2016-01-01

    The capacity of leaves to take up chemicals from the atmosphere and water influences how contaminants are transferred into food webs and soil. We provide a proof of concept of a passive dosing method to measure leaf/polydimethylsiloxane partition ratios (Kleaf/PDMS) for intact leaves, using...... polychlorinated biphenyls (PCBs) as model chemicals. Rhododendron leaves held in contact with PCB-loaded PDMS reached between 76 and 99% of equilibrium within 4 days for PCBs 3, 4, 28, 52, 101, 118, 138 and 180. Equilibrium Kleaf/PDMS extrapolated from the uptake kinetics measured over 4 days ranged from 0...... the variability in sorptive capacities of leaves that would improve descriptions of uptake of chemicals by leaves in multimedia fate models....

  10. The Train Driver Recovery Problem - a Set Partitioning Based Model and Solution Method

    DEFF Research Database (Denmark)

    Rezanova, Natalia Jurjevna; Ryan, David

    2010-01-01

    The need to recover a train driver schedule occurs during major disruptions in the daily railway operations. Based on data from the Danish passenger railway operator DSB S-tog A/S, a solution method to the train driver recovery problem (TDRP) is developed. The TDRP is formulated as a set...... branching strategy using the depth-first search of the Branch & Bound tree. The LP relaxation of the TDRP possesses strong integer properties. We present test scenarios generated from the historical real-life operations data of DSB S-tog A/S. The numerical results show that all but one tested instances...... partitioning problem. We define a disruption neighbourhood by identifying a small set of drivers and train tasks directly affected by the disruption. Based on the disruption neighbourhood, the TDRP model is formed and solved. If the TDRP solution provides a feasible recovery for the drivers within...

  11. Development of a high-order finite volume method with multiblock partition techniques

    Directory of Open Access Journals (Sweden)

    E. M. Lemos

    2012-03-01

    Full Text Available This work deals with a new numerical methodology to solve the Navier-Stokes equations based on a finite volume method applied to structured meshes with co-located grids. High-order schemes used to approximate advective, diffusive and non-linear terms, connected with multiblock partition techniques, are the main contributions of this paper. Combination of these two techniques resulted in a computer code that involves high accuracy due the high-order schemes and great flexibility to generate locally refined meshes based on the multiblock approach. This computer code has been able to obtain results with higher or equal accuracy in comparison with results obtained using classical procedures, with considerably less computational effort.

  12. Evaluation of Oceanic Transport Statistics By Use of Transient Tracers and Bayesian Methods

    Science.gov (United States)

    Trossman, D. S.; Thompson, L.; Mecking, S.; Bryan, F.; Peacock, S.

    2013-12-01

    Key variables that quantify the time scales over which atmospheric signals penetrate into the oceanic interior and their uncertainties are computed using Bayesian methods and transient tracers from both models and observations. First, the mean residence times, subduction rates, and formation rates of Subtropical Mode Water (STMW) and Subpolar Mode Water (SPMW) in the North Atlantic and Subantarctic Mode Water (SAMW) in the Southern Ocean are estimated by combining a model and observations of chlorofluorocarbon-11 (CFC-11) via Bayesian Model Averaging (BMA), statistical technique that weights model estimates according to how close they agree with observations. Second, a Bayesian method is presented to find two oceanic transport parameters associated with the age distribution of ocean waters, the transit-time distribution (TTD), by combining an eddying global ocean model's estimate of the TTD with hydrographic observations of CFC-11, temperature, and salinity. Uncertainties associated with objectively mapping irregularly spaced bottle data are quantified by making use of a thin-plate spline and then propagated via the two Bayesian techniques. It is found that the subduction of STMW, SPMW, and SAMW is mostly an advective process, but up to about one-third of STMW subduction likely owes to non-advective processes. Also, while the formation of STMW is mostly due to subduction, the formation of SPMW is mostly due to other processes. About half of the formation of SAMW is due to subduction and half is due to other processes. A combination of air-sea flux, acting on relatively short time scales, and turbulent mixing, acting on a wide range of time scales, is likely the dominant SPMW erosion mechanism. Air-sea flux is likely responsible for most STMW erosion, and turbulent mixing is likely responsible for most SAMW erosion. Two oceanic transport parameters, the mean age of a water parcel and the half-variance associated with the TTD, estimated using the model's tracers as

  13. Study on shielded pump system failure analysis method based on Bayesian network

    International Nuclear Information System (INIS)

    Bao Yilan; Huang Gaofeng; Tong Lili; Cao Xuewu

    2012-01-01

    This paper applies Bayesian network to the system failure analysis, with an aim to improve knowledge representation of the uncertainty logic and multi-fault states in system failure analysis. A Bayesian network for shielded pump failure analysis is presented, conducting fault parameter learning, updating Bayesian network parameter based on new samples. Finally, through the Bayesian network inference, vulnerability in this system, the largest possible failure modes, and the fault probability are obtained. The powerful ability of Bayesian network to analyze system fault is illustrated by examples. (authors)

  14. Guideline for Bayesian Net based Software Fault Estimation Method for Reactor Protection System

    International Nuclear Information System (INIS)

    Eom, Heung Seop; Park, Gee Yong; Jang, Seung Cheol

    2011-01-01

    The purpose of this paper is to provide a preliminary guideline for the estimation of software faults in a safety-critical software, for example, reactor protection system's software. As the fault estimation method is based on Bayesian Net which intensively uses subjective probability and informal data, it is necessary to define formal procedure of the method to minimize the variability of the results. The guideline describes assumptions, limitations and uncertainties, and the product of the fault estimation method. The procedure for conducting a software fault-estimation method is then outlined, highlighting the major tasks involved. The contents of the guideline are based on our own experience and a review of research guidelines developed for a PSA

  15. Bayesian prediction of future ice sheet volume using local approximation Markov chain Monte Carlo methods

    Science.gov (United States)

    Davis, A. D.; Heimbach, P.; Marzouk, Y.

    2017-12-01

    We develop a Bayesian inverse modeling framework for predicting future ice sheet volume with associated formal uncertainty estimates. Marine ice sheets are drained by fast-flowing ice streams, which we simulate using a flowline model. Flowline models depend on geometric parameters (e.g., basal topography), parameterized physical processes (e.g., calving laws and basal sliding), and climate parameters (e.g., surface mass balance), most of which are unknown or uncertain. Given observations of ice surface velocity and thickness, we define a Bayesian posterior distribution over static parameters, such as basal topography. We also define a parameterized distribution over variable parameters, such as future surface mass balance, which we assume are not informed by the data. Hyperparameters are used to represent climate change scenarios, and sampling their distributions mimics internal variation. For example, a warming climate corresponds to increasing mean surface mass balance but an individual sample may have periods of increasing or decreasing surface mass balance. We characterize the predictive distribution of ice volume by evaluating the flowline model given samples from the posterior distribution and the distribution over variable parameters. Finally, we determine the effect of climate change on future ice sheet volume by investigating how changing the hyperparameters affects the predictive distribution. We use state-of-the-art Bayesian computation to address computational feasibility. Characterizing the posterior distribution (using Markov chain Monte Carlo), sampling the full range of variable parameters and evaluating the predictive model is prohibitively expensive. Furthermore, the required resolution of the inferred basal topography may be very high, which is often challenging for sampling methods. Instead, we leverage regularity in the predictive distribution to build a computationally cheaper surrogate over the low dimensional quantity of interest (future ice

  16. Predicting uncertainty in future marine ice sheet volume using Bayesian statistical methods

    Science.gov (United States)

    Davis, A. D.

    2015-12-01

    The marine ice instability can trigger rapid retreat of marine ice streams. Recent observations suggest that marine ice systems in West Antarctica have begun retreating. However, unknown ice dynamics, computationally intensive mathematical models, and uncertain parameters in these models make predicting retreat rate and ice volume difficult. In this work, we fuse current observational data with ice stream/shelf models to develop probabilistic predictions of future grounded ice sheet volume. Given observational data (e.g., thickness, surface elevation, and velocity) and a forward model that relates uncertain parameters (e.g., basal friction and basal topography) to these observations, we use a Bayesian framework to define a posterior distribution over the parameters. A stochastic predictive model then propagates uncertainties in these parameters to uncertainty in a particular quantity of interest (QoI)---here, the volume of grounded ice at a specified future time. While the Bayesian approach can in principle characterize the posterior predictive distribution of the QoI, the computational cost of both the forward and predictive models makes this effort prohibitively expensive. To tackle this challenge, we introduce a new Markov chain Monte Carlo method that constructs convergent approximations of the QoI target density in an online fashion, yielding accurate characterizations of future ice sheet volume at significantly reduced computational cost.Our second goal is to attribute uncertainty in these Bayesian predictions to uncertainties in particular parameters. Doing so can help target data collection, for the purpose of constraining the parameters that contribute most strongly to uncertainty in the future volume of grounded ice. For instance, smaller uncertainties in parameters to which the QoI is highly sensitive may account for more variability in the prediction than larger uncertainties in parameters to which the QoI is less sensitive. We use global sensitivity

  17. Photoacoustic discrimination of vascular and pigmented lesions using classical and Bayesian methods

    Science.gov (United States)

    Swearingen, Jennifer A.; Holan, Scott H.; Feldman, Mary M.; Viator, John A.

    2010-01-01

    Discrimination of pigmented and vascular lesions in skin can be difficult due to factors such as size, subungual location, and the nature of lesions containing both melanin and vascularity. Misdiagnosis may lead to precancerous or cancerous lesions not receiving proper medical care. To aid in the rapid and accurate diagnosis of such pathologies, we develop a photoacoustic system to determine the nature of skin lesions in vivo. By irradiating skin with two laser wavelengths, 422 and 530 nm, we induce photoacoustic responses, and the relative response at these two wavelengths indicates whether the lesion is pigmented or vascular. This response is due to the distinct absorption spectrum of melanin and hemoglobin. In particular, pigmented lesions have ratios of photoacoustic amplitudes of approximately 1.4 to 1 at the two wavelengths, while vascular lesions have ratios of about 4.0 to 1. Furthermore, we consider two statistical methods for conducting classification of lesions: standard multivariate analysis classification techniques and a Bayesian-model-based approach. We study 15 human subjects with eight vascular and seven pigmented lesions. Using the classical method, we achieve a perfect classification rate, while the Bayesian approach has an error rate of 20%.

  18. Estimated value of insurance premium due to Citarum River flood by using Bayesian method

    Science.gov (United States)

    Sukono; Aisah, I.; Tampubolon, Y. R. H.; Napitupulu, H.; Supian, S.; Subiyanto; Sidi, P.

    2018-03-01

    Citarum river flood in South Bandung, West Java Indonesia, often happens every year. It causes property damage, producing economic loss. The risk of loss can be mitigated by following the flood insurance program. In this paper, we discussed about the estimated value of insurance premiums due to Citarum river flood by Bayesian method. It is assumed that the risk data for flood losses follows the Pareto distribution with the right fat-tail. The estimation of distribution model parameters is done by using Bayesian method. First, parameter estimation is done with assumption that prior comes from Gamma distribution family, while observation data follow Pareto distribution. Second, flood loss data is simulated based on the probability of damage in each flood affected area. The result of the analysis shows that the estimated premium value of insurance based on pure premium principle is as follows: for the loss value of IDR 629.65 million of premium IDR 338.63 million; for a loss of IDR 584.30 million of its premium IDR 314.24 million; and the loss value of IDR 574.53 million of its premium IDR 308.95 million. The premium value estimator can be used as neither a reference in the decision of reasonable premium determination, so as not to incriminate the insured, nor it result in loss of the insurer.

  19. Bayesian risk-based decision method for model validation under uncertainty

    International Nuclear Information System (INIS)

    Jiang Xiaomo; Mahadevan, Sankaran

    2007-01-01

    This paper develops a decision-making methodology for computational model validation, considering the risk of using the current model, data support for the current model, and cost of acquiring new information to improve the model. A Bayesian decision theory-based method is developed for this purpose, using a likelihood ratio as the validation metric for model assessment. An expected risk or cost function is defined as a function of the decision costs, and the likelihood and prior of each hypothesis. The risk is minimized through correctly assigning experimental data to two decision regions based on the comparison of the likelihood ratio with a decision threshold. A Bayesian validation metric is derived based on the risk minimization criterion. Two types of validation tests are considered: pass/fail tests and system response value measurement tests. The methodology is illustrated for the validation of reliability prediction models in a tension bar and an engine blade subjected to high cycle fatigue. The proposed method can effectively integrate optimal experimental design into model validation to simultaneously reduce the cost and improve the accuracy of reliability model assessment

  20. Two modified symplectic partitioned Runge-Kutta methods for solving the elastic wave equation

    Science.gov (United States)

    Su, Bo; Tuo, Xianguo; Xu, Ling

    2017-08-01

    Based on a modified strategy, two modified symplectic partitioned Runge-Kutta (PRK) methods are proposed for the temporal discretization of the elastic wave equation. The two symplectic schemes are similar in form but are different in nature. After the spatial discretization of the elastic wave equation, the ordinary Hamiltonian formulation for the elastic wave equation is presented. The PRK scheme is then applied for time integration. An additional term associated with spatial discretization is inserted into the different stages of the PRK scheme. Theoretical analyses are conducted to evaluate the numerical dispersion and stability of the two novel PRK methods. A finite difference method is used to approximate the spatial derivatives since the two schemes are independent of the spatial discretization technique used. The numerical solutions computed by the two new schemes are compared with those computed by a conventional symplectic PRK. The numerical results, which verify the new method, are superior to those generated by traditional conventional methods in seismic wave modeling.

  1. Multiple Attribute Group Decision-Making Methods Based on Trapezoidal Fuzzy Two-Dimensional Linguistic Partitioned Bonferroni Mean Aggregation Operators.

    Science.gov (United States)

    Yin, Kedong; Yang, Benshuo; Li, Xuemei

    2018-01-24

    In this paper, we investigate multiple attribute group decision making (MAGDM) problems where decision makers represent their evaluation of alternatives by trapezoidal fuzzy two-dimensional uncertain linguistic variable. To begin with, we introduce the definition, properties, expectation, operational laws of trapezoidal fuzzy two-dimensional linguistic information. Then, to improve the accuracy of decision making in some case where there are a sort of interrelationship among the attributes, we analyze partition Bonferroni mean (PBM) operator in trapezoidal fuzzy two-dimensional variable environment and develop two operators: trapezoidal fuzzy two-dimensional linguistic partitioned Bonferroni mean (TF2DLPBM) aggregation operator and trapezoidal fuzzy two-dimensional linguistic weighted partitioned Bonferroni mean (TF2DLWPBM) aggregation operator. Furthermore, we develop a novel method to solve MAGDM problems based on TF2DLWPBM aggregation operator. Finally, a practical example is presented to illustrate the effectiveness of this method and analyses the impact of different parameters on the results of decision-making.

  2. Partition functions in even dimensional AdS via quasinormal mode methods

    International Nuclear Information System (INIS)

    Keeler, Cynthia; Ng, Gim Seng

    2014-01-01

    In this note, we calculate the one-loop determinant for a massive scalar (with conformal dimension Δ) in even-dimensional AdS d+1 space, using the quasinormal mode method developed in http://dx.doi.org/10.1088/0264-9381/27/12/125001 by Denef, Hartnoll, and Sachdev. Working first in two dimensions on the related Euclidean hyperbolic plane H 2 , we find a series of zero modes for negative real values of Δ whose presence indicates a series of poles in the one-loop partition function Z(Δ) in the Δ complex plane; these poles contribute temperature-independent terms to the thermal AdS partition function computed in http://dx.doi.org/10.1088/0264-9381/27/12/125001. Our results match those in a series of papers by Camporesi and Higuchi, as well as Gopakumar et al. http://dx.doi.org/10.1007/JHEP11(2011)010 and Banerjee et al. http://dx.doi.org/10.1007/JHEP03(2011)147. We additionally examine the meaning of these zero modes, finding that they Wick-rotate to quasinormal modes of the AdS 2 black hole. They are also interpretable as matrix elements of the discrete series representations of SO(2,1) in the space of smooth functions on S 1 . We generalize our results to general even dimensional AdS 2n , again finding a series of zero modes which are related to discrete series representations of SO(2n,1), the motion group of H 2n .

  3. Model Based Beamforming and Bayesian Inversion Signal Processing Methods for Seismic Localization of Underground Source

    DEFF Research Database (Denmark)

    Oh, Geok Lian

    properties such as the elastic wave speeds and soil densities. One processing method is casting the estimation problem into an inverse problem to solve for the unknown material parameters. The forward model for the seismic signals used in the literatures include ray tracing methods that consider only...... density values of the discretized ground medium, which leads to time-consuming computations and instability behaviour of the inversion process. In addition, the geophysics inverse problem is generally ill-posed due to non-exact forward model that introduces errors. The Bayesian inversion method through...... the first arrivals of the reflected compressional P-waves from the subsurface structures, or 3D elastic wave models that model all the seismic wave components. The ray tracing forward model formulation is linear, whereas the full 3D elastic wave model leads to a nonlinear inversion problem. In this Ph...

  4. A Modified Method Combined with a Support Vector Machine and Bayesian Algorithms in Biological Information

    Directory of Open Access Journals (Sweden)

    Wen-Gang Zhou

    2015-06-01

    Full Text Available With the deep research of genomics and proteomics, the number of new protein sequences has expanded rapidly. With the obvious shortcomings of high cost and low efficiency of the traditional experimental method, the calculation method for protein localization prediction has attracted a lot of attention due to its convenience and low cost. In the machine learning techniques, neural network and support vector machine (SVM are often used as learning tools. Due to its complete theoretical framework, SVM has been widely applied. In this paper, we make an improvement on the existing machine learning algorithm of the support vector machine algorithm, and a new improved algorithm has been developed, combined with Bayesian algorithms. The proposed algorithm can improve calculation efficiency, and defects of the original algorithm are eliminated. According to the verification, the method has proved to be valid. At the same time, it can reduce calculation time and improve prediction efficiency.

  5. Online probabilistic operational safety assessment of multi-mode engineering systems using Bayesian methods

    International Nuclear Information System (INIS)

    Lin, Yufei; Chen, Maoyin; Zhou, Donghua

    2013-01-01

    In the past decades, engineering systems become more and more complex, and generally work at different operational modes. Since incipient fault can lead to dangerous accidents, it is crucial to develop strategies for online operational safety assessment. However, the existing online assessment methods for multi-mode engineering systems commonly assume that samples are independent, which do not hold for practical cases. This paper proposes a probabilistic framework of online operational safety assessment of multi-mode engineering systems with sample dependency. To begin with, a Gaussian mixture model (GMM) is used to characterize multiple operating modes. Then, based on the definition of safety index (SI), the SI for one single mode is calculated. At last, the Bayesian method is presented to calculate the posterior probabilities belonging to each operating mode with sample dependency. The proposed assessment strategy is applied in two examples: one is the aircraft gas turbine, another is an industrial dryer. Both examples illustrate the efficiency of the proposed method

  6. A calibration and data assimilation method using the Bayesian MARS emulator

    International Nuclear Information System (INIS)

    Stripling, H.F.; McClarren, R.G.; Kuranz, C.C.; Grosskopf, M.J.; Rutter, E.; Torralva, B.R.

    2013-01-01

    Highlights: ► We outline a transparent, flexible method for the calibration of uncertain inputs to computer models. ► We account for model, data, emulator, and measurement uncertainties. ► The method produces improved predictive results, which are validated using leave one-out experiments. ► Our implementation leverages the Bayesian MARS emulator, but any emulator may be substituted. -- Abstract: We present a method for calibrating the uncertain inputs to a computer model using available experimental data. The goal of the procedure is to estimate the posterior distribution of the uncertain inputs such that when samples from the posterior are used as inputs to future model runs, the model is more likely to replicate (or predict) the experimental response. The calibration is performed by sampling the space of the uncertain inputs, using the computer model (or, more likely, an emulator for the computer model) to assign weights to the samples, and applying the weights to produce the posterior distributions and generate predictions of new experiments with confidence bounds. The method is similar to Metropolis–Hastings calibration methods with independently sampled updates, except that we generate samples beforehand and replace the candidate acceptance routine with a weighting scheme. We apply our method to the calibration of a Hyades 2D model of laser energy deposition in beryllium. We employ a Bayesian Multivariate Adaptive Regression Splines (BMARS) emulator as a surrogate for Hyades 2D. We treat a range of uncertainties in our application, including uncertainties in the experimental inputs, experimental measurement error, and systematic experimental timing errors. The resulting posterior distributions agree with our existing intuition, and we validate the results by performing a series of leave-one-out predictions. We find that the calibrated predictions are considerably more accurate and less uncertain than blind sampling of the forward model alone.

  7. Bayesian methods for addressing long-standing problems in associative learning: The case of PREE.

    Science.gov (United States)

    Blanco, Fernando; Moris, Joaquín

    2017-07-20

    Most associative models typically assume that learning can be understood as a gradual change in associative strength that captures the situation into one single parameter, or representational state. We will call this view single-state learning. However, there is ample evidence showing that under many circumstances different relationships that share features can be learned independently, and animals can quickly switch between expressing one or another. We will call this multiple-state learning. Theoretically, it is understudied because it needs a different data analysis approach from those usually employed. In this paper, we present a Bayesian model of the Partial Reinforcement Extinction Effect (PREE) that can test the predictions of the multiple-state view. This implies estimating the moment of change in the responses (from the acquisition to the extinction performance), both at the individual and at the group levels. We used this model to analyze data from a PREE experiment with three levels of reinforcement during acquisition (100%, 75% and 50%). We found differences in the estimated moment of switch between states during extinction, so that it was delayed after leaner partial reinforcement schedules. The finding is compatible with the multiple-state view. It is the first time, to our knowledge, that the predictions from the multiple-state view are tested directly. The paper also aims to show the benefits that Bayesian methods can bring to the associative learning field.

  8. Evolutionary Analysis of Dengue Serotype 2 Viruses Using Phylogenetic and Bayesian Methods from New Delhi, India.

    Directory of Open Access Journals (Sweden)

    Nazia Afreen

    2016-03-01

    Full Text Available Dengue fever is the most important arboviral disease in the tropical and sub-tropical countries of the world. Delhi, the metropolitan capital state of India, has reported many dengue outbreaks, with the last outbreak occurring in 2013. We have recently reported predominance of dengue virus serotype 2 during 2011-2014 in Delhi. In the present study, we report molecular characterization and evolutionary analysis of dengue serotype 2 viruses which were detected in 2011-2014 in Delhi. Envelope genes of 42 DENV-2 strains were sequenced in the study. All DENV-2 strains grouped within the Cosmopolitan genotype and further clustered into three lineages; Lineage I, II and III. Lineage III replaced lineage I during dengue fever outbreak of 2013. Further, a novel mutation Thr404Ile was detected in the stem region of the envelope protein of a single DENV-2 strain in 2014. Nucleotide substitution rate and time to the most recent common ancestor were determined by molecular clock analysis using Bayesian methods. A change in effective population size of Indian DENV-2 viruses was investigated through Bayesian skyline plot. The study will be a vital road map for investigation of epidemiology and evolutionary pattern of dengue viruses in India.

  9. Bayesian calibration of terrestrial ecosystem models: a study of advanced Markov chain Monte Carlo methods

    Science.gov (United States)

    Lu, Dan; Ricciuto, Daniel; Walker, Anthony; Safta, Cosmin; Munger, William

    2017-09-01

    Calibration of terrestrial ecosystem models is important but challenging. Bayesian inference implemented by Markov chain Monte Carlo (MCMC) sampling provides a comprehensive framework to estimate model parameters and associated uncertainties using their posterior distributions. The effectiveness and efficiency of the method strongly depend on the MCMC algorithm used. In this work, a differential evolution adaptive Metropolis (DREAM) algorithm is used to estimate posterior distributions of 21 parameters for the data assimilation linked ecosystem carbon (DALEC) model using 14 years of daily net ecosystem exchange data collected at the Harvard Forest Environmental Measurement Site eddy-flux tower. The calibration of DREAM results in a better model fit and predictive performance compared to the popular adaptive Metropolis (AM) scheme. Moreover, DREAM indicates that two parameters controlling autumn phenology have multiple modes in their posterior distributions while AM only identifies one mode. The application suggests that DREAM is very suitable to calibrate complex terrestrial ecosystem models, where the uncertain parameter size is usually large and existence of local optima is always a concern. In addition, this effort justifies the assumptions of the error model used in Bayesian calibration according to the residual analysis. The result indicates that a heteroscedastic, correlated, Gaussian error model is appropriate for the problem, and the consequent constructed likelihood function can alleviate the underestimation of parameter uncertainty that is usually caused by using uncorrelated error models.

  10. Fast gradient-based methods for Bayesian reconstruction of transmission and emission PET images

    International Nuclear Information System (INIS)

    Mumcuglu, E.U.; Leahy, R.; Zhou, Z.; Cherry, S.R.

    1994-01-01

    The authors describe conjugate gradient algorithms for reconstruction of transmission and emission PET images. The reconstructions are based on a Bayesian formulation, where the data are modeled as a collection of independent Poisson random variables and the image is modeled using a Markov random field. A conjugate gradient algorithm is used to compute a maximum a posteriori (MAP) estimate of the image by maximizing over the posterior density. To ensure nonnegativity of the solution, a penalty function is used to convert the problem to one of unconstrained optimization. Preconditioners are used to enhance convergence rates. These methods generally achieve effective convergence in 15--25 iterations. Reconstructions are presented of an 18 FDG whole body scan from data collected using a Siemens/CTI ECAT931 whole body system. These results indicate significant improvements in emission image quality using the Bayesian approach, in comparison to filtered backprojection, particularly when reprojections of the MAP transmission image are used in place of the standard attenuation correction factors

  11. Efficient nonparametric and asymptotic Bayesian model selection methods for attributed graph clustering

    KAUST Repository

    Xu, Zhiqiang

    2017-02-16

    Attributed graph clustering, also known as community detection on attributed graphs, attracts much interests recently due to the ubiquity of attributed graphs in real life. Many existing algorithms have been proposed for this problem, which are either distance based or model based. However, model selection in attributed graph clustering has not been well addressed, that is, most existing algorithms assume the cluster number to be known a priori. In this paper, we propose two efficient approaches for attributed graph clustering with automatic model selection. The first approach is a popular Bayesian nonparametric method, while the second approach is an asymptotic method based on a recently proposed model selection criterion, factorized information criterion. Experimental results on both synthetic and real datasets demonstrate that our approaches for attributed graph clustering with automatic model selection significantly outperform the state-of-the-art algorithm.

  12. Efficient nonparametric and asymptotic Bayesian model selection methods for attributed graph clustering

    KAUST Repository

    Xu, Zhiqiang; Cheng, James; Xiao, Xiaokui; Fujimaki, Ryohei; Muraoka, Yusuke

    2017-01-01

    Attributed graph clustering, also known as community detection on attributed graphs, attracts much interests recently due to the ubiquity of attributed graphs in real life. Many existing algorithms have been proposed for this problem, which are either distance based or model based. However, model selection in attributed graph clustering has not been well addressed, that is, most existing algorithms assume the cluster number to be known a priori. In this paper, we propose two efficient approaches for attributed graph clustering with automatic model selection. The first approach is a popular Bayesian nonparametric method, while the second approach is an asymptotic method based on a recently proposed model selection criterion, factorized information criterion. Experimental results on both synthetic and real datasets demonstrate that our approaches for attributed graph clustering with automatic model selection significantly outperform the state-of-the-art algorithm.

  13. Statistical analysis using the Bayesian nonparametric method for irradiation embrittlement of reactor pressure vessels

    Energy Technology Data Exchange (ETDEWEB)

    Takamizawa, Hisashi, E-mail: takamizawa.hisashi@jaea.go.jp; Itoh, Hiroto, E-mail: ito.hiroto@jaea.go.jp; Nishiyama, Yutaka, E-mail: nishiyama.yutaka93@jaea.go.jp

    2016-10-15

    In order to understand neutron irradiation embrittlement in high fluence regions, statistical analysis using the Bayesian nonparametric (BNP) method was performed for the Japanese surveillance and material test reactor irradiation database. The BNP method is essentially expressed as an infinite summation of normal distributions, with input data being subdivided into clusters with identical statistical parameters, such as mean and standard deviation, for each cluster to estimate shifts in ductile-to-brittle transition temperature (DBTT). The clusters typically depend on chemical compositions, irradiation conditions, and the irradiation embrittlement. Specific variables contributing to the irradiation embrittlement include the content of Cu, Ni, P, Si, and Mn in the pressure vessel steels, neutron flux, neutron fluence, and irradiation temperatures. It was found that the measured shifts of DBTT correlated well with the calculated ones. Data associated with the same materials were subdivided into the same clusters even if neutron fluences were increased.

  14. A non-conventional watershed partitioning method for semi-distributed hydrological modelling: the package ALADHYN

    Science.gov (United States)

    Menduni, Giovanni; Pagani, Alessandro; Rulli, Maria Cristina; Rosso, Renzo

    2002-02-01

    The extraction of the river network from a digital elevation model (DEM) plays a fundamental role in modelling spatially distributed hydrological processes. The present paper deals with a new two-step procedure based on the preliminary identification of an ideal drainage network (IDN) from contour lines through a variable mesh size, and the further extraction of the actual drainage network (AND) from the IDN using land morphology. The steepest downslope direction search is used to identify individual channels, which are further merged into a network path draining to a given node of the IDN. The contributing area, peaks and saddles are determined by means of a steepest upslope direction search. The basin area is thus partitioned into physically based finite elements enclosed by irregular polygons. Different methods, i.e. the constant and variable threshold area methods, the contour line curvature method, and a topologic method descending from the Hortonian ordering scheme, are used to extract the ADN from the IDN. The contour line curvature method is shown to provide the most appropriate method from a comparison with field surveys. Using the ADN one can model the hydrological response of any sub-basin using a semi-distributed approach. The model presented here combines storm abstraction by the SCS-CN method with surface runoff routing as a geomorphological dispersion process. This is modelled using the gamma instantaneous unit hydrograph as parameterized by river geomorphology. The results are implemented using a project-oriented software facility for the Analysis of LAnd Digital HYdrological Networks (ALADHYN).

  15. Estimation of octanol/water partition coefficient and aqueous solubility of environmental chemicals using molecular fingerprints and machine learning methods

    Science.gov (United States)

    Octanol/water partition coefficient (logP) and aqueous solubility (logS) are two important parameters in pharmacology and toxicology studies, and experimental measurements are usually time-consuming and expensive. In the present research, novel methods are presented for the estim...

  16. A computer program for uncertainty analysis integrating regression and Bayesian methods

    Science.gov (United States)

    Lu, Dan; Ye, Ming; Hill, Mary C.; Poeter, Eileen P.; Curtis, Gary

    2014-01-01

    This work develops a new functionality in UCODE_2014 to evaluate Bayesian credible intervals using the Markov Chain Monte Carlo (MCMC) method. The MCMC capability in UCODE_2014 is based on the FORTRAN version of the differential evolution adaptive Metropolis (DREAM) algorithm of Vrugt et al. (2009), which estimates the posterior probability density function of model parameters in high-dimensional and multimodal sampling problems. The UCODE MCMC capability provides eleven prior probability distributions and three ways to initialize the sampling process. It evaluates parametric and predictive uncertainties and it has parallel computing capability based on multiple chains to accelerate the sampling process. This paper tests and demonstrates the MCMC capability using a 10-dimensional multimodal mathematical function, a 100-dimensional Gaussian function, and a groundwater reactive transport model. The use of the MCMC capability is made straightforward and flexible by adopting the JUPITER API protocol. With the new MCMC capability, UCODE_2014 can be used to calculate three types of uncertainty intervals, which all can account for prior information: (1) linear confidence intervals which require linearity and Gaussian error assumptions and typically 10s–100s of highly parallelizable model runs after optimization, (2) nonlinear confidence intervals which require a smooth objective function surface and Gaussian observation error assumptions and typically 100s–1,000s of partially parallelizable model runs after optimization, and (3) MCMC Bayesian credible intervals which require few assumptions and commonly 10,000s–100,000s or more partially parallelizable model runs. Ready access allows users to select methods best suited to their work, and to compare methods in many circumstances.

  17. Partition function zeros of the one-dimensional Potts model: the recursive method

    International Nuclear Information System (INIS)

    Ghulghazaryan, R G; Ananikian, N S

    2003-01-01

    The Yang-Lee, Fisher and Potts zeros of the one-dimensional Q-state Potts model are studied using the theory of dynamical systems. An exact recurrence relation for the partition function is derived. It is shown that zeros of the partition function may be associated with neutral fixed points of the recurrence relation. Further, a general equation for zeros of the partition function is found and a classification of the Yang-Lee, Fisher and Potts zeros is given. It is shown that the Fisher zeros in a nonzero magnetic field are located on several lines in the complex temperature plane and that the number of these lines depends on the value of the magnetic field. Analytical expressions for the densities of the Yang-Lee, Fisher and Potts zeros are derived. It is shown that densities of all types of zeros of the partition function are singular at the edge singularity points with the same critical exponent

  18. VizieR Online Data Catalog: Bayesian method for detecting stellar flares (Pitkin+, 2014)

    Science.gov (United States)

    Pitkin, M.; Williams, D.; Fletcher, L.; Grant, S. D. T.

    2015-05-01

    We present a Bayesian-odds-ratio-based algorithm for detecting stellar flares in light-curve data. We assume flares are described by a model in which there is a rapid rise with a half-Gaussian profile, followed by an exponential decay. Our signal model also contains a polynomial background model required to fit underlying light-curve variations in the data, which could otherwise partially mimic a flare. We characterize the false alarm probability and efficiency of this method under the assumption that any unmodelled noise in the data is Gaussian, and compare it with a simpler thresholding method based on that used in Walkowicz et al. We find our method has a significant increase in detection efficiency for low signal-to-noise ratio (S/N) flares. For a conservative false alarm probability our method can detect 95 per cent of flares with S/N less than 20, as compared to S/N of 25 for the simpler method. We also test how well the assumption of Gaussian noise holds by applying the method to a selection of 'quiet' Kepler stars. As an example we have applied our method to a selection of stars in Kepler Quarter 1 data. The method finds 687 flaring stars with a total of 1873 flares after vetos have been applied. For these flares we have made preliminary characterizations of their durations and and S/N. (1 data file).

  19. A Bayesian method and its variational approximation for prediction of genomic breeding values in multiple traits

    Directory of Open Access Journals (Sweden)

    Hayashi Takeshi

    2013-01-01

    Full Text Available Abstract Background Genomic selection is an effective tool for animal and plant breeding, allowing effective individual selection without phenotypic records through the prediction of genomic breeding value (GBV. To date, genomic selection has focused on a single trait. However, actual breeding often targets multiple correlated traits, and, therefore, joint analysis taking into consideration the correlation between traits, which might result in more accurate GBV prediction than analyzing each trait separately, is suitable for multi-trait genomic selection. This would require an extension of the prediction model for single-trait GBV to multi-trait case. As the computational burden of multi-trait analysis is even higher than that of single-trait analysis, an effective computational method for constructing a multi-trait prediction model is also needed. Results We described a Bayesian regression model incorporating variable selection for jointly predicting GBVs of multiple traits and devised both an MCMC iteration and variational approximation for Bayesian estimation of parameters in this multi-trait model. The proposed Bayesian procedures with MCMC iteration and variational approximation were referred to as MCBayes and varBayes, respectively. Using simulated datasets of SNP genotypes and phenotypes for three traits with high and low heritabilities, we compared the accuracy in predicting GBVs between multi-trait and single-trait analyses as well as between MCBayes and varBayes. The results showed that, compared to single-trait analysis, multi-trait analysis enabled much more accurate GBV prediction for low-heritability traits correlated with high-heritability traits, by utilizing the correlation structure between traits, while the prediction accuracy for uncorrelated low-heritability traits was comparable or less with multi-trait analysis in comparison with single-trait analysis depending on the setting for prior probability that a SNP has zero

  20. Bayesian analysis of general failure data from an ageing distribution: advances in numerical methods

    International Nuclear Information System (INIS)

    Procaccia, H.; Villain, B.; Clarotti, C.A.

    1996-01-01

    EDF and ENEA carried out a joint research program for developing the numerical methods and computer codes needed for Bayesian analysis of component-lives in the case of ageing. Early results of this study were presented at ESREL'94. Since then the following further steps have been gone: input data have been generalized to the case that observed lives are censored both on the right and on the left; allowable life distributions are Weibull and gamma - their parameters are both unknown and can be statistically dependent; allowable priors are histograms relative to different parametrizations of the life distribution of concern; first-and-second-order-moments of the posterior distributions can be computed. In particular the covariance will give some important information about the degree of the statistical dependence between the parameters of interest. An application of the code to the appearance of a stress corrosion cracking in a tube of the PWR Steam Generator system is presented. (authors)

  1. The determination of nuclear charge distributions using a Bayesian maximum entropy method

    International Nuclear Information System (INIS)

    Macaulay, V.A.; Buck, B.

    1995-01-01

    We treat the inference of nuclear charge densities from measurements of elastic electron scattering cross sections. In order to get the most reliable information from expensively acquired, incomplete and noisy measurements, we use Bayesian probability theory. Very little prior information about the charge densities is assumed. We derive a prior probability distribution which is a generalization of a form used widely in image restoration based on the entropy of a physical density. From the posterior distribution of possible densities, we select the most probable one, and show how error bars can be evaluated. These have very reasonable properties, such as increasing without bound as hypotheses about finer scale structures are included in the hypothesis space. The methods are demonstrated by using data on the nuclei 4 He and 12 C. (orig.)

  2. An urban flood risk assessment method using the Bayesian Network approach

    DEFF Research Database (Denmark)

    Åström, Helena Lisa Alexandra

    and water resources management studies, whereas climate risk studies have not yet fully adapted the BN method. A BN is a graphical model that utilizes causal relationships to describe the overall system where risk occurs. A BN can be further extended into a Bayesian Influence diagram (ID) by including...... for inclusion of multiple hazards in FRAs. Lastly, the inclusion of multiple hazards in FRA may be challenging, among others because concurrent events are rare. However, with climate change, the annual variation of hazards may change, and concurrent events may become more frequent. Large-scale atmospheric...... circulation influences local and regional climate and is considered an important factor when aiming at improving our understanding of local weather conditions and the occurrence of extreme events. Hence, this thesis presents a study that explores the relationship between flood generating hazards and large...

  3. Physics-based, Bayesian sequential detection method and system for radioactive contraband

    Science.gov (United States)

    Candy, James V; Axelrod, Michael C; Breitfeller, Eric F; Chambers, David H; Guidry, Brian L; Manatt, Douglas R; Meyer, Alan W; Sale, Kenneth E

    2014-03-18

    A distributed sequential method and system for detecting and identifying radioactive contraband from highly uncertain (noisy) low-count, radionuclide measurements, i.e. an event mode sequence (EMS), using a statistical approach based on Bayesian inference and physics-model-based signal processing based on the representation of a radionuclide as a monoenergetic decomposition of monoenergetic sources. For a given photon event of the EMS, the appropriate monoenergy processing channel is determined using a confidence interval condition-based discriminator for the energy amplitude and interarrival time and parameter estimates are used to update a measured probability density function estimate for a target radionuclide. A sequential likelihood ratio test is then used to determine one of two threshold conditions signifying that the EMS is either identified as the target radionuclide or not, and if not, then repeating the process for the next sequential photon event of the EMS until one of the two threshold conditions is satisfied.

  4. Model estimation of claim risk and premium for motor vehicle insurance by using Bayesian method

    Science.gov (United States)

    Sukono; Riaman; Lesmana, E.; Wulandari, R.; Napitupulu, H.; Supian, S.

    2018-01-01

    Risk models need to be estimated by the insurance company in order to predict the magnitude of the claim and determine the premiums charged to the insured. This is intended to prevent losses in the future. In this paper, we discuss the estimation of risk model claims and motor vehicle insurance premiums using Bayesian methods approach. It is assumed that the frequency of claims follow a Poisson distribution, while a number of claims assumed to follow a Gamma distribution. The estimation of parameters of the distribution of the frequency and amount of claims are made by using Bayesian methods. Furthermore, the estimator distribution of frequency and amount of claims are used to estimate the aggregate risk models as well as the value of the mean and variance. The mean and variance estimator that aggregate risk, was used to predict the premium eligible to be charged to the insured. Based on the analysis results, it is shown that the frequency of claims follow a Poisson distribution with parameter values λ is 5.827. While a number of claims follow the Gamma distribution with parameter values p is 7.922 and θ is 1.414. Therefore, the obtained values of the mean and variance of the aggregate claims respectively are IDR 32,667,489.88 and IDR 38,453,900,000,000.00. In this paper the prediction of the pure premium eligible charged to the insured is obtained, which amounting to IDR 2,722,290.82. The prediction of the claims and premiums aggregate can be used as a reference for the insurance company’s decision-making in management of reserves and premiums of motor vehicle insurance.

  5. Estimation of parameter uncertainty for an activated sludge model using Bayesian inference: a comparison with the frequentist method.

    Science.gov (United States)

    Zonta, Zivko J; Flotats, Xavier; Magrí, Albert

    2014-08-01

    The procedure commonly used for the assessment of the parameters included in activated sludge models (ASMs) relies on the estimation of their optimal value within a confidence region (i.e. frequentist inference). Once optimal values are estimated, parameter uncertainty is computed through the covariance matrix. However, alternative approaches based on the consideration of the model parameters as probability distributions (i.e. Bayesian inference), may be of interest. The aim of this work is to apply (and compare) both Bayesian and frequentist inference methods when assessing uncertainty for an ASM-type model, which considers intracellular storage and biomass growth, simultaneously. Practical identifiability was addressed exclusively considering respirometric profiles based on the oxygen uptake rate and with the aid of probabilistic global sensitivity analysis. Parameter uncertainty was thus estimated according to both the Bayesian and frequentist inferential procedures. Results were compared in order to evidence the strengths and weaknesses of both approaches. Since it was demonstrated that Bayesian inference could be reduced to a frequentist approach under particular hypotheses, the former can be considered as a more generalist methodology. Hence, the use of Bayesian inference is encouraged for tackling inferential issues in ASM environments.

  6. A fault diagnosis system for PV power station based on global partitioned gradually approximation method

    Science.gov (United States)

    Wang, S.; Zhang, X. N.; Gao, D. D.; Liu, H. X.; Ye, J.; Li, L. R.

    2016-08-01

    As the solar photovoltaic (PV) power is applied extensively, more attentions are paid to the maintenance and fault diagnosis of PV power plants. Based on analysis of the structure of PV power station, the global partitioned gradually approximation method is proposed as a fault diagnosis algorithm to determine and locate the fault of PV panels. The PV array is divided into 16x16 blocks and numbered. On the basis of modularly processing of the PV array, the current values of each block are analyzed. The mean current value of each block is used for calculating the fault weigh factor. The fault threshold is defined to determine the fault, and the shade is considered to reduce the probability of misjudgments. A fault diagnosis system is designed and implemented with LabVIEW. And it has some functions including the data realtime display, online check, statistics, real-time prediction and fault diagnosis. Through the data from PV plants, the algorithm is verified. The results show that the fault diagnosis results are accurate, and the system works well. The validity and the possibility of the system are verified by the results as well. The developed system will be benefit for the maintenance and management of large scale PV array.

  7. Development of quantitative analytical methods for the control of actinides in a pyrochemical partitioning process

    International Nuclear Information System (INIS)

    Abousahl, S.; Belle, P. van; Eberle, H.; Ottmar, H.; Lynch, B.; Vallet, P.; Mayer, K.; Ougier, M.

    2005-01-01

    Advanced nuclear fuel cycles are being developed in order to reduce the long-term radiotoxicity of highly radioactive waste. Pyrochemical partitioning techniques appear particularly attractive for advanced fuel cycles in which the minor actinides are recycled. The electrochemical processes of practical importance are the electrorefining process and the liquid-liquid extraction of transuranic (TRU) elements from fission products using either non-miscible molten metal or molten salt-metal phases. Analytical methods for the accurate assay of actinide elements in these matrices needed to be developed. A quantitative assay is required in order to establish a material balance for process development and - at a later stage - for accountancy and control purposes. To this end radiometric techniques such as energy-dispersive X-ray fluorescence analysis (XRF), neutron coincidence counting (NCC) and high-resolution gamma spectrometry (HRGS) were extensively employed for the quantitative determination of actinides (U, Np, Pu, Am, Cm) in process samples. Comparative analyses were performed using inductively coupled plasma mass spectrometry (ICP-MS). The respective samples were available in small quantities (≅ 100 mg) either in the form of eutectic salt or in metallic form with Cd, Zr or Bi as major metallic matrix constituents. (orig.)

  8. A Hybrid Optimization Method for Solving Bayesian Inverse Problems under Uncertainty.

    Directory of Open Access Journals (Sweden)

    Kai Zhang

    Full Text Available In this paper, we investigate the application of a new method, the Finite Difference and Stochastic Gradient (Hybrid method, for history matching in reservoir models. History matching is one of the processes of solving an inverse problem by calibrating reservoir models to dynamic behaviour of the reservoir in which an objective function is formulated based on a Bayesian approach for optimization. The goal of history matching is to identify the minimum value of an objective function that expresses the misfit between the predicted and measured data of a reservoir. To address the optimization problem, we present a novel application using a combination of the stochastic gradient and finite difference methods for solving inverse problems. The optimization is constrained by a linear equation that contains the reservoir parameters. We reformulate the reservoir model's parameters and dynamic data by operating the objective function, the approximate gradient of which can guarantee convergence. At each iteration step, we obtain the relatively 'important' elements of the gradient, which are subsequently substituted by the values from the Finite Difference method through comparing the magnitude of the components of the stochastic gradient, which forms a new gradient, and we subsequently iterate with the new gradient. Through the application of the Hybrid method, we efficiently and accurately optimize the objective function. We present a number numerical simulations in this paper that show that the method is accurate and computationally efficient.

  9. Locating disease genes using Bayesian variable selection with the Haseman-Elston method

    Directory of Open Access Journals (Sweden)

    He Qimei

    2003-12-01

    Full Text Available Abstract Background We applied stochastic search variable selection (SSVS, a Bayesian model selection method, to the simulated data of Genetic Analysis Workshop 13. We used SSVS with the revisited Haseman-Elston method to find the markers linked to the loci determining change in cholesterol over time. To study gene-gene interaction (epistasis and gene-environment interaction, we adopted prior structures, which incorporate the relationship among the predictors. This allows SSVS to search in the model space more efficiently and avoid the less likely models. Results In applying SSVS, instead of looking at the posterior distribution of each of the candidate models, which is sensitive to the setting of the prior, we ranked the candidate variables (markers according to their marginal posterior probability, which was shown to be more robust to the prior. Compared with traditional methods that consider one marker at a time, our method considers all markers simultaneously and obtains more favorable results. Conclusions We showed that SSVS is a powerful method for identifying linked markers using the Haseman-Elston method, even for weak effects. SSVS is very effective because it does a smart search over the entire model space.

  10. The continual reassessment method: comparison of Bayesian stopping rules for dose-ranging studies.

    Science.gov (United States)

    Zohar, S; Chevret, S

    2001-10-15

    The continual reassessment method (CRM) provides a Bayesian estimation of the maximum tolerated dose (MTD) in phase I clinical trials and is also used to estimate the minimal efficacy dose (MED) in phase II clinical trials. In this paper we propose Bayesian stopping rules for the CRM, based on either posterior or predictive probability distributions that can be applied sequentially during the trial. These rules aim at early detection of either the mis-choice of dose range or a prefixed gain in the point estimate or accuracy of estimated probability of response associated with the MTD (or MED). They were compared through a simulation study under six situations that could represent the underlying unknown dose-response (either toxicity or failure) relationship, in terms of sample size, probability of correct selection and bias of the response probability associated to the MTD (or MED). Our results show that the stopping rules act correctly, with early stopping by using the two first rules based on the posterior distribution when the actual underlying dose-response relationship is far from that initially supposed, while the rules based on predictive gain functions provide a discontinuation of inclusions whatever the actual dose-response curve after 20 patients on average, that is, depending mostly on the accumulated data. The stopping rules were then applied to a data set from a dose-ranging phase II clinical trial aiming at estimating the MED dose of midazolam in the sedation of infants during cardiac catheterization. All these findings suggest the early use of the two first rules to detect a mis-choice of dose range, while they confirm the requirement of including at least 20 patients at the same dose to reach an accurate estimate of MTD (MED). A two-stage design is under study. Copyright 2001 John Wiley & Sons, Ltd.

  11. A Bayesian least-squares support vector machine method for predicting the remaining useful life of a microwave component

    Directory of Open Access Journals (Sweden)

    Fuqiang Sun

    2017-01-01

    Full Text Available Rapid and accurate lifetime prediction of critical components in a system is important to maintaining the system’s reliable operation. To this end, many lifetime prediction methods have been developed to handle various failure-related data collected in different situations. Among these methods, machine learning and Bayesian updating are the most popular ones. In this article, a Bayesian least-squares support vector machine method that combines least-squares support vector machine with Bayesian inference is developed for predicting the remaining useful life of a microwave component. A degradation model describing the change in the component’s power gain over time is developed, and the point and interval remaining useful life estimates are obtained considering a predefined failure threshold. In our case study, the radial basis function neural network approach is also implemented for comparison purposes. The results indicate that the Bayesian least-squares support vector machine method is more precise and stable in predicting the remaining useful life of this type of components.

  12. Bayesian data analysis for newcomers.

    Science.gov (United States)

    Kruschke, John K; Liddell, Torrin M

    2018-02-01

    This article explains the foundational concepts of Bayesian data analysis using virtually no mathematical notation. Bayesian ideas already match your intuitions from everyday reasoning and from traditional data analysis. Simple examples of Bayesian data analysis are presented that illustrate how the information delivered by a Bayesian analysis can be directly interpreted. Bayesian approaches to null-value assessment are discussed. The article clarifies misconceptions about Bayesian methods that newcomers might have acquired elsewhere. We discuss prior distributions and explain how they are not a liability but an important asset. We discuss the relation of Bayesian data analysis to Bayesian models of mind, and we briefly discuss what methodological problems Bayesian data analysis is not meant to solve. After you have read this article, you should have a clear sense of how Bayesian data analysis works and the sort of information it delivers, and why that information is so intuitive and useful for drawing conclusions from data.

  13. Estimation of Fine Particulate Matter in Taipei Using Landuse Regression and Bayesian Maximum Entropy Methods

    Directory of Open Access Journals (Sweden)

    Yi-Ming Kuo

    2011-06-01

    Full Text Available Fine airborne particulate matter (PM2.5 has adverse effects on human health. Assessing the long-term effects of PM2.5 exposure on human health and ecology is often limited by a lack of reliable PM2.5 measurements. In Taipei, PM2.5 levels were not systematically measured until August, 2005. Due to the popularity of geographic information systems (GIS, the landuse regression method has been widely used in the spatial estimation of PM concentrations. This method accounts for the potential contributing factors of the local environment, such as traffic volume. Geostatistical methods, on other hand, account for the spatiotemporal dependence among the observations of ambient pollutants. This study assesses the performance of the landuse regression model for the spatiotemporal estimation of PM2.5 in the Taipei area. Specifically, this study integrates the landuse regression model with the geostatistical approach within the framework of the Bayesian maximum entropy (BME method. The resulting epistemic framework can assimilate knowledge bases including: (a empirical-based spatial trends of PM concentration based on landuse regression, (b the spatio-temporal dependence among PM observation information, and (c site-specific PM observations. The proposed approach performs the spatiotemporal estimation of PM2.5 levels in the Taipei area (Taiwan from 2005–2007.

  14. Estimation of fine particulate matter in Taipei using landuse regression and bayesian maximum entropy methods.

    Science.gov (United States)

    Yu, Hwa-Lung; Wang, Chih-Hsih; Liu, Ming-Che; Kuo, Yi-Ming

    2011-06-01

    Fine airborne particulate matter (PM2.5) has adverse effects on human health. Assessing the long-term effects of PM2.5 exposure on human health and ecology is often limited by a lack of reliable PM2.5 measurements. In Taipei, PM2.5 levels were not systematically measured until August, 2005. Due to the popularity of geographic information systems (GIS), the landuse regression method has been widely used in the spatial estimation of PM concentrations. This method accounts for the potential contributing factors of the local environment, such as traffic volume. Geostatistical methods, on other hand, account for the spatiotemporal dependence among the observations of ambient pollutants. This study assesses the performance of the landuse regression model for the spatiotemporal estimation of PM2.5 in the Taipei area. Specifically, this study integrates the landuse regression model with the geostatistical approach within the framework of the Bayesian maximum entropy (BME) method. The resulting epistemic framework can assimilate knowledge bases including: (a) empirical-based spatial trends of PM concentration based on landuse regression, (b) the spatio-temporal dependence among PM observation information, and (c) site-specific PM observations. The proposed approach performs the spatiotemporal estimation of PM2.5 levels in the Taipei area (Taiwan) from 2005-2007.

  15. Effective updating process of seismic fragilities using Bayesian method and information entropy

    International Nuclear Information System (INIS)

    Kato, Masaaki; Takata, Takashi; Yamaguchi, Akira

    2008-01-01

    Seismic probabilistic safety assessment (SPSA) is an effective method for evaluating overall performance of seismic safety of a plant. Seismic fragilities are estimated to quantify the seismically induced accident sequences. It is a great concern that the SPSA results involve uncertainties, a part of which comes from the uncertainty in the seismic fragility of equipment and systems. A straightforward approach to reduce the uncertainty is to perform a seismic qualification test and to reflect the results on the seismic fragility estimate. In this paper, we propose a figure-of-merit to find the most cost-effective condition of the seismic qualification tests about the acceleration level and number of components tested. Then a mathematical method to reflect the test results on the fragility update is developed. A Bayesian method is used for the fragility update procedure. Since a lognormal distribution that is used for the fragility model does not have a Bayes conjugate function, a parameterization method is proposed so that the posterior distribution expresses the characteristics of the fragility. The information entropy is used as the figure-of-merit to express importance of obtained evidence. It is found that the information entropy is strongly associated with the uncertainty of the fragility. (author)

  16. On the partitioning method and the perturbation quantum theory - discrete spectra

    International Nuclear Information System (INIS)

    Logrado, P.G.

    1982-05-01

    Lower and upper bounds to eigenvalues of the Schroedinger equation H Ψ = E Ψ (H = H 0 + V) and the convergence condition, in Schonberg's perturbation theory, are presented. These results are obtained using the partitioning technique. It is presented for the first time a perturbation treatment obtained when the reference function in the partitioning technique is chosen to be a true eigenfunction Ψ. The convergence condition and upper and lower bounds for the true eigenvalues E are derived in this formulation. The concept of the reaction and wave operators is also discussed. (author)

  17. DRABAL: novel method to mine large high-throughput screening assays using Bayesian active learning

    KAUST Repository

    Soufan, Othman

    2016-11-10

    Background Mining high-throughput screening (HTS) assays is key for enhancing decisions in the area of drug repositioning and drug discovery. However, many challenges are encountered in the process of developing suitable and accurate methods for extracting useful information from these assays. Virtual screening and a wide variety of databases, methods and solutions proposed to-date, did not completely overcome these challenges. This study is based on a multi-label classification (MLC) technique for modeling correlations between several HTS assays, meaning that a single prediction represents a subset of assigned correlated labels instead of one label. Thus, the devised method provides an increased probability for more accurate predictions of compounds that were not tested in particular assays. Results Here we present DRABAL, a novel MLC solution that incorporates structure learning of a Bayesian network as a step to model dependency between the HTS assays. In this study, DRABAL was used to process more than 1.4 million interactions of over 400,000 compounds and analyze the existing relationships between five large HTS assays from the PubChem BioAssay Database. Compared to different MLC methods, DRABAL significantly improves the F1Score by about 22%, on average. We further illustrated usefulness and utility of DRABAL through screening FDA approved drugs and reported ones that have a high probability to interact with several targets, thus enabling drug-multi-target repositioning. Specifically DRABAL suggests the Thiabendazole drug as a common activator of the NCP1 and Rab-9A proteins, both of which are designed to identify treatment modalities for the Niemann–Pick type C disease. Conclusion We developed a novel MLC solution based on a Bayesian active learning framework to overcome the challenge of lacking fully labeled training data and exploit actual dependencies between the HTS assays. The solution is motivated by the need to model dependencies between existing

  18. A functional-dependencies-based Bayesian networks learning method and its application in a mobile commerce system.

    Science.gov (United States)

    Liao, Stephen Shaoyi; Wang, Huai Qing; Li, Qiu Dan; Liu, Wei Yi

    2006-06-01

    This paper presents a new method for learning Bayesian networks from functional dependencies (FD) and third normal form (3NF) tables in relational databases. The method sets up a linkage between the theory of relational databases and probabilistic reasoning models, which is interesting and useful especially when data are incomplete and inaccurate. The effectiveness and practicability of the proposed method is demonstrated by its implementation in a mobile commerce system.

  19. A Bayesian approach to model uncertainty

    International Nuclear Information System (INIS)

    Buslik, A.

    1994-01-01

    A Bayesian approach to model uncertainty is taken. For the case of a finite number of alternative models, the model uncertainty is equivalent to parameter uncertainty. A derivation based on Savage's partition problem is given

  20. Using Bayesian methods to predict climate impacts on groundwater availability and agricultural production in Punjab, India

    Science.gov (United States)

    Russo, T. A.; Devineni, N.; Lall, U.

    2015-12-01

    Lasting success of the Green Revolution in Punjab, India relies on continued availability of local water resources. Supplying primarily rice and wheat for the rest of India, Punjab supports crop irrigation with a canal system and groundwater, which is vastly over-exploited. The detailed data required to physically model future impacts on water supplies agricultural production is not readily available for this region, therefore we use Bayesian methods to estimate hydrologic properties and irrigation requirements for an under-constrained mass balance model. Using measured values of historical precipitation, total canal water delivery, crop yield, and water table elevation, we present a method using a Markov chain Monte Carlo (MCMC) algorithm to solve for a distribution of values for each unknown parameter in a conceptual mass balance model. Due to heterogeneity across the state, and the resolution of input data, we estimate model parameters at the district-scale using spatial pooling. The resulting model is used to predict the impact of precipitation change scenarios on groundwater availability under multiple cropping options. Predicted groundwater declines vary across the state, suggesting that crop selection and water management strategies should be determined at a local scale. This computational method can be applied in data-scarce regions across the world, where water resource management is required to resolve competition between food security and available resources in a changing climate.

  1. An automated method for estimating reliability of grid systems using Bayesian networks

    International Nuclear Information System (INIS)

    Doguc, Ozge; Emmanuel Ramirez-Marquez, Jose

    2012-01-01

    Grid computing has become relevant due to its applications to large-scale resource sharing, wide-area information transfer, and multi-institutional collaborating. In general, in grid computing a service requests the use of a set of resources, available in a grid, to complete certain tasks. Although analysis tools and techniques for these types of systems have been studied, grid reliability analysis is generally computation-intensive to obtain due to the complexity of the system. Moreover, conventional reliability models have some common assumptions that cannot be applied to the grid systems. Therefore, new analytical methods are needed for effective and accurate assessment of grid reliability. This study presents a new method for estimating grid service reliability, which does not require prior knowledge about the grid system structure unlike the previous studies. Moreover, the proposed method does not rely on any assumptions about the link and node failure rates. This approach is based on a data-mining algorithm, the K2, to discover the grid system structure from raw historical system data, that allows to find minimum resource spanning trees (MRST) within the grid then, uses Bayesian networks (BN) to model the MRST and estimate grid service reliability.

  2. Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data.

    Science.gov (United States)

    O'Reilly, Joseph E; Puttick, Mark N; Parry, Luke; Tanner, Alastair R; Tarver, James E; Fleming, James; Pisani, Davide; Donoghue, Philip C J

    2016-04-01

    Different analytical methods can yield competing interpretations of evolutionary history and, currently, there is no definitive method for phylogenetic reconstruction using morphological data. Parsimony has been the primary method for analysing morphological data, but there has been a resurgence of interest in the likelihood-based Mk-model. Here, we test the performance of the Bayesian implementation of the Mk-model relative to both equal and implied-weight implementations of parsimony. Using simulated morphological data, we demonstrate that the Mk-model outperforms equal-weights parsimony in terms of topological accuracy, and implied-weights performs the most poorly. However, the Mk-model produces phylogenies that have less resolution than parsimony methods. This difference in the accuracy and precision of parsimony and Bayesian approaches to topology estimation needs to be considered when selecting a method for phylogeny reconstruction. © 2016 The Authors.

  3. bNEAT: a Bayesian network method for detecting epistatic interactions in genome-wide association studies

    Directory of Open Access Journals (Sweden)

    Chen Xue-wen

    2011-07-01

    Full Text Available Abstract Background Detecting epistatic interactions plays a significant role in improving pathogenesis, prevention, diagnosis and treatment of complex human diseases. A recent study in automatic detection of epistatic interactions shows that Markov Blanket-based methods are capable of finding genetic variants strongly associated with common diseases and reducing false positives when the number of instances is large. Unfortunately, a typical dataset from genome-wide association studies consists of very limited number of examples, where current methods including Markov Blanket-based method may perform poorly. Results To address small sample problems, we propose a Bayesian network-based approach (bNEAT to detect epistatic interactions. The proposed method also employs a Branch-and-Bound technique for learning. We apply the proposed method to simulated datasets based on four disease models and a real dataset. Experimental results show that our method outperforms Markov Blanket-based methods and other commonly-used methods, especially when the number of samples is small. Conclusions Our results show bNEAT can obtain a strong power regardless of the number of samples and is especially suitable for detecting epistatic interactions with slight or no marginal effects. The merits of the proposed approach lie in two aspects: a suitable score for Bayesian network structure learning that can reflect higher-order epistatic interactions and a heuristic Bayesian network structure learning method.

  4. Bayesian Methods for the Physical Sciences. Learning from Examples in Astronomy and Physics.

    Science.gov (United States)

    Andreon, Stefano; Weaver, Brian

    2015-05-01

    Chapter 1: This chapter presents some basic steps for performing a good statistical analysis, all summarized in about one page. Chapter 2: This short chapter introduces the basics of probability theory inan intuitive fashion using simple examples. It also illustrates, again with examples, how to propagate errors and the difference between marginal and profile likelihoods. Chapter 3: This chapter introduces the computational tools and methods that we use for sampling from the posterior distribution. Since all numerical computations, and Bayesian ones are no exception, may end in errors, we also provide a few tips to check that the numerical computation is sampling from the posterior distribution. Chapter 4: Many of the concepts of building, running, and summarizing the resultsof a Bayesian analysis are described with this step-by-step guide using a basic (Gaussian) model. The chapter also introduces examples using Poisson and Binomial likelihoods, and how to combine repeated independent measurements. Chapter 5: All statistical analyses make assumptions, and Bayesian analyses are no exception. This chapter emphasizes that results depend on data and priors (assumptions). We illustrate this concept with examples where the prior plays greatly different roles, from major to negligible. We also provide some advice on how to look for information useful for sculpting the prior. Chapter 6: In this chapter we consider examples for which we want to estimate more than a single parameter. These common problems include estimating location and spread. We also consider examples that require the modeling of two populations (one we are interested in and a nuisance population) or averaging incompatible measurements. We also introduce quite complex examples dealing with upper limits and with a larger-than-expected scatter. Chapter 7: Rarely is a sample randomly selected from the population we wish to study. Often, samples are affected by selection effects, e.g., easier

  5. 40 CFR 799.6756 - TSCA partition coefficient (n-octanol/water), generator column method.

    Science.gov (United States)

    2010-07-01

    ... using the CLogP3 computer program in paragraph (e)(9) of this section. 4 Hawker and Connell (1988... (B) Constant temperature bath with circulation pump-bath and capable of controlling temperature to 25...-partition coefficient correlation. Environmental Science and Technology 14:1227-1229 (1980). (2) Bruggemann...

  6. Simple Method to Determine the Partition Coefficient of Naphthenic Acid in Oil/Water

    DEFF Research Database (Denmark)

    Bitsch-Larsen, Anders; Andersen, Simon Ivar

    2008-01-01

    The partition coefficient for technical grade naphthenic acid in water/n-decane at 295 K has been determined (K-wo = 2.1 center dot 10(-4)) using a simple experimental technique with large extraction volumes (0.09 m(3) of water). Furthermore, nonequilibrium values at different pH values...

  7. Digitized Onondaga Lake Dissolved Oxygen Concentrations and Model Simulated Values using Bayesian Monte Carlo Methods

    Data.gov (United States)

    U.S. Environmental Protection Agency — The dataset is lake dissolved oxygen concentrations obtained form plots published by Gelda et al. (1996) and lake reaeration model simulated values using Bayesian...

  8. BAYESIAN DATA AUGMENTATION DOSE FINDING WITH CONTINUAL REASSESSMENT METHOD AND DELAYED TOXICITY

    Science.gov (United States)

    Liu, Suyu; Yin, Guosheng; Yuan, Ying

    2014-01-01

    A major practical impediment when implementing adaptive dose-finding designs is that the toxicity outcome used by the decision rules may not be observed shortly after the initiation of the treatment. To address this issue, we propose the data augmentation continual re-assessment method (DA-CRM) for dose finding. By naturally treating the unobserved toxicities as missing data, we show that such missing data are nonignorable in the sense that the missingness depends on the unobserved outcomes. The Bayesian data augmentation approach is used to sample both the missing data and model parameters from their posterior full conditional distributions. We evaluate the performance of the DA-CRM through extensive simulation studies, and also compare it with other existing methods. The results show that the proposed design satisfactorily resolves the issues related to late-onset toxicities and possesses desirable operating characteristics: treating patients more safely, and also selecting the maximum tolerated dose with a higher probability. The new DA-CRM is illustrated with two phase I cancer clinical trials. PMID:24707327

  9. Coding Partitions

    Directory of Open Access Journals (Sweden)

    Fabio Burderi

    2007-05-01

    Full Text Available Motivated by the study of decipherability conditions for codes weaker than Unique Decipherability (UD, we introduce the notion of coding partition. Such a notion generalizes that of UD code and, for codes that are not UD, allows to recover the ``unique decipherability" at the level of the classes of the partition. By tacking into account the natural order between the partitions, we define the characteristic partition of a code X as the finest coding partition of X. This leads to introduce the canonical decomposition of a code in at most one unambiguouscomponent and other (if any totally ambiguouscomponents. In the case the code is finite, we give an algorithm for computing its canonical partition. This, in particular, allows to decide whether a given partition of a finite code X is a coding partition. This last problem is then approached in the case the code is a rational set. We prove its decidability under the hypothesis that the partition contains a finite number of classes and each class is a rational set. Moreover we conjecture that the canonical partition satisfies such a hypothesis. Finally we consider also some relationships between coding partitions and varieties of codes.

  10. Overlapping community detection in weighted networks via a Bayesian approach

    Science.gov (United States)

    Chen, Yi; Wang, Xiaolong; Xiang, Xin; Tang, Buzhou; Chen, Qingcai; Fan, Shixi; Bu, Junzhao

    2017-02-01

    Complex networks as a powerful way to represent complex systems have been widely studied during the past several years. One of the most important tasks of complex network analysis is to detect communities embedded in networks. In the real world, weighted networks are very common and may contain overlapping communities where a node is allowed to belong to multiple communities. In this paper, we propose a novel Bayesian approach, called the Bayesian mixture network (BMN) model, to detect overlapping communities in weighted networks. The advantages of our method are (i) providing soft-partition solutions in weighted networks; (ii) providing soft memberships, which quantify 'how strongly' a node belongs to a community. Experiments on a large number of real and synthetic networks show that our model has the ability in detecting overlapping communities in weighted networks and is competitive with other state-of-the-art models at shedding light on community partition.

  11. Bayesian approach to inverse statistical mechanics

    Science.gov (United States)

    Habeck, Michael

    2014-05-01

    Inverse statistical mechanics aims to determine particle interactions from ensemble properties. This article looks at this inverse problem from a Bayesian perspective and discusses several statistical estimators to solve it. In addition, a sequential Monte Carlo algorithm is proposed that draws the interaction parameters from their posterior probability distribution. The posterior probability involves an intractable partition function that is estimated along with the interactions. The method is illustrated for inverse problems of varying complexity, including the estimation of a temperature, the inverse Ising problem, maximum entropy fitting, and the reconstruction of molecular interaction potentials.

  12. Itô-SDE MCMC method for Bayesian characterization of errors associated with data limitations in stochastic expansion methods for uncertainty quantification

    Science.gov (United States)

    Arnst, M.; Abello Álvarez, B.; Ponthot, J.-P.; Boman, R.

    2017-11-01

    This paper is concerned with the characterization and the propagation of errors associated with data limitations in polynomial-chaos-based stochastic methods for uncertainty quantification. Such an issue can arise in uncertainty quantification when only a limited amount of data is available. When the available information does not suffice to accurately determine the probability distributions that must be assigned to the uncertain variables, the Bayesian method for assigning these probability distributions becomes attractive because it allows the stochastic model to account explicitly for insufficiency of the available information. In previous work, such applications of the Bayesian method had already been implemented by using the Metropolis-Hastings and Gibbs Markov Chain Monte Carlo (MCMC) methods. In this paper, we present an alternative implementation, which uses an alternative MCMC method built around an Itô stochastic differential equation (SDE) that is ergodic for the Bayesian posterior. We draw together from the mathematics literature a number of formal properties of this Itô SDE that lend support to its use in the implementation of the Bayesian method, and we describe its discretization, including the choice of the free parameters, by using the implicit Euler method. We demonstrate the proposed methodology on a problem of uncertainty quantification in a complex nonlinear engineering application relevant to metal forming.

  13. A hierarchical method for Bayesian inference of rate parameters from shock tube data: Application to the study of the reaction of hydroxyl with 2-methylfuran

    KAUST Repository

    Kim, Daesang; El Gharamti, Iman; Hantouche, Mireille; Elwardani, Ahmed Elsaid; Farooq, Aamir; Bisetti, Fabrizio; Knio, Omar

    2017-01-01

    We developed a novel two-step hierarchical method for the Bayesian inference of the rate parameters of a target reaction from time-resolved concentration measurements in shock tubes. The method was applied to the calibration of the parameters

  14. Bayesian Inference for Functional Dynamics Exploring in fMRI Data

    Directory of Open Access Journals (Sweden)

    Xuan Guo

    2016-01-01

    Full Text Available This paper aims to review state-of-the-art Bayesian-inference-based methods applied to functional magnetic resonance imaging (fMRI data. Particularly, we focus on one specific long-standing challenge in the computational modeling of fMRI datasets: how to effectively explore typical functional interactions from fMRI time series and the corresponding boundaries of temporal segments. Bayesian inference is a method of statistical inference which has been shown to be a powerful tool to encode dependence relationships among the variables with uncertainty. Here we provide an introduction to a group of Bayesian-inference-based methods for fMRI data analysis, which were designed to detect magnitude or functional connectivity change points and to infer their functional interaction patterns based on corresponding temporal boundaries. We also provide a comparison of three popular Bayesian models, that is, Bayesian Magnitude Change Point Model (BMCPM, Bayesian Connectivity Change Point Model (BCCPM, and Dynamic Bayesian Variable Partition Model (DBVPM, and give a summary of their applications. We envision that more delicate Bayesian inference models will be emerging and play increasingly important roles in modeling brain functions in the years to come.

  15. Development of A Bayesian Geostatistical Data Assimilation Method and Application to the Hanford 300 Area

    Science.gov (United States)

    Murakami, Haruko

    Probabilistic risk assessment of groundwater contamination requires us to incorporate large and diverse datasets at the site into the stochastic modeling of flow and transport for prediction. In quantifying the uncertainty in our predictions, we must not only combine the best estimates of the parameters based on each dataset, but also integrate the uncertainty associated with each dataset caused by measurement errors and limited number of measurements. This dissertation presents a Bayesian geostatistical data assimilation method that integrates various types of field data for characterizing heterogeneous hydrological properties. It quantifies the parameter uncertainty as a posterior distribution conditioned on all the datasets, which can be directly used in stochastic simulations to compute possible outcomes of flow and transport processes. The goal of this framework is to remove the discontinuity between data analysis and prediction. Such a direct connection between data and prediction also makes it possible to evaluate the worth of each dataset or combined worth of multiple datasets. The synthetic studies described here confirm that the data assimilation method introduced in this dissertation successfully captures the true parameter values and predicted values within the posterior distribution. The shape of the inferred posterior distributions from the method indicates the importance of estimating the entire distribution in fully accounting for parameter uncertainty. The method is then applied to integrate multiple types of datasets at the Hanford 300 Area for characterizing a three-dimensional heterogeneous hydraulic conductivity field. Comparing the results based on the different numbers or combinations of datasets shows that increasing data do not always contribute in a straightforward way to improving the posterior distribution: increasing numbers of the same data type would not necessarily be beneficial above a certain number, and also the combined effect of

  16. Merging daily sea surface temperature data from multiple satellites using a Bayesian maximum entropy method

    Science.gov (United States)

    Tang, Shaolei; Yang, Xiaofeng; Dong, Di; Li, Ziwei

    2015-12-01

    Sea surface temperature (SST) is an important variable for understanding interactions between the ocean and the atmosphere. SST fusion is crucial for acquiring SST products of high spatial resolution and coverage. This study introduces a Bayesian maximum entropy (BME) method for blending daily SSTs from multiple satellite sensors. A new spatiotemporal covariance model of an SST field is built to integrate not only single-day SSTs but also time-adjacent SSTs. In addition, AVHRR 30-year SST climatology data are introduced as soft data at the estimation points to improve the accuracy of blended results within the BME framework. The merged SSTs, with a spatial resolution of 4 km and a temporal resolution of 24 hours, are produced in the Western Pacific Ocean region to demonstrate and evaluate the proposed methodology. Comparisons with in situ drifting buoy observations show that the merged SSTs are accurate and the bias and root-mean-square errors for the comparison are 0.15°C and 0.72°C, respectively.

  17. Prediction of Nepsilon-acetylation on internal lysines implemented in Bayesian Discriminant Method.

    Science.gov (United States)

    Li, Ao; Xue, Yu; Jin, Changjiang; Wang, Minghui; Yao, Xuebiao

    2006-12-01

    Protein acetylation is an important and reversible post-translational modification (PTM), and it governs a variety of cellular dynamics and plasticity. Experimental identification of acetylation sites is labor-intensive and often limited by the availability of reagents such as acetyl-specific antibodies and optimization of enzymatic reactions. Computational analyses may facilitate the identification of potential acetylation sites and provide insights into further experimentation. In this manuscript, we present a novel protein acetylation prediction program named PAIL, prediction of acetylation on internal lysines, implemented in a BDM (Bayesian Discriminant Method) algorithm. The accuracies of PAIL are 85.13%, 87.97%, and 89.21% at low, medium, and high thresholds, respectively. Both Jack-Knife validation and n-fold cross-validation have been performed to show that PAIL is accurate and robust. Taken together, we propose that PAIL is a novel predictor for identification of protein acetylation sites and may serve as an important tool to study the function of protein acetylation. PAIL has been implemented in PHP and is freely available on a web server at: http://bioinformatics.lcd-ustc.org/pail.

  18. Prediction of Nε-acetylation on internal lysines implemented in Bayesian Discriminant Method

    Science.gov (United States)

    Li, Ao; Xue, Yu; Jin, Changjiang; Wang, Minghui; Yao, Xuebiao

    2007-01-01

    Protein acetylation is an important and reversible post-translational modification (PTM), and it governs a variety of cellular dynamics and plasticity. Experimental identification of acetylation sites is labor-intensive and often limited by the availability reagents such as acetyl-specific antibodies and optimization of enzymatic reactions. Computational analyses may facilitate the identification of potential acetylation sites and provide insights into further experimentation. In this manuscript, we present a novel protein acetylation prediction program named PAIL, prediction of acetylation on internal lysines, implemented in a BDM (Bayesian Discriminant Method) algorithm. The accuracies of PAIL are 85.13%, 87.97% and 89.21% at low, medium and high thresholds, respectively. Both Jack-Knife validation and n-fold cross validation have been performed to show that PAIL is accurate and robust. Taken together, we propose that PAIL is a novel predictor for identification of protein acetylation sites and may serve as an important tool to study the function of protein acetylation. PAIL has been implemented in PHP and is freely available on a web server at: http://bioinformatics.lcd-ustc.org/pail. PMID:17045240

  19. Alternative method of highway traffic safety analysis for developing countries using delphi technique and Bayesian network.

    Science.gov (United States)

    Mbakwe, Anthony C; Saka, Anthony A; Choi, Keechoo; Lee, Young-Jae

    2016-08-01

    Highway traffic accidents all over the world result in more than 1.3 million fatalities annually. An alarming number of these fatalities occurs in developing countries. There are many risk factors that are associated with frequent accidents, heavy loss of lives, and property damage in developing countries. Unfortunately, poor record keeping practices are very difficult obstacle to overcome in striving to obtain a near accurate casualty and safety data. In light of the fact that there are numerous accident causes, any attempts to curb the escalating death and injury rates in developing countries must include the identification of the primary accident causes. This paper, therefore, seeks to show that the Delphi Technique is a suitable alternative method that can be exploited in generating highway traffic accident data through which the major accident causes can be identified. In order to authenticate the technique used, Korea, a country that underwent similar problems when it was in its early stages of development in addition to the availability of excellent highway safety records in its database, is chosen and utilized for this purpose. Validation of the methodology confirms the technique is suitable for application in developing countries. Furthermore, the Delphi Technique, in combination with the Bayesian Network Model, is utilized in modeling highway traffic accidents and forecasting accident rates in the countries of research. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Development of a partitioning method for the management of high-level liquid waste

    International Nuclear Information System (INIS)

    Kubota, M.; Dojiri, S.; Yamaguchi, I.; Morita, Y.; Yamagishi, I.; Kobayashi, T.; Tani, S.

    1989-01-01

    Fundamental studies especially focused on the separation of neptunium and technetium have been carried out to construct the advanced partitioning process of fractioning elements in a high-level liquid waste into four groups: transuranium elements, technetium-noble metals, strontium-cesium, and other elements. For the separation of neptunium by solvent extraction, DIDPA proved excellent for extracting Np(V), and its extraction rate was accelerated by hydrogen peroxide. Np(V) was found to be also separated quantitatively as precipitate with oxalic acid. For the separation of technetium, the denitration with formic acid was effective in precipitating it along with noble metals, and the adsorption with activated carbon was also effective for quantitative separation. Through these fundamental studies, the advanced partitioning process is presented as the candidate to be examined with an actual high-level liquid waste

  1. Bayesian statistics an introduction

    CERN Document Server

    Lee, Peter M

    2012-01-01

    Bayesian Statistics is the school of thought that combines prior beliefs with the likelihood of a hypothesis to arrive at posterior beliefs. The first edition of Peter Lee’s book appeared in 1989, but the subject has moved ever onwards, with increasing emphasis on Monte Carlo based techniques. This new fourth edition looks at recent techniques such as variational methods, Bayesian importance sampling, approximate Bayesian computation and Reversible Jump Markov Chain Monte Carlo (RJMCMC), providing a concise account of the way in which the Bayesian approach to statistics develops as wel

  2. The effect of different evapotranspiration methods on portraying soil water dynamics and ET partitioning in a semi-arid environment in Northwest China

    OpenAIRE

    Yu, L.; Zeng, Yijian; Su, Zhongbo; Cai, H.; Zheng, Z.

    2016-01-01

    Different methods for assessing evapotranspiration (ET) can significantly affect the performance of land surface models in portraying soil water dynamics and ET partitioning. An accurate understanding of the impact a method has is crucial to determining the effectiveness of an irrigation scheme. Two ET methods are discussed: one is based on reference crop evapotranspiration (ET0) theory, uses leaf area index (LAI) for partitioning into soil evaporation and transpiration, and...

  3. Learning to Recommend Point-of-Interest with the Weighted Bayesian Personalized Ranking Method in LBSNs

    Directory of Open Access Journals (Sweden)

    Lei Guo

    2017-02-01

    Full Text Available Point-of-interest (POI recommendation has been well studied in recent years. However, most of the existing methods focus on the recommendation scenarios where users can provide explicit feedback. In most cases, however, the feedback is not explicit, but implicit. For example, we can only get a user’s check-in behaviors from the history of what POIs she/he has visited, but never know how much she/he likes and why she/he does not like them. Recently, some researchers have noticed this problem and began to learn the user preferences from the partial order of POIs. However, these works give equal weight to each POI pair and cannot distinguish the contributions from different POI pairs. Intuitively, for the two POIs in a POI pair, the larger the frequency difference of being visited and the farther the geographical distance between them, the higher the contribution of this POI pair to the ranking function. Based on the above observations, we propose a weighted ranking method for POI recommendation. Specifically, we first introduce a Bayesian personalized ranking criterion designed for implicit feedback to POI recommendation. To fully utilize the partial order of POIs, we then treat the cost function in a weighted way, that is give each POI pair a different weight according to their frequency of being visited and the geographical distance between them. Data analysis and experimental results on two real-world datasets demonstrate the existence of user preference on different POI pairs and the effectiveness of our weighted ranking method.

  4. A Laplace method for under-determined Bayesian optimal experimental designs

    KAUST Repository

    Long, Quan

    2014-12-17

    In Long et al. (2013), a new method based on the Laplace approximation was developed to accelerate the estimation of the post-experimental expected information gains (Kullback–Leibler divergence) in model parameters and predictive quantities of interest in the Bayesian framework. A closed-form asymptotic approximation of the inner integral and the order of the corresponding dominant error term were obtained in the cases where the parameters are determined by the experiment. In this work, we extend that method to the general case where the model parameters cannot be determined completely by the data from the proposed experiments. We carry out the Laplace approximations in the directions orthogonal to the null space of the Jacobian matrix of the data model with respect to the parameters, so that the information gain can be reduced to an integration against the marginal density of the transformed parameters that are not determined by the experiments. Furthermore, the expected information gain can be approximated by an integration over the prior, where the integrand is a function of the posterior covariance matrix projected over the aforementioned orthogonal directions. To deal with the issue of dimensionality in a complex problem, we use either Monte Carlo sampling or sparse quadratures for the integration over the prior probability density function, depending on the regularity of the integrand function. We demonstrate the accuracy, efficiency and robustness of the proposed method via several nonlinear under-determined test cases. They include the designs of the scalar parameter in a one dimensional cubic polynomial function with two unidentifiable parameters forming a linear manifold, and the boundary source locations for impedance tomography in a square domain, where the unknown parameter is the conductivity, which is represented as a random field.

  5. Fast Bayesian Inference in Dirichlet Process Mixture Models.

    Science.gov (United States)

    Wang, Lianming; Dunson, David B

    2011-01-01

    There has been increasing interest in applying Bayesian nonparametric methods in large samples and high dimensions. As Markov chain Monte Carlo (MCMC) algorithms are often infeasible, there is a pressing need for much faster algorithms. This article proposes a fast approach for inference in Dirichlet process mixture (DPM) models. Viewing the partitioning of subjects into clusters as a model selection problem, we propose a sequential greedy search algorithm for selecting the partition. Then, when conjugate priors are chosen, the resulting posterior conditionally on the selected partition is available in closed form. This approach allows testing of parametric models versus nonparametric alternatives based on Bayes factors. We evaluate the approach using simulation studies and compare it with four other fast nonparametric methods in the literature. We apply the proposed approach to three datasets including one from a large epidemiologic study. Matlab codes for the simulation and data analyses using the proposed approach are available online in the supplemental materials.

  6. Sharp Boundary Inversion of 2D Magnetotelluric Data using Bayesian Method.

    Science.gov (United States)

    Zhou, S.; Huang, Q.

    2017-12-01

    Normally magnetotelluric(MT) inversion method cannot show the distribution of underground resistivity with clear boundary, even if there are obviously different blocks. Aiming to solve this problem, we develop a Bayesian structure to inverse 2D MT sharp boundary data, using boundary location and inside resistivity as the random variables. Firstly, we use other MT inversion results, like ModEM, to analyze the resistivity distribution roughly. Then, we select the suitable random variables and change its data format to traditional staggered grid parameters, which can be used to do finite difference forward part. Finally, we can shape the posterior probability density(PPD), which contains all the prior information and model-data correlation, by Markov Chain Monte Carlo(MCMC) sampling from prior distribution. The depth, resistivity and their uncertainty can be valued. It also works for sensibility estimation. We applied the method to a synthetic case, which composes two large abnormal blocks in a trivial background. We consider the boundary smooth and the near true model weight constrains that mimic joint inversion or constrained inversion, then we find that the model results a more precise and focused depth distribution. And we also test the inversion without constrains and find that the boundary could also be figured, though not as well. Both inversions have a good valuation of resistivity. The constrained result has a lower root mean square than ModEM inversion result. The data sensibility obtained via PPD shows that the resistivity is the most sensible, center depth comes second and both sides are the worst.

  7. A Bayesian method for comparing and combining binary classifiers in the absence of a gold standard

    Directory of Open Access Journals (Sweden)

    Keith Jonathan M

    2012-07-01

    Full Text Available Abstract Background Many problems in bioinformatics involve classification based on features such as sequence, structure or morphology. Given multiple classifiers, two crucial questions arise: how does their performance compare, and how can they best be combined to produce a better classifier? A classifier can be evaluated in terms of sensitivity and specificity using benchmark, or gold standard, data, that is, data for which the true classification is known. However, a gold standard is not always available. Here we demonstrate that a Bayesian model for comparing medical diagnostics without a gold standard can be successfully applied in the bioinformatics domain, to genomic scale data sets. We present a new implementation, which unlike previous implementations is applicable to any number of classifiers. We apply this model, for the first time, to the problem of finding the globally optimal logical combination of classifiers. Results We compared three classifiers of protein subcellular localisation, and evaluated our estimates of sensitivity and specificity against estimates obtained using a gold standard. The method overestimated sensitivity and specificity with only a small discrepancy, and correctly ranked the classifiers. Diagnostic tests for swine flu were then compared on a small data set. Lastly, classifiers for a genome-wide association study of macular degeneration with 541094 SNPs were analysed. In all cases, run times were feasible, and results precise. The optimal logical combination of classifiers was also determined for all three data sets. Code and data are available from http://bioinformatics.monash.edu.au/downloads/. Conclusions The examples demonstrate the methods are suitable for both small and large data sets, applicable to the wide range of bioinformatics classification problems, and robust to dependence between classifiers. In all three test cases, the globally optimal logical combination of the classifiers was found to be

  8. Application of Bayesian methods to habitat selection modeling of the northern spotted owl in California: new statistical methods for wildlife research

    Science.gov (United States)

    Howard B. Stauffer; Cynthia J. Zabel; Jeffrey R. Dunk

    2005-01-01

    We compared a set of competing logistic regression habitat selection models for Northern Spotted Owls (Strix occidentalis caurina) in California. The habitat selection models were estimated, compared, evaluated, and tested using multiple sample datasets collected on federal forestlands in northern California. We used Bayesian methods in interpreting...

  9. Fault Localization Method by Partitioning Memory Using Memory Map and the Stack for Automotive ECU Software Testing

    Directory of Open Access Journals (Sweden)

    Kwanhyo Kim

    2016-09-01

    Full Text Available Recently, the usage of the automotive Electronic Control Unit (ECU and its software in cars is increasing. Therefore, as the functional complexity of such software increases, so does the likelihood of software-related faults. Therefore, it is important to ensure the reliability of ECU software in order to ensure automobile safety. For this reason, systematic testing methods are required that can guarantee software quality. However, it is difficult to locate a fault during testing with the current ECU development system because a tester performs the black-box testing using a Hardware-in-the-Loop (HiL simulator. Consequently, developers consume a large amount of money and time for debugging because they perform debugging without any information about the location of the fault. In this paper, we propose a method for localizing the fault utilizing memory information during black-box testing. This is likely to be of use to developers who debug automotive software. In order to observe whether symbols stored in the memory have been updated, the memory is partitioned by a memory map and the stack, thus the fault candidate region is reduced. A memory map method has the advantage of being able to finely partition the memory, and the stack method can partition the memory without a memory map. We validated these methods by applying these to HiL testing of the ECU for a body control system. The preliminary results indicate that a memory map and the stack reduce the possible fault locations to 22% and 19% of the updated memory, respectively.

  10. Bayesian programming

    CERN Document Server

    Bessiere, Pierre; Ahuactzin, Juan Manuel; Mekhnacha, Kamel

    2013-01-01

    Probability as an Alternative to Boolean LogicWhile logic is the mathematical foundation of rational reasoning and the fundamental principle of computing, it is restricted to problems where information is both complete and certain. However, many real-world problems, from financial investments to email filtering, are incomplete or uncertain in nature. Probability theory and Bayesian computing together provide an alternative framework to deal with incomplete and uncertain data. Decision-Making Tools and Methods for Incomplete and Uncertain DataEmphasizing probability as an alternative to Boolean

  11. Spatiotemporal fusion of multiple-satellite aerosol optical depth (AOD) products using Bayesian maximum entropy method

    Science.gov (United States)

    Tang, Qingxin; Bo, Yanchen; Zhu, Yuxin

    2016-04-01

    Merging multisensor aerosol optical depth (AOD) products is an effective way to produce more spatiotemporally complete and accurate AOD products. A spatiotemporal statistical data fusion framework based on a Bayesian maximum entropy (BME) method was developed for merging satellite AOD products in East Asia. The advantages of the presented merging framework are that it not only utilizes the spatiotemporal autocorrelations but also explicitly incorporates the uncertainties of the AOD products being merged. The satellite AOD products used for merging are the Moderate Resolution Imaging Spectroradiometer (MODIS) Collection 5.1 Level-2 AOD products (MOD04_L2) and the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) Deep Blue Level 2 AOD products (SWDB_L2). The results show that the average completeness of the merged AOD data is 95.2%,which is significantly superior to the completeness of MOD04_L2 (22.9%) and SWDB_L2 (20.2%). By comparing the merged AOD to the Aerosol Robotic Network AOD records, the results show that the correlation coefficient (0.75), root-mean-square error (0.29), and mean bias (0.068) of the merged AOD are close to those (the correlation coefficient (0.82), root-mean-square error (0.19), and mean bias (0.059)) of the MODIS AOD. In the regions where both MODIS and SeaWiFS have valid observations, the accuracy of the merged AOD is higher than those of MODIS and SeaWiFS AODs. Even in regions where both MODIS and SeaWiFS AODs are missing, the accuracy of the merged AOD is also close to the accuracy of the regions where both MODIS and SeaWiFS have valid observations.

  12. A new 3-D ray tracing method based on LTI using successive partitioning of cell interfaces and traveltime gradients

    Science.gov (United States)

    Zhang, Dong; Zhang, Ting-Ting; Zhang, Xiao-Lei; Yang, Yan; Hu, Ying; Qin, Qian-Qing

    2013-05-01

    We present a new method of three-dimensional (3-D) seismic ray tracing, based on an improvement to the linear traveltime interpolation (LTI) ray tracing algorithm. This new technique involves two separate steps. The first involves a forward calculation based on the LTI method and the dynamic successive partitioning scheme, which is applied to calculate traveltimes on cell boundaries and assumes a wavefront that expands from the source to all grid nodes in the computational domain. We locate several dynamic successive partition points on a cell's surface, the traveltimes of which can be calculated by linear interpolation between the vertices of the cell's boundary. The second is a backward step that uses Fermat's principle and the fact that the ray path is always perpendicular to the wavefront and follows the negative traveltime gradient. In this process, the first-arriving ray path can be traced from the receiver to the source along the negative traveltime gradient, which can be calculated by reconstructing the continuous traveltime field with cubic B-spline interpolation. This new 3-D ray tracing method is compared with the LTI method and the shortest path method (SPM) through a number of numerical experiments. These comparisons show obvious improvements to computed traveltimes and ray paths, both in precision and computational efficiency.

  13. Evidence of major genes affecting stress response in rainbow trout using Bayesian methods of complex segregation analysis

    DEFF Research Database (Denmark)

    Vallejo, R L; Rexroad III, C E; Silverstein, J T

    2009-01-01

    As a first step toward the genetic mapping of QTL affecting stress response variation in rainbow trout, we performed complex segregation analyses (CSA) fitting mixed inheritance models of plasma cortisol by using Bayesian methods in large full-sib families of rainbow trout. To date, no studies have...... been conducted to determine the mode of inheritance of stress response as measured by plasma cortisol response when using a crowding stress paradigm and CSA in rainbow trout. The main objective of this study was to determine the mode of inheritance of plasma cortisol after a crowding stress....... The results from fitting mixed inheritance models with Bayesian CSA suggest that 1 or more major genes with dominant cortisol-decreasing alleles and small additive genetic effects of a large number of independent genes likely underlie the genetic variation of plasma cortisol in the rainbow trout families...

  14. A New Method to Quantify the Isotopic Signature of Leaf Transpiration: Implications for Landscape-Scale Evapotranspiration Partitioning Studies

    Science.gov (United States)

    Wang, L.; Good, S. P.; Caylor, K. K.

    2010-12-01

    Characterizing the constituent components of evapotranspiration is crucial to better understand ecosystem-level water budgets and water use dynamics. Isotope based evapotranspiration partitioning methods are promising but their utility lies in the accurate estimation of the isotopic composition of underlying transpiration and evaporation. Here we report a new method to quantify the isotopic signature of leaf transpiration under field conditions. This method utilizes a commercially available laser-based isotope analyzer and a transparent leaf chamber, modified from Licor conifer leaf chamber. The method is based on the water mass balance in ambient air and leaf transpired air. We verified the method using “artificial leaves” and glassline extracted samples. The method provides a new and direct way to estimate leaf transpiration isotopic signatures and it has wide applications in ecology, hydrology and plant physiology.

  15. New Bayesian inference method using two steps of Markov chain Monte Carlo and its application to shock tube experiment data of Furan oxidation

    KAUST Repository

    Kim, Daesang; El Gharamti, Iman; Bisetti, Fabrizio; Farooq, Aamir; Knio, Omar

    2016-01-01

    A new Bayesian inference method has been developed and applied to Furan shock tube experimental data for efficient statistical inferences of the Arrhenius parameters of two OH radical consumption reactions. The collected experimental data, which

  16. Optimum Inductive Methods. A study in Inductive Probability, Bayesian Statistics, and Verisimilitude.

    NARCIS (Netherlands)

    Festa, Roberto

    1992-01-01

    According to the Bayesian view, scientific hypotheses must be appraised in terms of their posterior probabilities relative to the available experimental data. Such posterior probabilities are derived from the prior probabilities of the hypotheses by applying Bayes'theorem. One of the most important

  17. A Bayesian analysis of rare B decays with advanced Monte Carlo methods

    International Nuclear Information System (INIS)

    Beaujean, Frederik

    2012-01-01

    Searching for new physics in rare B meson decays governed by b → s transitions, we perform a model-independent global fit of the short-distance couplings C 7 , C 9 , and C 10 of the ΔB=1 effective field theory. We assume the standard-model set of b → sγ and b → sl + l - operators with real-valued C i . A total of 59 measurements by the experiments BaBar, Belle, CDF, CLEO, and LHCb of observables in B→K * γ, B→K (*) l + l - , and B s →μ + μ - decays are used in the fit. Our analysis is the first of its kind to harness the full power of the Bayesian approach to probability theory. All main sources of theory uncertainty explicitly enter the fit in the form of nuisance parameters. We make optimal use of the experimental information to simultaneously constrain theWilson coefficients as well as hadronic form factors - the dominant theory uncertainty. Generating samples from the posterior probability distribution to compute marginal distributions and predict observables by uncertainty propagation is a formidable numerical challenge for two reasons. First, the posterior has multiple well separated maxima and degeneracies. Second, the computation of the theory predictions is very time consuming. A single posterior evaluation requires O(1s), and a few million evaluations are needed. Population Monte Carlo (PMC) provides a solution to both issues; a mixture density is iteratively adapted to the posterior, and samples are drawn in a massively parallel way using importance sampling. The major shortcoming of PMC is the need for cogent knowledge of the posterior at the initial stage. In an effort towards a general black-box Monte Carlo sampling algorithm, we present a new method to extract the necessary information in a reliable and automatic manner from Markov chains with the help of hierarchical clustering. Exploiting the latest 2012 measurements, the fit reveals a flipped-sign solution in addition to a standard-model-like solution for the couplings C i . The

  18. A Bayesian analysis of rare B decays with advanced Monte Carlo methods

    Energy Technology Data Exchange (ETDEWEB)

    Beaujean, Frederik

    2012-11-12

    Searching for new physics in rare B meson decays governed by b {yields} s transitions, we perform a model-independent global fit of the short-distance couplings C{sub 7}, C{sub 9}, and C{sub 10} of the {Delta}B=1 effective field theory. We assume the standard-model set of b {yields} s{gamma} and b {yields} sl{sup +}l{sup -} operators with real-valued C{sub i}. A total of 59 measurements by the experiments BaBar, Belle, CDF, CLEO, and LHCb of observables in B{yields}K{sup *}{gamma}, B{yields}K{sup (*)}l{sup +}l{sup -}, and B{sub s}{yields}{mu}{sup +}{mu}{sup -} decays are used in the fit. Our analysis is the first of its kind to harness the full power of the Bayesian approach to probability theory. All main sources of theory uncertainty explicitly enter the fit in the form of nuisance parameters. We make optimal use of the experimental information to simultaneously constrain theWilson coefficients as well as hadronic form factors - the dominant theory uncertainty. Generating samples from the posterior probability distribution to compute marginal distributions and predict observables by uncertainty propagation is a formidable numerical challenge for two reasons. First, the posterior has multiple well separated maxima and degeneracies. Second, the computation of the theory predictions is very time consuming. A single posterior evaluation requires O(1s), and a few million evaluations are needed. Population Monte Carlo (PMC) provides a solution to both issues; a mixture density is iteratively adapted to the posterior, and samples are drawn in a massively parallel way using importance sampling. The major shortcoming of PMC is the need for cogent knowledge of the posterior at the initial stage. In an effort towards a general black-box Monte Carlo sampling algorithm, we present a new method to extract the necessary information in a reliable and automatic manner from Markov chains with the help of hierarchical clustering. Exploiting the latest 2012 measurements, the fit

  19. Genetic Properties of Some Economic Traits in Isfahan Native Fowl Using Bayesian and REML Methods

    Directory of Open Access Journals (Sweden)

    Salehinasab M

    2015-12-01

    Full Text Available The objective of the present study was to estimate heritability values for some performance and egg quality traits of native fowl in Isfahan breeding center using REML and Bayesian approaches. The records were about 51521 and 975 for performance and egg quality traits, respectively. At the first step, variance components were estimated for body weight at hatch (BW0, body weight at 8 weeks of age (BW8, weight at sexual maturity (WSM, egg yolk weight (YW, egg Haugh unit and eggshell thickness, via REML approach using ASREML software. At the second step, the same traits were analyzed via Bayesian approach using Gibbs3f90 software. In both approaches six different animal models were applied and the best model was determined using likelihood ratio test (LRT and deviance information criterion (DIC for REML and Bayesian approaches, respectively. Heritability estimates for BW0, WSM and ST were the same in both approaches. For BW0, LRT and DIC indexes confirmed that the model consisting maternal genetic, permanent environmental and direct genetic effects was significantly better than other models. For WSM, a model consisting of maternal permanent environmental effect in addition to direct genetic effect was the best. For shell thickness, the basic model consisting direct genetic effect was the best. The results for BW8, YW and Haugh unit, were different between the two approaches. The reason behind this tiny differences was that the convergence could not be achieved for some models in REML approach and thus for these traits the Bayesian approach estimated the variance components more accurately. The results indicated that ignoring maternal effects, overestimates the direct genetic variance and heritability for most of the traits. Also, the Bayesian-based software could take more variance components into account.

  20. Inside-sediment partitioning of PAH, PCB and organochlorine compounds and inferences on sampling and normalization methods

    International Nuclear Information System (INIS)

    Opel, Oliver; Palm, Wolf-Ulrich; Steffen, Dieter; Ruck, Wolfgang K.L.

    2011-01-01

    Comparability of sediment analyses for semivolatile organic substances is still low. Neither screening of the sediments nor organic-carbon based normalization is sufficient to obtain comparable results. We are showing the interdependency of grain-size effects with inside-sediment organic-matter distribution for PAH, PCB and organochlorine compounds. Surface sediment samples collected by Van-Veen grab were sieved and analyzed for 16 PAH, 6 PCB and 18 organochlorine pesticides (OCP) as well as organic-matter content. Since bulk concentrations are influenced by grain-size effects themselves, we used a novel normalization method based on the sum of concentrations in the separate grain-size fractions of the sediments. By calculating relative normalized concentrations, it was possible to clearly show underlying mechanisms throughout a heterogeneous set of samples. Furthermore, we were able to show that, for comparability, screening at <125 μm is best suited and can be further improved by additional organic-carbon normalization. - Research highlights: → New method for the comparison of heterogeneous sets of sediment samples. → Assessment of organic pollutants partitioning mechanisms in sediments. → Proposed method for more comparable sediment sampling. - Inside-sediment partitioning mechanisms are shown using a new mathematical approach and discussed in terms of sediment sampling and normalization.

  1. A model partitioning method based on dynamic decoupling for the efficient simulation of multibody systems

    Energy Technology Data Exchange (ETDEWEB)

    Papadopoulos, Alessandro Vittorio, E-mail: alessandro.papadopoulos@control.lth.se [Lund University, Department of Automatic Control (Sweden); Leva, Alberto, E-mail: alberto.leva@polimi.it [Politecnico di Milano, Dipartimento di Elettronica, Informazione e Bioingegneria (Italy)

    2015-06-15

    The presence of different time scales in a dynamic model significantly hampers the efficiency of its simulation. In multibody systems the fact is particularly relevant, as the mentioned time scales may be very different, due, for example, to the coexistence of mechanical components controled by electronic drive units, and may also appear in conjunction with significant nonlinearities. This paper proposes a systematic technique, based on the principles of dynamic decoupling, to partition a model based on the time scales that are relevant for the particular simulation studies to be performed and as transparently as possible for the user. In accordance with said purpose, peculiar to the technique is its neat separation into two parts: a structural analysis of the model, which is general with respect to any possible simulation scenario, and a subsequent decoupled integration, which can conversely be (easily) tailored to the study at hand. Also, since the technique does not aim at reducing but rather at partitioning the model, the state space and the physical interpretation of the dynamic variables are inherently preserved. Moreover, the proposed analysis allows us to define some novel indices relative to the separability of the system, thereby extending the idea of “stiffness” in a way that is particularly keen to its use for the improvement of simulation efficiency, be the envisaged integration scheme monolithic, parallel, or even based on cosimulation. Finally, thanks to the way the analysis phase is conceived, the technique is naturally applicable to both linear and nonlinear models. The paper contains a methodological presentation of the proposed technique, which is related to alternatives available in the literature so as to evidence the peculiarities just sketched, and some application examples illustrating the achieved advantages and motivating the major design choice from an operational viewpoint.

  2. A hybrid segmentation method for partitioning the liver based on 4D DCE-MR images

    Science.gov (United States)

    Zhang, Tian; Wu, Zhiyi; Runge, Jurgen H.; Lavini, Cristina; Stoker, Jaap; van Gulik, Thomas; Cieslak, Kasia P.; van Vliet, Lucas J.; Vos, Frans M.

    2018-03-01

    The Couinaud classification of hepatic anatomy partitions the liver into eight functionally independent segments. Detection and segmentation of the hepatic vein (HV), portal vein (PV) and inferior vena cava (IVC) plays an important role in the subsequent delineation of the liver segments. To facilitate pharmacokinetic modeling of the liver based on the same data, a 4D DCE-MR scan protocol was selected. This yields images with high temporal resolution but low spatial resolution. Since the liver's vasculature consists of many tiny branches, segmentation of these images is challenging. The proposed framework starts with registration of the 4D DCE-MRI series followed by region growing from manually annotated seeds in the main branches of key blood vessels in the liver. It calculates the Pearson correlation between the time intensity curves (TICs) of a seed and all voxels. A maximum correlation map for each vessel is obtained by combining the correlation maps for all branches of the same vessel through a maximum selection per voxel. The maximum correlation map is incorporated in a level set scheme to individually delineate the main vessels. Subsequently, the eight liver segments are segmented based on three vertical intersecting planes fit through the three skeleton branches of HV and IVC's center of mass as well as a horizontal plane fit through the skeleton of PV. Our segmentation regarding delineation of the vessels is more accurate than the results of two state-of-the-art techniques on five subjects in terms of the average symmetric surface distance (ASSD) and modified Hausdorff distance (MHD). Furthermore, the proposed liver partitioning achieves large overlap with manual reference segmentations (expressed in Dice Coefficient) in all but a small minority of segments (mean values between 87% and 94% for segments 2-8). The lower mean overlap for segment 1 (72%) is due to the limited spatial resolution of our DCE-MR scan protocol.

  3. Bayesian Probability Theory

    Science.gov (United States)

    von der Linden, Wolfgang; Dose, Volker; von Toussaint, Udo

    2014-06-01

    Preface; Part I. Introduction: 1. The meaning of probability; 2. Basic definitions; 3. Bayesian inference; 4. Combinatrics; 5. Random walks; 6. Limit theorems; 7. Continuous distributions; 8. The central limit theorem; 9. Poisson processes and waiting times; Part II. Assigning Probabilities: 10. Transformation invariance; 11. Maximum entropy; 12. Qualified maximum entropy; 13. Global smoothness; Part III. Parameter Estimation: 14. Bayesian parameter estimation; 15. Frequentist parameter estimation; 16. The Cramer-Rao inequality; Part IV. Testing Hypotheses: 17. The Bayesian way; 18. The frequentist way; 19. Sampling distributions; 20. Bayesian vs frequentist hypothesis tests; Part V. Real World Applications: 21. Regression; 22. Inconsistent data; 23. Unrecognized signal contributions; 24. Change point problems; 25. Function estimation; 26. Integral equations; 27. Model selection; 28. Bayesian experimental design; Part VI. Probabilistic Numerical Techniques: 29. Numerical integration; 30. Monte Carlo methods; 31. Nested sampling; Appendixes; References; Index.

  4. Evaluating a Bayesian approach to improve accuracy of individual photographic identification methods using ecological distribution data

    Directory of Open Access Journals (Sweden)

    Richard Stafford

    2011-04-01

    Full Text Available Photographic identification of individual organisms can be possible from natural body markings. Data from photo-ID can be used to estimate important ecological and conservation metrics such as population sizes, home ranges or territories. However, poor quality photographs or less well-studied individuals can result in a non-unique ID, potentially confounding several similar looking individuals. Here we present a Bayesian approach that uses known data about previous sightings of individuals at specific sites as priors to help assess the problems of obtaining a non-unique ID. Using a simulation of individuals with different confidence of correct ID we evaluate the accuracy of Bayesian modified (posterior probabilities. However, in most cases, the accuracy of identification decreases. Although this technique is unsuccessful, it does demonstrate the importance of computer simulations in testing such hypotheses in ecology.

  5. Bayesian Network Assessment Method for Civil Aviation Safety Based on Flight Delays

    OpenAIRE

    Huawei Wang; Jun Gao

    2013-01-01

    Flight delays and safety are the principal contradictions in the sound development of civil aviation. Flight delays often come up and induce civil aviation safety risk simultaneously. Based on flight delays, the random characteristics of civil aviation safety risk are analyzed. Flight delays have been deemed to a potential safety hazard. The change rules and characteristics of civil aviation safety risk based on flight delays have been analyzed. Bayesian networks (BN) have been used to build ...

  6. Statistics: a Bayesian perspective

    National Research Council Canada - National Science Library

    Berry, Donald A

    1996-01-01

    ...: it is the only introductory textbook based on Bayesian ideas, it combines concepts and methods, it presents statistics as a means of integrating data into the significant process, it develops ideas...

  7. Bayesian psychometric scaling

    NARCIS (Netherlands)

    Fox, Gerardus J.A.; van den Berg, Stéphanie Martine; Veldkamp, Bernard P.; Irwing, P.; Booth, T.; Hughes, D.

    2015-01-01

    In educational and psychological studies, psychometric methods are involved in the measurement of constructs, and in constructing and validating measurement instruments. Assessment results are typically used to measure student proficiency levels and test characteristics. Recently, Bayesian item

  8. 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.

  9. Removal of radionuclides from partitioning waste solutions by adsorption and catalytic oxidation methods

    Energy Technology Data Exchange (ETDEWEB)

    Yamagishi, Isao; Yamaguchi, Isoo [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Kubota, Masumitsu [Research Organization for Information Science and Technology (RIST), Tokai, Ibaraki (Japan)

    2000-09-01

    Adsorption of radionuclides with inorganic ion exchangers and catalytic oxidation of a complexant were studied for the decontamination of waste solutions generated in past partitioning tests with high-level liquid waste. Granulated ferrocyanide and titanic acid were used for adsorption of Cs and Sr, respectively, from an alkaline solution resulting from direct neutralization of an acidic waste solution. Both Na and Ba inhibited adsorption of Sr but Na did not that of Cs. These exchangers adsorbed Cs and Sr at low concentration with distribution coefficients of more than 10{sup 4}ml/g from 2M Na solution of pH11. Overall decontamination factors (DFs) of Cs and total {beta} nuclides exceeded 10{sup 5} and 10{sup 3}, respectively, at the neutralization-adsorption step of actual waste solutions free from a complexant. The DF of total {alpha} nuclides was less than 10{sup 3} for a waste solution containing diethylenetriaminepentaacetic acid (DTPA). DTPA was rapidly oxidized by nitric acid in the presence of a platinum catalyst, and radionuclides were removed as precipitates by neutralization of the resultant solution. The DF of {alpha} nuclides increased to 8x10{sup 4} by addition of the oxidation step. The DFs of Sb and Co were quite low through the adsorption step. A synthesized Ti-base exchanger (PTC) could remove Sb with the DF of more than 4x10{sup 3}. (author)

  10. General Method of Using Bayesian Nets for a Software Reliability Assessment in Varying SW Development Life cycle

    International Nuclear Information System (INIS)

    Eom, Heung Seop; Chang, Seung Cheol

    2008-01-01

    Bayesian Net (BN) has been used in many researches to predict software defects, because it allows all the evidence to be taken into account. However one of the serious difficulties in the earlier works was that the user had to build a different BN for each software development life cycle. This limits the practical use of BN in the field. One way to solve this problem is the use of general BN templates which are not restricted to a particular software life cycle. This paper describes a method for this purpose on the strength of Object- Oriented BN (OOBN) and Dynamic BN (DBN) technique

  11. A combined evidence Bayesian method for human ancestry inference applied to Afro-Colombians.

    Science.gov (United States)

    Rishishwar, Lavanya; Conley, Andrew B; Vidakovic, Brani; Jordan, I King

    2015-12-15

    Uniparental genetic markers, mitochondrial DNA (mtDNA) and Y chromosomal DNA, are widely used for the inference of human ancestry. However, the resolution of ancestral origins based on mtDNA haplotypes is limited by the fact that such haplotypes are often found to be distributed across wide geographical regions. We have addressed this issue here by combining two sources of ancestry information that have typically been considered separately: historical records regarding population origins and genetic information on mtDNA haplotypes. To combine these distinct data sources, we applied a Bayesian approach that considers historical records, in the form of prior probabilities, together with data on the geographical distribution of mtDNA haplotypes, formulated as likelihoods, to yield ancestry assignments from posterior probabilities. This combined evidence Bayesian approach to ancestry assignment was evaluated for its ability to accurately assign sub-continental African ancestral origins to Afro-Colombians based on their mtDNA haplotypes. We demonstrate that the incorporation of historical prior probabilities via this analytical framework can provide for substantially increased resolution in sub-continental African ancestry assignment for members of this population. In addition, a personalized approach to ancestry assignment that involves the tuning of priors to individual mtDNA haplotypes yields even greater resolution for individual ancestry assignment. Despite the fact that Colombia has a large population of Afro-descendants, the ancestry of this community has been understudied relative to populations with primarily European and Native American ancestry. Thus, the application of the kind of combined evidence approach developed here to the study of ancestry in the Afro-Colombian population has the potential to be impactful. The formal Bayesian analytical framework we propose for combining historical and genetic information also has the potential to be widely applied

  12. Bayesian computation with R

    CERN Document Server

    Albert, Jim

    2009-01-01

    There has been a dramatic growth in the development and application of Bayesian inferential methods. Some of this growth is due to the availability of powerful simulation-based algorithms to summarize posterior distributions. There has been also a growing interest in the use of the system R for statistical analyses. R's open source nature, free availability, and large number of contributor packages have made R the software of choice for many statisticians in education and industry. Bayesian Computation with R introduces Bayesian modeling by the use of computation using the R language. The earl

  13. Development of partitioning method. Adsorption of cesium with mordenite in acidic media

    Energy Technology Data Exchange (ETDEWEB)

    Donnet, L.; Morita, Yasuji; Yamagishi, Isao; Kubota, Masumitsu [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    1998-10-01

    Adsorption of cesium with mordenite from a acidic solution, typically from a 0.5 mol/L nitric acid solution, was studied to examine the possibility to design a new separation scheme for partitioning of high-level liquid waste. Batch adsorption experiments showed that three mordenites examined (natural mordenite and two synthetic mordenites Zeolon 900Na and 900H) have very close behavior with the parameters of adsorption kinetics, the saturation capacity by Langmuir equation, the distribution coefficient of Cs and adsorption of other elements. In the Cs adsorption with the natural mordenite at 0.5 mol/L nitric acid, distribution coefficient was 1150 ml/g and the saturation capacity was 0.64 mmol/g. In the adsorption of Cs on column using the natural mordenite, the flow rate of the Cs solution modified only the 5% breakthrough point and gave no influence on the total capacity of Cs. Column experiments with a mixed solution of Cs, Rb, Na, Ba, Sr, Cr, Ni, Ru, Rh and Pd showed that cesium was adsorbed very selectively. Only about 4% of rubidium in a molar ratio were retained in the column. The total quantity of Cs and Rb adsorbed was 0.51 mmol/g at 0.5 mol/L nitric acid. Elution of Cs (and Rb) with 4 mol/L nitric acid was performed against the column of the loaded natural mordenite. The adsorbed Cs and Rb were well eluted, and a good mass balance was obtained between the adsorbed quantity by breakthrough curves and the quantity found in the eluate. (author)

  14. Support agnostic Bayesian matching pursuit for block sparse signals

    KAUST Repository

    Masood, Mudassir

    2013-05-01

    A fast matching pursuit method using a Bayesian approach is introduced for block-sparse signal recovery. This method performs Bayesian estimates of block-sparse signals even when the distribution of active blocks is non-Gaussian or unknown. It is agnostic to the distribution of active blocks in the signal and utilizes a priori statistics of additive noise and the sparsity rate of the signal, which are shown to be easily estimated from data and no user intervention is required. The method requires a priori knowledge of block partition and utilizes a greedy approach and order-recursive updates of its metrics to find the most dominant sparse supports to determine the approximate minimum mean square error (MMSE) estimate of the block-sparse signal. Simulation results demonstrate the power and robustness of our proposed estimator. © 2013 IEEE.

  15. Water isotope partitioning and ecohydrologic separation in mixed conifer forest explored with a centrifugation water extraction method

    Science.gov (United States)

    Bowers, W.; Mercer, J.; Pleasants, M.; Williams, D. G.

    2017-12-01

    Isotopic partitioning of water within soil into tightly and loosely bound fractions has been proposed to explain differences between isotopic water sources used by plants and those that contribute to streams and ground water, the basis for the "two water worlds" hypothesis. We examined the isotope ratio values of water in trees, bulk soil, mobile water collected from soil lysimeters, stream water, and GW at three different hillslopes in a mixed conifer forest in southeastern Wyoming, USA. Hillslopes differed in aspect and topographic position with corresponding differences in surface energy balance, snowmelt timing, and duration of soil moisture during the dry summer. The isotopic results support the partitioning of water within the soil; trees apparently used a different pool of water for transpiration than that recovered from soil lysimeters and the source was not resolved with the isotopic signature of the water that was extracted from bulk soil via cryogenic vacuum distillation. Separating and measuring the isotope ratios values in these pools would test the assumption that the tightly bound water within the soil has the same isotopic signature as the water transpired by the trees. We employed a centrifugation approach to separate water within the soil held at different tensions by applying stepwise increases in rotational velocity and pressures to the bulk soil samples. Effluent and the remaining water (cryogenically extracted) at each step were compared. We first applied the centrifugation method in a simple lab experiment using sandy loam soil and separate introductions of two isotopically distinct waters. We then applied the method to soil collected from the montane hillslopes. For the lab experiment, we predicted that effluents would have distinct isotopic signatures, with the last effluent and extracted water more closely representing the isotopic signature of the first water applied. For our field samples, we predicted that the isotopic signature of the

  16. Current trends in Bayesian methodology with applications

    CERN Document Server

    Upadhyay, Satyanshu K; Dey, Dipak K; Loganathan, Appaia

    2015-01-01

    Collecting Bayesian material scattered throughout the literature, Current Trends in Bayesian Methodology with Applications examines the latest methodological and applied aspects of Bayesian statistics. The book covers biostatistics, econometrics, reliability and risk analysis, spatial statistics, image analysis, shape analysis, Bayesian computation, clustering, uncertainty assessment, high-energy astrophysics, neural networking, fuzzy information, objective Bayesian methodologies, empirical Bayes methods, small area estimation, and many more topics.Each chapter is self-contained and focuses on

  17. Bayesian methods for the design and interpretation of clinical trials in very rare diseases

    Science.gov (United States)

    Hampson, Lisa V; Whitehead, John; Eleftheriou, Despina; Brogan, Paul

    2014-01-01

    This paper considers the design and interpretation of clinical trials comparing treatments for conditions so rare that worldwide recruitment efforts are likely to yield total sample sizes of 50 or fewer, even when patients are recruited over several years. For such studies, the sample size needed to meet a conventional frequentist power requirement is clearly infeasible. Rather, the expectation of any such trial has to be limited to the generation of an improved understanding of treatment options. We propose a Bayesian approach for the conduct of rare-disease trials comparing an experimental treatment with a control where patient responses are classified as a success or failure. A systematic elicitation from clinicians of their beliefs concerning treatment efficacy is used to establish Bayesian priors for unknown model parameters. The process of determining the prior is described, including the possibility of formally considering results from related trials. As sample sizes are small, it is possible to compute all possible posterior distributions of the two success rates. A number of allocation ratios between the two treatment groups can be considered with a view to maximising the prior probability that the trial concludes recommending the new treatment when in fact it is non-inferior to control. Consideration of the extent to which opinion can be changed, even by data from the best feasible design, can help to determine whether such a trial is worthwhile. © 2014 The Authors. Statistics in Medicine published by John Wiley & Sons, Ltd. PMID:24957522

  18. On the application of the partition of unity method for nonlocal response of low-dimensional structures

    Science.gov (United States)

    Natarajan, Sundararajan

    2014-12-01

    The main objectives of the paper are to (1) present an overview of nonlocal integral elasticity and Aifantis gradient elasticity theory and (2) discuss the application of partition of unity methods to study the response of low-dimensional structures. We present different choices of approximation functions for gradient elasticity, namely Lagrange intepolants, moving least-squares approximants and non-uniform rational B-splines. Next, we employ these approximation functions to study the response of nanobeams based on Euler-Bernoulli and Timoshenko theories as well as to study nanoplates based on first-order shear deformation theory. The response of nanobeams and nanoplates is studied using Eringen's nonlocal elasticity theory. The influence of the nonlocal parameter, the beam and the plate aspect ratio and the boundary conditions on the global response is numerically studied. The influence of a crack on the axial vibration and buckling characteristics of nanobeams is also numerically studied.

  19. [Determination of six main components in compound theophylline tablet by convolution curve method after prior separation by column partition chromatography

    Science.gov (United States)

    Zhang, S. Y.; Wang, G. F.; Wu, Y. T.; Baldwin, K. M. (Principal Investigator)

    1993-01-01

    On a partition chromatographic column in which the support is Kieselguhr and the stationary phase is sulfuric acid solution (2 mol/L), three components of compound theophylline tablet were simultaneously eluted by chloroform and three other components were simultaneously eluted by ammonia-saturated chloroform. The two mixtures were determined by computer-aided convolution curve method separately. The corresponding average recovery and relative standard deviation of the six components were as follows: 101.6, 1.46% for caffeine; 99.7, 0.10% for phenacetin; 100.9, 1.31% for phenobarbitone; 100.2, 0.81% for theophylline; 99.9, 0.81% for theobromine and 100.8, 0.48% for aminopyrine.

  20. Improving the reliability of POD curves in NDI methods using a Bayesian inversion approach for uncertainty quantification

    Science.gov (United States)

    Ben Abdessalem, A.; Jenson, F.; Calmon, P.

    2016-02-01

    This contribution provides an example of the possible advantages of adopting a Bayesian inversion approach to uncertainty quantification in nondestructive inspection methods. In such problem, the uncertainty associated to the random parameters is not always known and needs to be characterised from scattering signal measurements. The uncertainties may then correctly propagated in order to determine a reliable probability of detection curve. To this end, we establish a general Bayesian framework based on a non-parametric maximum likelihood function formulation and some priors from expert knowledge. However, the presented inverse problem is time-consuming and computationally intensive. To cope with this difficulty, we replace the real model by a surrogate one in order to speed-up the model evaluation and to make the problem to be computationally feasible for implementation. The least squares support vector regression is adopted as metamodelling technique due to its robustness to deal with non-linear problems. We illustrate the usefulness of this methodology through the control of tube with enclosed defect using ultrasonic inspection method.

  1. "K"-Balance Partitioning: An Exact Method with Applications to Generalized Structural Balance and Other Psychological Contexts

    Science.gov (United States)

    Brusco, Michael; Steinley, Douglas

    2010-01-01

    Structural balance theory (SBT) has maintained a venerable status in the psychological literature for more than 5 decades. One important problem pertaining to SBT is the approximation of structural or generalized balance via the partitioning of the vertices of a signed graph into "K" clusters. This "K"-balance partitioning problem also has more…

  2. Partitioning in P-T concept

    International Nuclear Information System (INIS)

    Zhang Peilu; Qi Zhanshun; Zhu Zhixuan

    2000-01-01

    Comparison of dry- and water-method for partitioning fission products and minor actinides from the spent fuels, and description of advance of dry-method were done. Partitioning process, some typical concept and some results of dry-method were described. The problems fond in dry-method up to now were pointed out. The partitioning study program was suggested

  3. Automated potentiometric titrations in KCl/water-saturated octanol: method for quantifying factors influencing ion-pair partitioning.

    Science.gov (United States)

    Scherrer, Robert A; Donovan, Stephen F

    2009-04-01

    The knowledge base of factors influencing ion pair partitioning is very sparse, primarily because of the difficulty in determining accurate log P(I) values of desirable low molecular weight (MW) reference compounds. We have developed a potentiometric titration procedure in KCl/water-saturated octanol that provides a link to log P(I) through the thermodynamic cycle of ionization and partitioning. These titrations have the advantage of being independent of the magnitude of log P, while maintaining a reproducibility of a few hundredths of a log P in the calculated difference between log P neutral and log P ion pair (diff (log P(N - I))). Simple model compounds can be used. The titration procedure is described in detail, along with a program for calculating pK(a)'' values incorporating the ionization of water in octanol. Hydrogen bonding and steric factors have a greater influence on ion pairs than they do on neutral species, yet these factors are missing from current programs used to calculate log P(I) and log D. In contrast to the common assumption that diff (log P(N - I)) is the same for all amines, they can actually vary more than 3 log units, as in our examples. A major factor affecting log P(I) is the ability of water and the counterion to approach the charge center. Bulky substituents near the charge center have a negative influence on log P(I). On the other hand, hydrogen bonding groups near the charge center have the opposite effect by lowering the free energy of the ion pair. The use of this titration method to determine substituent ion pair stabilization values (IPS) should bring about more accurate log D calculations and encourage species-specific QSAR involving log D(N) and log D(I). This work also brings attention to the fascinating world of nature's highly stabilized ion pairs.

  4. Automated Potentiometric Titrations in KCl/Water-Saturated Octanol: Method for Quantifying Factors Influencing Ion-Pair Partitioning

    Science.gov (United States)

    2009-01-01

    The knowledge base of factors influencing ion pair partitioning is very sparse, primarily because of the difficulty in determining accurate log PI values of desirable low molecular weight (MW) reference compounds. We have developed a potentiometric titration procedure in KCl/water-saturated octanol that provides a link to log PI through the thermodynamic cycle of ionization and partitioning. These titrations have the advantage of being independent of the magnitude of log P, while maintaining a reproducibility of a few hundredths of a log P in the calculated difference between log P neutral and log P ion pair (diff (log PN − I)). Simple model compounds can be used. The titration procedure is described in detail, along with a program for calculating pKa′′ values incorporating the ionization of water in octanol. Hydrogen bonding and steric factors have a greater influence on ion pairs than they do on neutral species, yet these factors are missing from current programs used to calculate log PI and log D. In contrast to the common assumption that diff (log PN − I) is the same for all amines, they can actually vary more than 3 log units, as in our examples. A major factor affecting log PI is the ability of water and the counterion to approach the charge center. Bulky substituents near the charge center have a negative influence on log PI. On the other hand, hydrogen bonding groups near the charge center have the opposite effect by lowering the free energy of the ion pair. The use of this titration method to determine substituent ion pair stabilization values (IPS) should bring about more accurate log D calculations and encourage species-specific QSAR involving log DN and log DI. This work also brings attention to the fascinating world of nature’s highly stabilized ion pairs. PMID:19265385

  5. A Bayesian method for inferring transmission chains in a partially observed epidemic.

    Energy Technology Data Exchange (ETDEWEB)

    Marzouk, Youssef M.; Ray, Jaideep

    2008-10-01

    We present a Bayesian approach for estimating transmission chains and rates in the Abakaliki smallpox epidemic of 1967. The epidemic affected 30 individuals in a community of 74; only the dates of appearance of symptoms were recorded. Our model assumes stochastic transmission of the infections over a social network. Distinct binomial random graphs model intra- and inter-compound social connections, while disease transmission over each link is treated as a Poisson process. Link probabilities and rate parameters are objects of inference. Dates of infection and recovery comprise the remaining unknowns. Distributions for smallpox incubation and recovery periods are obtained from historical data. Using Markov chain Monte Carlo, we explore the joint posterior distribution of the scalar parameters and provide an expected connectivity pattern for the social graph and infection pathway.

  6. Bayesian methods for the physical sciences learning from examples in astronomy and physics

    CERN Document Server

    Andreon, Stefano

    2015-01-01

    Statistical literacy is critical for the modern researcher in Physics and Astronomy. This book empowers researchers in these disciplines by providing the tools they will need to analyze their own data. Chapters in this book provide a statistical base from which to approach new problems, including numerical advice and a profusion of examples. The examples are engaging analyses of real-world problems taken from modern astronomical research. The examples are intended to be starting points for readers as they learn to approach their own data and research questions. Acknowledging that scientific progress now hinges on the availability of data and the possibility to improve previous analyses, data and code are distributed throughout the book. The JAGS symbolic language used throughout the book makes it easy to perform Bayesian analysis and is particularly valuable as readers may use it in a myriad of scenarios through slight modifications.

  7. Bayesian methods for the combination of core sampling data with historical models for tank characterization

    International Nuclear Information System (INIS)

    York, J.C.; Remund, K.M.; Chen, G.; Simpson, B.C.; Brown, T.M.

    1995-07-01

    A wide variety of information is available on the contents of the nuclear waste tanks at the Hanford site. This report describes an attempt to combine several sources of information using a Bayesian statistical approach. This methodology allows the combination of multiple disparate information sources. After each source of information is summarized in terms of a probability distribution function (pdf), Bayes' theorem is applied to combine them. This approach has been applied to characterizing tanks B-110, B-111, and B-201. These tanks were chosen for their simple waste matrices: B-110 and B-111 contain mostly 2C waste, and B-201 contains mostly 224 waste. Additionally,, the results of this analysis axe used to make predictions for tank T-111 (which contains both 2C and 224 waste). These predictions are compared to the estimates based on core samples from tank T-111

  8. A Bayesian method to mine spatial data sets to evaluate the vulnerability of human beings to catastrophic risk.

    Science.gov (United States)

    Li, Lianfa; Wang, Jinfeng; Leung, Hareton; Zhao, Sisi

    2012-06-01

    Vulnerability of human beings exposed to a catastrophic disaster is affected by multiple factors that include hazard intensity, environment, and individual characteristics. The traditional approach to vulnerability assessment, based on the aggregate-area method and unsupervised learning, cannot incorporate spatial information; thus, vulnerability can be only roughly assessed. In this article, we propose Bayesian network (BN) and spatial analysis techniques to mine spatial data sets to evaluate the vulnerability of human beings. In our approach, spatial analysis is leveraged to preprocess the data; for example, kernel density analysis (KDA) and accumulative road cost surface modeling (ARCSM) are employed to quantify the influence of geofeatures on vulnerability and relate such influence to spatial distance. The knowledge- and data-based BN provides a consistent platform to integrate a variety of factors, including those extracted by KDA and ARCSM to model vulnerability uncertainty. We also consider the model's uncertainty and use the Bayesian model average and Occam's Window to average the multiple models obtained by our approach to robust prediction of the risk and vulnerability. We compare our approach with other probabilistic models in the case study of seismic risk and conclude that our approach is a good means to mining spatial data sets for evaluating vulnerability. © 2012 Society for Risk Analysis.

  9. Peak Bagging of red giant stars observed by Kepler: first results with a new method based on Bayesian nested sampling

    Science.gov (United States)

    Corsaro, Enrico; De Ridder, Joris

    2015-09-01

    The peak bagging analysis, namely the fitting and identification of single oscillation modes in stars' power spectra, coupled to the very high-quality light curves of red giant stars observed by Kepler, can play a crucial role for studying stellar oscillations of different flavor with an unprecedented level of detail. A thorough study of stellar oscillations would thus allow for deeper testing of stellar structure models and new insights in stellar evolution theory. However, peak bagging inferences are in general very challenging problems due to the large number of observed oscillation modes, hence of free parameters that can be involved in the fitting models. Efficiency and robustness in performing the analysis is what may be needed to proceed further. For this purpose, we developed a new code implementing the Nested Sampling Monte Carlo (NSMC) algorithm, a powerful statistical method well suited for Bayesian analyses of complex problems. In this talk we show the peak bagging of a sample of high signal-to-noise red giant stars by exploiting recent Kepler datasets and a new criterion for the detection of an oscillation mode based on the computation of the Bayesian evidence. Preliminary results for frequencies and lifetimes for single oscillation modes, together with acoustic glitches, are therefore presented.

  10. Bayesian methods to restore and re build images: application to gamma-graphy and to photofission tomography

    International Nuclear Information System (INIS)

    Stawinski, G.

    1998-01-01

    Bayesian algorithms are developed to solve inverse problems in gamma imaging and photofission tomography. The first part of this work is devoted to the modeling of our measurement systems. Two models have been found for both applications: the first one is a simple conventional model and the second one is a cascaded point process model. EM and MCMC Bayesian algorithms for image restoration and image reconstruction have been developed for these models and compared. The cascaded point process model does not improve significantly the results previously obtained by the classical model. To original approaches have been proposed, which increase the results previously obtained. The first approach uses an inhomogeneous Markov Random Field as a prior law, and makes the regularization parameter spatially vary. However, the problem of the estimation of hyper-parameters has not been solved. In the case of the deconvolution of point sources, a second approach has been proposed, which introduces a high level prior model. The picture is modeled as a list of objects, whose parameters and number are unknown. The results obtained with this method are more accurate than those obtained with the conventional Markov Random Field prior model and require less computational costs. (author)

  11. Peak Bagging of red giant stars observed by Kepler: first results with a new method based on Bayesian nested sampling

    Directory of Open Access Journals (Sweden)

    Corsaro Enrico

    2015-01-01

    Full Text Available The peak bagging analysis, namely the fitting and identification of single oscillation modes in stars’ power spectra, coupled to the very high-quality light curves of red giant stars observed by Kepler, can play a crucial role for studying stellar oscillations of different flavor with an unprecedented level of detail. A thorough study of stellar oscillations would thus allow for deeper testing of stellar structure models and new insights in stellar evolution theory. However, peak bagging inferences are in general very challenging problems due to the large number of observed oscillation modes, hence of free parameters that can be involved in the fitting models. Efficiency and robustness in performing the analysis is what may be needed to proceed further. For this purpose, we developed a new code implementing the Nested Sampling Monte Carlo (NSMC algorithm, a powerful statistical method well suited for Bayesian analyses of complex problems. In this talk we show the peak bagging of a sample of high signal-to-noise red giant stars by exploiting recent Kepler datasets and a new criterion for the detection of an oscillation mode based on the computation of the Bayesian evidence. Preliminary results for frequencies and lifetimes for single oscillation modes, together with acoustic glitches, are therefore presented.

  12. A Bayesian Method for Short-Term Probabilistic Forecasting of Photovoltaic Generation in Smart Grid Operation and Control

    Directory of Open Access Journals (Sweden)

    Gabriella Ferruzzi

    2013-02-01

    Full Text Available A new short-term probabilistic forecasting method is proposed to predict the probability density function of the hourly active power generated by a photovoltaic system. Firstly, the probability density function of the hourly clearness index is forecasted making use of a Bayesian auto regressive time series model; the model takes into account the dependence of the solar radiation on some meteorological variables, such as the cloud cover and humidity. Then, a Monte Carlo simulation procedure is used to evaluate the predictive probability density function of the hourly active power by applying the photovoltaic system model to the random sampling of the clearness index distribution. A numerical application demonstrates the effectiveness and advantages of the proposed forecasting method.

  13. A pseudo-statistical approach to treat choice uncertainty: the example of partitioning allocation methods

    NARCIS (Netherlands)

    Mendoza Beltran, A.; Heijungs, R.; Guinée, J.; Tukker, A.

    2016-01-01

    Purpose: Despite efforts to treat uncertainty due to methodological choices in life cycle assessment (LCA) such as standardization, one-at-a-time (OAT) sensitivity analysis, and analytical and statistical methods, no method exists that propagate this source of uncertainty for all relevant processes

  14. Research on Large-Scale Road Network Partition and Route Search Method Combined with Traveler Preferences

    Directory of Open Access Journals (Sweden)

    De-Xin Yu

    2013-01-01

    Full Text Available Combined with improved Pallottino parallel algorithm, this paper proposes a large-scale route search method, which considers travelers’ route choice preferences. And urban road network is decomposed into multilayers effectively. Utilizing generalized travel time as road impedance function, the method builds a new multilayer and multitasking road network data storage structure with object-oriented class definition. Then, the proposed path search algorithm is verified by using the real road network of Guangzhou city as an example. By the sensitive experiments, we make a comparative analysis of the proposed path search method with the current advanced optimal path algorithms. The results demonstrate that the proposed method can increase the road network search efficiency by more than 16% under different search proportion requests, node numbers, and computing process numbers, respectively. Therefore, this method is a great breakthrough in the guidance field of urban road network.

  15. A comparison of different quasi-newton acceleration methods for partitioned multi-physics codes

    CSIR Research Space (South Africa)

    Haelterman, R

    2018-02-01

    Full Text Available & structures, 88/7, pp. 446–457 (2010) 8. J.E. Dennis, J.J. More´, Quasi-Newton methods: motivation and theory. SIAM Rev. 19, pp. 46–89 (1977) A Comparison of Quasi-Newton Acceleration Methods 15 9. J.E. Dennis, R.B. Schnabel, Least Change Secant Updates... Dois Metodos de Broyden. Mat. Apl. Comput. 1/2, pp. 135– 143 (1982) 25. J.M. Martinez, A quasi-Newton method with modification of one column per iteration. Com- puting 33, pp. 353–362 (1984) 26. J.M. Martinez, M.C. Zambaldi, An Inverse Column...

  16. Evaluation of errors in prior mean and variance in the estimation of integrated circuit failure rates using Bayesian methods

    Science.gov (United States)

    Fletcher, B. C.

    1972-01-01

    The critical point of any Bayesian analysis concerns the choice and quantification of the prior information. The effects of prior data on a Bayesian analysis are studied. Comparisons of the maximum likelihood estimator, the Bayesian estimator, and the known failure rate are presented. The results of the many simulated trails are then analyzed to show the region of criticality for prior information being supplied to the Bayesian estimator. In particular, effects of prior mean and variance are determined as a function of the amount of test data available.

  17. Schinus terebinthifolius countercurrent chromatography (Part III): Method transfer from small countercurrent chromatography column to preparative centrifugal partition chromatography ones as a part of method development.

    Science.gov (United States)

    das Neves Costa, Fernanda; Hubert, Jane; Borie, Nicolas; Kotland, Alexis; Hewitson, Peter; Ignatova, Svetlana; Renault, Jean-Hugues

    2017-03-03

    Countercurrent chromatography (CCC) and centrifugal partition chromatography (CPC) are support free liquid-liquid chromatography techniques sharing the same basic principles and features. Method transfer has previously been demonstrated for both techniques but never from one to another. This study aimed to show such a feasibility using fractionation of Schinus terebinthifolius berries dichloromethane extract as a case study. Heptane - ethyl acetate - methanol -water (6:1:6:1, v/v/v/v) was used as solvent system with masticadienonic and 3β-masticadienolic acids as target compounds. The optimized separation methodology previously described in Part I and II, was scaled up from an analytical hydrodynamic CCC column (17.4mL) to preparative hydrostatic CPC instruments (250mL and 303mL) as a part of method development. Flow-rate and sample loading were further optimized on CPC. Mobile phase linear velocity is suggested as a transfer invariant parameter if the CPC column contains sufficient number of partition cells. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Applications of Bayesian Phylodynamic Methods in a Recent U.S. Porcine Reproductive and Respiratory Syndrome Virus Outbreak

    Directory of Open Access Journals (Sweden)

    Mohammad A. Alkhamis

    2016-02-01

    Full Text Available Classical phylogenetic methods such as neighbor-joining or maximum likelihood trees, provide limited inferences about the evolution of important pathogens and ignore important evolutionary parameters and uncertainties, which in turn limits decision making related to surveillance, control and prevention resources. Bayesian phylodynamic models have recently been used to test research hypothesis related to evolution of infectious agents. However, few studies have attempted to model the evolutionary dynamics of porcine reproductive and respiratory syndrome virus (PRRSV and, to the authors’ knowledge, no attempt has been made to use large volumes of routinely collected data, sometimes referred to as big data, in the context of animal disease surveillance. The objective of this study was to explore and discuss the applications of Bayesian phylodynamic methods for modeling the evolution and spread of a notable 1-7-4 RFLP-type PRRSV between 2014 and 2015. A convenience sample of 288 ORF5 sequences was collected from 5 swine production systems in the United States between September 2003 and March 2015. Using coalescence and discrete trait phylodynamic models, we were able to infer population growth and demographic history of the virus, identified the most likely ancestral system (root state posterior probability = 0.95 and revealed significant dispersal routes (Bayes factor > 6 of viral exchange among systems. Results indicate that currently circulating viruses are evolving rapidly, and show a higher level of relative genetic diversity over time, when compared to earlier relatives. Biological soundness of model results is supported by the finding that sow farms were responsible for PRRSV spread within the systems. Such results can’t be obtained by traditional phylogenetic methods, and therefore, our results provide a methodological framework for molecular epidemiological modeling of new PRRSV outbreaks and demonstrate the prospects of phylodynamic

  19. Bayesian Utilitarianism

    OpenAIRE

    ZHOU, Lin

    1996-01-01

    In this paper I consider social choices under uncertainty. I prove that any social choice rule that satisfies independence of irrelevant alternatives, translation invariance, and weak anonymity is consistent with ex post Bayesian utilitarianism

  20. Quantitative methods in ethnobotany and ethnopharmacology: considering the overall flora--hypothesis testing for over- and underused plant families with the Bayesian approach.

    Science.gov (United States)

    Weckerle, Caroline S; Cabras, Stefano; Castellanos, Maria Eugenia; Leonti, Marco

    2011-09-01

    We introduce and explain the advantages of the Bayesian approach and exemplify the method with an analysis of the medicinal flora of Campania, Italy. The Bayesian approach is a new method, which allows to compare medicinal floras with the overall flora of a given area and to investigate over- and underused plant families. In contrast to previously used methods (regression analysis and binomial method) it considers the inherent uncertainty around the analyzed data. The medicinal flora with 423 species was compiled based on nine studies on local medicinal plant use in Campania. The total flora comprises 2237 species belonging to 128 families. Statistical analysis was performed with the Bayesian method and the binomial method. An approximated χ(2)-test was used to analyze the relationship between use categories and higher taxonomic groups. Among the larger plant families we find the Lamiaceae, Rosaceae, and Malvaceae, to be overused in the local medicine of Campania and the Orchidaceae, Caryophyllaceae, Poaceae, and Fabaceae to be underused compared to the overall flora. Furthermore, do specific medicinal uses tend to be correlated with taxonomic plant groups. For example, are the Monocots heavily used for urological complaints. Testing for over- and underused taxonomic groups of a flora with the Bayesian method is easy to adopt and can readily be calculated in excel spreadsheets using the excel function Inverse beta (INV.BETA). In contrast to the binomial method the presented method is also suitable for small datasets. With larger datasets the two methods tend to converge. However, results are generally more conservative with the Bayesian method pointing out fewer families as over- or underused. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  1. Partitioning sparse rectangular matrices for parallel processing

    Energy Technology Data Exchange (ETDEWEB)

    Kolda, T.G.

    1998-05-01

    The authors are interested in partitioning sparse rectangular matrices for parallel processing. The partitioning problem has been well-studied in the square symmetric case, but the rectangular problem has received very little attention. They will formalize the rectangular matrix partitioning problem and discuss several methods for solving it. They will extend the spectral partitioning method for symmetric matrices to the rectangular case and compare this method to three new methods -- the alternating partitioning method and two hybrid methods. The hybrid methods will be shown to be best.

  2. Digital halftoning methods for selectively partitioning error into achromatic and chromatic channels

    Science.gov (United States)

    Mulligan, Jeffrey B.

    1990-01-01

    A method is described for reducing the visibility of artifacts arising in the display of quantized color images on CRT displays. The method is based on the differential spatial sensitivity of the human visual system to chromatic and achromatic modulations. Because the visual system has the highest spatial and temporal acuity for the luminance component of an image, a technique which will reduce luminance artifacts at the expense of introducing high-frequency chromatic errors is sought. A method based on controlling the correlations between the quantization errors in the individual phosphor images is explored. The luminance component is greatest when the phosphor errors are positively correlated, and is minimized when the phosphor errors are negatively correlated. The greatest effect of the correlation is obtained when the intensity quantization step sizes of the individual phosphors have equal luminances. For the ordered dither algorithm, a version of the method can be implemented by simply inverting the matrix of thresholds for one of the color components.

  3. A composite experimental dynamic substructuring method based on partitioned algorithms and localized Lagrange multipliers

    Science.gov (United States)

    Abbiati, Giuseppe; La Salandra, Vincenzo; Bursi, Oreste S.; Caracoglia, Luca

    2018-02-01

    Successful online hybrid (numerical/physical) dynamic substructuring simulations have shown their potential in enabling realistic dynamic analysis of almost any type of non-linear structural system (e.g., an as-built/isolated viaduct, a petrochemical piping system subjected to non-stationary seismic loading, etc.). Moreover, owing to faster and more accurate testing equipment, a number of different offline experimental substructuring methods, operating both in time (e.g. the impulse-based substructuring) and frequency domains (i.e. the Lagrange multiplier frequency-based substructuring), have been employed in mechanical engineering to examine dynamic substructure coupling. Numerous studies have dealt with the above-mentioned methods and with consequent uncertainty propagation issues, either associated with experimental errors or modelling assumptions. Nonetheless, a limited number of publications have systematically cross-examined the performance of the various Experimental Dynamic Substructuring (EDS) methods and the possibility of their exploitation in a complementary way to expedite a hybrid experiment/numerical simulation. From this perspective, this paper performs a comparative uncertainty propagation analysis of three EDS algorithms for coupling physical and numerical subdomains with a dual assembly approach based on localized Lagrange multipliers. The main results and comparisons are based on a series of Monte Carlo simulations carried out on a five-DoF linear/non-linear chain-like systems that include typical aleatoric uncertainties emerging from measurement errors and excitation loads. In addition, we propose a new Composite-EDS (C-EDS) method to fuse both online and offline algorithms into a unique simulator. Capitalizing from the results of a more complex case study composed of a coupled isolated tank-piping system, we provide a feasible way to employ the C-EDS method when nonlinearities and multi-point constraints are present in the emulated system.

  4. Using Bayesian network and AHP method as a marketing approach tools in defining tourists’ preferences

    Directory of Open Access Journals (Sweden)

    Nataša Papić-Blagojević

    2012-04-01

    Full Text Available Marketing approach is associated to market conditions and achieving long term profitability of a company by satisfying consumers’ needs. This approach in tourism does not have to be related only to promoting one touristic destination, but is associated to relation between travel agency and its clients too. It considers that travel agencies adjust their offers to their clients’ needs. In that sense, it is important to analyze the behavior of tourists in the earlier periods with consideration of their preferences. Using Bayesian network, it could be graphically displayed the connection between tourists who have similar taste and relationships between them. On the other hand, the analytic hierarchy process (AHP is used to rank tourist attractions, with also relying on past experience. In this paper we examine possible applications of these two models in tourism in Serbia. The example is hypothetical, but it will serve as a base for future research. Three types of tourism are chosen as a representative in Vojvodina: Cultural, Rural and Business tourism, because they are the bright spot of touristic development in this area. Applied on these forms, analytic hierarchy process has shown its strength in predicting tourists’ preferences.

  5. Development of the Bayesian method for unavailability inference. The new inferential theory and the examples of inference using BWR outage data in Japan

    International Nuclear Information System (INIS)

    Nakamura, Makoto

    2009-01-01

    It is important for Level 1 PSA to quantify input reliability parameters and their uncertainty. Bayesian methods for inference of system/component unavailability, however, are not well studied. At present practitioners allocate the uncertainty (i.e. error factor) of the unavailability based on engineering judgment. Systematic methods based on Bayesian statistics are needed for quantification of such uncertainty. In this study we have developed a new method for Bayesian inference of unavailability, where the posterior of system/component unavailability is described by the inverted gamma distribution. We show that the average of the posterior comes close to the point estimate of the unavailability as the number of outages goes to infinity. That indicates validity of the new method. Using plant data recorded in NUCIA, we have applied the new method to inference of system unavailability under unplanned outages due to violations of LCO at BWRs in Japan. According to the inference results, the unavailability is populated in the order of 10 -5 -10 -4 and the error factor is within 1-2. Thus, the new Bayesian method allows one to quantify magnitudes and widths (i.e. error factor) of uncertainty distributions of unavailability. (author)

  6. A multivariate nonlinear mixed effects method for analyzing energy partitioning in growing pigs

    DEFF Research Database (Denmark)

    Strathe, Anders Bjerring; Danfær, Allan Christian; Chwalibog, André

    2010-01-01

    to the multivariate nonlinear regression model because the MNLME method accounted for correlated errors associated with PD and LD measurements and could also include the random effect of animal. It is recommended that multivariate models used to quantify energy metabolism in growing pigs should account for animal......Simultaneous equations have become increasingly popular for describing the effects of nutrition on the utilization of ME for protein (PD) and lipid deposition (LD) in animals. The study developed a multivariate nonlinear mixed effects (MNLME) framework and compared it with an alternative method...... for estimating parameters in simultaneous equations that described energy metabolism in growing pigs, and then proposed new PD and LD equations. The general statistical framework was implemented in the NLMIXED procedure in SAS. Alternative PD and LD equations were also developed, which assumed...

  7. Bayesian model averaging method for evaluating associations between air pollution and respiratory mortality: a time-series study.

    Science.gov (United States)

    Fang, Xin; Li, Runkui; Kan, Haidong; Bottai, Matteo; Fang, Fang; Cao, Yang

    2016-08-16

    To demonstrate an application of Bayesian model averaging (BMA) with generalised additive mixed models (GAMM) and provide a novel modelling technique to assess the association between inhalable coarse particles (PM10) and respiratory mortality in time-series studies. A time-series study using regional death registry between 2009 and 2010. 8 districts in a large metropolitan area in Northern China. 9559 permanent residents of the 8 districts who died of respiratory diseases between 2009 and 2010. Per cent increase in daily respiratory mortality rate (MR) per interquartile range (IQR) increase of PM10 concentration and corresponding 95% confidence interval (CI) in single-pollutant and multipollutant (including NOx, CO) models. The Bayesian model averaged GAMM (GAMM+BMA) and the optimal GAMM of PM10, multipollutants and principal components (PCs) of multipollutants showed comparable results for the effect of PM10 on daily respiratory MR, that is, one IQR increase in PM10 concentration corresponded to 1.38% vs 1.39%, 1.81% vs 1.83% and 0.87% vs 0.88% increase, respectively, in daily respiratory MR. However, GAMM+BMA gave slightly but noticeable wider CIs for the single-pollutant model (-1.09 to 4.28 vs -1.08 to 3.93) and the PCs-based model (-2.23 to 4.07 vs -2.03 vs 3.88). The CIs of the multiple-pollutant model from two methods are similar, that is, -1.12 to 4.85 versus -1.11 versus 4.83. The BMA method may represent a useful tool for modelling uncertainty in time-series studies when evaluating the effect of air pollution on fatal health outcomes. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  8. A novel method for the determination of adsorption partition coefficients of minor gases in a shale sample by headspace gas chromatography.

    Science.gov (United States)

    Zhang, Chun-Yun; Hu, Hui-Chao; Chai, Xin-Sheng; Pan, Lei; Xiao, Xian-Ming

    2013-10-04

    A novel method has been developed for the determination of adsorption partition coefficient (Kd) of minor gases in shale. The method uses samples of two different sizes (masses) of the same material, from which the partition coefficient of the gas can be determined from two independent headspace gas chromatographic (HS-GC) measurements. The equilibrium for the model gas (ethane) was achieved in 5h at 120°C. The method also involves establishing an equation based on the Kd at higher equilibrium temperature, from which the Kd at lower temperature can be calculated. Although the HS-GC method requires some time and effort, it is simpler and quicker than the isothermal adsorption method that is in widespread use today. As a result, the method is simple and practical and can be a valuable tool for shale gas-related research and applications. Copyright © 2013 Elsevier B.V. All rights reserved.

  9. Sources of CO{sub 2} efflux from soil and review of partitioning methods

    Energy Technology Data Exchange (ETDEWEB)

    Kuzyakov, Y. [University of Hohenheim, Stuttgart (Germany). Institute of Soil Science and Land Evaluation

    2006-03-15

    Five main biogenic sources of CO{sub 2} efflux from soils have been distinguished and described according to their turnover rates and the mean residence time of carbon. They are root respiration, rhizomicrobial respiration, decomposition of plant residues, the priming effect induced by root exudation or by addition of plant residues, and basal respiration by microbial decomposition of soil organic matter (SOM). These sources can be grouped in several combinations to summarize CO{sub 2} efflux from the soil including: root-derived CO{sub 2}, plant-derived CO{sub 2}, SOM-derived CO{sub 2}, rhizosphere respiration, heterotrophic microbial respiration (respiration by heterotrophs), and respiration by autotrophs. These distinctions are important because without separation of SOM-derived CO{sub 2} from plant-derived CO{sub 2}, measurements of total soil respiration have very limited value for evaluation of the soil as a source or sink of atmospheric CO{sub 2} and for interpreting the sources of CO{sub 2} and the fate of carbon within soils and ecosystems. Additionally, the processes linked to the five sources of CO{sub 2} efflux from soil have various responses to environmental variables and consequently to global warming. This review describes the basic principles and assumptions of the following methods which allow SOM-derived and root-derived CO{sub 2} efflux to be separated under laboratory and field conditions: root exclusion techniques, shading and clipping, tree girdling, regression, component integration, excised roots and in situ root respiration; continuous and pulse labeling, {sup 13}C natural abundance and FACE, and radiocarbon dating and bomb-{sup 14}C. A short sections cover the separation of the respiration of autotrophs and that of heterotrophs, i.e. the separation of actual root respiration from microbial respiration, as well as methods allowing the amount of CO{sub 2} evolved by decomposition of plant residues and by priming effects to be estimated. All

  10. Sources of CO2 efflux from soil and review of partitioning methods

    International Nuclear Information System (INIS)

    Kuzyakov, Y.

    2006-01-01

    Five main biogenic sources of CO 2 efflux from soils have been distinguished and described according to their turnover rates and the mean residence time of carbon. They are root respiration, rhizomicrobial respiration, decomposition of plant residues, the priming effect induced by root exudation or by addition of plant residues, and basal respiration by microbial decomposition of soil organic matter (SOM). These sources can be grouped in several combinations to summarize CO 2 efflux from the soil including: root-derived CO 2 , plant-derived CO 2 , SOM-derived CO 2 , rhizosphere respiration, heterotrophic microbial respiration (respiration by heterotrophs), and respiration by autotrophs. These distinctions are important because without separation of SOM-derived CO 2 from plant-derived CO 2 , measurements of total soil respiration have very limited value for evaluation of the soil as a source or sink of atmospheric CO 2 and for interpreting the sources of CO 2 and the fate of carbon within soils and ecosystems. Additionally, the processes linked to the five sources of CO 2 efflux from soil have various responses to environmental variables and consequently to global warming. This review describes the basic principles and assumptions of the following methods which allow SOM-derived and root-derived CO 2 efflux to be separated under laboratory and field conditions: root exclusion techniques, shading and clipping, tree girdling, regression, component integration, excised roots and in situ root respiration; continuous and pulse labeling, 13 C natural abundance and FACE, and radiocarbon dating and bomb- 14 C. A short sections cover the separation of the respiration of autotrophs and that of heterotrophs, i.e. the separation of actual root respiration from microbial respiration, as well as methods allowing the amount of CO 2 evolved by decomposition of plant residues and by priming effects to be estimated. All these methods have been evaluated according to their inherent

  11. The Train Driver Recovery Problem - a Set Partitioning Based Model and Solution Method

    DEFF Research Database (Denmark)

    Rezanova, Natalia Jurjevna; Ryan, David

    The need to recover a train driver schedule occurs during major disruptions in the daily railway operations. Using data from the train driver schedule of the Danish passenger railway operator DSB S-tog A/S, a solution method to the Train Driver Recovery Problem (TDRP) is developed. The TDRP...... the depth-first search of the Branch & Bound tree. Preliminarily results are encouraging, showing that nearly all tested real-life instances produce integer solutions to the LP relaxation and solutions are found within a few seconds....

  12. Towards Improving the Efficiency of Bayesian Model Averaging Analysis for Flow in Porous Media via the Probabilistic Collocation Method

    Directory of Open Access Journals (Sweden)

    Liang Xue

    2018-04-01

    Full Text Available The characterization of flow in subsurface porous media is associated with high uncertainty. To better quantify the uncertainty of groundwater systems, it is necessary to consider the model uncertainty. Multi-model uncertainty analysis can be performed in the Bayesian model averaging (BMA framework. However, the BMA analysis via Monte Carlo method is time consuming because it requires many forward model evaluations. A computationally efficient BMA analysis framework is proposed by using the probabilistic collocation method to construct a response surface model, where the log hydraulic conductivity field and hydraulic head are expanded into polynomials through Karhunen–Loeve and polynomial chaos methods. A synthetic test is designed to validate the proposed response surface analysis method. The results show that the posterior model weight and the key statistics in BMA framework can be accurately estimated. The relative errors of mean and total variance in the BMA analysis results are just approximately 0.013% and 1.18%, but the proposed method can be 16 times more computationally efficient than the traditional BMA method.

  13. Bayesian analysis in plant pathology.

    Science.gov (United States)

    Mila, A L; Carriquiry, A L

    2004-09-01

    ABSTRACT Bayesian methods are currently much discussed and applied in several disciplines from molecular biology to engineering. Bayesian inference is the process of fitting a probability model to a set of data and summarizing the results via probability distributions on the parameters of the model and unobserved quantities such as predictions for new observations. In this paper, after a short introduction of Bayesian inference, we present the basic features of Bayesian methodology using examples from sequencing genomic fragments and analyzing microarray gene-expressing levels, reconstructing disease maps, and designing experiments.

  14. Effect of partitioning the nonfiber carbohydrate fraction and neutral detergent fiber method on digestibility of carbohydrates by dairy cows.

    Science.gov (United States)

    Tebbe, A W; Faulkner, M J; Weiss, W P

    2017-08-01

    Many nutrition models rely on summative equations to estimate feed and diet energy concentrations. These models partition feed into nutrient fractions and multiply the fractions by their estimated true digestibility, and the digestible mass provided by each fraction is then summed and converted to an energy value. Nonfiber carbohydrate (NFC) is used in many models. Although it behaves as a nutritionally uniform fraction, it is a heterogeneous mixture of components. To reduce the heterogeneity, we partitioned NFC into starch and residual organic matter (ROM), which is calculated as 100 - CP - LCFA - ash - starch - NDF, where crude protein (CP), long-chain fatty acids (LCFA), ash, starch, and neutral detergent fiber (NDF) are a percentage of DM. However, the true digestibility of ROM is unknown, and because NDF is contaminated with both ash and CP, those components are subtracted twice. The effect of ash and CP contamination of NDF on in vivo digestibility of NDF and ROM was evaluated using data from 2 total-collection digestibility experiments using lactating dairy cows. Digestibility of NDF was greater when it was corrected for ash and CP than without correction. Conversely, ROM apparent digestibility decreased when NDF was corrected for contamination. Although correcting for contamination statistically increased NDF digestibility, the effect was small; the average increase was 3.4%. The decrease in ROM digestibility was 7.4%. True digestibility of ROM is needed to incorporate ROM into summative equations. Data from multiple digestibility experiments (38 diets) using dairy cows were collated, and ROM concentrations were regressed on concentration of digestible ROM (ROM was calculated without adjusting for ash and CP contamination). The estimated true digestibility coefficient of ROM was 0.96 (SE = 0.021), and metabolic fecal ROM was 3.43 g/100 g of dry matter intake (SE = 0.30). Using a smaller data set (7 diets), estimated true digestibility of ROM when calculated

  15. Lifetime estimates of a fusion reactor first wall by linear damage summation and strain range partitioning methods

    International Nuclear Information System (INIS)

    Liu, K.C.; Grossbeck, M.L.

    1979-01-01

    A generalized model of a first wall made of 20% cold-worked steel was examined for neutron wall loadings ranging from 2 to 5 MW/m 2 . A spectrum of simplified on-off duty cycles was assumed with a 95% burn time. Independent evaluations of cyclic lifetimes were based on two methods: the method of linear damage summation currently being employed for use in ASME high-temperature design Code Case N-47 and that of strain range partitioning being studied for inclusion in the design code. An important point is that the latter method can incorporate a known decrease in ductility for materials subject to irradiation as a parameter, so low-cycle fatigue behavior can be estimated for irradiated material. Lifetimes predicted by the two methods agree reasonably well despite their diversity in concept. Lack of high-cycle fatigue data for the material tested at temperatures within the range of our interest precludes making conclusions on the accuracy of the predicted results, but such data are forthcoming. The analysis includes stress relaxation due to thermal and irradiation-induced creep. Reduced ductility values from irradiations that simulate the environment of the first wall of a fusion reactor were used to estimate the lifetime of the first wall under irradiation. These results indicate that 20% cold-worked type 316 stainless steel could be used as a first-wall material meeting a 8 to 10 MW-year/m 2 lifetime goal for a neutron wall loading of about 2 MW-year/m 2 and a maximum temperature of about 500 0 C

  16. Bayesian and Classical Machine Learning Methods: A Comparison for Tree Species Classification with LiDAR Waveform Signatures

    Directory of Open Access Journals (Sweden)

    Tan Zhou

    2017-12-01

    Full Text Available A plethora of information contained in full-waveform (FW Light Detection and Ranging (LiDAR data offers prospects for characterizing vegetation structures. This study aims to investigate the capacity of FW LiDAR data alone for tree species identification through the integration of waveform metrics with machine learning methods and Bayesian inference. Specifically, we first conducted automatic tree segmentation based on the waveform-based canopy height model (CHM using three approaches including TreeVaW, watershed algorithms and the combination of TreeVaW and watershed (TW algorithms. Subsequently, the Random forests (RF and Conditional inference forests (CF models were employed to identify important tree-level waveform metrics derived from three distinct sources, such as raw waveforms, composite waveforms, the waveform-based point cloud and the combined variables from these three sources. Further, we discriminated tree (gray pine, blue oak, interior live oak and shrub species through the RF, CF and Bayesian multinomial logistic regression (BMLR using important waveform metrics identified in this study. Results of the tree segmentation demonstrated that the TW algorithms outperformed other algorithms for delineating individual tree crowns. The CF model overcomes waveform metrics selection bias caused by the RF model which favors correlated metrics and enhances the accuracy of subsequent classification. We also found that composite waveforms are more informative than raw waveforms and waveform-based point cloud for characterizing tree species in our study area. Both classical machine learning methods (the RF and CF and the BMLR generated satisfactory average overall accuracy (74% for the RF, 77% for the CF and 81% for the BMLR and the BMLR slightly outperformed the other two methods. However, these three methods suffered from low individual classification accuracy for the blue oak which is prone to being misclassified as the interior live oak due

  17. A multi-solver quasi-Newton method for the partitioned simulation of fluid-structure interaction

    International Nuclear Information System (INIS)

    Degroote, J; Annerel, S; Vierendeels, J

    2010-01-01

    In partitioned fluid-structure interaction simulations, the flow equations and the structural equations are solved separately. Consequently, the stresses and displacements on both sides of the fluid-structure interface are not automatically in equilibrium. Coupling techniques like Aitken relaxation and the Interface Block Quasi-Newton method with approximate Jacobians from Least-Squares models (IBQN-LS) enforce this equilibrium, even with black-box solvers. However, all existing coupling techniques use only one flow solver and one structural solver. To benefit from the large number of multi-core processors in modern clusters, a new Multi-Solver Interface Block Quasi-Newton (MS-IBQN-LS) algorithm has been developed. This algorithm uses more than one flow solver and structural solver, each running in parallel on a number of cores. One-dimensional and three-dimensional numerical experiments demonstrate that the run time of a simulation decreases as the number of solvers increases, albeit at a slower pace. Hence, the presented multi-solver algorithm accelerates fluid-structure interaction calculations by increasing the number of solvers, especially when the run time does not decrease further if more cores are used per solver.

  18. Diagnostic analysis of turbulent boundary layer data by a trivariate Lagrangian partitioning method

    Energy Technology Data Exchange (ETDEWEB)

    Welsh, P.T. [Florida State Univ., Tallahassee, FL (United States)

    1994-12-31

    The rapid scientific and technological advances in meteorological theory and modeling predominantly have occurred on the large (or synoptic) scale flow characterized by the extratropical cyclone. Turbulent boundary layer flows, in contrast, have been slower in developing both theoretically and in accuracy for several reasons. There are many existing problems in boundary layer models, among them are limits to computational power available, the inability to handle countergradient fluxes, poor growth matching to real boundary layers, and inaccuracy in calculating the diffusion of scalar concentrations. Such transport errors exist within the boundary layer as well as into the free atmosphere above. This research uses a new method, which can provide insight into these problems, and ultimately improve boundary layer models. There are several potential applications of the insights provided by this approach, among them are estimation of cloud contamination of satellite remotely sensed surface parameters, improved flux and vertical transport calculations, and better understanding of the diurnal boundary layer growth process and its hysteresis cycle.

  19. Methods for identifying SNP interactions: a review on variations of Logic Regression, Random Forest and Bayesian logistic regression.

    Science.gov (United States)

    Chen, Carla Chia-Ming; Schwender, Holger; Keith, Jonathan; Nunkesser, Robin; Mengersen, Kerrie; Macrossan, Paula

    2011-01-01

    Due to advancements in computational ability, enhanced technology and a reduction in the price of genotyping, more data are being generated for understanding genetic associations with diseases and disorders. However, with the availability of large data sets comes the inherent challenges of new methods of statistical analysis and modeling. Considering a complex phenotype may be the effect of a combination of multiple loci, various statistical methods have been developed for identifying genetic epistasis effects. Among these methods, logic regression (LR) is an intriguing approach incorporating tree-like structures. Various methods have built on the original LR to improve different aspects of the model. In this study, we review four variations of LR, namely Logic Feature Selection, Monte Carlo Logic Regression, Genetic Programming for Association Studies, and Modified Logic Regression-Gene Expression Programming, and investigate the performance of each method using simulated and real genotype data. We contrast these with another tree-like approach, namely Random Forests, and a Bayesian logistic regression with stochastic search variable selection.

  20. Bayesian Inference on Gravitational Waves

    Directory of Open Access Journals (Sweden)

    Asad Ali

    2015-12-01

    Full Text Available The Bayesian approach is increasingly becoming popular among the astrophysics data analysis communities. However, the Pakistan statistics communities are unaware of this fertile interaction between the two disciplines. Bayesian methods have been in use to address astronomical problems since the very birth of the Bayes probability in eighteenth century. Today the Bayesian methods for the detection and parameter estimation of gravitational waves have solid theoretical grounds with a strong promise for the realistic applications. This article aims to introduce the Pakistan statistics communities to the applications of Bayesian Monte Carlo methods in the analysis of gravitational wave data with an  overview of the Bayesian signal detection and estimation methods and demonstration by a couple of simplified examples.

  1. Search for transient ultralight dark matter signatures with networks of precision measurement devices using a Bayesian statistics method

    Science.gov (United States)

    Roberts, B. M.; Blewitt, G.; Dailey, C.; Derevianko, A.

    2018-04-01

    We analyze the prospects of employing a distributed global network of precision measurement devices as a dark matter and exotic physics observatory. In particular, we consider the atomic clocks of the global positioning system (GPS), consisting of a constellation of 32 medium-Earth orbit satellites equipped with either Cs or Rb microwave clocks and a number of Earth-based receiver stations, some of which employ highly-stable H-maser atomic clocks. High-accuracy timing data is available for almost two decades. By analyzing the satellite and terrestrial atomic clock data, it is possible to search for transient signatures of exotic physics, such as "clumpy" dark matter and dark energy, effectively transforming the GPS constellation into a 50 000 km aperture sensor array. Here we characterize the noise of the GPS satellite atomic clocks, describe the search method based on Bayesian statistics, and test the method using simulated clock data. We present the projected discovery reach using our method, and demonstrate that it can surpass the existing constrains by several order of magnitude for certain models. Our method is not limited in scope to GPS or atomic clock networks, and can also be applied to other networks of precision measurement devices.

  2. Bayesian grid matching

    DEFF Research Database (Denmark)

    Hartelius, Karsten; Carstensen, Jens Michael

    2003-01-01

    A method for locating distorted grid structures in images is presented. The method is based on the theories of template matching and Bayesian image restoration. The grid is modeled as a deformable template. Prior knowledge of the grid is described through a Markov random field (MRF) model which r...

  3. Supplementary Material for: DRABAL: novel method to mine large high-throughput screening assays using Bayesian active learning

    KAUST Repository

    Soufan, Othman

    2016-01-01

    Abstract Background Mining high-throughput screening (HTS) assays is key for enhancing decisions in the area of drug repositioning and drug discovery. However, many challenges are encountered in the process of developing suitable and accurate methods for extracting useful information from these assays. Virtual screening and a wide variety of databases, methods and solutions proposed to-date, did not completely overcome these challenges. This study is based on a multi-label classification (MLC) technique for modeling correlations between several HTS assays, meaning that a single prediction represents a subset of assigned correlated labels instead of one label. Thus, the devised method provides an increased probability for more accurate predictions of compounds that were not tested in particular assays. Results Here we present DRABAL, a novel MLC solution that incorporates structure learning of a Bayesian network as a step to model dependency between the HTS assays. In this study, DRABAL was used to process more than 1.4 million interactions of over 400,000 compounds and analyze the existing relationships between five large HTS assays from the PubChem BioAssay Database. Compared to different MLC methods, DRABAL significantly improves the F1Score by about 22%, on average. We further illustrated usefulness and utility of DRABAL through screening FDA approved drugs and reported ones that have a high probability to interact with several targets, thus enabling drug-multi-target repositioning. Specifically DRABAL suggests the Thiabendazole drug as a common activator of the NCP1 and Rab-9A proteins, both of which are designed to identify treatment modalities for the Niemannâ Pick type C disease. Conclusion We developed a novel MLC solution based on a Bayesian active learning framework to overcome the challenge of lacking fully labeled training data and exploit actual dependencies between the HTS assays. The solution is motivated by the need to model dependencies between

  4. Evidence Estimation for Bayesian Partially Observed MRFs

    NARCIS (Netherlands)

    Chen, Y.; Welling, M.

    2013-01-01

    Bayesian estimation in Markov random fields is very hard due to the intractability of the partition function. The introduction of hidden units makes the situation even worse due to the presence of potentially very many modes in the posterior distribution. For the first time we propose a

  5. Development of partitioning method

    International Nuclear Information System (INIS)

    Kondo, Yasuo; Kubota, Masumitsu; Abe, Tadashi; Nagato, Kotaro.

    1991-09-01

    Spent fuels from nuclear power stations contain many useful elements, which can be utilized as heat and irradiation sources, radioisotope, elemental resource, etc. Their recovery from spent fuel and effective uses have the advantages in not only converting the radioactive waste to beneficial resources but also promoting rationalization of the management and disposal of the radioactive wastes. In present study, published literature related to recovery and utilization of useful elements in spent fuel was mainly surveyed, present states and trends in their research and development were analyzed, and their future prospects were conjectured. Research and development on recovery and utilization of useful elements are being continued mainly in USA, Europe and Japan. A transportable food irradiator with Cs-137 and an electric power source with Sr-90 for remote weather station are typical examples in major past applications. However, research and development on recovery and utilization are not so much active and the future efforts should be expected hereafter. Present study was conducted under the auspices of the Science and Technology Agency of Japan. (author)

  6. Development of partitioning method

    International Nuclear Information System (INIS)

    Morita, Yasuji; Kubota, Masumitsu

    1989-10-01

    Behavior of Fe in the extraction process with diisodecyl phosphoric acid (DIDPA) was studied from various aspects of the extraction rates, the third phase formation, the continuous extraction using a mixer-settler and also the back extraction. Dependence of the extraction rates of Fe on nitric acid concentration, extractant concentration and temperature was examined by batchwise procedure. The extraction rate of Fe was a little greater than that of Np, of which behavior is determined by extraction rate like Fe. Therefore, under the condition where Np is quantitatively extracted, Fe is also extracted together with Np. The third phase formation by Fe could be suppressed by limiting Fe concentrations or raising temperatures. The behavior of Fe in the continuous extraction using a mixer-settler could be explained by the results of batchwise experiment on the extraction rates. Iron extracted with DIDPA could be back-extracted with oxalic acid. The rate of this back-extraction was slightly slow, but the distribution ratio soon becomes small enough for back-extraction even at room temperature. (author)

  7. Estimation of Mental Disorders Prevalence in High School Students Using Small Area Methods: A Hierarchical Bayesian Approach

    Directory of Open Access Journals (Sweden)

    Ali Reza Soltanian

    2016-08-01

    Full Text Available Background Adolescence is one of the most important periods in the course of human evolution and the prevalence of mental disorders among adolescence in different regions of Iran, especially in southern Iran. Objectives This study was conducted to determine the prevalence of mental disorders among high school students in Bushehr province, south of Iran. Methods In this cross-sectional study, 286 high school students were recruited by a multi-stage random sampling in Bushehr province in 2015. A general health questionnaire (GHQ-28 was used to assess mental disorders. The small area method, under the hierarchical Bayesian approach, was used to determine the prevalence of mental disorders and data analysis. Results From 286 questionnaires only 182 were completely filed and evaluated (the response rate was 70.5%. Of the students, 58.79% and 41.21% were male and female, respectively. Of all students, the prevalence of mental disorders in Bushehr, Dayyer, Deylam, Kangan, Dashtestan, Tangestan, Genaveh, and Dashty were 0.48, 0.42, 0.45, 0.52, 0.41, 0.47, 0.42, and 0.43, respectively. Conclusions Based on this study, the prevalence of mental disorders among adolescents was increasing in Bushehr Province counties. The lack of a national policy in this way is a serious obstacle to mental health and wellbeing access.

  8. An evolutionary game theoretical model shows the limitations of the additive partitioning method for interpreting biodiversity experiments

    NARCIS (Netherlands)

    Vermeulen, Peter J.; Ruijven, van Jasper; Anten, Niels P.R.; Werf, van der Wopke; Satake, Akiko

    2017-01-01

    1.The relationship between diversity and ecosystem functioning is often analysed by partitioning the change in species performance in mixtures into a complementarity effect (CE) and a selection effect (SE). There is continuing ambiguity in the literature on the interpretation of these effects,

  9. Creep-fatigue life prediction for different heats of Type 304 stainless steel by linear-damage rule, strain-range partitioning method, and damage-rate approach

    International Nuclear Information System (INIS)

    Maiya, P.S.

    1978-07-01

    The creep-fatigue life results for five different heats of Type 304 stainless steel at 593 0 C (1100 0 F), generated under push-pull conditions in the axial strain-control mode, are presented. The life predictions for the various heats based on the linear-damage rule, strain-range partitioning method, and damage-rate approach are discussed. The appropriate material properties required for computation of fatigue life are also included

  10. N3 Bias Field Correction Explained as a Bayesian Modeling Method

    DEFF Research Database (Denmark)

    Larsen, Christian Thode; Iglesias, Juan Eugenio; Van Leemput, Koen

    2014-01-01

    Although N3 is perhaps the most widely used method for MRI bias field correction, its underlying mechanism is in fact not well understood. Specifically, the method relies on a relatively heuristic recipe of alternating iterative steps that does not optimize any particular objective function. In t...

  11. Bayesian Exponential Smoothing.

    OpenAIRE

    Forbes, C.S.; Snyder, R.D.; Shami, R.S.

    2000-01-01

    In this paper, a Bayesian version of the exponential smoothing method of forecasting is proposed. The approach is based on a state space model containing only a single source of error for each time interval. This model allows us to improve current practices surrounding exponential smoothing by providing both point predictions and measures of the uncertainty surrounding them.

  12. Novel medium-throughput technique for investigating drug-cyclodextrin complexation by pH-metric titration using the partition coefficient method.

    Science.gov (United States)

    Dargó, Gergő; Boros, Krisztina; Péter, László; Malanga, Milo; Sohajda, Tamás; Szente, Lajos; Balogh, György T

    2018-05-05

    The present study was aimed to develop a medium-throughput screening technique for investigation of cyclodextrin (CD)-active pharmaceutical ingredient (API) complexes. Dual-phase potentiometric lipophilicity measurement, as gold standard technique, was combined with the partition coefficient method (plotting the reciprocal of partition coefficients of APIs as a function of CD concentration). A general equation was derived for determination of stability constants of 1:1 CD-API complexes (K 1:1,CD ) based on solely the changes of partition coefficients (logP o/w N -logP app N ), without measurement of the actual API concentrations. Experimentally determined logP value (-1.64) of 6-deoxy-6[(5/6)-fluoresceinylthioureido]-HPBCD (FITC-NH-HPBCD) was used to estimate the logP value (≈ -2.5 to -3) of (2-hydroxypropyl)-ß-cyclodextrin (HPBCD). The results suggested that the amount of HPBCD can be considered to be inconsequential in the octanol phase. The decrease of octanol volume due to the octanol-CD complexation was considered, thus a corrected octanol-water phase ratio was also introduced. The K 1:1,CD values obtained by this developed method showed a good accordance with the results from other orthogonal methods. Copyright © 2018 Elsevier B.V. All rights reserved.

  13. A Bayesian nonrigid registration method to enhance intraoperative target definition in image-guided prostate procedures through uncertainty characterization

    International Nuclear Information System (INIS)

    Pursley, Jennifer; Risholm, Petter; Fedorov, Andriy; Tuncali, Kemal; Fennessy, Fiona M.; Wells, William M. III; Tempany, Clare M.; Cormack, Robert A.

    2012-01-01

    Purpose: This study introduces a probabilistic nonrigid registration method for use in image-guided prostate brachytherapy. Intraoperative imaging for prostate procedures, usually transrectal ultrasound (TRUS), is typically inferior to diagnostic-quality imaging of the pelvis such as endorectal magnetic resonance imaging (MRI). MR images contain superior detail of the prostate boundaries and provide substructure features not otherwise visible. Previous efforts to register diagnostic prostate images with the intraoperative coordinate system have been deterministic and did not offer a measure of the registration uncertainty. The authors developed a Bayesian registration method to estimate the posterior distribution on deformations and provide a case-specific measure of the associated registration uncertainty. Methods: The authors adapted a biomechanical-based probabilistic nonrigid method to register diagnostic to intraoperative images by aligning a physician's segmentations of the prostate in the two images. The posterior distribution was characterized with a Markov Chain Monte Carlo method; the maximum a posteriori deformation and the associated uncertainty were estimated from the collection of deformation samples drawn from the posterior distribution. The authors validated the registration method using a dataset created from ten patients with MRI-guided prostate biopsies who had both diagnostic and intraprocedural 3 Tesla MRI scans. The accuracy and precision of the estimated posterior distribution on deformations were evaluated from two predictive distance distributions: between the deformed central zone-peripheral zone (CZ-PZ) interface and the physician-labeled interface, and based on physician-defined landmarks. Geometric margins on the registration of the prostate's peripheral zone were determined from the posterior predictive distance to the CZ-PZ interface separately for the base, mid-gland, and apical regions of the prostate. Results: The authors observed

  14. A Laplace method for under-determined Bayesian optimal experimental designs

    KAUST Repository

    Long, Quan; Scavino, Marco; Tempone, Raul; Wang, Suojin

    2014-01-01

    In Long et al. (2013), a new method based on the Laplace approximation was developed to accelerate the estimation of the post-experimental expected information gains (Kullback–Leibler divergence) in model parameters and predictive quantities

  15. DRABAL: novel method to mine large high-throughput screening assays using Bayesian active learning

    KAUST Repository

    Soufan, Othman; Ba Alawi, Wail; Afeef, Moataz A.; Essack, Magbubah; Kalnis, Panos; Bajic, Vladimir B.

    2016-01-01

    Mining high-throughput screening (HTS) assays is key for enhancing decisions in the area of drug repositioning and drug discovery. However, many challenges are encountered in the process of developing suitable and accurate methods

  16. Spatiotemporal analysis and mapping of oral cancer risk in changhua county (taiwan): an application of generalized bayesian maximum entropy method.

    Science.gov (United States)

    Yu, Hwa-Lung; Chiang, Chi-Ting; Lin, Shu-De; Chang, Tsun-Kuo

    2010-02-01

    Incidence rate of oral cancer in Changhua County is the highest among the 23 counties of Taiwan during 2001. However, in health data analysis, crude or adjusted incidence rates of a rare event (e.g., cancer) for small populations often exhibit high variances and are, thus, less reliable. We proposed a generalized Bayesian Maximum Entropy (GBME) analysis of spatiotemporal disease mapping under conditions of considerable data uncertainty. GBME was used to study the oral cancer population incidence in Changhua County (Taiwan). Methodologically, GBME is based on an epistematics principles framework and generates spatiotemporal estimates of oral cancer incidence rates. In a way, it accounts for the multi-sourced uncertainty of rates, including small population effects, and the composite space-time dependence of rare events in terms of an extended Poisson-based semivariogram. The results showed that GBME analysis alleviates the noises of oral cancer data from population size effect. Comparing to the raw incidence data, the maps of GBME-estimated results can identify high risk oral cancer regions in Changhua County, where the prevalence of betel quid chewing and cigarette smoking is relatively higher than the rest of the areas. GBME method is a valuable tool for spatiotemporal disease mapping under conditions of uncertainty. 2010 Elsevier Inc. All rights reserved.

  17. About approximation of integer factorization problem by the combination fixed-point iteration method and Bayesian rounding for quantum cryptography

    Science.gov (United States)

    Ogorodnikov, Yuri; Khachay, Michael; Pljonkin, Anton

    2018-04-01

    We describe the possibility of employing the special case of the 3-SAT problem stemming from the well known integer factorization problem for the quantum cryptography. It is known, that for every instance of our 3-SAT setting the given 3-CNF is satisfiable by a unique truth assignment, and the goal is to find this assignment. Since the complexity status of the factorization problem is still undefined, development of approximation algorithms and heuristics adopts interest of numerous researchers. One of promising approaches to construction of approximation techniques is based on real-valued relaxation of the given 3-CNF followed by minimizing of the appropriate differentiable loss function, and subsequent rounding of the fractional minimizer obtained. Actually, algorithms developed this way differ by the rounding scheme applied on their final stage. We propose a new rounding scheme based on Bayesian learning. The article shows that the proposed method can be used to determine the security in quantum key distribution systems. In the quantum distribution the Shannon rules is applied and the factorization problem is paramount when decrypting secret keys.

  18. Application of a Bayesian/generalised least-squares method to generate correlations between independent neutron fission yield data

    International Nuclear Information System (INIS)

    Fiorito, L.; Diez, C.; Cabellos, O.; Stankovskiy, A.; Van den Eynde, G.; Labeau, P.E.

    2014-01-01

    Fission product yields are fundamental parameters for several nuclear engineering calculations and in particular for burn-up/activation problems. The impact of their uncertainties was widely studied in the past and evaluations were released, although still incomplete. Recently, the nuclear community expressed the need for full fission yield covariance matrices to produce inventory calculation results that take into account the complete uncertainty data. In this work, we studied and applied a Bayesian/generalised least-squares method for covariance generation, and compared the generated uncertainties to the original data stored in the JEFF-3.1.2 library. Then, we focused on the effect of fission yield covariance information on fission pulse decay heat results for thermal fission of 235 U. Calculations were carried out using different codes (ACAB and ALEPH-2) after introducing the new covariance values. Results were compared with those obtained with the uncertainty data currently provided by the library. The uncertainty quantification was performed with the Monte Carlo sampling technique. Indeed, correlations between fission yields strongly affect the statistics of decay heat. (authors)

  19. Bayesian inference with ecological applications

    CERN Document Server

    Link, William A

    2009-01-01

    This text is written to provide a mathematically sound but accessible and engaging introduction to Bayesian inference specifically for environmental scientists, ecologists and wildlife biologists. It emphasizes the power and usefulness of Bayesian methods in an ecological context. The advent of fast personal computers and easily available software has simplified the use of Bayesian and hierarchical models . One obstacle remains for ecologists and wildlife biologists, namely the near absence of Bayesian texts written specifically for them. The book includes many relevant examples, is supported by software and examples on a companion website and will become an essential grounding in this approach for students and research ecologists. Engagingly written text specifically designed to demystify a complex subject Examples drawn from ecology and wildlife research An essential grounding for graduate and research ecologists in the increasingly prevalent Bayesian approach to inference Companion website with analyt...

  20. Estimation of Land Surface Temperature through Blending MODIS and AMSR-E Data with the Bayesian Maximum Entropy Method

    Directory of Open Access Journals (Sweden)

    Xiaokang Kou

    2016-01-01

    Full Text Available Land surface temperature (LST plays a major role in the study of surface energy balances. Remote sensing techniques provide ways to monitor LST at large scales. However, due to atmospheric influences, significant missing data exist in LST products retrieved from satellite thermal infrared (TIR remotely sensed data. Although passive microwaves (PMWs are able to overcome these atmospheric influences while estimating LST, the data are constrained by low spatial resolution. In this study, to obtain complete and high-quality LST data, the Bayesian Maximum Entropy (BME method was introduced to merge 0.01° and 0.25° LSTs inversed from MODIS and AMSR-E data, respectively. The result showed that the missing LSTs in cloudy pixels were filled completely, and the availability of merged LSTs reaches 100%. Because the depths of LST and soil temperature measurements are different, before validating the merged LST, the station measurements were calibrated with an empirical equation between MODIS LST and 0~5 cm soil temperatures. The results showed that the accuracy of merged LSTs increased with the increasing quantity of utilized data, and as the availability of utilized data increased from 25.2% to 91.4%, the RMSEs of the merged data decreased from 4.53 °C to 2.31 °C. In addition, compared with the filling gap method in which MODIS LST gaps were filled with AMSR-E LST directly, the merged LSTs from the BME method showed better spatial continuity. The different penetration depths of TIR and PMWs may influence fusion performance and still require further studies.

  1. Bayesian methods for meta-analysis of causal relationships estimated using genetic instrumental variables

    DEFF Research Database (Denmark)

    Burgess, Stephen; Thompson, Simon G; Thompson, Grahame

    2010-01-01

    Genetic markers can be used as instrumental variables, in an analogous way to randomization in a clinical trial, to estimate the causal relationship between a phenotype and an outcome variable. Our purpose is to extend the existing methods for such Mendelian randomization studies to the context o...

  2. Correction the Bias of Odds Ratio resulting from the Misclassification of Exposures in the Study of Environmental Risk Factors of Lung Cancer using Bayesian Methods

    Directory of Open Access Journals (Sweden)

    Alireza Abadi

    2015-07-01

    Full Text Available Background & Objective: Inability to measure exact exposure in epidemiological studies is a common problem in many studies, especially cross-sectional studies. Depending on the extent of misclassification, results may be affected. Existing methods for solving this problem require a lot of time and money and it is not practical for some of the exposures. Recently, new methods have been proposed in 1:1 matched case–control studies that have solved these problems to some extent. In the present study we have aimed to extend the existing Bayesian method to adjust for misclassification in matched case–control Studies with 1:2 matching. Methods: Here, the standard Dirichlet prior distribution for a multinomial model was extended to allow the data of exposure–disease (OR parameter to be imported into the model excluding other parameters. Information that exist in literature about association between exposure and disease were used as prior information about OR. In order to correct the misclassification Sensitivity Analysis was accomplished and the results were obtained under three Bayesian Methods. Results: The results of naïve Bayesian model were similar to the classic model. The second Bayesian model by employing prior information about the OR, was heavily affected by these information. The third proposed model provides maximum bias adjustment for the risk of heavy metals, smoking and drug abuse. This model showed that heavy metals are not an important risk factor although raw model (logistic regression Classic detected this exposure as an influencing factor on the incidence of lung cancer. Sensitivity analysis showed that third model is robust regarding to different levels of Sensitivity and Specificity. Conclusion: The present study showed that although in most of exposures the results of the second and third model were similar but the proposed model would be able to correct the misclassification to some extent.

  3. Data Analytics of Mobile Serious Games: Applying Bayesian Data Analysis Methods

    Directory of Open Access Journals (Sweden)

    Heide Lukosch

    2018-03-01

    Full Text Available Traditional teaching methods in the field of resuscitation training show some limitations, while teaching the right actions in critical situations could increase the number of people saved after a cardiac arrest. For our study, we developed a mobile game to support the transfer of theoretical knowledge on resuscitation.  The game has been tested at three schools of further education. A number of data has been collected from 171 players. To analyze this large data set from different sources and quality, different types of data modeling and analyses had to be applied. This approach showed its usefulness in analyzing the large set of data from different sources. It revealed some interesting findings, such as that female players outperformed the male ones, and that the game fostering informal, self-directed is equally efficient as the traditional formal learning method.

  4. FPGA Acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods

    Directory of Open Access Journals (Sweden)

    Bakos Jason D

    2010-04-01

    Full Text Available Abstract Background Likelihood (ML-based phylogenetic inference has become a popular method for estimating the evolutionary relationships among species based on genomic sequence data. This method is used in applications such as RAxML, GARLI, MrBayes, PAML, and PAUP. The Phylogenetic Likelihood Function (PLF is an important kernel computation for this method. The PLF consists of a loop with no conditional behavior or dependencies between iterations. As such it contains a high potential for exploiting parallelism using micro-architectural techniques. In this paper, we describe a technique for mapping the PLF and supporting logic onto a Field Programmable Gate Array (FPGA-based co-processor. By leveraging the FPGA's on-chip DSP modules and the high-bandwidth local memory attached to the FPGA, the resultant co-processor can accelerate ML-based methods and outperform state-of-the-art multi-core processors. Results We use the MrBayes 3 tool as a framework for designing our co-processor. For large datasets, we estimate that our accelerated MrBayes, if run on a current-generation FPGA, achieves a 10× speedup relative to software running on a state-of-the-art server-class microprocessor. The FPGA-based implementation achieves its performance by deeply pipelining the likelihood computations, performing multiple floating-point operations in parallel, and through a natural log approximation that is chosen specifically to leverage a deeply pipelined custom architecture. Conclusions Heterogeneous computing, which combines general-purpose processors with special-purpose co-processors such as FPGAs and GPUs, is a promising approach for high-performance phylogeny inference as shown by the growing body of literature in this field. FPGAs in particular are well-suited for this task because of their low power consumption as compared to many-core processors and Graphics Processor Units (GPUs 1.

  5. A Hamiltonian Monte–Carlo method for Bayesian inference of supermassive black hole binaries

    International Nuclear Information System (INIS)

    Porter, Edward K; Carré, Jérôme

    2014-01-01

    We investigate the use of a Hamiltonian Monte–Carlo to map out the posterior density function for supermassive black hole binaries. While previous Markov Chain Monte–Carlo (MCMC) methods, such as Metropolis–Hastings MCMC, have been successfully employed for a number of different gravitational wave sources, these methods are essentially random walk algorithms. The Hamiltonian Monte–Carlo treats the inverse likelihood surface as a ‘gravitational potential’ and by introducing canonical positions and momenta, dynamically evolves the Markov chain by solving Hamilton's equations of motion. This method is not as widely used as other MCMC algorithms due to the necessity of calculating gradients of the log-likelihood, which for most applications results in a bottleneck that makes the algorithm computationally prohibitive. We circumvent this problem by using accepted initial phase-space trajectory points to analytically fit for each of the individual gradients. Eliminating the waveform generation needed for the numerical derivatives reduces the total number of required templates for a 10 6 iteration chain from ∼10 9 to ∼10 6 . The result is in an implementation of the Hamiltonian Monte–Carlo that is faster, and more efficient by a factor of approximately the dimension of the parameter space, than a Hessian MCMC. (paper)

  6. Present status of partitioning developments

    International Nuclear Information System (INIS)

    Nakamura, Haruto; Kubota, Masumitsu; Tachimori, Shoichi

    1978-09-01

    Evolution and development of the concept of partitioning of high-level liquid wastes (HLLW) in nuclear fuel reprocessing are reviewed historically from the early phase of separating useful radioisotopes from HLLW to the recent phase of eliminating hazardous nuclides such as transuranium elements for safe waste disposal. Since the criteria in determining the nuclides for elimination and the respective decontamination factors are important in the strategy of partitioning, current views on the criteria are summarized. As elimination of the transuranium is most significant in the partitioning, various methods available of separating them from fission products are evaluated. (auth.)

  7. Bayesian methods for jointly estimating genomic breeding values of one continuous and one threshold trait.

    Directory of Open Access Journals (Sweden)

    Chonglong Wang

    Full Text Available Genomic selection has become a useful tool for animal and plant breeding. Currently, genomic evaluation is usually carried out using a single-trait model. However, a multi-trait model has the advantage of using information on the correlated traits, leading to more accurate genomic prediction. To date, joint genomic prediction for a continuous and a threshold trait using a multi-trait model is scarce and needs more attention. Based on the previously proposed methods BayesCπ for single continuous trait and BayesTCπ for single threshold trait, we developed a novel method based on a linear-threshold model, i.e., LT-BayesCπ, for joint genomic prediction of a continuous trait and a threshold trait. Computing procedures of LT-BayesCπ using Markov Chain Monte Carlo algorithm were derived. A simulation study was performed to investigate the advantages of LT-BayesCπ over BayesCπ and BayesTCπ with regard to the accuracy of genomic prediction on both traits. Factors affecting the performance of LT-BayesCπ were addressed. The results showed that, in all scenarios, the accuracy of genomic prediction obtained from LT-BayesCπ was significantly increased for the threshold trait compared to that from single trait prediction using BayesTCπ, while the accuracy for the continuous trait was comparable with that from single trait prediction using BayesCπ. The proposed LT-BayesCπ could be a method of choice for joint genomic prediction of one continuous and one threshold trait.

  8. A method for risk-informed safety significance categorization using the analytic hierarchy process and bayesian belief networks

    International Nuclear Information System (INIS)

    Ha, Jun Su; Seong, Poong Hyun

    2004-01-01

    A risk-informed safety significance categorization (RISSC) is to categorize structures, systems, or components (SSCs) of a nuclear power plant (NPP) into two or more groups, according to their safety significance using both probabilistic and deterministic insights. In the conventional methods for the RISSC, the SSCs are quantitatively categorized according to their importance measures for the initial categorization. The final decisions (categorizations) of SSCs, however, are qualitatively made by an expert panel through discussions and adjustments of opinions by using the probabilistic insights compiled in the initial categorization process and combining the probabilistic insights with the deterministic insights. Therefore, owing to the qualitative and linear decision-making process, the conventional methods have the demerits as follows: (1) they are very costly in terms of time and labor, (2) it is not easy to reach the final decision, when the opinions of the experts are in conflict and (3) they have an overlapping process due to the linear paradigm (the categorization is performed twice - first, by the engineers who propose the method, and second, by the expert panel). In this work, a method for RISSC using the analytic hierarchy process (AHP) and bayesian belief networks (BBN) is proposed to overcome the demerits of the conventional methods and to effectively arrive at a final decision (or categorization). By using the AHP and BBN, the expert panel takes part in the early stage of the categorization (that is, the quantification process) and the safety significance based on both probabilistic and deterministic insights is quantified. According to that safety significance, SSCs are quantitatively categorized into three categories such as high safety significant category (Hi), potentially safety significant category (Po), or low safety significant category (Lo). The proposed method was applied to the components such as CC-V073, CV-V530, and SI-V644 in Ulchin Unit

  9. Learning to Recommend Point-of-Interest with the Weighted Bayesian Personalized Ranking Method in LBSNs

    OpenAIRE

    Lei Guo; Haoran Jiang; Xinhua Wang; Fangai Liu

    2017-01-01

    Point-of-interest (POI) recommendation has been well studied in recent years. However, most of the existing methods focus on the recommendation scenarios where users can provide explicit feedback. In most cases, however, the feedback is not explicit, but implicit. For example, we can only get a user’s check-in behaviors from the history of what POIs she/he has visited, but never know how much she/he likes and why she/he does not like them. Recently, some researchers have noticed this problem ...

  10. A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases

    Directory of Open Access Journals (Sweden)

    Karp Peter D

    2004-06-01

    Full Text Available Abstract Background The PathoLogic program constructs Pathway/Genome databases by using a genome's annotation to predict the set of metabolic pathways present in an organism. PathoLogic determines the set of reactions composing those pathways from the enzymes annotated in the organism's genome. Most annotation efforts fail to assign function to 40–60% of sequences. In addition, large numbers of sequences may have non-specific annotations (e.g., thiolase family protein. Pathway holes occur when a genome appears to lack the enzymes needed to catalyze reactions in a pathway. If a protein has not been assigned a specific function during the annotation process, any reaction catalyzed by that protein will appear as a missing enzyme or pathway hole in a Pathway/Genome database. Results We have developed a method that efficiently combines homology and pathway-based evidence to identify candidates for filling pathway holes in Pathway/Genome databases. Our program not only identifies potential candidate sequences for pathway holes, but combines data from multiple, heterogeneous sources to assess the likelihood that a candidate has the required function. Our algorithm emulates the manual sequence annotation process, considering not only evidence from homology searches, but also considering evidence from genomic context (i.e., is the gene part of an operon? and functional context (e.g., are there functionally-related genes nearby in the genome? to determine the posterior belief that a candidate has the required function. The method can be applied across an entire metabolic pathway network and is generally applicable to any pathway database. The program uses a set of sequences encoding the required activity in other genomes to identify candidate proteins in the genome of interest, and then evaluates each candidate by using a simple Bayes classifier to determine the probability that the candidate has the desired function. We achieved 71% precision at a

  11. Topics in Bayesian statistics and maximum entropy

    International Nuclear Information System (INIS)

    Mutihac, R.; Cicuttin, A.; Cerdeira, A.; Stanciulescu, C.

    1998-12-01

    Notions of Bayesian decision theory and maximum entropy methods are reviewed with particular emphasis on probabilistic inference and Bayesian modeling. The axiomatic approach is considered as the best justification of Bayesian analysis and maximum entropy principle applied in natural sciences. Particular emphasis is put on solving the inverse problem in digital image restoration and Bayesian modeling of neural networks. Further topics addressed briefly include language modeling, neutron scattering, multiuser detection and channel equalization in digital communications, genetic information, and Bayesian court decision-making. (author)

  12. Application of Bayesian Method in Validation of TTM Decisional Balance and Self-Efficacy Constructs to Improve Nutritional Behavior in Yazdian Prediabetes

    Directory of Open Access Journals (Sweden)

    Hossein Fallahzadeh

    2017-07-01

    Full Text Available Introduction: To introduce Bayesian method in validation of transtheoretical model’s Self-Efficacy and Decisional Balance for nutritional behavior improvement among Prediabetes with ordinal data. Methods: This is an Experimental trial with parallel design and sample was included 220 Prediabetes who Participated in screening program and had over 30 years old, fasting blood glucose ranged 100-125 and at least elementary Education. We used OpenBugs 3.2.3 to fit Bayesian ordinal factor analysis to achieve validation of TTM’s decisional balance and self-efficacy. Results: All of the factor loadings corresponded to mentioned constructs was significant at α= 0.05%. That support validation of the Constructs. Correlation between Pros and Cons was not significant(-0.076, 0.007.Furthermore a specific statistical model for ordinal data created that can estimate odds ratios and marginal Probabilities for each choice of any item in questionnaire. Conclusion: Thanks to benefits of Bayesian method in use of prior information such as Meta-analysis and other resources, In comparison to similar studies that used standard or other factor analysis for ordinal data, our results had good accuracy(with aspect to standard deviation even with lower sample size.so the results can be used  in future clinical researches.

  13. CONTROL BASED ON NUMERICAL METHODS AND RECURSIVE BAYESIAN ESTIMATION IN A CONTINUOUS ALCOHOLIC FERMENTATION PROCESS

    Directory of Open Access Journals (Sweden)

    Olga L. Quintero

    Full Text Available Biotechnological processes represent a challenge in the control field, due to their high nonlinearity. In particular, continuous alcoholic fermentation from Zymomonas mobilis (Z.m presents a significant challenge. This bioprocess has high ethanol performance, but it exhibits an oscillatory behavior in process variables due to the influence of inhibition dynamics (rate of ethanol concentration over biomass, substrate, and product concentrations. In this work a new solution for control of biotechnological variables in the fermentation process is proposed, based on numerical methods and linear algebra. In addition, an improvement to a previously reported state estimator, based on particle filtering techniques, is used in the control loop. The feasibility estimator and its performance are demonstrated in the proposed control loop. This methodology makes it possible to develop a controller design through the use of dynamic analysis with a tested biomass estimator in Z.m and without the use of complex calculations.

  14. A Bayesian method to rank different model forecasts of the same volcanic ash cloud: Chapter 24

    Science.gov (United States)

    Denlinger, Roger P.; Webley, P.; Mastin, Larry G.; Schwaiger, Hans F.

    2012-01-01

    Volcanic eruptions often spew fine ash high into the atmosphere, where it is carried downwind, forming long ash clouds that disrupt air traffic and pose a hazard to air travel. To mitigate such hazards, the community studying ash hazards must assess risk of ash ingestion for any flight path and provide robust and accurate forecasts of volcanic ash dispersal. We provide a quantitative and objective method to evaluate the efficacy of ash dispersal estimates from different models, using Bayes theorem to assess the predictions that each model makes about ash dispersal. We incorporate model and measurement uncertainty and produce a posterior probability for model input parameters. The integral of the posterior over all possible combinations of model inputs determines the evidence for each model and is used to compare models. We compare two different types of transport models, an Eulerian model (Ash3d) and a Langrangian model (PUFF), as applied to the 2010 eruptions of Eyjafjallajökull volcano in Iceland. The evidence for each model benefits from common physical characteristics of ash dispersal from an eruption column and provides a measure of how well each model forecasts cloud transport. Given the complexity of the wind fields, we find that the differences between these models depend upon the differences in the way the models disperse ash into the wind from the source plume. With continued observation, the accuracy of the estimates made by each model increases, increasing the efficacy of each model’s ability to simulate ash dispersal.

  15. Strength Reduction Method for Stability Analysis of Local Discontinuous Rock Mass with Iterative Method of Partitioned Finite Element and Interface Boundary Element

    Directory of Open Access Journals (Sweden)

    Tongchun Li

    2015-01-01

    element is proposed to solve the safety factor of local discontinuous rock mass. Slope system is divided into several continuous bodies and local discontinuous interface boundaries. Each block is treated as a partition of the system and contacted by discontinuous joints. The displacements of blocks are chosen as basic variables and the rigid displacements in the centroid of blocks are chosen as motion variables. The contact forces on interface boundaries and the rigid displacements to the centroid of each body are chosen as mixed variables and solved iteratively using the interface boundary equations. Flexibility matrix is formed through PFE according to the contact states of nodal pairs and spring flexibility is used to reflect the influence of weak structural plane so that nonlinear iteration is only limited to the possible contact region. With cohesion and friction coefficient reduced gradually, the states of all nodal pairs at the open or slip state for the first time are regarded as failure criterion, which can decrease the effect of subjectivity in determining safety factor. Examples are used to verify the validity of the proposed method.

  16. Unique Path Partitions

    DEFF Research Database (Denmark)

    Bessenrodt, Christine; Olsson, Jørn Børling; Sellers, James A.

    2013-01-01

    We give a complete classification of the unique path partitions and study congruence properties of the function which enumerates such partitions.......We give a complete classification of the unique path partitions and study congruence properties of the function which enumerates such partitions....

  17. High-throughput determination of octanol/water partition coefficients using a shake-flask method and novel two-phase solvent system.

    Science.gov (United States)

    Morikawa, Go; Suzuka, Chihiro; Shoji, Atsushi; Shibusawa, Yoichi; Yanagida, Akio

    2016-01-05

    A high-throughput method for determining the octanol/water partition coefficient (P(o/w)) of a large variety of compounds exhibiting a wide range in hydrophobicity was established. The method combines a simple shake-flask method with a novel two-phase solvent system comprising an acetonitrile-phosphate buffer (0.1 M, pH 7.4)-1-octanol (25:25:4, v/v/v; AN system). The AN system partition coefficients (K(AN)) of 51 standard compounds for which log P(o/w) (at pH 7.4; log D) values had been reported were determined by single two-phase partitioning in test tubes, followed by measurement of the solute concentration in both phases using an automatic flow injection-ultraviolet detection system. The log K(AN) values were closely related to reported log D values, and the relationship could be expressed by the following linear regression equation: log D=2.8630 log K(AN) -0.1497(n=51). The relationship reveals that log D values (+8 to -8) for a large variety of highly hydrophobic and/or hydrophilic compounds can be estimated indirectly from the narrow range of log K(AN) values (+3 to -3) determined using the present method. Furthermore, log K(AN) values for highly polar compounds for which no log D values have been reported, such as amino acids, peptides, proteins, nucleosides, and nucleotides, can be estimated using the present method. The wide-ranging log D values (+5.9 to -7.5) of these molecules were estimated for the first time from their log K(AN) values and the above regression equation. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Bayesian mixture modeling of significant p values: A meta-analytic method to estimate the degree of contamination from H₀.

    Science.gov (United States)

    Gronau, Quentin Frederik; Duizer, Monique; Bakker, Marjan; Wagenmakers, Eric-Jan

    2017-09-01

    Publication bias and questionable research practices have long been known to corrupt the published record. One method to assess the extent of this corruption is to examine the meta-analytic collection of significant p values, the so-called p -curve (Simonsohn, Nelson, & Simmons, 2014a). Inspired by statistical research on false-discovery rates, we propose a Bayesian mixture model analysis of the p -curve. Our mixture model assumes that significant p values arise either from the null-hypothesis H ₀ (when their distribution is uniform) or from the alternative hypothesis H1 (when their distribution is accounted for by a simple parametric model). The mixture model estimates the proportion of significant results that originate from H ₀, but it also estimates the probability that each specific p value originates from H ₀. We apply our model to 2 examples. The first concerns the set of 587 significant p values for all t tests published in the 2007 volumes of Psychonomic Bulletin & Review and the Journal of Experimental Psychology: Learning, Memory, and Cognition; the mixture model reveals that p values higher than about .005 are more likely to stem from H ₀ than from H ₁. The second example concerns 159 significant p values from studies on social priming and 130 from yoked control studies. The results from the yoked controls confirm the findings from the first example, whereas the results from the social priming studies are difficult to interpret because they are sensitive to the prior specification. To maximize accessibility, we provide a web application that allows researchers to apply the mixture model to any set of significant p values. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  19. Monitoring county-level chlamydia incidence in Texas, 2004 – 2005: application of empirical Bayesian smoothing and Exploratory Spatial Data Analysis (ESDA methods

    Directory of Open Access Journals (Sweden)

    Owens Chantelle J

    2009-02-01

    Full Text Available Abstract Background Chlamydia continues to be the most prevalent disease in the United States. Effective spatial monitoring of chlamydia incidence is important for successful implementation of control and prevention programs. The objective of this study is to apply Bayesian smoothing and exploratory spatial data analysis (ESDA methods to monitor Texas county-level chlamydia incidence rates by examining spatiotemporal patterns. We used county-level data on chlamydia incidence (for all ages, gender and races from the National Electronic Telecommunications System for Surveillance (NETSS for 2004 and 2005. Results Bayesian-smoothed chlamydia incidence rates were spatially dependent both in levels and in relative changes. Erath county had significantly (p 300 cases per 100,000 residents than its contiguous neighbors (195 or less in both years. Gaines county experienced the highest relative increase in smoothed rates (173% – 139 to 379. The relative change in smoothed chlamydia rates in Newton county was significantly (p Conclusion Bayesian smoothing and ESDA methods can assist programs in using chlamydia surveillance data to identify outliers, as well as relevant changes in chlamydia incidence in specific geographic units. Secondly, it may also indirectly help in assessing existing differences and changes in chlamydia surveillance systems over time.

  20. Supplementary Material for: DRABAL: novel method to mine large high-throughput screening assays using Bayesian active learning

    KAUST Repository

    Soufan, Othman; Ba Alawi, Wail; Afeef, Moataz A.; Essack, Magbubah; Kalnis, Panos; Bajic, Vladimir B.

    2016-01-01

    of compounds that were not tested in particular assays. Results Here we present DRABAL, a novel MLC solution that incorporates structure learning of a Bayesian network as a step to model dependency between the HTS assays. In this study, DRABAL was used

  1. Applied Bayesian hierarchical methods

    National Research Council Canada - National Science Library

    Congdon, P

    2010-01-01

    .... It also incorporates BayesX code, which is particularly useful in nonlinear regression. To demonstrate MCMC sampling from first principles, the author includes worked examples using the R package...

  2. Manual hierarchical clustering of regional geochemical data using a Bayesian finite mixture model

    International Nuclear Information System (INIS)

    Ellefsen, Karl J.; Smith, David B.

    2016-01-01

    Interpretation of regional scale, multivariate geochemical data is aided by a statistical technique called “clustering.” We investigate a particular clustering procedure by applying it to geochemical data collected in the State of Colorado, United States of America. The clustering procedure partitions the field samples for the entire survey area into two clusters. The field samples in each cluster are partitioned again to create two subclusters, and so on. This manual procedure generates a hierarchy of clusters, and the different levels of the hierarchy show geochemical and geological processes occurring at different spatial scales. Although there are many different clustering methods, we use Bayesian finite mixture modeling with two probability distributions, which yields two clusters. The model parameters are estimated with Hamiltonian Monte Carlo sampling of the posterior probability density function, which usually has multiple modes. Each mode has its own set of model parameters; each set is checked to ensure that it is consistent both with the data and with independent geologic knowledge. The set of model parameters that is most consistent with the independent geologic knowledge is selected for detailed interpretation and partitioning of the field samples. - Highlights: • We evaluate a clustering procedure by applying it to geochemical data. • The procedure generates a hierarchy of clusters. • Different levels of the hierarchy show geochemical processes at different spatial scales. • The clustering method is Bayesian finite mixture modeling. • Model parameters are estimated with Hamiltonian Monte Carlo sampling.

  3. Bayesian Networks and Influence Diagrams

    DEFF Research Database (Denmark)

    Kjærulff, Uffe Bro; Madsen, Anders Læsø

     Probabilistic networks, also known as Bayesian networks and influence diagrams, have become one of the most promising technologies in the area of applied artificial intelligence, offering intuitive, efficient, and reliable methods for diagnosis, prediction, decision making, classification......, troubleshooting, and data mining under uncertainty. Bayesian Networks and Influence Diagrams: A Guide to Construction and Analysis provides a comprehensive guide for practitioners who wish to understand, construct, and analyze intelligent systems for decision support based on probabilistic networks. Intended...

  4. Sparse reconstruction using distribution agnostic bayesian matching pursuit

    KAUST Repository

    Masood, Mudassir; Al-Naffouri, Tareq Y.

    2013-01-01

    A fast matching pursuit method using a Bayesian approach is introduced for sparse signal recovery. This method performs Bayesian estimates of sparse signals even when the signal prior is non-Gaussian or unknown. It is agnostic on signal statistics

  5. Subjective Bayesian Beliefs

    DEFF Research Database (Denmark)

    Antoniou, Constantinos; Harrison, Glenn W.; Lau, Morten I.

    2015-01-01

    A large literature suggests that many individuals do not apply Bayes’ Rule when making decisions that depend on them correctly pooling prior information and sample data. We replicate and extend a classic experimental study of Bayesian updating from psychology, employing the methods of experimenta...... economics, with careful controls for the confounding effects of risk aversion. Our results show that risk aversion significantly alters inferences on deviations from Bayes’ Rule....

  6. Introduction to Bayesian statistics

    CERN Document Server

    Koch, Karl-Rudolf

    2007-01-01

    This book presents Bayes' theorem, the estimation of unknown parameters, the determination of confidence regions and the derivation of tests of hypotheses for the unknown parameters. It does so in a simple manner that is easy to comprehend. The book compares traditional and Bayesian methods with the rules of probability presented in a logical way allowing an intuitive understanding of random variables and their probability distributions to be formed.

  7. Iterative Bayesian Model Averaging: a method for the application of survival analysis to high-dimensional microarray data

    Directory of Open Access Journals (Sweden)

    Raftery Adrian E

    2009-02-01

    Full Text Available Abstract Background Microarray technology is increasingly used to identify potential biomarkers for cancer prognostics and diagnostics. Previously, we have developed the iterative Bayesian Model Averaging (BMA algorithm for use in classification. Here, we extend the iterative BMA algorithm for application to survival analysis on high-dimensional microarray data. The main goal in applying survival analysis to microarray data is to determine a highly predictive model of patients' time to event (such as death, relapse, or metastasis using a small number of selected genes. Our multivariate procedure combines the effectiveness of multiple contending models by calculating the weighted average of their posterior probability distributions. Our results demonstrate that our iterative BMA algorithm for survival analysis achieves high prediction accuracy while consistently selecting a small and cost-effective number of predictor genes. Results We applied the iterative BMA algorithm to two cancer datasets: breast cancer and diffuse large B-cell lymphoma (DLBCL data. On the breast cancer data, the algorithm selected a total of 15 predictor genes across 84 contending models from the training data. The maximum likelihood estimates of the selected genes and the posterior probabilities of the selected models from the training data were used to divide patients in the test (or validation dataset into high- and low-risk categories. Using the genes and models determined from the training data, we assigned patients from the test data into highly distinct risk groups (as indicated by a p-value of 7.26e-05 from the log-rank test. Moreover, we achieved comparable results using only the 5 top selected genes with 100% posterior probabilities. On the DLBCL data, our iterative BMA procedure selected a total of 25 genes across 3 contending models from the training data. Once again, we assigned the patients in the validation set to significantly distinct risk groups (p

  8. Bayesian Graphical Models

    DEFF Research Database (Denmark)

    Jensen, Finn Verner; Nielsen, Thomas Dyhre

    2016-01-01

    Mathematically, a Bayesian graphical model is a compact representation of the joint probability distribution for a set of variables. The most frequently used type of Bayesian graphical models are Bayesian networks. The structural part of a Bayesian graphical model is a graph consisting of nodes...

  9. Source partitioning of methane emissions and its seasonality in the U.S. Midwest

    Science.gov (United States)

    Zichong Chen; Timothy J. Griffis; John M. Baker; Dylan B. Millet; Jeffrey D. Wood; Edward J. Dlugokencky; Arlyn E. Andrews; Colm Sweeney; Cheng Hu; Randall K. Kolka

    2018-01-01

    The methane (CH4) budget and its source partitioning are poorly constrained in the Midwestern United States. We used tall tower (185 m) aerodynamic flux measurements and atmospheric scale factor Bayesian inversions to constrain the monthly budget and to partition the total budget into natural (e.g., wetlands) and anthropogenic (e.g., livestock,...

  10. [On the partition of acupuncture academic schools].

    Science.gov (United States)

    Yang, Pengyan; Luo, Xi; Xia, Youbing

    2016-05-01

    Nowadays extensive attention has been paid on the research of acupuncture academic schools, however, a widely accepted method of partition of acupuncture academic schools is still in need. In this paper, the methods of partition of acupuncture academic schools in the history have been arranged, and three typical methods of"partition of five schools" "partition of eighteen schools" and "two-stage based partition" are summarized. After adeep analysis on the disadvantages and advantages of these three methods, a new method of partition of acupuncture academic schools that is called "three-stage based partition" is proposed. In this method, after the overall acupuncture academic schools are divided into an ancient stage, a modern stage and a contemporary stage, each schoolis divided into its sub-school category. It is believed that this method of partition can remedy the weaknesses ofcurrent methods, but also explore a new model of inheritance and development under a different aspect through thedifferentiation and interaction of acupuncture academic schools at three stages.

  11. Bayesian nonparametric data analysis

    CERN Document Server

    Müller, Peter; Jara, Alejandro; Hanson, Tim

    2015-01-01

    This book reviews nonparametric Bayesian methods and models that have proven useful in the context of data analysis. Rather than providing an encyclopedic review of probability models, the book’s structure follows a data analysis perspective. As such, the chapters are organized by traditional data analysis problems. In selecting specific nonparametric models, simpler and more traditional models are favored over specialized ones. The discussed methods are illustrated with a wealth of examples, including applications ranging from stylized examples to case studies from recent literature. The book also includes an extensive discussion of computational methods and details on their implementation. R code for many examples is included in on-line software pages.

  12. Robust Bayesian detection of unmodelled bursts

    International Nuclear Information System (INIS)

    Searle, Antony C; Sutton, Patrick J; Tinto, Massimo; Woan, Graham

    2008-01-01

    We develop a Bayesian treatment of the problem of detecting unmodelled gravitational wave bursts using the new global network of interferometric detectors. We also compare this Bayesian treatment with existing coherent methods, and demonstrate that the existing methods make implicit assumptions on the distribution of signals that make them sub-optimal for realistic signal populations

  13. Quantifying the uncertainty in discharge data using hydraulic knowledge and uncertain gaugings: a Bayesian method named BaRatin

    Science.gov (United States)

    Le Coz, Jérôme; Renard, Benjamin; Bonnifait, Laurent; Branger, Flora; Le Boursicaud, Raphaël; Horner, Ivan; Mansanarez, Valentin; Lang, Michel; Vigneau, Sylvain

    2015-04-01

    River discharge is a crucial variable for Hydrology: as the output variable of most hydrologic models, it is used for sensitivity analyses, model structure identification, parameter estimation, data assimilation, prediction, etc. A major difficulty stems from the fact that river discharge is not measured continuously. Instead, discharge time series used by hydrologists are usually based on simple stage-discharge relations (rating curves) calibrated using a set of direct stage-discharge measurements (gaugings). In this presentation, we present a Bayesian approach (cf. Le Coz et al., 2014) to build such hydrometric rating curves, to estimate the associated uncertainty and to propagate this uncertainty to discharge time series. The three main steps of this approach are described: (1) Hydraulic analysis: identification of the hydraulic controls that govern the stage-discharge relation, identification of the rating curve equation and specification of prior distributions for the rating curve parameters; (2) Rating curve estimation: Bayesian inference of the rating curve parameters, accounting for the individual uncertainties of available gaugings, which often differ according to the discharge measurement procedure and the flow conditions; (3) Uncertainty propagation: quantification of the uncertainty in discharge time series, accounting for both the rating curve uncertainties and the uncertainty of recorded stage values. The rating curve uncertainties combine the parametric uncertainties and the remnant uncertainties that reflect the limited accuracy of the mathematical model used to simulate the physical stage-discharge relation. In addition, we also discuss current research activities, including the treatment of non-univocal stage-discharge relationships (e.g. due to hydraulic hysteresis, vegetation growth, sudden change of the geometry of the section, etc.). An operational version of the BaRatin software and its graphical interface are made available free of charge on

  14. Classification algorithms using adaptive partitioning

    KAUST Repository

    Binev, Peter; Cohen, Albert; Dahmen, Wolfgang; DeVore, Ronald

    2014-01-01

    © 2014 Institute of Mathematical Statistics. Algorithms for binary classification based on adaptive tree partitioning are formulated and analyzed for both their risk performance and their friendliness to numerical implementation. The algorithms can be viewed as generating a set approximation to the Bayes set and thus fall into the general category of set estimators. In contrast with the most studied tree-based algorithms, which utilize piecewise constant approximation on the generated partition [IEEE Trans. Inform. Theory 52 (2006) 1335.1353; Mach. Learn. 66 (2007) 209.242], we consider decorated trees, which allow us to derive higher order methods. Convergence rates for these methods are derived in terms the parameter - of margin conditions and a rate s of best approximation of the Bayes set by decorated adaptive partitions. They can also be expressed in terms of the Besov smoothness β of the regression function that governs its approximability by piecewise polynomials on adaptive partition. The execution of the algorithms does not require knowledge of the smoothness or margin conditions. Besov smoothness conditions are weaker than the commonly used Holder conditions, which govern approximation by nonadaptive partitions, and therefore for a given regression function can result in a higher rate of convergence. This in turn mitigates the compatibility conflict between smoothness and margin parameters.

  15. Classification algorithms using adaptive partitioning

    KAUST Repository

    Binev, Peter

    2014-12-01

    © 2014 Institute of Mathematical Statistics. Algorithms for binary classification based on adaptive tree partitioning are formulated and analyzed for both their risk performance and their friendliness to numerical implementation. The algorithms can be viewed as generating a set approximation to the Bayes set and thus fall into the general category of set estimators. In contrast with the most studied tree-based algorithms, which utilize piecewise constant approximation on the generated partition [IEEE Trans. Inform. Theory 52 (2006) 1335.1353; Mach. Learn. 66 (2007) 209.242], we consider decorated trees, which allow us to derive higher order methods. Convergence rates for these methods are derived in terms the parameter - of margin conditions and a rate s of best approximation of the Bayes set by decorated adaptive partitions. They can also be expressed in terms of the Besov smoothness β of the regression function that governs its approximability by piecewise polynomials on adaptive partition. The execution of the algorithms does not require knowledge of the smoothness or margin conditions. Besov smoothness conditions are weaker than the commonly used Holder conditions, which govern approximation by nonadaptive partitions, and therefore for a given regression function can result in a higher rate of convergence. This in turn mitigates the compatibility conflict between smoothness and margin parameters.

  16. Bayesian theory and applications

    CERN Document Server

    Dellaportas, Petros; Polson, Nicholas G; Stephens, David A

    2013-01-01

    The development of hierarchical models and Markov chain Monte Carlo (MCMC) techniques forms one of the most profound advances in Bayesian analysis since the 1970s and provides the basis for advances in virtually all areas of applied and theoretical Bayesian statistics. This volume guides the reader along a statistical journey that begins with the basic structure of Bayesian theory, and then provides details on most of the past and present advances in this field. The book has a unique format. There is an explanatory chapter devoted to each conceptual advance followed by journal-style chapters that provide applications or further advances on the concept. Thus, the volume is both a textbook and a compendium of papers covering a vast range of topics. It is appropriate for a well-informed novice interested in understanding the basic approach, methods and recent applications. Because of its advanced chapters and recent work, it is also appropriate for a more mature reader interested in recent applications and devel...

  17. 12th Brazilian Meeting on Bayesian Statistics

    CERN Document Server

    Louzada, Francisco; Rifo, Laura; Stern, Julio; Lauretto, Marcelo

    2015-01-01

    Through refereed papers, this volume focuses on the foundations of the Bayesian paradigm; their comparison to objectivistic or frequentist Statistics counterparts; and the appropriate application of Bayesian foundations. This research in Bayesian Statistics is applicable to data analysis in biostatistics, clinical trials, law, engineering, and the social sciences. EBEB, the Brazilian Meeting on Bayesian Statistics, is held every two years by the ISBrA, the International Society for Bayesian Analysis, one of the most active chapters of the ISBA. The 12th meeting took place March 10-14, 2014 in Atibaia. Interest in foundations of inductive Statistics has grown recently in accordance with the increasing availability of Bayesian methodological alternatives. Scientists need to deal with the ever more difficult choice of the optimal method to apply to their problem. This volume shows how Bayes can be the answer. The examination and discussion on the foundations work towards the goal of proper application of Bayesia...

  18. Bayesian disease mapping: hierarchical modeling in spatial epidemiology

    National Research Council Canada - National Science Library

    Lawson, Andrew

    2013-01-01

    .... Exploring these new developments, Bayesian Disease Mapping: Hierarchical Modeling in Spatial Epidemiology, Second Edition provides an up-to-date, cohesive account of the full range of Bayesian disease mapping methods and applications...

  19. COMPUTING VERTICES OF INTEGER PARTITION POLYTOPES

    Directory of Open Access Journals (Sweden)

    A. S. Vroublevski

    2015-01-01

    Full Text Available The paper describes a method of generating vertices of the polytopes of integer partitions that was used by the authors to calculate all vertices and support vertices of the partition polytopes for all n ≤ 105 and all knapsack partitions of n ≤ 165. The method avoids generating all partitions of n. The vertices are determined with the help of sufficient and necessary conditions; in the hard cases, the well-known program Polymake is used. Some computational aspects are exposed in more detail. These are the algorithm for checking the criterion that characterizes partitions that are convex combinations of two other partitions; the way of using two combinatorial operations that transform the known vertices to the new ones; and employing the Polymake to recognize a limited number (for small n of partitions that need three or more other partitions for being convexly expressed. We discuss the computational results on the numbers of vertices and support vertices of the partition polytopes and some appealing problems these results give rise to.

  20. 3rd Bayesian Young Statisticians Meeting

    CERN Document Server

    Lanzarone, Ettore; Villalobos, Isadora; Mattei, Alessandra

    2017-01-01

    This book is a selection of peer-reviewed contributions presented at the third Bayesian Young Statisticians Meeting, BAYSM 2016, Florence, Italy, June 19-21. The meeting provided a unique opportunity for young researchers, M.S. students, Ph.D. students, and postdocs dealing with Bayesian statistics to connect with the Bayesian community at large, to exchange ideas, and to network with others working in the same field. The contributions develop and apply Bayesian methods in a variety of fields, ranging from the traditional (e.g., biostatistics and reliability) to the most innovative ones (e.g., big data and networks).

  1. A hierarchical method for Bayesian inference of rate parameters from shock tube data: Application to the study of the reaction of hydroxyl with 2-methylfuran

    KAUST Repository

    Kim, Daesang

    2017-06-22

    We developed a novel two-step hierarchical method for the Bayesian inference of the rate parameters of a target reaction from time-resolved concentration measurements in shock tubes. The method was applied to the calibration of the parameters of the reaction of hydroxyl with 2-methylfuran, which is studied experimentally via absorption measurements of the OH radical\\'s concentration following shock-heating. In the first step of the approach, each shock tube experiment is treated independently to infer the posterior distribution of the rate constant and error hyper-parameter that best explains the OH signal. In the second step, these posterior distributions are sampled to calibrate the parameters appearing in the Arrhenius reaction model for the rate constant. Furthermore, the second step is modified and repeated in order to explore alternative rate constant models and to assess the effect of uncertainties in the reflected shock\\'s temperature. Comparisons of the estimates obtained via the proposed methodology against the common least squares approach are presented. The relative merits of the novel Bayesian framework are highlighted, especially with respect to the opportunity to utilize the posterior distributions of the parameters in future uncertainty quantification studies.

  2. Bayesian artificial intelligence

    CERN Document Server

    Korb, Kevin B

    2010-01-01

    Updated and expanded, Bayesian Artificial Intelligence, Second Edition provides a practical and accessible introduction to the main concepts, foundation, and applications of Bayesian networks. It focuses on both the causal discovery of networks and Bayesian inference procedures. Adopting a causal interpretation of Bayesian networks, the authors discuss the use of Bayesian networks for causal modeling. They also draw on their own applied research to illustrate various applications of the technology.New to the Second EditionNew chapter on Bayesian network classifiersNew section on object-oriente

  3. Bayesian artificial intelligence

    CERN Document Server

    Korb, Kevin B

    2003-01-01

    As the power of Bayesian techniques has become more fully realized, the field of artificial intelligence has embraced Bayesian methodology and integrated it to the point where an introduction to Bayesian techniques is now a core course in many computer science programs. Unlike other books on the subject, Bayesian Artificial Intelligence keeps mathematical detail to a minimum and covers a broad range of topics. The authors integrate all of Bayesian net technology and learning Bayesian net technology and apply them both to knowledge engineering. They emphasize understanding and intuition but also provide the algorithms and technical background needed for applications. Software, exercises, and solutions are available on the authors' website.

  4. The Bayesian Covariance Lasso.

    Science.gov (United States)

    Khondker, Zakaria S; Zhu, Hongtu; Chu, Haitao; Lin, Weili; Ibrahim, Joseph G

    2013-04-01

    Estimation of sparse covariance matrices and their inverse subject to positive definiteness constraints has drawn a lot of attention in recent years. The abundance of high-dimensional data, where the sample size ( n ) is less than the dimension ( d ), requires shrinkage estimation methods since the maximum likelihood estimator is not positive definite in this case. Furthermore, when n is larger than d but not sufficiently larger, shrinkage estimation is more stable than maximum likelihood as it reduces the condition number of the precision matrix. Frequentist methods have utilized penalized likelihood methods, whereas Bayesian approaches rely on matrix decompositions or Wishart priors for shrinkage. In this paper we propose a new method, called the Bayesian Covariance Lasso (BCLASSO), for the shrinkage estimation of a precision (covariance) matrix. We consider a class of priors for the precision matrix that leads to the popular frequentist penalties as special cases, develop a Bayes estimator for the precision matrix, and propose an efficient sampling scheme that does not precalculate boundaries for positive definiteness. The proposed method is permutation invariant and performs shrinkage and estimation simultaneously for non-full rank data. Simulations show that the proposed BCLASSO performs similarly as frequentist methods for non-full rank data.

  5. New phiomorph rodents from the latest Eocene of Egypt, and the impact of Bayesian "clock"-based phylogenetic methods on estimates of basal hystricognath relationships and biochronology.

    Science.gov (United States)

    Sallam, Hesham M; Seiffert, Erik R

    2016-01-01

    The Fayum Depression of Egypt has yielded fossils of hystricognathous rodents from multiple Eocene and Oligocene horizons that range in age from ∼37 to ∼30 Ma and document several phases in the early evolution of crown Hystricognathi and one of its major subclades, Phiomorpha. Here we describe two new genera and species of basal phiomorphs, Birkamys korai and Mubhammys vadumensis, based on rostra and maxillary and mandibular remains from the terminal Eocene (∼34 Ma) Fayum Locality 41 (L-41). Birkamys is the smallest known Paleogene hystricognath, has very simple molars, and, like derived Oligocene-to-Recent phiomorphs (but unlike contemporaneous and older taxa) apparently retained dP(4)∕4 late into life, with no evidence for P(4)∕4 eruption or formation. Mubhammys is very similar in dental morphology to Birkamys, and also shows no evidence for P(4)∕4 formation or eruption, but is considerably larger. Though parsimony analysis with all characters equally weighted places Birkamys and Mubhammys as sister taxa of extant Thryonomys to the exclusion of much younger relatives of that genus, all other methods (standard Bayesian inference, Bayesian "tip-dating," and parsimony analysis with scaled transitions between "fixed" and polymorphic states) place these species in more basal positions within Hystricognathi, as sister taxa of Oligocene-to-Recent phiomorphs. We also employ tip-dating as a means for estimating the ages of early hystricognath-bearing localities, many of which are not well-constrained by geological, geochronological, or biostratigraphic evidence. By simultaneously taking into account phylogeny, evolutionary rates, and uniform priors that appropriately encompass the range of possible ages for fossil localities, dating of tips in this Bayesian framework allows paleontologists to move beyond vague and assumption-laden "stage of evolution" arguments in biochronology to provide relatively rigorous age assessments of poorly-constrained faunas. This

  6. New phiomorph rodents from the latest Eocene of Egypt, and the impact of Bayesian “clock”-based phylogenetic methods on estimates of basal hystricognath relationships and biochronology

    Directory of Open Access Journals (Sweden)

    Hesham M. Sallam

    2016-03-01

    Full Text Available The Fayum Depression of Egypt has yielded fossils of hystricognathous rodents from multiple Eocene and Oligocene horizons that range in age from ∼37 to ∼30 Ma and document several phases in the early evolution of crown Hystricognathi and one of its major subclades, Phiomorpha. Here we describe two new genera and species of basal phiomorphs, Birkamys korai and Mubhammys vadumensis, based on rostra and maxillary and mandibular remains from the terminal Eocene (∼34 Ma Fayum Locality 41 (L-41. Birkamys is the smallest known Paleogene hystricognath, has very simple molars, and, like derived Oligocene-to-Recent phiomorphs (but unlike contemporaneous and older taxa apparently retained dP4∕4 late into life, with no evidence for P4∕4 eruption or formation. Mubhammys is very similar in dental morphology to Birkamys, and also shows no evidence for P4∕4 formation or eruption, but is considerably larger. Though parsimony analysis with all characters equally weighted places Birkamys and Mubhammys as sister taxa of extant Thryonomys to the exclusion of much younger relatives of that genus, all other methods (standard Bayesian inference, Bayesian “tip-dating,” and parsimony analysis with scaled transitions between “fixed” and polymorphic states place these species in more basal positions within Hystricognathi, as sister taxa of Oligocene-to-Recent phiomorphs. We also employ tip-dating as a means for estimating the ages of early hystricognath-bearing localities, many of which are not well-constrained by geological, geochronological, or biostratigraphic evidence. By simultaneously taking into account phylogeny, evolutionary rates, and uniform priors that appropriately encompass the range of possible ages for fossil localities, dating of tips in this Bayesian framework allows paleontologists to move beyond vague and assumption-laden “stage of evolution” arguments in biochronology to provide relatively rigorous age assessments of poorly

  7. New phiomorph rodents from the latest Eocene of Egypt, and the impact of Bayesian “clock”-based phylogenetic methods on estimates of basal hystricognath relationships and biochronology

    Science.gov (United States)

    2016-01-01

    The Fayum Depression of Egypt has yielded fossils of hystricognathous rodents from multiple Eocene and Oligocene horizons that range in age from ∼37 to ∼30 Ma and document several phases in the early evolution of crown Hystricognathi and one of its major subclades, Phiomorpha. Here we describe two new genera and species of basal phiomorphs, Birkamys korai and Mubhammys vadumensis, based on rostra and maxillary and mandibular remains from the terminal Eocene (∼34 Ma) Fayum Locality 41 (L-41). Birkamys is the smallest known Paleogene hystricognath, has very simple molars, and, like derived Oligocene-to-Recent phiomorphs (but unlike contemporaneous and older taxa) apparently retained dP4∕4 late into life, with no evidence for P4∕4 eruption or formation. Mubhammys is very similar in dental morphology to Birkamys, and also shows no evidence for P4∕4 formation or eruption, but is considerably larger. Though parsimony analysis with all characters equally weighted places Birkamys and Mubhammys as sister taxa of extant Thryonomys to the exclusion of much younger relatives of that genus, all other methods (standard Bayesian inference, Bayesian “tip-dating,” and parsimony analysis with scaled transitions between “fixed” and polymorphic states) place these species in more basal positions within Hystricognathi, as sister taxa of Oligocene-to-Recent phiomorphs. We also employ tip-dating as a means for estimating the ages of early hystricognath-bearing localities, many of which are not well-constrained by geological, geochronological, or biostratigraphic evidence. By simultaneously taking into account phylogeny, evolutionary rates, and uniform priors that appropriately encompass the range of possible ages for fossil localities, dating of tips in this Bayesian framework allows paleontologists to move beyond vague and assumption-laden “stage of evolution” arguments in biochronology to provide relatively rigorous age assessments of poorly-constrained faunas

  8. An alternative method to isolate protease and phospholipase A2 toxins from snake venoms based on partitioning of aqueous two-phase systems

    Directory of Open Access Journals (Sweden)

    GN Gómez

    2012-01-01

    Full Text Available Snake venoms are rich sources of active proteins that have been employed in the diagnosis and treatment of health disorders and antivenom therapy. Developing countries demand fast economical downstream processes for the purification of this biomolecule type without requiring sophisticated equipment. We developed an alternative, simple and easy to scale-up method, able to purify simultaneously protease and phospholipase A2 toxins from Bothrops alternatus venom. It comprises a multiple-step partition procedure with polyethylene-glycol/phosphate aqueous two-phase systems followed by a gel filtration chromatographic step. Two single bands in SDS-polyacrylamide gel electrophoresis and increased proteolytic and phospholipase A2 specific activities evidence the homogeneity of the isolated proteins.

  9. Using Bayesian belief networks in adaptive management.

    Science.gov (United States)

    J.B. Nyberg; B.G. Marcot; R. Sulyma

    2006-01-01

    Bayesian belief and decision networks are relatively new modeling methods that are especially well suited to adaptive-management applications, but they appear not to have been widely used in adaptive management to date. Bayesian belief networks (BBNs) can serve many purposes for practioners of adaptive management, from illustrating system relations conceptually to...

  10. 2nd Bayesian Young Statisticians Meeting

    CERN Document Server

    Bitto, Angela; Kastner, Gregor; Posekany, Alexandra

    2015-01-01

    The Second Bayesian Young Statisticians Meeting (BAYSM 2014) and the research presented here facilitate connections among researchers using Bayesian Statistics by providing a forum for the development and exchange of ideas. WU Vienna University of Business and Economics hosted BAYSM 2014 from September 18th to 19th. The guidance of renowned plenary lecturers and senior discussants is a critical part of the meeting and this volume, which follows publication of contributions from BAYSM 2013. The meeting's scientific program reflected the variety of fields in which Bayesian methods are currently employed or could be introduced in the future. Three brilliant keynote lectures by Chris Holmes (University of Oxford), Christian Robert (Université Paris-Dauphine), and Mike West (Duke University), were complemented by 24 plenary talks covering the major topics Dynamic Models, Applications, Bayesian Nonparametrics, Biostatistics, Bayesian Methods in Economics, and Models and Methods, as well as a lively poster session ...

  11. Bayesian dynamic mediation analysis.

    Science.gov (United States)

    Huang, Jing; Yuan, Ying

    2017-12-01

    Most existing methods for mediation analysis assume that mediation is a stationary, time-invariant process, which overlooks the inherently dynamic nature of many human psychological processes and behavioral activities. In this article, we consider mediation as a dynamic process that continuously changes over time. We propose Bayesian multilevel time-varying coefficient models to describe and estimate such dynamic mediation effects. By taking the nonparametric penalized spline approach, the proposed method is flexible and able to accommodate any shape of the relationship between time and mediation effects. Simulation studies show that the proposed method works well and faithfully reflects the true nature of the mediation process. By modeling mediation effect nonparametrically as a continuous function of time, our method provides a valuable tool to help researchers obtain a more complete understanding of the dynamic nature of the mediation process underlying psychological and behavioral phenomena. We also briefly discuss an alternative approach of using dynamic autoregressive mediation model to estimate the dynamic mediation effect. The computer code is provided to implement the proposed Bayesian dynamic mediation analysis. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  12. Approximate Bayesian computation.

    Directory of Open Access Journals (Sweden)

    Mikael Sunnåker

    Full Text Available Approximate Bayesian computation (ABC constitutes a class of computational methods rooted in Bayesian statistics. In all model-based statistical inference, the likelihood function is of central importance, since it expresses the probability of the observed data under a particular statistical model, and thus quantifies the support data lend to particular values of parameters and to choices among different models. For simple models, an analytical formula for the likelihood function can typically be derived. However, for more complex models, an analytical formula might be elusive or the likelihood function might be computationally very costly to evaluate. ABC methods bypass the evaluation of the likelihood function. In this way, ABC methods widen the realm of models for which statistical inference can be considered. ABC methods are mathematically well-founded, but they inevitably make assumptions and approximations whose impact needs to be carefully assessed. Furthermore, the wider application domain of ABC exacerbates the challenges of parameter estimation and model selection. ABC has rapidly gained popularity over the last years and in particular for the analysis of complex problems arising in biological sciences (e.g., in population genetics, ecology, epidemiology, and systems biology.

  13. Bayesian Mediation Analysis

    OpenAIRE

    Yuan, Ying; MacKinnon, David P.

    2009-01-01

    This article proposes Bayesian analysis of mediation effects. Compared to conventional frequentist mediation analysis, the Bayesian approach has several advantages. First, it allows researchers to incorporate prior information into the mediation analysis, thus potentially improving the efficiency of estimates. Second, under the Bayesian mediation analysis, inference is straightforward and exact, which makes it appealing for studies with small samples. Third, the Bayesian approach is conceptua...

  14. Bayesian benefits with JASP

    NARCIS (Netherlands)

    Marsman, M.; Wagenmakers, E.-J.

    2017-01-01

    We illustrate the Bayesian approach to data analysis using the newly developed statistical software program JASP. With JASP, researchers are able to take advantage of the benefits that the Bayesian framework has to offer in terms of parameter estimation and hypothesis testing. The Bayesian

  15. A Fast Iterative Bayesian Inference Algorithm for Sparse Channel Estimation

    DEFF Research Database (Denmark)

    Pedersen, Niels Lovmand; Manchón, Carles Navarro; Fleury, Bernard Henri

    2013-01-01

    representation of the Bessel K probability density function; a highly efficient, fast iterative Bayesian inference method is then applied to the proposed model. The resulting estimator outperforms other state-of-the-art Bayesian and non-Bayesian estimators, either by yielding lower mean squared estimation error...

  16. A Gentle Introduction to Bayesian Analysis : Applications to Developmental Research

    NARCIS (Netherlands)

    Van de Schoot, Rens; Kaplan, David; Denissen, Jaap; Asendorpf, Jens B.; Neyer, Franz J.; van Aken, Marcel A G

    2014-01-01

    Bayesian statistical methods are becoming ever more popular in applied and fundamental research. In this study a gentle introduction to Bayesian analysis is provided. It is shown under what circumstances it is attractive to use Bayesian estimation, and how to interpret properly the results. First,

  17. A gentle introduction to Bayesian analysis : Applications to developmental research

    NARCIS (Netherlands)

    van de Schoot, R.; Kaplan, D.; Denissen, J.J.A.; Asendorpf, J.B.; Neyer, F.J.; van Aken, M.A.G.

    2014-01-01

    Bayesian statistical methods are becoming ever more popular in applied and fundamental research. In this study a gentle introduction to Bayesian analysis is provided. It is shown under what circumstances it is attractive to use Bayesian estimation, and how to interpret properly the results. First,

  18. A default Bayesian hypothesis test for ANOVA designs

    NARCIS (Netherlands)

    Wetzels, R.; Grasman, R.P.P.P.; Wagenmakers, E.J.

    2012-01-01

    This article presents a Bayesian hypothesis test for analysis of variance (ANOVA) designs. The test is an application of standard Bayesian methods for variable selection in regression models. We illustrate the effect of various g-priors on the ANOVA hypothesis test. The Bayesian test for ANOVA

  19. Nonparametric Bayesian inference in biostatistics

    CERN Document Server

    Müller, Peter

    2015-01-01

    As chapters in this book demonstrate, BNP has important uses in clinical sciences and inference for issues like unknown partitions in genomics. Nonparametric Bayesian approaches (BNP) play an ever expanding role in biostatistical inference from use in proteomics to clinical trials. Many research problems involve an abundance of data and require flexible and complex probability models beyond the traditional parametric approaches. As this book's expert contributors show, BNP approaches can be the answer. Survival Analysis, in particular survival regression, has traditionally used BNP, but BNP's potential is now very broad. This applies to important tasks like arrangement of patients into clinically meaningful subpopulations and segmenting the genome into functionally distinct regions. This book is designed to both review and introduce application areas for BNP. While existing books provide theoretical foundations, this book connects theory to practice through engaging examples and research questions. Chapters c...

  20. A new method to quantify and compare the multiple components of fitness--a study case with kelp niche partition by divergent microstage adaptations to temperature.

    Directory of Open Access Journals (Sweden)

    Vasco M N C S Vieira

    Full Text Available Management of crops, commercialized or protected species, plagues or life-cycle evolution are subjects requiring comparisons among different demographic strategies. The simpler methods fail in relating changes in vital rates with changes in population viability whereas more complex methods lack accuracy by neglecting interactions among vital rates.The difference between the fitness (evaluated by the population growth rate λ of two alternative demographies is decomposed into the contributions of the differences between the pair-wised vital rates and their interactions. This is achieved through a full Taylor expansion (i.e. remainder = 0 of the demographic model. The significance of each term is determined by permutation tests under the null hypothesis that all demographies come from the same pool.An example is given with periodic demographic matrices of the microscopic haploid phase of two kelp cryptic species observed to partition their niche occupation along the Chilean coast. The method provided clear and synthetic results showing conditional differentiation of reproduction is an important driver for their differences in fitness along the latitudinal temperature gradient. But it also demonstrated that interactions among vital rates cannot be neglected as they compose a significant part of the differences between demographies.This method allows researchers to access the effects of multiple effective changes in a life-cycle from only two experiments. Evolutionists can determine with confidence the effective causes for changes in fitness whereas population managers can determine best strategies from simpler experimental designs.

  1. Bayesian natural language semantics and pragmatics

    CERN Document Server

    Zeevat, Henk

    2015-01-01

    The contributions in this volume focus on the Bayesian interpretation of natural languages, which is widely used in areas of artificial intelligence, cognitive science, and computational linguistics. This is the first volume to take up topics in Bayesian Natural Language Interpretation and make proposals based on information theory, probability theory, and related fields. The methodologies offered here extend to the target semantic and pragmatic analyses of computational natural language interpretation. Bayesian approaches to natural language semantics and pragmatics are based on methods from signal processing and the causal Bayesian models pioneered by especially Pearl. In signal processing, the Bayesian method finds the most probable interpretation by finding the one that maximizes the product of the prior probability and the likelihood of the interpretation. It thus stresses the importance of a production model for interpretation as in Grice's contributions to pragmatics or in interpretation by abduction.

  2. Probability biases as Bayesian inference

    Directory of Open Access Journals (Sweden)

    Andre; C. R. Martins

    2006-11-01

    Full Text Available In this article, I will show how several observed biases in human probabilistic reasoning can be partially explained as good heuristics for making inferences in an environment where probabilities have uncertainties associated to them. Previous results show that the weight functions and the observed violations of coalescing and stochastic dominance can be understood from a Bayesian point of view. We will review those results and see that Bayesian methods should also be used as part of the explanation behind other known biases. That means that, although the observed errors are still errors under the be understood as adaptations to the solution of real life problems. Heuristics that allow fast evaluations and mimic a Bayesian inference would be an evolutionary advantage, since they would give us an efficient way of making decisions. %XX In that sense, it should be no surprise that humans reason with % probability as it has been observed.

  3. Bayesian analysis of CCDM models

    Science.gov (United States)

    Jesus, J. F.; Valentim, R.; Andrade-Oliveira, F.

    2017-09-01

    Creation of Cold Dark Matter (CCDM), in the context of Einstein Field Equations, produces a negative pressure term which can be used to explain the accelerated expansion of the Universe. In this work we tested six different spatially flat models for matter creation using statistical criteria, in light of SNe Ia data: Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC) and Bayesian Evidence (BE). These criteria allow to compare models considering goodness of fit and number of free parameters, penalizing excess of complexity. We find that JO model is slightly favoured over LJO/ΛCDM model, however, neither of these, nor Γ = 3αH0 model can be discarded from the current analysis. Three other scenarios are discarded either because poor fitting or because of the excess of free parameters. A method of increasing Bayesian evidence through reparameterization in order to reducing parameter degeneracy is also developed.

  4. Bayesian analysis of CCDM models

    Energy Technology Data Exchange (ETDEWEB)

    Jesus, J.F. [Universidade Estadual Paulista (Unesp), Câmpus Experimental de Itapeva, Rua Geraldo Alckmin 519, Vila N. Sra. de Fátima, Itapeva, SP, 18409-010 Brazil (Brazil); Valentim, R. [Departamento de Física, Instituto de Ciências Ambientais, Químicas e Farmacêuticas—ICAQF, Universidade Federal de São Paulo (UNIFESP), Unidade José Alencar, Rua São Nicolau No. 210, Diadema, SP, 09913-030 Brazil (Brazil); Andrade-Oliveira, F., E-mail: jfjesus@itapeva.unesp.br, E-mail: valentim.rodolfo@unifesp.br, E-mail: felipe.oliveira@port.ac.uk [Institute of Cosmology and Gravitation—University of Portsmouth, Burnaby Road, Portsmouth, PO1 3FX United Kingdom (United Kingdom)

    2017-09-01

    Creation of Cold Dark Matter (CCDM), in the context of Einstein Field Equations, produces a negative pressure term which can be used to explain the accelerated expansion of the Universe. In this work we tested six different spatially flat models for matter creation using statistical criteria, in light of SNe Ia data: Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC) and Bayesian Evidence (BE). These criteria allow to compare models considering goodness of fit and number of free parameters, penalizing excess of complexity. We find that JO model is slightly favoured over LJO/ΛCDM model, however, neither of these, nor Γ = 3α H {sub 0} model can be discarded from the current analysis. Three other scenarios are discarded either because poor fitting or because of the excess of free parameters. A method of increasing Bayesian evidence through reparameterization in order to reducing parameter degeneracy is also developed.

  5. Estudo da prevalência da tuberculose: uso de métodos bayesianos Study of the prevalence of tuberculosis using Bayesian methods

    Directory of Open Access Journals (Sweden)

    Jorge Alberto Achcar

    2003-12-01

    Full Text Available Neste artigo, apresentamos estimadores bayesianos para a prevalência de tuberculose usando métodos computacionais de simulação de amostras da distribuição a posteriori de interesse. Em especial, consideramos o uso do amostrador de Gibbs para simular amostras da distribuição a posteriori, e daí encontramos, em uma forma simples, inferências precisas para a prevalência de tuberculose. Em uma aplicação, analisamos os resultados do exame de Rx do tórax no diagnóstico da tuberculose. Com essa aplicação, verificamos que os estimadores bayesianos são simples de se obter e apresentam grande precisão. O uso de métodos computacionais para simulação de amostras como o caso do amostrador de Gibbs tem sido recentemente muito utilizado para análise bayesiana de modelos em bioestatística. Essas técnicas de simulação usando o amostrador de Gibbs são facilmente implementadas e não exigem muito conhecimento computacional, podendo ser programadas em qualquer software disponível. Além disso, essas técnicas podem ser consideradas para o estudo da prevalência de outras doenças.In this paper we present Bayesian estimators of the prevalence of tuberculosis using computational methods for simulation of samples of posterior distribution of interest. We especially considered the Gibbs sampling algorithm to generate samples of posterior distribution, and from these samples we obtained accurate inferences for the prevalence of tuberculosis. In an application, we analyzed the results of lung X-ray tests in the diagnosis of tuberculosis. With this application, we verified that Bayesian estimators are more accurate than some existing estimators usually considered by health researchers. The use of computational methods for simulation of samples as the case of the Gibbs sampling algorithm is becoming very popular for Bayesian analysis in biostatistics. These simulation techniques using the Gibbs sampling algorithm are easily implemented and do

  6. Hyainailourine and teratodontine cranial material from the late Eocene of Egypt and the application of parsimony and Bayesian methods to the phylogeny and biogeography of Hyaenodonta (Placentalia, Mammalia).

    Science.gov (United States)

    Borths, Matthew R; Holroyd, Patricia A; Seiffert, Erik R

    2016-01-01

    Hyaenodonta is a diverse, extinct group of carnivorous mammals that included weasel- to rhinoceros-sized species. The oldest-known hyaenodont fossils are from the middle Paleocene of North Africa and the antiquity of the group in Afro-Arabia led to the hypothesis that it originated there and dispersed to Asia, Europe, and North America. Here we describe two new hyaenodont species based on the oldest hyaenodont cranial specimens known from Afro-Arabia. The material was collected from the latest Eocene Locality 41 (L-41, ∼34 Ma) in the Fayum Depression, Egypt. Akhnatenavus nefertiticyon sp. nov. has specialized, hypercarnivorous molars and an elongate cranial vault. In A. nefertiticyon the tallest, piercing cusp on M 1 -M 2 is the paracone. Brychotherium ephalmos gen. et sp. nov. has more generalized molars that retain the metacone and complex talonids. In B. ephalmos the tallest, piercing cusp on M 1 -M 2 is the metacone. We incorporate this new material into a series of phylogenetic analyses using a character-taxon matrix that includes novel dental, cranial, and postcranial characters, and samples extensively from the global record of the group. The phylogenetic analysis includes the first application of Bayesian methods to hyaenodont relationships. B. ephalmos is consistently placed within Teratodontinae, an Afro-Arabian clade with several generalist and hypercarnivorous forms, and Akhnatenavus is consistently recovered in Hyainailourinae as part of an Afro-Arabian radiation. The phylogenetic results suggest that hypercarnivory evolved independently three times within Hyaenodonta: in Teratodontinae, in Hyainailourinae, and in Hyaenodontinae. Teratodontines are consistently placed in a close relationship with Hyainailouridae (Hyainailourinae + Apterodontinae) to the exclusion of "proviverrines," hyaenodontines, and several North American clades, and we propose that the superfamily Hyainailouroidea be used to describe this relationship. Using the topologies

  7. The Bayesian Approach to Association

    Science.gov (United States)

    Arora, N. S.

    2017-12-01

    The Bayesian approach to Association focuses mainly on quantifying the physics of the domain. In the case of seismic association for instance let X be the set of all significant events (above some threshold) and their attributes, such as location, time, and magnitude, Y1 be the set of detections that are caused by significant events and their attributes such as seismic phase, arrival time, amplitude etc., Y2 be the set of detections that are not caused by significant events, and finally Y be the set of observed detections We would now define the joint distribution P(X, Y1, Y2, Y) = P(X) P(Y1 | X) P(Y2) I(Y = Y1 + Y2) ; where the last term simply states that Y1 and Y2 are a partitioning of Y. Given the above joint distribution the inference problem is simply to find the X, Y1, and Y2 that maximizes posterior probability P(X, Y1, Y2| Y) which reduces to maximizing P(X) P(Y1 | X) P(Y2) I(Y = Y1 + Y2). In this expression P(X) captures our prior belief about event locations. P(Y1 | X) captures notions of travel time, residual error distributions as well as detection and mis-detection probabilities. While P(Y2) captures the false detection rate of our seismic network. The elegance of this approach is that all of the assumptions are stated clearly in the model for P(X), P(Y1|X) and P(Y2). The implementation of the inference is merely a by-product of this model. In contrast some of the other methods such as GA hide a number of assumptions in the implementation details of the inference - such as the so called "driver cells." The other important aspect of this approach is that all seismic knowledge including knowledge from other domains such as infrasound and hydroacoustic can be included in the same model. So, we don't need to separately account for misdetections or merge seismic and infrasound events as a separate step. Finally, it should be noted that the objective of automatic association is to simplify the job of humans who are publishing seismic bulletins based on this

  8. Bayesian analysis of rare events

    Energy Technology Data Exchange (ETDEWEB)

    Straub, Daniel, E-mail: straub@tum.de; Papaioannou, Iason; Betz, Wolfgang

    2016-06-01

    In many areas of engineering and science there is an interest in predicting the probability of rare events, in particular in applications related to safety and security. Increasingly, such predictions are made through computer models of physical systems in an uncertainty quantification framework. Additionally, with advances in IT, monitoring and sensor technology, an increasing amount of data on the performance of the systems is collected. This data can be used to reduce uncertainty, improve the probability estimates and consequently enhance the management of rare events and associated risks. Bayesian analysis is the ideal method to include the data into the probabilistic model. It ensures a consistent probabilistic treatment of uncertainty, which is central in the prediction of rare events, where extrapolation from the domain of observation is common. We present a framework for performing Bayesian updating of rare event probabilities, termed BUS. It is based on a reinterpretation of the classical rejection-sampling approach to Bayesian analysis, which enables the use of established methods for estimating probabilities of rare events. By drawing upon these methods, the framework makes use of their computational efficiency. These methods include the First-Order Reliability Method (FORM), tailored importance sampling (IS) methods and Subset Simulation (SuS). In this contribution, we briefly review these methods in the context of the BUS framework and investigate their applicability to Bayesian analysis of rare events in different settings. We find that, for some applications, FORM can be highly efficient and is surprisingly accurate, enabling Bayesian analysis of rare events with just a few model evaluations. In a general setting, BUS implemented through IS and SuS is more robust and flexible.

  9. A Bayesian method for characterizing distributed micro-releases: II. inference under model uncertainty with short time-series data.

    Energy Technology Data Exchange (ETDEWEB)

    Marzouk, Youssef; Fast P. (Lawrence Livermore National Laboratory, Livermore, CA); Kraus, M. (Peterson AFB, CO); Ray, J. P.

    2006-01-01

    Terrorist attacks using an aerosolized pathogen preparation have gained credibility as a national security concern after the anthrax attacks of 2001. The ability to characterize such attacks, i.e., to estimate the number of people infected, the time of infection, and the average dose received, is important when planning a medical response. We address this question of characterization by formulating a Bayesian inverse problem predicated on a short time-series of diagnosed patients exhibiting symptoms. To be of relevance to response planning, we limit ourselves to 3-5 days of data. In tests performed with anthrax as the pathogen, we find that these data are usually sufficient, especially if the model of the outbreak used in the inverse problem is an accurate one. In some cases the scarcity of data may initially support outbreak characterizations at odds with the true one, but with sufficient data the correct inferences are recovered; in other words, the inverse problem posed and its solution methodology are consistent. We also explore the effect of model error-situations for which the model used in the inverse problem is only a partially accurate representation of the outbreak; here, the model predictions and the observations differ by more than a random noise. We find that while there is a consistent discrepancy between the inferred and the true characterizations, they are also close enough to be of relevance when planning a response.

  10. Bayesian networks: a new method for the modeling of bibliographic knowledge: application to fall risk assessment in geriatric patients.

    Science.gov (United States)

    Lalande, Laure; Bourguignon, Laurent; Carlier, Chloé; Ducher, Michel

    2013-06-01

    Falls in geriatry are associated with important morbidity, mortality and high healthcare costs. Because of the large number of variables related to the risk of falling, determining patients at risk is a difficult challenge. The aim of this work was to validate a tool to detect patients with high risk of fall using only bibliographic knowledge. Thirty articles corresponding to 160 studies were used to modelize fall risk. A retrospective case-control cohort including 288 patients (88 ± 7 years) and a prospective cohort including 106 patients (89 ± 6 years) from two geriatric hospitals were used to validate the performances of our model. We identified 26 variables associated with an increased risk of fall. These variables were split into illnesses, medications, and environment. The combination of the three associated scores gives a global fall score. The sensitivity and the specificity were 31.4, 81.6, 38.5, and 90 %, respectively, for the retrospective and the prospective cohort. The performances of the model are similar to results observed with already existing prediction tools using model adjustment to data from numerous cohort studies. This work demonstrates that knowledge from the literature can be synthesized with Bayesian networks.

  11. Use of Bayesian Methods to Analyze and Visualize Content Uniformity Capability Versus United States Pharmacopeia and ASTM Standards.

    Science.gov (United States)

    Hofer, Jeffrey D; Rauk, Adam P

    2017-02-01

    The purpose of this work was to develop a straightforward and robust approach to analyze and summarize the ability of content uniformity data to meet different criteria. A robust Bayesian statistical analysis methodology is presented which provides a concise and easily interpretable visual summary of the content uniformity analysis results. The visualization displays individual batch analysis results and shows whether there is high confidence that different content uniformity criteria could be met a high percentage of the time in the future. The 3 tests assessed are as follows: (a) United States Pharmacopeia Uniformity of Dosage Units , (b) a specific ASTM E2810 Sampling Plan 1 criterion to potentially be used for routine release testing, and (c) another specific ASTM E2810 Sampling Plan 2 criterion to potentially be used for process validation. The approach shown here could readily be used to create similar result summaries for other potential criteria. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

  12. Advancing Dose-Response Assessment Methods for Environmental Regulatory Impact Analysis: A Bayesian Belief Network Approach Applied to Inorganic Arsenic.

    Science.gov (United States)

    Zabinski, Joseph W; Garcia-Vargas, Gonzalo; Rubio-Andrade, Marisela; Fry, Rebecca C; Gibson, Jacqueline MacDonald

    2016-05-10

    Dose-response functions used in regulatory risk assessment are based on studies of whole organisms and fail to incorporate genetic and metabolomic data. Bayesian belief networks (BBNs) could provide a powerful framework for incorporating such data, but no prior research has examined this possibility. To address this gap, we develop a BBN-based model predicting birthweight at gestational age from arsenic exposure via drinking water and maternal metabolic indicators using a cohort of 200 pregnant women from an arsenic-endemic region of Mexico. We compare BBN predictions to those of prevailing slope-factor and reference-dose approaches. The BBN outperforms prevailing approaches in balancing false-positive and false-negative rates. Whereas the slope-factor approach had 2% sensitivity and 99% specificity and the reference-dose approach had 100% sensitivity and 0% specificity, the BBN's sensitivity and specificity were 71% and 30%, respectively. BBNs offer a promising opportunity to advance health risk assessment by incorporating modern genetic and metabolomic data.

  13. New PDE-based methods for image enhancement using SOM and Bayesian inference in various discretization schemes

    International Nuclear Information System (INIS)

    Karras, D A; Mertzios, G B

    2009-01-01

    A novel approach is presented in this paper for improving anisotropic diffusion PDE models, based on the Perona–Malik equation. A solution is proposed from an engineering perspective to adaptively estimate the parameters of the regularizing function in this equation. The goal of such a new adaptive diffusion scheme is to better preserve edges when the anisotropic diffusion PDE models are applied to image enhancement tasks. The proposed adaptive parameter estimation in the anisotropic diffusion PDE model involves self-organizing maps and Bayesian inference to define edge probabilities accurately. The proposed modifications attempt to capture not only simple edges but also difficult textural edges and incorporate their probability in the anisotropic diffusion model. In the context of the application of PDE models to image processing such adaptive schemes are closely related to the discrete image representation problem and the investigation of more suitable discretization algorithms using constraints derived from image processing theory. The proposed adaptive anisotropic diffusion model illustrates these concepts when it is numerically approximated by various discretization schemes in a database of magnetic resonance images (MRI), where it is shown to be efficient in image filtering and restoration applications

  14. Partitioning of oxygen uptake between the gills and skin in fish larvae: a novel method for estimating cutaneous oxygen uptake.

    Science.gov (United States)

    Rombough, P J

    1998-06-01

    The goal of this study was to develop an alternative to the traditional rubber dam method for measuring cutaneous oxygen uptake in bimodally respiring (skin + gills) fish larvae. The method tested involved using microelectrodes to measure the PO2 gradient in the diffusive boundary layer adjacent to seven positions on the skin surface (one on the head, two on the yolk sac, two on the trunk, one at the base of the dorsal fin-fold and one on the proximal portion of the caudal fin-fold) of rainbow trout (Oncorhynchus mykiss) larvae in still water. The PO2 gradient (deltaPO2/delta x, where x is the distance from the skin surface) was then used to calculate area-specific rate of O2 uptake (.MO2/A) according to the Fick equation, .MO2/A=Dbeta(deltaPO2/deltax), where A is the cross-sectional area of the boundary layer, D is the diffusion coefficient and beta is the capacitance coefficient for O2 in water. The accuracy of the method was assessed by comparing it with the rubber dam method. After correcting for differences in body mass, the two methods gave essentially identical results. According to the boundary layer method, the mean (+/-95 % CI) rate of O2 uptake across the skin of newly hatched rainbow trout at 10 degrees C is 3.13+/-0.18 microg O2 cm-2h-1 (N=265). The corresponding value obtained using the rubber dam method was 3. 36+/-0.35 microg O2 cm-2 h-1 (N=27). The advantages of the boundary layer method are that it can be used with smaller, more delicate larvae and that variables, such as flow rate, that can affect the efficiency of gas exchange can be regulated more precisely. The boundary layer method also permits examination of regional differences in exchange efficiency, although in still water such differences do not appear to be significant in trout larvae. The mean steepness of the PO2 gradient in the boundary layer and, hence, the mean rate of area-specific O2 uptake were essentially the same (P>0.05) at all seven locations tested in this study. The

  15. Bayesian NL interpretation and learning

    NARCIS (Netherlands)

    Zeevat, H.

    2011-01-01

    Everyday natural language communication is normally successful, even though contemporary computational linguistics has shown that NL is characterised by very high degree of ambiguity and the results of stochastic methods are not good enough to explain the high success rate. Bayesian natural language

  16. Bayesian optimization for computationally extensive probability distributions.

    Science.gov (United States)

    Tamura, Ryo; Hukushima, Koji

    2018-01-01

    An efficient method for finding a better maximizer of computationally extensive probability distributions is proposed on the basis of a Bayesian optimization technique. A key idea of the proposed method is to use extreme values of acquisition functions by Gaussian processes for the next training phase, which should be located near a local maximum or a global maximum of the probability distribution. Our Bayesian optimization technique is applied to the posterior distribution in the effective physical model estimation, which is a computationally extensive probability distribution. Even when the number of sampling points on the posterior distributions is fixed to be small, the Bayesian optimization provides a better maximizer of the posterior distributions in comparison to those by the random search method, the steepest descent method, or the Monte Carlo method. Furthermore, the Bayesian optimization improves the results efficiently by combining the steepest descent method and thus it is a powerful tool to search for a better maximizer of computationally extensive probability distributions.

  17. Cation solvation with quantum chemical effects modeled by a size-consistent multi-partitioning quantum mechanics/molecular mechanics method.

    Science.gov (United States)

    Watanabe, Hiroshi C; Kubillus, Maximilian; Kubař, Tomáš; Stach, Robert; Mizaikoff, Boris; Ishikita, Hiroshi

    2017-07-21

    In the condensed phase, quantum chemical properties such as many-body effects and intermolecular charge fluctuations are critical determinants of the solvation structure and dynamics. Thus, a quantum mechanical (QM) molecular description is required for both solute and solvent to incorporate these properties. However, it is challenging to conduct molecular dynamics (MD) simulations for condensed systems of sufficient scale when adapting QM potentials. To overcome this problem, we recently developed the size-consistent multi-partitioning (SCMP) quantum mechanics/molecular mechanics (QM/MM) method and realized stable and accurate MD simulations, using the QM potential to a benchmark system. In the present study, as the first application of the SCMP method, we have investigated the structures and dynamics of Na + , K + , and Ca 2+ solutions based on nanosecond-scale sampling, a sampling 100-times longer than that of conventional QM-based samplings. Furthermore, we have evaluated two dynamic properties, the diffusion coefficient and difference spectra, with high statistical certainty. Furthermore the calculation of these properties has not previously been possible within the conventional QM/MM framework. Based on our analysis, we have quantitatively evaluated the quantum chemical solvation effects, which show distinct differences between the cations.

  18. (Bostrychus sinensis) and partitioned Bayesian analysis of Eleotri

    Indian Academy of Sciences (India)

    2013-08-12

    Aug 12, 2013 ... breeding fish, but few molecular studies have been conducted ... 2008). Puta- tive origin of L-strand replication and control region were determined by ..... cernible DHU stem in the B. sinensis mitochondrial genome, which was ...

  19. Application of the Monte Carlo method for building up models for octanol-water partition coefficient of platinum complexes

    Science.gov (United States)

    Toropov, Andrey A.; Toropova, Alla P.

    2018-06-01

    Predictive model of logP for Pt(II) and Pt(IV) complexes built up with the Monte Carlo method using the CORAL software has been validated with six different splits into the training and validation sets. The improving of the predictive potential of models for six different splits has been obtained using so-called index of ideality of correlation. The suggested models give possibility to extract molecular features, which cause the increase or vice versa decrease of the logP.

  20. A note on the relationships between multiple imputation, maximum likelihood and fully Bayesian methods for missing responses in linear regression models.

    Science.gov (United States)

    Chen, Qingxia; Ibrahim, Joseph G

    2014-07-01

    Multiple Imputation, Maximum Likelihood and Fully Bayesian methods are the three most commonly used model-based approaches in missing data problems. Although it is easy to show that when the responses are missing at random (MAR), the complete case analysis is unbiased and efficient, the aforementioned methods are still commonly used in practice for this setting. To examine the performance of and relationships between these three methods in this setting, we derive and investigate small sample and asymptotic expressions of the estimates and standard errors, and fully examine how these estimates are related for the three approaches in the linear regression model when the responses are MAR. We show that when the responses are MAR in the linear model, the estimates of the regression coefficients using these three methods are asymptotically equivalent to the complete case estimates under general conditions. One simulation and a real data set from a liver cancer clinical trial are given to compare the properties of these methods when the responses are MAR.

  1. Bayesian nonparametric hierarchical modeling.

    Science.gov (United States)

    Dunson, David B

    2009-04-01

    In biomedical research, hierarchical models are very widely used to accommodate dependence in multivariate and longitudinal data and for borrowing of information across data from different sources. A primary concern in hierarchical modeling is sensitivity to parametric assumptions, such as linearity and normality of the random effects. Parametric assumptions on latent variable distributions can be challenging to check and are typically unwarranted, given available prior knowledge. This article reviews some recent developments in Bayesian nonparametric methods motivated by complex, multivariate and functional data collected in biomedical studies. The author provides a brief review of flexible parametric approaches relying on finite mixtures and latent class modeling. Dirichlet process mixture models are motivated by the need to generalize these approaches to avoid assuming a fixed finite number of classes. Focusing on an epidemiology application, the author illustrates the practical utility and potential of nonparametric Bayes methods.

  2. An overview on Approximate Bayesian computation*

    Directory of Open Access Journals (Sweden)

    Baragatti Meïli

    2014-01-01

    Full Text Available Approximate Bayesian computation techniques, also called likelihood-free methods, are one of the most satisfactory approach to intractable likelihood problems. This overview presents recent results since its introduction about ten years ago in population genetics.

  3. Monte Carlo Bayesian inference on a statistical model of sub-gridcolumn moisture variability using high-resolution cloud observations. Part 1: Method

    Science.gov (United States)

    Norris, Peter M.; da Silva, Arlindo M.

    2018-01-01

    A method is presented to constrain a statistical model of sub-gridcolumn moisture variability using high-resolution satellite cloud data. The method can be used for large-scale model parameter estimation or cloud data assimilation. The gridcolumn model includes assumed probability density function (PDF) intra-layer horizontal variability and a copula-based inter-layer correlation model. The observables used in the current study are Moderate Resolution Imaging Spectroradiometer (MODIS) cloud-top pressure, brightness temperature and cloud optical thickness, but the method should be extensible to direct cloudy radiance assimilation for a small number of channels. The algorithm is a form of Bayesian inference with a Markov chain Monte Carlo (MCMC) approach to characterizing the posterior distribution. This approach is especially useful in cases where the background state is clear but cloudy observations exist. In traditional linearized data assimilation methods, a subsaturated background cannot produce clouds via any infinitesimal equilibrium perturbation, but the Monte Carlo approach is not gradient-based and allows jumps into regions of non-zero cloud probability. The current study uses a skewed-triangle distribution for layer moisture. The article also includes a discussion of the Metropolis and multiple-try Metropolis versions of MCMC. PMID:29618847

  4. Monte Carlo Bayesian Inference on a Statistical Model of Sub-Gridcolumn Moisture Variability Using High-Resolution Cloud Observations. Part 1: Method

    Science.gov (United States)

    Norris, Peter M.; Da Silva, Arlindo M.

    2016-01-01

    A method is presented to constrain a statistical model of sub-gridcolumn moisture variability using high-resolution satellite cloud data. The method can be used for large-scale model parameter estimation or cloud data assimilation. The gridcolumn model includes assumed probability density function (PDF) intra-layer horizontal variability and a copula-based inter-layer correlation model. The observables used in the current study are Moderate Resolution Imaging Spectroradiometer (MODIS) cloud-top pressure, brightness temperature and cloud optical thickness, but the method should be extensible to direct cloudy radiance assimilation for a small number of channels. The algorithm is a form of Bayesian inference with a Markov chain Monte Carlo (MCMC) approach to characterizing the posterior distribution. This approach is especially useful in cases where the background state is clear but cloudy observations exist. In traditional linearized data assimilation methods, a subsaturated background cannot produce clouds via any infinitesimal equilibrium perturbation, but the Monte Carlo approach is not gradient-based and allows jumps into regions of non-zero cloud probability. The current study uses a skewed-triangle distribution for layer moisture. The article also includes a discussion of the Metropolis and multiple-try Metropolis versions of MCMC.

  5. Benchmark of the non-parametric Bayesian deconvolution method implemented in the SINBAD code for X/γ rays spectra processing

    Energy Technology Data Exchange (ETDEWEB)

    Rohée, E. [CEA, LIST, Laboratoire Capteurs et Architectures Electroniques, F-91191 Gif-sur-Yvette (France); Coulon, R., E-mail: romain.coulon@cea.fr [CEA, LIST, Laboratoire Capteurs et Architectures Electroniques, F-91191 Gif-sur-Yvette (France); Carrel, F. [CEA, LIST, Laboratoire Capteurs et Architectures Electroniques, F-91191 Gif-sur-Yvette (France); Dautremer, T.; Barat, E.; Montagu, T. [CEA, LIST, Laboratoire de Modélisation et Simulation des Systèmes, F-91191 Gif-sur-Yvette (France); Normand, S. [CEA, DAM, Le Ponant, DPN/STXN, F-75015 Paris (France); Jammes, C. [CEA, DEN, Cadarache, DER/SPEx/LDCI, F-13108 Saint-Paul-lez-Durance (France)

    2016-11-11

    Radionuclide identification and quantification are a serious concern for many applications as for in situ monitoring at nuclear facilities, laboratory analysis, special nuclear materials detection, environmental monitoring, and waste measurements. High resolution gamma-ray spectrometry based on high purity germanium diode detectors is the best solution available for isotopic identification. Over the last decades, methods have been developed to improve gamma spectra analysis. However, some difficulties remain in the analysis when full energy peaks are folded together with high ratio between their amplitudes, and when the Compton background is much larger compared to the signal of a single peak. In this context, this study deals with the comparison between a conventional analysis based on “iterative peak fitting deconvolution” method and a “nonparametric Bayesian deconvolution” approach developed by the CEA LIST and implemented into the SINBAD code. The iterative peak fit deconvolution is used in this study as a reference method largely validated by industrial standards to unfold complex spectra from HPGe detectors. Complex cases of spectra are studied from IAEA benchmark protocol tests and with measured spectra. The SINBAD code shows promising deconvolution capabilities compared to the conventional method without any expert parameter fine tuning.

  6. A Study on the Quantitative Assessment Method of Software Requirement Documents Using Software Engineering Measures and Bayesian Belief Networks

    International Nuclear Information System (INIS)

    Eom, Heung Seop; Kang, Hyun Gook; Park, Ki Hong; Kwon, Kee Choon; Chang, Seung Cheol

    2005-01-01

    One of the major challenges in using the digital systems in a NPP is the reliability estimation of safety critical software embedded in the digital safety systems. Precise quantitative assessment of the reliability of safety critical software is nearly impossible, since many of the aspects to be considered are of qualitative nature and not directly measurable, but they have to be estimated for a practical use. Therefore an expert's judgment plays an important role in estimating the reliability of the software embedded in safety-critical systems in practice, because they can deal with all the diverse evidence relevant to the reliability and can perform an inference based on the evidence. But, in general, the experts' way of combining the diverse evidence and performing an inference is usually informal and qualitative, which is hard to discuss and will eventually lead to a debate about the conclusion. We have been carrying out research on a quantitative assessment of the reliability of safety critical software using Bayesian Belief Networks (BBN). BBN has been proven to be a useful modeling formalism because a user can represent a complex set of events and relationships in a fashion that can easily be interpreted by others. In the previous works we have assessed a software requirement specification of a reactor protection system by using our BBN-based assessment model. The BBN model mainly employed an expert's subjective probabilities as inputs. In the process of assessing the software requirement documents we found out that the BBN model was excessively dependent on experts' subjective judgments in a large part. Therefore, to overcome the weakness of our methodology we employed conventional software engineering measures into the BBN model as shown in this paper. The quantitative relationship between the conventional software measures and the reliability of software were not identified well in the past. Then recently there appeared a few researches on a ranking of

  7. Towards cleaner methods for the production of Mo-99 using refractory ceramics and its relevance to actinide partitioning and transmutation

    Energy Technology Data Exchange (ETDEWEB)

    Luca, V.; Dos Santos, L.; Vaccaro, J. [Comision Nacional de Energia Atomica, Centro Atomico Constituyentes, Av. General Paz 1499, 1650 San Martin, Buenos Aires (Argentina)

    2016-07-01

    Mo-99 is the most utilized isotope in nuclear medicine accounting for over 30 million medical diagnostic procedures annually worldwide. The process for the production of Mo-99 through fission of U-235 normally involves the irradiation of UAl{sub x} dispersion plate fuel in a research reactor, the subsequent dissolution of the fuel plate, the selective separation of the Mo-99 from all of the other fission products and possibly also the recovery of U-235 for future reuse. Compared to the amount of product recovered, copious radioactive waste is generated during the Mo-99 production process. Gaseous wastes are produced at the head-end during the plate dissolution and several liquid wastes are produced during the recovering of Mo-99 using solid extractants, typically polymeric ion exchange resins, which themselves constitute an additional waste stream. It would be extremely advantageous to devise a new process that generates little or no waste. We have been working on a new strategy for the production of fission Mo-99 that involves replacing the dispersion plate targets that are used in the traditional process with inert or active matrix fuel particles that do not need to be dissolved. In one embodiment of the strategy the preparation of new highly porous ZrC{sub x} and graphite-ZrC{sub x} composite target kernels are used that are prepared through polymer templating. The surface properties of these porous materials have been studied and are such that they can be easily loaded with uranium, or for that matter, with any other actinide. In our work we are exploring the possibility of selectively extracting the Mo-99 from the irradiated target kernels by either solution or gas-phase methods and then easily recover the uranium. The fission product-containing kernels can be oxidized in air to generate ZrO{sub 2} that can act as a stable host material either alone or as part of a multiphase ceramic matrix or possibly even as an actinide transmutation host. At the conceptual

  8. MCMC for parameters estimation by bayesian approach

    International Nuclear Information System (INIS)

    Ait Saadi, H.; Ykhlef, F.; Guessoum, A.

    2011-01-01

    This article discusses the parameter estimation for dynamic system by a Bayesian approach associated with Markov Chain Monte Carlo methods (MCMC). The MCMC methods are powerful for approximating complex integrals, simulating joint distributions, and the estimation of marginal posterior distributions, or posterior means. The MetropolisHastings algorithm has been widely used in Bayesian inference to approximate posterior densities. Calibrating the proposal distribution is one of the main issues of MCMC simulation in order to accelerate the convergence.

  9. Understanding Computational Bayesian Statistics

    CERN Document Server

    Bolstad, William M

    2011-01-01

    A hands-on introduction to computational statistics from a Bayesian point of view Providing a solid grounding in statistics while uniquely covering the topics from a Bayesian perspective, Understanding Computational Bayesian Statistics successfully guides readers through this new, cutting-edge approach. With its hands-on treatment of the topic, the book shows how samples can be drawn from the posterior distribution when the formula giving its shape is all that is known, and how Bayesian inferences can be based on these samples from the posterior. These ideas are illustrated on common statistic

  10. An introduction to using Bayesian linear regression with clinical data.

    Science.gov (United States)

    Baldwin, Scott A; Larson, Michael J

    2017-11-01

    Statistical training psychology focuses on frequentist methods. Bayesian methods are an alternative to standard frequentist methods. This article provides researchers with an introduction to fundamental ideas in Bayesian modeling. We use data from an electroencephalogram (EEG) and anxiety study to illustrate Bayesian models. Specifically, the models examine the relationship between error-related negativity (ERN), a particular event-related potential, and trait anxiety. Methodological topics covered include: how to set up a regression model in a Bayesian framework, specifying priors, examining convergence of the model, visualizing and interpreting posterior distributions, interval estimates, expected and predicted values, and model comparison tools. We also discuss situations where Bayesian methods can outperform frequentist methods as well has how to specify more complicated regression models. Finally, we conclude with recommendations about reporting guidelines for those using Bayesian methods in their own research. We provide data and R code for replicating our analyses. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. An approximate inversion method of geoelectrical sounding data using linear and bayesian statistical approaches. Examples of Tritrivakely volcanic lake and Mahitsy area (central part of Madagascar)

    International Nuclear Information System (INIS)

    Ranaivo Nomenjanahary, F.; Rakoto, H.; Ratsimbazafy, J.B.

    1994-08-01

    This paper is concerned with resistivity sounding measurements performed from single site (vertical sounding) or from several sites (profiles) within a bounded area. The objective is to present an accurate information about the study area and to estimate the likelihood of the produced quantitative models. The achievement of this objective obviously requires quite relevant data and processing methods. It also requires interpretation methods which should take into account the probable effect of an heterogeneous structure. In front of such difficulties, the interpretation of resistivity sounding data inevitably involves the use of inversion methods. We suggest starting the interpretation in simple situation (1-D approximation), and using the rough but correct model obtained as an a-priori model for any more refined interpretation. Related to this point of view, special attention should be paid for the inverse problem applied to the resistivity sounding data. This inverse problem is nonlinear, while linearity inherent in the functional response used to describe the physical experiment. Two different approaches are used to build an approximate but higher dimensional inversion of geoelectrical data: the linear approach and the bayesian statistical approach. Some illustrations of their application in resistivity sounding data acquired at Tritrivakely volcanic lake (single site) and at Mahitsy area (several sites) will be given. (author). 28 refs, 7 figs

  12. Bayesian estimates of linkage disequilibrium

    Directory of Open Access Journals (Sweden)

    Abad-Grau María M

    2007-06-01

    Full Text Available Abstract Background The maximum likelihood estimator of D' – a standard measure of linkage disequilibrium – is biased toward disequilibrium, and the bias is particularly evident in small samples and rare haplotypes. Results This paper proposes a Bayesian estimation of D' to address this problem. The reduction of the bias is achieved by using a prior distribution on the pair-wise associations between single nucleotide polymorphisms (SNPs that increases the likelihood of equilibrium with increasing physical distances between pairs of SNPs. We show how to compute the Bayesian estimate using a stochastic estimation based on MCMC methods, and also propose a numerical approximation to the Bayesian estimates that can be used to estimate patterns of LD in large datasets of SNPs. Conclusion Our Bayesian estimator of D' corrects the bias toward disequilibrium that affects the maximum likelihood estimator. A consequence of this feature is a more objective view about the extent of linkage disequilibrium in the human genome, and a more realistic number of tagging SNPs to fully exploit the power of genome wide association studies.

  13. The Benefits of Adaptive Partitioning for Parallel AMR Applications

    Energy Technology Data Exchange (ETDEWEB)

    Steensland, Johan [Sandia National Lab. (SNL-CA), Livermore, CA (United States). Advanced Software Research and Development

    2008-07-01

    Parallel adaptive mesh refinement methods potentially lead to realistic modeling of complex three-dimensional physical phenomena. However, the dynamics inherent in these methods present significant challenges in data partitioning and load balancing. Significant human resources, including time, effort, experience, and knowledge, are required for determining the optimal partitioning technique for each new simulation. In reality, scientists resort to using the on-board partitioner of the computational framework, or to using the partitioning industry standard, ParMetis. Adaptive partitioning refers to repeatedly selecting, configuring and invoking the optimal partitioning technique at run-time, based on the current state of the computer and application. In theory, adaptive partitioning automatically delivers superior performance and eliminates the need for repeatedly spending valuable human resources for determining the optimal static partitioning technique. In practice, however, enabling frameworks are non-existent due to the inherent significant inter-disciplinary research challenges. This paper presents a study of a simple implementation of adaptive partitioning and discusses implied potential benefits from the perspective of common groups of users within computational science. The study is based on a large set of data derived from experiments including six real-life, multi-time-step adaptive applications from various scientific domains, five complementing and fundamentally different partitioning techniques, a large set of parameters corresponding to a wide spectrum of computing environments, and a flexible cost function that considers the relative impact of multiple partitioning metrics and diverse partitioning objectives. The results show that even a simple implementation of adaptive partitioning can automatically generate results statistically equivalent to the best static partitioning. Thus, it is possible to effectively eliminate the problem of determining the

  14. Bayesian models a statistical primer for ecologists

    CERN Document Server

    Hobbs, N Thompson

    2015-01-01

    Bayesian modeling has become an indispensable tool for ecological research because it is uniquely suited to deal with complexity in a statistically coherent way. This textbook provides a comprehensive and accessible introduction to the latest Bayesian methods-in language ecologists can understand. Unlike other books on the subject, this one emphasizes the principles behind the computations, giving ecologists a big-picture understanding of how to implement this powerful statistical approach. Bayesian Models is an essential primer for non-statisticians. It begins with a definition of probabili

  15. An imprecise Dirichlet model for Bayesian analysis of failure data including right-censored observations

    International Nuclear Information System (INIS)

    Coolen, F.P.A.

    1997-01-01

    This paper is intended to make researchers in reliability theory aware of a recently introduced Bayesian model with imprecise prior distributions for statistical inference on failure data, that can also be considered as a robust Bayesian model. The model consists of a multinomial distribution with Dirichlet priors, making the approach basically nonparametric. New results for the model are presented, related to right-censored observations, where estimation based on this model is closely related to the product-limit estimator, which is an important statistical method to deal with reliability or survival data including right-censored observations. As for the product-limit estimator, the model considered in this paper aims at not using any information other than that provided by observed data, but our model fits into the robust Bayesian context which has the advantage that all inferences can be based on probabilities or expectations, or bounds for probabilities or expectations. The model uses a finite partition of the time-axis, and as such it is also related to life-tables

  16. The efficacy and safety of triple inhaled treatment in patients with chronic obstructive pulmonary disease: a systematic review and meta-analysis using Bayesian methods

    Directory of Open Access Journals (Sweden)

    Kwak MS

    2015-11-01

    Full Text Available Min-Sun Kwak,1 Eunyoung Kim,2 Eun Jin Jang,3 Hyun Jung Kim,4 Chang-Hoon Lee5 1Department of Internal Medicine, Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, Republic of Korea; 2Department of Statistics, Kyungpook National University, Daegu, Republic of Korea; 3Department of Information Statistics, Andong National University, Andong, Republic of Korea; 4Department of Preventive Medicine, College of Medicine, Korea University, Seoul, Republic of Korea; 5Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea Purpose: Although tiotropium (TIO and inhaled corticosteroid (ICS/long-acting β-agonists are frequently prescribed together, the efficacy of “triple therapy” has not been scientifically demonstrated. We conducted a systematic review and meta-analysis using Bayesian methods to compare triple therapy and TIO monotherapy.Methods: We searched the MEDLINE, EMBASE, and Cochrane Library databases for randomized controlled trials comparing the efficacy and safety of triple therapy and TIO monotherapy in patients with chronic obstructive pulmonary disease (COPD. We conducted a meta-analysis to compare the effectiveness and safety of triple therapy and TIO monotherapy using Bayesian random effects models.Results: Seven trials were included, and the risk of bias in the majority of the studies was acceptable. There were no statistically significant differences in the incidence of death and acute exacerbation of disease in the triple therapy and TIO monotherapy groups. Triple therapy improved the prebronchodilator forced expiratory volume in 1 second (mean difference [MD], 63.68 mL; 95% credible interval [CrI], 45.29–82.73, and patients receiving triple therapy showed more improvement in St George Respiratory Questionnaire scores (MD, -3.11 points; 95% Cr

  17. New Bayesian inference method using two steps of Markov chain Monte Carlo and its application to shock tube experiment data of Furan oxidation

    KAUST Repository

    Kim, Daesang

    2016-01-06

    A new Bayesian inference method has been developed and applied to Furan shock tube experimental data for efficient statistical inferences of the Arrhenius parameters of two OH radical consumption reactions. The collected experimental data, which consist of time series signals of OH radical concentrations of 14 shock tube experiments, may require several days for MCMC computations even with the support of a fast surrogate of the combustion simulation model, while the new method reduces it to several hours by splitting the process into two steps of MCMC: the first inference of rate constants and the second inference of the Arrhenius parameters. Each step has low dimensional parameter spaces and the second step does not need the executions of the combustion simulation. Furthermore, the new approach has more flexibility in choosing the ranges of the inference parameters, and the higher speed and flexibility enable the more accurate inferences and the analyses of the propagation of errors in the measured temperatures and the alignment of the experimental time to the inference results.

  18. Bayesian Mediation Analysis

    Science.gov (United States)

    Yuan, Ying; MacKinnon, David P.

    2009-01-01

    In this article, we propose Bayesian analysis of mediation effects. Compared with conventional frequentist mediation analysis, the Bayesian approach has several advantages. First, it allows researchers to incorporate prior information into the mediation analysis, thus potentially improving the efficiency of estimates. Second, under the Bayesian…

  19. The Bayesian Score Statistic

    NARCIS (Netherlands)

    Kleibergen, F.R.; Kleijn, R.; Paap, R.

    2000-01-01

    We propose a novel Bayesian test under a (noninformative) Jeffreys'priorspecification. We check whether the fixed scalar value of the so-calledBayesian Score Statistic (BSS) under the null hypothesis is aplausiblerealization from its known and standardized distribution under thealternative. Unlike

  20. A Bayesian modelling method for post-processing daily sub-seasonal to seasonal rainfall forecasts from global climate models and evaluation for 12 Australian catchments

    Directory of Open Access Journals (Sweden)

    A. Schepen

    2018-03-01

    Full Text Available Rainfall forecasts are an integral part of hydrological forecasting systems at sub-seasonal to seasonal timescales. In seasonal forecasting, global climate models (GCMs are now the go-to source for rainfall forecasts. For hydrological applications however, GCM forecasts are often biased and unreliable in uncertainty spread, and calibration is therefore required before use. There are sophisticated statistical techniques for calibrating monthly and seasonal aggregations of the forecasts. However, calibration of seasonal forecasts at the daily time step typically uses very simple statistical methods or climate analogue methods. These methods generally lack the sophistication to achieve unbiased, reliable and coherent forecasts of daily amounts and seasonal accumulated totals. In this study, we propose and evaluate a Rainfall Post-Processing method for Seasonal forecasts (RPP-S, which is based on the Bayesian joint probability modelling approach for calibrating daily forecasts and the Schaake Shuffle for connecting the daily ensemble members of different lead times. We apply the method to post-process ACCESS-S forecasts for 12 perennial and ephemeral catchments across Australia and for 12 initialisation dates. RPP-S significantly reduces bias in raw forecasts and improves both skill and reliability. RPP-S forecasts are also more skilful and reliable than forecasts derived from ACCESS-S forecasts that have been post-processed using quantile mapping, especially for monthly and seasonal accumulations. Several opportunities to improve the robustness and skill of RPP-S are identified. The new RPP-S post-processed forecasts will be used in ensemble sub-seasonal to seasonal streamflow applications.

  1. A Bayesian modelling method for post-processing daily sub-seasonal to seasonal rainfall forecasts from global climate models and evaluation for 12 Australian catchments

    Science.gov (United States)

    Schepen, Andrew; Zhao, Tongtiegang; Wang, Quan J.; Robertson, David E.

    2018-03-01

    Rainfall forecasts are an integral part of hydrological forecasting systems at sub-seasonal to seasonal timescales. In seasonal forecasting, global climate models (GCMs) are now the go-to source for rainfall forecasts. For hydrological applications however, GCM forecasts are often biased and unreliable in uncertainty spread, and calibration is therefore required before use. There are sophisticated statistical techniques for calibrating monthly and seasonal aggregations of the forecasts. However, calibration of seasonal forecasts at the daily time step typically uses very simple statistical methods or climate analogue methods. These methods generally lack the sophistication to achieve unbiased, reliable and coherent forecasts of daily amounts and seasonal accumulated totals. In this study, we propose and evaluate a Rainfall Post-Processing method for Seasonal forecasts (RPP-S), which is based on the Bayesian joint probability modelling approach for calibrating daily forecasts and the Schaake Shuffle for connecting the daily ensemble members of different lead times. We apply the method to post-process ACCESS-S forecasts for 12 perennial and ephemeral catchments across Australia and for 12 initialisation dates. RPP-S significantly reduces bias in raw forecasts and improves both skill and reliability. RPP-S forecasts are also more skilful and reliable than forecasts derived from ACCESS-S forecasts that have been post-processed using quantile mapping, especially for monthly and seasonal accumulations. Several opportunities to improve the robustness and skill of RPP-S are identified. The new RPP-S post-processed forecasts will be used in ensemble sub-seasonal to seasonal streamflow applications.

  2. Comparison of salting-out and sugaring-out liquid-liquid extraction methods for the partition of 10-hydroxy-2-decenoic acid in royal jelly and their co-extracted protein content.

    Science.gov (United States)

    Tu, Xijuan; Sun, Fanyi; Wu, Siyuan; Liu, Weiyi; Gao, Zhaosheng; Huang, Shaokang; Chen, Wenbin

    2018-01-15

    Homogeneous liquid-liquid extraction (h-LLE) has been receiving considerable attention as a sample preparation method due to its simple and fast partition of compounds with a wide range of polarities. To better understand the differences between the two h-LLE extraction approaches, salting-out assisted liquid-liquid extraction (SALLE) and sugaring-out assisted liquid-liquid extraction (SULLE), have been compared for the partition of 10-hydroxy-2-decenoic acid (10-HDA) from royal jelly, and for the co-extraction of proteins. Effects of the amount of phase partition agents and the concentration of acetonitrile (ACN) on the h-LLE were discussed. Results showed that partition efficiency of 10-HDA depends on the phase ratio in both SALLE and SULLE. Though the partition triggered by NaCl and glucose is less efficient than MgSO 4 in the 50% (v/v) ACN-water mixture, their extraction yields can be improved to be similar with that in MgSO 4 SALLE by increasing the initial concentration of ACN in the ACN-water mixture. The content of co-extracted protein was correlated with water concentration in the obtained upper phase. MgSO 4 showed the largest protein co-extraction at the low concentration of salt. Glucose exhibited a large protein co-extraction in the high phase ratio condition. Furthermore, NaCl with high initial ACN concentration is recommended because it produced high extraction yield for 10-HDA and the lowest amount of co-extracted protein. These observations would be valuable for the sample preparation of royal jelly. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. A Bayesian classifier for symbol recognition

    OpenAIRE

    Barrat , Sabine; Tabbone , Salvatore; Nourrissier , Patrick

    2007-01-01

    URL : http://www.buyans.com/POL/UploadedFile/134_9977.pdf; International audience; We present in this paper an original adaptation of Bayesian networks to symbol recognition problem. More precisely, a descriptor combination method, which enables to improve significantly the recognition rate compared to the recognition rates obtained by each descriptor, is presented. In this perspective, we use a simple Bayesian classifier, called naive Bayes. In fact, probabilistic graphical models, more spec...

  4. Bayesian target tracking based on particle filter

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    For being able to deal with the nonlinear or non-Gaussian problems, particle filters have been studied by many researchers. Based on particle filter, the extended Kalman filter (EKF) proposal function is applied to Bayesian target tracking. Markov chain Monte Carlo (MCMC) method, the resampling step, etc novel techniques are also introduced into Bayesian target tracking. And the simulation results confirm the improved particle filter with these techniques outperforms the basic one.

  5. PAQ: Partition Analysis of Quasispecies.

    Science.gov (United States)

    Baccam, P; Thompson, R J; Fedrigo, O; Carpenter, S; Cornette, J L

    2001-01-01

    The complexities of genetic data may not be accurately described by any single analytical tool. Phylogenetic analysis is often used to study the genetic relationship among different sequences. Evolutionary models and assumptions are invoked to reconstruct trees that describe the phylogenetic relationship among sequences. Genetic databases are rapidly accumulating large amounts of sequences. Newly acquired sequences, which have not yet been characterized, may require preliminary genetic exploration in order to build models describing the evolutionary relationship among sequences. There are clustering techniques that rely less on models of evolution, and thus may provide nice exploratory tools for identifying genetic similarities. Some of the more commonly used clustering methods perform better when data can be grouped into mutually exclusive groups. Genetic data from viral quasispecies, which consist of closely related variants that differ by small changes, however, may best be partitioned by overlapping groups. We have developed an intuitive exploratory program, Partition Analysis of Quasispecies (PAQ), which utilizes a non-hierarchical technique to partition sequences that are genetically similar. PAQ was used to analyze a data set of human immunodeficiency virus type 1 (HIV-1) envelope sequences isolated from different regions of the brain and another data set consisting of the equine infectious anemia virus (EIAV) regulatory gene rev. Analysis of the HIV-1 data set by PAQ was consistent with phylogenetic analysis of the same data, and the EIAV rev variants were partitioned into two overlapping groups. PAQ provides an additional tool which can be used to glean information from genetic data and can be used in conjunction with other tools to study genetic similarities and genetic evolution of viral quasispecies.

  6. Bayesian methods to restore and re build images: application to gamma-graphy and to photofission tomography; Methodes bayesiennes pour la restauration et la reconstruction d`images application a la gammagraphie et a la tomographie par photofissions

    Energy Technology Data Exchange (ETDEWEB)

    Stawinski, G

    1998-10-26

    Bayesian algorithms are developed to solve inverse problems in gamma imaging and photofission tomography. The first part of this work is devoted to the modeling of our measurement systems. Two models have been found for both applications: the first one is a simple conventional model and the second one is a cascaded point process model. EM and MCMC Bayesian algorithms for image restoration and image reconstruction have been developed for these models and compared. The cascaded point process model does not improve significantly the results previously obtained by the classical model. To original approaches have been proposed, which increase the results previously obtained. The first approach uses an inhomogeneous Markov Random Field as a prior law, and makes the regularization parameter spatially vary. However, the problem of the estimation of hyper-parameters has not been solved. In the case of the deconvolution of point sources, a second approach has been proposed, which introduces a high level prior model. The picture is modeled as a list of objects, whose parameters and number are unknown. The results obtained with this method are more accurate than those obtained with the conventional Markov Random Field prior model and require less computational costs. (author)

  7. Assessment of myocardial metabolic rate of glucose by means of Bayesian ICA and Markov Chain Monte Carlo methods in small animal PET imaging

    Science.gov (United States)

    Berradja, Khadidja; Boughanmi, Nabil

    2016-09-01

    In dynamic cardiac PET FDG studies the assessment of myocardial metabolic rate of glucose (MMRG) requires the knowledge of the blood input function (IF). IF can be obtained by manual or automatic blood sampling and cross calibrated with PET. These procedures are cumbersome, invasive and generate uncertainties. The IF is contaminated by spillover of radioactivity from the adjacent myocardium and this could cause important error in the estimated MMRG. In this study, we show that the IF can be extracted from the images in a rat heart study with 18F-fluorodeoxyglucose (18F-FDG) by means of Independent Component Analysis (ICA) based on Bayesian theory and Markov Chain Monte Carlo (MCMC) sampling method (BICA). Images of the heart from rats were acquired with the Sherbrooke small animal PET scanner. A region of interest (ROI) was drawn around the rat image and decomposed into blood and tissue using BICA. The Statistical study showed that there is a significant difference (p corrupted with spillover.

  8. Efficient Bayesian inference of subsurface flow models using nested sampling and sparse polynomial chaos surrogates

    KAUST Repository

    Elsheikh, Ahmed H.; Hoteit, Ibrahim; Wheeler, Mary Fanett

    2014-01-01

    An efficient Bayesian calibration method based on the nested sampling (NS) algorithm and non-intrusive polynomial chaos method is presented. Nested sampling is a Bayesian sampling algorithm that builds a discrete representation of the posterior

  9. The metabolic network of Clostridium acetobutylicum: Comparison of the approximate Bayesian computation via sequential Monte Carlo (ABC-SMC) and profile likelihood estimation (PLE) methods for determinability analysis.

    Science.gov (United States)

    Thorn, Graeme J; King, John R

    2016-01-01

    The Gram-positive bacterium Clostridium acetobutylicum is an anaerobic endospore-forming species which produces acetone, butanol and ethanol via the acetone-butanol (AB) fermentation process, leading to biofuels including butanol. In previous work we looked to estimate the parameters in an ordinary differential equation model of the glucose metabolism network using data from pH-controlled continuous culture experiments. Here we combine two approaches, namely the approximate Bayesian computation via an existing sequential Monte Carlo (ABC-SMC) method (to compute credible intervals for the parameters), and the profile likelihood estimation (PLE) (to improve the calculation of confidence intervals for the same parameters), the parameters in both cases being derived from experimental data from forward shift experiments. We also apply the ABC-SMC method to investigate which of the models introduced previously (one non-sporulation and four sporulation models) have the greatest strength of evidence. We find that the joint approximate posterior distribution of the parameters determines the same parameters as previously, including all of the basal and increased enzyme production rates and enzyme reaction activity parameters, as well as the Michaelis-Menten kinetic parameters for glucose ingestion, while other parameters are not as well-determined, particularly those connected with the internal metabolites acetyl-CoA, acetoacetyl-CoA and butyryl-CoA. We also find that the approximate posterior is strongly non-Gaussian, indicating that our previous assumption of elliptical contours of the distribution is not valid, which has the effect of reducing the numbers of pairs of parameters that are (linearly) correlated with each other. Calculations of confidence intervals using the PLE method back this up. Finally, we find that all five of our models are equally likely, given the data available at present. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Correct Bayesian and frequentist intervals are similar

    International Nuclear Information System (INIS)

    Atwood, C.L.

    1986-01-01

    This paper argues that Bayesians and frequentists will normally reach numerically similar conclusions, when dealing with vague data or sparse data. It is shown that both statistical methodologies can deal reasonably with vague data. With sparse data, in many important practical cases Bayesian interval estimates and frequentist confidence intervals are approximately equal, although with discrete data the frequentist intervals are somewhat longer. This is not to say that the two methodologies are equally easy to use: The construction of a frequentist confidence interval may require new theoretical development. Bayesians methods typically require numerical integration, perhaps over many variables. Also, Bayesian can easily fall into the trap of over-optimism about their amount of prior knowledge. But in cases where both intervals are found correctly, the two intervals are usually not very different. (orig.)

  11. Implementing the Bayesian paradigm in risk analysis

    International Nuclear Information System (INIS)

    Aven, T.; Kvaloey, J.T.

    2002-01-01

    The Bayesian paradigm comprises a unified and consistent framework for analyzing and expressing risk. Yet, we see rather few examples of applications where the full Bayesian setting has been adopted with specifications of priors of unknown parameters. In this paper, we discuss some of the practical challenges of implementing Bayesian thinking and methods in risk analysis, emphasizing the introduction of probability models and parameters and associated uncertainty assessments. We conclude that there is a need for a pragmatic view in order to 'successfully' apply the Bayesian approach, such that we can do the assignments of some of the probabilities without adopting the somewhat sophisticated procedure of specifying prior distributions of parameters. A simple risk analysis example is presented to illustrate ideas

  12. A Fast Numerical Method for Max-Convolution and the Application to Efficient Max-Product Inference in Bayesian Networks.

    Science.gov (United States)

    Serang, Oliver

    2015-08-01

    Observations depending on sums of random variables are common throughout many fields; however, no efficient solution is currently known for performing max-product inference on these sums of general discrete distributions (max-product inference can be used to obtain maximum a posteriori estimates). The limiting step to max-product inference is the max-convolution problem (sometimes presented in log-transformed form and denoted as "infimal convolution," "min-convolution," or "convolution on the tropical semiring"), for which no O(k log(k)) method is currently known. Presented here is an O(k log(k)) numerical method for estimating the max-convolution of two nonnegative vectors (e.g., two probability mass functions), where k is the length of the larger vector. This numerical max-convolution method is then demonstrated by performing fast max-product inference on a convolution tree, a data structure for performing fast inference given information on the sum of n discrete random variables in O(nk log(nk)log(n)) steps (where each random variable has an arbitrary prior distribution on k contiguous possible states). The numerical max-convolution method can be applied to specialized classes of hidden Markov models to reduce the runtime of computing the Viterbi path from nk(2) to nk log(k), and has potential application to the all-pairs shortest paths problem.

  13. Curriculum-Based Measurement of Reading: An Evaluation of Frequentist and Bayesian Methods to Model Progress Monitoring Data

    Science.gov (United States)

    Christ, Theodore J.; Desjardins, Christopher David

    2018-01-01

    Curriculum-Based Measurement of Oral Reading (CBM-R) is often used to monitor student progress and guide educational decisions. Ordinary least squares regression (OLSR) is the most widely used method to estimate the slope, or rate of improvement (ROI), even though published research demonstrates OLSR's lack of validity and reliability, and…

  14. Plane partition vesicles

    International Nuclear Information System (INIS)

    Rensburg, E J Janse van; Ma, J

    2006-01-01

    We examine partitions and their natural three-dimensional generalizations, plane partitions, as models of vesicles undergoing an inflation-deflation transition. The phase diagrams of these models include a critical point corresponding to an inflation-deflation transition, and exhibits multicritical scaling in the vicinity of a multicritical point located elsewhere on the critical curve. We determine the locations of the multicritical points by analysing the generating functions using analytic and numerical means. In addition, we determine the numerical values of the multicritical scaling exponents associated with the multicritical scaling regimes in these models

  15. Matrix string partition function

    CERN Document Server

    Kostov, Ivan K; Kostov, Ivan K.; Vanhove, Pierre

    1998-01-01

    We evaluate quasiclassically the Ramond partition function of Euclidean D=10 U(N) super Yang-Mills theory reduced to a two-dimensional torus. The result can be interpreted in terms of free strings wrapping the space-time torus, as expected from the point of view of Matrix string theory. We demonstrate that, when extrapolated to the ultraviolet limit (small area of the torus), the quasiclassical expressions reproduce exactly the recently obtained expression for the partition of the completely reduced SYM theory, including the overall numerical factor. This is an evidence that our quasiclassical calculation might be exact.

  16. Systematics and morphological evolution within the moss family Bryaceae: a comparison between parsimony and Bayesian methods for reconstruction of ancestral character states.

    Science.gov (United States)

    Pedersen, Niklas; Holyoak, David T; Newton, Angela E

    2007-06-01

    The Bryaceae are a large cosmopolitan moss family including genera of significant morphological and taxonomic complexity. Phylogenetic relationships within the Bryaceae were reconstructed based on DNA sequence data from all three genomic compartments. In addition, maximum parsimony and Bayesian inference were employed to reconstruct ancestral character states of 38 morphological plus four habitat characters and eight insertion/deletion events. The recovered phylogenetic patterns are generally in accord with previous phylogenies based on chloroplast DNA sequence data and three major clades are identified. The first clade comprises Bryum bornholmense, B. rubens, B. caespiticium, and Plagiobryum. This corroborates the hypothesis suggested by previous studies that several Bryum species are more closely related to Plagiobryum than to the core Bryum species. The second clade includes Acidodontium, Anomobryum, and Haplodontium, while the third clade contains the core Bryum species plus Imbribryum. Within the latter clade, B. subapiculatum and B. tenuisetum form the sister clade to Imbribryum. Reconstructions of ancestral character states under maximum parsimony and Bayesian inference suggest fourteen morphological synapomorphies for the ingroup and synapomorphies are detected for most clades within the ingroup. Maximum parsimony and Bayesian reconstructions of ancestral character states are mostly congruent although Bayesian inference shows that the posterior probability of ancestral character states may decrease dramatically when node support is taken into account. Bayesian inference also indicates that reconstructions may be ambiguous at internal nodes for highly polymorphic characters.

  17. Bayesian inference on proportional elections.

    Directory of Open Access Journals (Sweden)

    Gabriel Hideki Vatanabe Brunello

    Full Text Available Polls for majoritarian voting systems usually show estimates of the percentage of votes for each candidate. However, proportional vote systems do not necessarily guarantee the candidate with the most percentage of votes will be elected. Thus, traditional methods used in majoritarian elections cannot be applied on proportional elections. In this context, the purpose of this paper was to perform a Bayesian inference on proportional elections considering the Brazilian system of seats distribution. More specifically, a methodology to answer the probability that a given party will have representation on the chamber of deputies was developed. Inferences were made on a Bayesian scenario using the Monte Carlo simulation technique, and the developed methodology was applied on data from the Brazilian elections for Members of the Legislative Assembly and Federal Chamber of Deputies in 2010. A performance rate was also presented to evaluate the efficiency of the methodology. Calculations and simulations were carried out using the free R statistical software.

  18. Development of an Origin Trace Method based on Bayesian Inference and Artificial Neural Network for Missing or Stolen Nuclear Materials

    Energy Technology Data Exchange (ETDEWEB)

    Bin, Yim Ho; Min, Lee Seung; Min, Kim Kyung; Jeong, Hong Yoon; Kim, Jae Kwang [Nuclear Security Div., Daejeon (Korea, Republic of)

    2014-05-15

    Thus, 'to put nuclear materials under control' is an important issue for prosperity mankind. Unfortunately, numbers of illicit trafficking of nuclear materials have been increased for decades. Consequently, security of nuclear materials is recently spotlighted. After the 2{sup nd} Nuclear Security Summit in Seoul in 2012, the president of Korea had showed his devotion to nuclear security. One of the main responses for nuclear security related interest of Korea was to develop a national nuclear forensic support system. International Atomic Energy Agency (IAEA) published the document of Nuclear Security Series No.2 'Nuclear Forensics Support' in 2006 to encourage international cooperation of all IAEA member states for tracking nuclear attributions. There are two main questions related to nuclear forensics to answer in the document. The first question is 'what type of material is it?', and the second one is 'where did the material come from?' Korea Nuclear Forensic Library (K-NFL) and mathematical methods to trace origins of missing or stolen nuclear materials (MSNMs) are being developed by Korea Institute of Nuclear Non-proliferation and Control (KINAC) to answer those questions. Although the K-NFL has been designed to perform many functions, K-NFL is being developed to effectively trace the origin of MSNMs and tested to validate suitability of trace methods. New fuels and spent fuels need each trace method because of the different nature of data acquisition. An inductive logic was found to be appropriate for new fuels, which had values as well as a bistable property. On the other hand, machine learning was suitable for spent fuels, which were unable to measure, and thus needed simulation.

  19. The role of representation in Bayesian reasoning: Correcting common misconceptions

    OpenAIRE

    Gigerenzer, G.; Hoffrage, U.

    2007-01-01

    The terms nested sets, partitive frequencies, inside-outside view, and dual processes add little but confusion to our original analysis (Gigerenzer & Hoffrage 1995; 1999). The idea of nested set was introduced because of an oversight; it simply rephrases two of our equations. Representation in terms of chances, in contrast, is a novel contribution yet consistent with our computational analysis - it uses exactly the same numbers as natural frequencies. We show that non-Bayesian reasoning in ch...

  20. Modeling framework for representing long-term effectiveness of best management practices in addressing hydrology and water quality problems: Framework development and demonstration using a Bayesian method

    Science.gov (United States)

    Liu, Yaoze; Engel, Bernard A.; Flanagan, Dennis C.; Gitau, Margaret W.; McMillan, Sara K.; Chaubey, Indrajeet; Singh, Shweta

    2018-05-01

    Best management practices (BMPs) are popular approaches used to improve hydrology and water quality. Uncertainties in BMP effectiveness over time may result in overestimating long-term efficiency in watershed planning strategies. To represent varying long-term BMP effectiveness in hydrologic/water quality models, a high level and forward-looking modeling framework was developed. The components in the framework consist of establishment period efficiency, starting efficiency, efficiency for each storm event, efficiency between maintenance, and efficiency over the life cycle. Combined, they represent long-term efficiency for a specific type of practice and specific environmental concern (runoff/pollutant). An approach for possible implementation of the framework was discussed. The long-term impacts of grass buffer strips (agricultural BMP) and bioretention systems (urban BMP) in reducing total phosphorus were simulated to demonstrate the framework. Data gaps were captured in estimating the long-term performance of the BMPs. A Bayesian method was used to match the simulated distribution of long-term BMP efficiencies with the observed distribution with the assumption that the observed data represented long-term BMP efficiencies. The simulated distribution matched the observed distribution well with only small total predictive uncertainties. With additional data, the same method can be used to further improve the simulation results. The modeling framework and results of this study, which can be adopted in hydrologic/water quality models to better represent long-term BMP effectiveness, can help improve decision support systems for creating long-term stormwater management strategies for watershed management projects.

  1. A Bayesian method to quantify azimuthal anisotropy model uncertainties: application to global azimuthal anisotropy in the upper mantle and transition zone

    Science.gov (United States)

    Yuan, K.; Beghein, C.

    2018-04-01

    Seismic anisotropy is a powerful tool to constrain mantle deformation, but its existence in the deep upper mantle and topmost lower mantle is still uncertain. Recent results from higher mode Rayleigh waves have, however, revealed the presence of 1 per cent azimuthal anisotropy between 300 and 800 km depth, and changes in azimuthal anisotropy across the mantle transition zone boundaries. This has important consequences for our understanding of mantle convection patterns and deformation of deep mantle material. Here, we propose a Bayesian method to model depth variations in azimuthal anisotropy and to obtain quantitative uncertainties on the fast seismic direction and anisotropy amplitude from phase velocity dispersion maps. We applied this new method to existing global fundamental and higher mode Rayleigh wave phase velocity maps to assess the likelihood of azimuthal anisotropy in the deep upper mantle and to determine whether previously detected changes in anisotropy at the transition zone boundaries are robustly constrained by those data. Our results confirm that deep upper-mantle azimuthal anisotropy is favoured and well constrained by the higher mode data employed. The fast seismic directions are in agreement with our previously published model. The data favour a model characterized, on average, by changes in azimuthal anisotropy at the top and bottom of the transition zone. However, this change in fast axes is not a global feature as there are regions of the model where the azimuthal anisotropy direction is unlikely to change across depths in the deep upper mantle. We were, however, unable to detect any clear pattern or connection with surface tectonics. Future studies will be needed to further improve the lateral resolution of this type of model at transition zone depths.

  2. A non-linear and stochastic response surface method for Bayesian estimation of uncertainty in soil moisture simulation from a land surface model

    Directory of Open Access Journals (Sweden)

    F. Hossain

    2004-01-01

    Full Text Available This study presents a simple and efficient scheme for Bayesian estimation of uncertainty in soil moisture simulation by a Land Surface Model (LSM. The scheme is assessed within a Monte Carlo (MC simulation framework based on the Generalized Likelihood Uncertainty Estimation (GLUE methodology. A primary limitation of using the GLUE method is the prohibitive computational burden imposed by uniform random sampling of the model's parameter distributions. Sampling is improved in the proposed scheme by stochastic modeling of the parameters' response surface that recognizes the non-linear deterministic behavior between soil moisture and land surface parameters. Uncertainty in soil moisture simulation (model output is approximated through a Hermite polynomial chaos expansion of normal random variables that represent the model's parameter (model input uncertainty. The unknown coefficients of the polynomial are calculated using limited number of model simulation runs. The calibrated polynomial is then used as a fast-running proxy to the slower-running LSM to predict the degree of representativeness of a randomly sampled model parameter set. An evaluation of the scheme's efficiency in sampling is made through comparison with the fully random MC sampling (the norm for GLUE and the nearest-neighborhood sampling technique. The scheme was able to reduce computational burden of random MC sampling for GLUE in the ranges of 10%-70%. The scheme was also found to be about 10% more efficient than the nearest-neighborhood sampling method in predicting a sampled parameter set's degree of representativeness. The GLUE based on the proposed sampling scheme did not alter the essential features of the uncertainty structure in soil moisture simulation. The scheme can potentially make GLUE uncertainty estimation for any LSM more efficient as it does not impose any additional structural or distributional assumptions.

  3. Doing bayesian data analysis a tutorial with R and BUGS

    CERN Document Server

    Kruschke, John K

    2011-01-01

    There is an explosion of interest in Bayesian statistics, primarily because recently created computational methods have finally made Bayesian analysis obtainable to a wide audience. Doing Bayesian Data Analysis, A Tutorial Introduction with R and BUGS provides an accessible approach to Bayesian data analysis, as material is explained clearly with concrete examples. The book begins with the basics, including essential concepts of probability and random sampling, and gradually progresses to advanced hierarchical modeling methods for realistic data. The text delivers comprehensive coverage of all

  4. Fast Bayesian optimal experimental design and its applications

    KAUST Repository

    Long, Quan

    2015-01-01

    We summarize our Laplace method and multilevel method of accelerating the computation of the expected information gain in a Bayesian Optimal Experimental Design (OED). Laplace method is a widely-used method to approximate an integration

  5. Estimating the spatial distribution of soil moisture based on Bayesian maximum entropy method with auxiliary data from remote sensing

    Science.gov (United States)

    Gao, Shengguo; Zhu, Zhongli; Liu, Shaomin; Jin, Rui; Yang, Guangchao; Tan, Lei

    2014-10-01

    Soil moisture (SM) plays a fundamental role in the land-atmosphere exchange process. Spatial estimation based on multi in situ (network) data is a critical way to understand the spatial structure and variation of land surface soil moisture. Theoretically, integrating densely sampled auxiliary data spatially correlated with soil moisture into the procedure of spatial estimation can improve its accuracy. In this study, we present a novel approach to estimate the spatial pattern of soil moisture by using the BME method based on wireless sensor network data and auxiliary information from ASTER (Terra) land surface temperature measurements. For comparison, three traditional geostatistic methods were also applied: ordinary kriging (OK), which used the wireless sensor network data only, regression kriging (RK) and ordinary co-kriging (Co-OK) which both integrated the ASTER land surface temperature as a covariate. In Co-OK, LST was linearly contained in the estimator, in RK, estimator is expressed as the sum of the regression estimate and the kriged estimate of the spatially correlated residual, but in BME, the ASTER land surface temperature was first retrieved as soil moisture based on the linear regression, then, the t-distributed prediction interval (PI) of soil moisture was estimated and used as soft data in probability form. The results indicate that all three methods provide reasonable estimations. Co-OK, RK and BME can provide a more accurate spatial estimation by integrating the auxiliary information Compared to OK. RK and BME shows more obvious improvement compared to Co-OK, and even BME can perform slightly better than RK. The inherent issue of spatial estimation (overestimation in the range of low values and underestimation in the range of high values) can also be further improved in both RK and BME. We can conclude that integrating auxiliary data into spatial estimation can indeed improve the accuracy, BME and RK take better advantage of the auxiliary

  6. The Partition of Multi-Resolution LOD Based on Qtm

    Science.gov (United States)

    Hou, M.-L.; Xing, H.-Q.; Zhao, X.-S.; Chen, J.

    2011-08-01

    The partition hierarch of Quaternary Triangular Mesh (QTM) determine the accuracy of spatial analysis and application based on QTM. In order to resolve the problem that the partition hierarch of QTM is limited by the level of the computer hardware, the new method that Multi- Resolution LOD (Level of Details) based on QTM will be discussed in this paper. This method can make the resolution of the cells varying with the viewpoint position by partitioning the cells of QTM, selecting the particular area according to the viewpoint; dealing with the cracks caused by different subdivisions, it satisfies the request of unlimited partition in part.

  7. THE PARTITION OF MULTI-RESOLUTION LOD BASED ON QTM

    Directory of Open Access Journals (Sweden)

    M.-L. Hou

    2012-08-01

    Full Text Available The partition hierarch of Quaternary Triangular Mesh (QTM determine the accuracy of spatial analysis and application based on QTM. In order to resolve the problem that the partition hierarch of QTM is limited by the level of the computer hardware, the new method that Multi- Resolution LOD (Level of Details based on QTM will be discussed in this paper. This method can make the resolution of the cells varying with the viewpoint position by partitioning the cells of QTM, selecting the particular area according to the viewpoint; dealing with the cracks caused by different subdivisions, it satisfies the request of unlimited partition in part.

  8. Noncausal Bayesian Vector Autoregression

    DEFF Research Database (Denmark)

    Lanne, Markku; Luoto, Jani

    We propose a Bayesian inferential procedure for the noncausal vector autoregressive (VAR) model that is capable of capturing nonlinearities and incorporating effects of missing variables. In particular, we devise a fast and reliable posterior simulator that yields the predictive distribution...

  9. Monotonicity Conditions for Multirate and Partitioned Explicit Runge-Kutta Schemes

    KAUST Repository

    Hundsdorfer, Willem; Mozartova, Anna; Savcenco, Valeriu

    2013-01-01

    of partitioned Runge-Kutta methods. It will also be seen that the incompatibility of consistency and mass-conservation holds for ‘genuine’ multirate schemes, but not for general partitioned methods.

  10. Learning Bayesian Networks with Incomplete Data by Augmentation

    OpenAIRE

    Adel, Tameem; de Campos, Cassio P.

    2016-01-01

    We present new algorithms for learning Bayesian networks from data with missing values using a data augmentation approach. An exact Bayesian network learning algorithm is obtained by recasting the problem into a standard Bayesian network learning problem without missing data. To the best of our knowledge, this is the first exact algorithm for this problem. As expected, the exact algorithm does not scale to large domains. We build on the exact method to create an approximate algorithm using a ...

  11. Bayesian emulation for optimization in multi-step portfolio decisions

    OpenAIRE

    Irie, Kaoru; West, Mike

    2016-01-01

    We discuss the Bayesian emulation approach to computational solution of multi-step portfolio studies in financial time series. "Bayesian emulation for decisions" involves mapping the technical structure of a decision analysis problem to that of Bayesian inference in a purely synthetic "emulating" statistical model. This provides access to standard posterior analytic, simulation and optimization methods that yield indirect solutions of the decision problem. We develop this in time series portf...

  12. Bayesian Networks An Introduction

    CERN Document Server

    Koski, Timo

    2009-01-01

    Bayesian Networks: An Introduction provides a self-contained introduction to the theory and applications of Bayesian networks, a topic of interest and importance for statisticians, computer scientists and those involved in modelling complex data sets. The material has been extensively tested in classroom teaching and assumes a basic knowledge of probability, statistics and mathematics. All notions are carefully explained and feature exercises throughout. Features include:.: An introduction to Dirichlet Distribution, Exponential Families and their applications.; A detailed description of learni

  13. A Bayesian encourages dropout

    OpenAIRE

    Maeda, Shin-ichi

    2014-01-01

    Dropout is one of the key techniques to prevent the learning from overfitting. It is explained that dropout works as a kind of modified L2 regularization. Here, we shed light on the dropout from Bayesian standpoint. Bayesian interpretation enables us to optimize the dropout rate, which is beneficial for learning of weight parameters and prediction after learning. The experiment result also encourages the optimization of the dropout.

  14. VLSI PARTITIONING ALGORITHM WITH ADAPTIVE CONTROL PARAMETER

    Directory of Open Access Journals (Sweden)

    P. N. Filippenko

    2013-03-01

    Full Text Available The article deals with the problem of very large-scale integration circuit partitioning. A graph is selected as a mathematical model describing integrated circuit. Modification of ant colony optimization algorithm is presented, which is used to solve graph partitioning problem. Ant colony optimization algorithm is an optimization method based on the principles of self-organization and other useful features of the ants’ behavior. The proposed search system is based on ant colony optimization algorithm with the improved method of the initial distribution and dynamic adjustment of the control search parameters. The experimental results and performance comparison show that the proposed method of very large-scale integration circuit partitioning provides the better search performance over other well known algorithms.

  15. A Bayesian Mixed-Methods Analysis of Basic Psychological Needs Satisfaction through Outdoor Learning and Its Influence on Motivational Behavior in Science Class

    Directory of Open Access Journals (Sweden)

    Ulrich Dettweiler

    2017-12-01

    Full Text Available Research has shown that outdoor educational interventions can lead to students' increased self-regulated motivational behavior. In this study, we searched into the satisfaction of basic psychological needs (BPN, i.e., autonomy support, the learners' experience of competence, and relatedness, both within the peer group and with their teachers, through outdoor learning. From 2014 to 2016, n = 281 students attended “research weeks” at a Student Science Lab in the Alpine National Park Berchtesgaden (Germany. The program is a curriculum-based one-week residential course, centered on a 2-day research expedition. Both before and after the course, students completed a composite questionnaire addressing BPN-satisfaction and overall motivational behavior in relation to the Self-Determination Index (SDI. At the latter time-point, students also reported on their experiences during the intervention. Questionnaire data was analyzed using a set of Bayesian General Linear Models with random effects. Those quantitative measures have been complemented by and contextualized with a set of qualitative survey methods. The results showed that the basic psychological needs influence the motivational behavior in both contexts equally, however on different scale levels. The basic needs satisfaction in the outdoor context is decisively higher than indoors. Moreover, the increment of competence-experience from the school context to the hands-on outdoor program appears to have the biggest impact to students' increased intrinsic motivation during the intervention. Increased autonomy support, student-teacher relations, and student-student relations have much less or no influence on the overall difference of motivational behavior. Gender does not influence the results. The contextualization partly supports those results and provide further explanation for the students' increased self-regulation in the outdoors. They add some explanatory thrust to the argument that outdoor

  16. The prediction of blood-tissue partitions, water-skin partitions and skin permeation for agrochemicals.

    Science.gov (United States)

    Abraham, Michael H; Gola, Joelle M R; Ibrahim, Adam; Acree, William E; Liu, Xiangli

    2014-07-01

    There is considerable interest in the blood-tissue distribution of agrochemicals, and a number of researchers have developed experimental methods for in vitro distribution. These methods involve the determination of saline-blood and saline-tissue partitions; not only are they indirect, but they do not yield the required in vivo distribution. The authors set out equations for gas-tissue and blood-tissue distribution, for partition from water into skin and for permeation from water through human skin. Together with Abraham descriptors for the agrochemicals, these equations can be used to predict values for all of these processes. The present predictions compare favourably with experimental in vivo blood-tissue distribution where available. The predictions require no more than simple arithmetic. The present method represents a much easier and much more economic way of estimating blood-tissue partitions than the method that uses saline-blood and saline-tissue partitions. It has the added advantages of yielding the required in vivo partitions and being easily extended to the prediction of partition of agrochemicals from water into skin and permeation from water through skin. © 2013 Society of Chemical Industry.

  17. An economic growth model based on financial credits distribution to the government economy priority sectors of each regency in Indonesia using hierarchical Bayesian method

    Science.gov (United States)

    Yasmirullah, Septia Devi Prihastuti; Iriawan, Nur; Sipayung, Feronika Rosalinda

    2017-11-01

    The success of regional economic establishment could be measured by economic growth. Since the Act No. 32 of 2004 has been implemented, unbalance economic among the regency in Indonesia is increasing. This condition is contrary different with the government goal to build society welfare through the economic activity development in each region. This research aims to examine economic growth through the distribution of bank credits to each Indonesia's regency. The data analyzed in this research is hierarchically structured data which follow normal distribution in first level. Two modeling approaches are employed in this research, a global-one level Bayesian approach and two-level hierarchical Bayesian approach. The result shows that hierarchical Bayesian has succeeded to demonstrate a better estimation than a global-one level Bayesian. It proves that the different economic growth in each province is significantly influenced by the variations of micro level characteristics in each province. These variations are significantly affected by cities and province characteristics in second level.

  18. Countering oversegmentation in partitioning-based connectivities

    NARCIS (Netherlands)

    Ouzounis, Georgios K.; Wilkinson, Michael H.F.

    2005-01-01

    A new theoretical development is presented for handling the over-segmentation problem in partitioning-based connected openings. The definition we propose treats singletons generated with the earlier method, as elements of a larger connected component. Unlike the existing formalism, this new method

  19. Bayesian uncertainty analyses of probabilistic risk models

    International Nuclear Information System (INIS)

    Pulkkinen, U.

    1989-01-01

    Applications of Bayesian principles to the uncertainty analyses are discussed in the paper. A short review of the most important uncertainties and their causes is provided. An application of the principle of maximum entropy to the determination of Bayesian prior distributions is described. An approach based on so called probabilistic structures is presented in order to develop a method of quantitative evaluation of modelling uncertainties. The method is applied to a small example case. Ideas for application areas for the proposed method are discussed

  20. Bayesian parameter estimation in probabilistic risk assessment

    International Nuclear Information System (INIS)

    Siu, Nathan O.; Kelly, Dana L.

    1998-01-01

    Bayesian statistical methods are widely used in probabilistic risk assessment (PRA) because of their ability to provide useful estimates of model parameters when data are sparse and because the subjective probability framework, from which these methods are derived, is a natural framework to address the decision problems motivating PRA. This paper presents a tutorial on Bayesian parameter estimation especially relevant to PRA. It summarizes the philosophy behind these methods, approaches for constructing likelihood functions and prior distributions, some simple but realistic examples, and a variety of cautions and lessons regarding practical applications. References are also provided for more in-depth coverage of various topics

  1. BAYESIAN BICLUSTERING FOR PATIENT STRATIFICATION.

    Science.gov (United States)

    Khakabimamaghani, Sahand; Ester, Martin

    2016-01-01

    The move from Empirical Medicine towards Personalized Medicine has attracted attention to Stratified Medicine (SM). Some methods are provided in the literature for patient stratification, which is the central task of SM, however, there are still significant open issues. First, it is still unclear if integrating different datatypes will help in detecting disease subtypes more accurately, and, if not, which datatype(s) are most useful for this task. Second, it is not clear how we can compare different methods of patient stratification. Third, as most of the proposed stratification methods are deterministic, there is a need for investigating the potential benefits of applying probabilistic methods. To address these issues, we introduce a novel integrative Bayesian biclustering method, called B2PS, for patient stratification and propose methods for evaluating the results. Our experimental results demonstrate the superiority of B2PS over a popular state-of-the-art method and the benefits of Bayesian approaches. Our results agree with the intuition that transcriptomic data forms a better basis for patient stratification than genomic data.

  2. Simultaneous discovery, estimation and prediction analysis of complex traits using a bayesian mixture model.

    Directory of Open Access Journals (Sweden)

    Gerhard Moser

    2015-04-01

    Full Text Available Gene discovery, estimation of heritability captured by SNP arrays, inference on genetic architecture and prediction analyses of complex traits are usually performed using different statistical models and methods, leading to inefficiency and loss of power. Here we use a Bayesian mixture model that simultaneously allows variant discovery, estimation of genetic variance explained by all variants and prediction of unobserved phenotypes in new samples. We apply the method to simulated data of quantitative traits and Welcome Trust Case Control Consortium (WTCCC data on disease and show that it provides accurate estimates of SNP-based heritability, produces unbiased estimators of risk in new samples, and that it can estimate genetic architecture by partitioning variation across hundreds to thousands of SNPs. We estimated that, depending on the trait, 2,633 to 9,411 SNPs explain all of the SNP-based heritability in the WTCCC diseases. The majority of those SNPs (>96% had small effects, confirming a substantial polygenic component to common diseases. The proportion of the SNP-based variance explained by large effects (each SNP explaining 1% of the variance varied markedly between diseases, ranging from almost zero for bipolar disorder to 72% for type 1 diabetes. Prediction analyses demonstrate that for diseases with major loci, such as type 1 diabetes and rheumatoid arthritis, Bayesian methods outperform profile scoring or mixed model approaches.

  3. Improving Transparency and Replication in Bayesian Statistics : The WAMBS-Checklist

    NARCIS (Netherlands)

    Depaoli, Sarah; van de Schoot, Rens

    2017-01-01

    Bayesian statistical methods are slowly creeping into all fields of science and are becoming ever more popular in applied research. Although it is very attractive to use Bayesian statistics, our personal experience has led us to believe that naively applying Bayesian methods can be dangerous for at

  4. Partitioning of unstructured meshes for load balancing

    International Nuclear Information System (INIS)

    Martin, O.C.; Otto, S.W.

    1994-01-01

    Many large-scale engineering and scientific calculations involve repeated updating of variables on an unstructured mesh. To do these types of computations on distributed memory parallel computers, it is necessary to partition the mesh among the processors so that the load balance is maximized and inter-processor communication time is minimized. This can be approximated by the problem, of partitioning a graph so as to obtain a minimum cut, a well-studied combinatorial optimization problem. Graph partitioning algorithms are discussed that give good but not necessarily optimum solutions. These algorithms include local search methods recursive spectral bisection, and more general purpose methods such as simulated annealing. It is shown that a general procedure enables to combine simulated annealing with Kernighan-Lin. The resulting algorithm is both very fast and extremely effective. (authors) 23 refs., 3 figs., 1 tab

  5. Inverse problems in the Bayesian framework

    International Nuclear Information System (INIS)

    Calvetti, Daniela; Somersalo, Erkki; Kaipio, Jari P

    2014-01-01

    The history of Bayesian methods dates back to the original works of Reverend Thomas Bayes and Pierre-Simon Laplace: the former laid down some of the basic principles on inverse probability in his classic article ‘An essay towards solving a problem in the doctrine of chances’ that was read posthumously in the Royal Society in 1763. Laplace, on the other hand, in his ‘Memoirs on inverse probability’ of 1774 developed the idea of updating beliefs and wrote down the celebrated Bayes’ formula in the form we know today. Although not identified yet as a framework for investigating inverse problems, Laplace used the formalism very much in the spirit it is used today in the context of inverse problems, e.g., in his study of the distribution of comets. With the evolution of computational tools, Bayesian methods have become increasingly popular in all fields of human knowledge in which conclusions need to be drawn based on incomplete and noisy data. Needless to say, inverse problems, almost by definition, fall into this category. Systematic work for developing a Bayesian inverse problem framework can arguably be traced back to the 1980s, (the original first edition being published by Elsevier in 1987), although articles on Bayesian methodology applied to inverse problems, in particular in geophysics, had appeared much earlier. Today, as testified by the articles in this special issue, the Bayesian methodology as a framework for considering inverse problems has gained a lot of popularity, and it has integrated very successfully with many traditional inverse problems ideas and techniques, providing novel ways to interpret and implement traditional procedures in numerical analysis, computational statistics, signal analysis and data assimilation. The range of applications where the Bayesian framework has been fundamental goes from geophysics, engineering and imaging to astronomy, life sciences and economy, and continues to grow. There is no question that Bayesian

  6. Low-Complexity Bayesian Estimation of Cluster-Sparse Channels

    KAUST Repository

    Ballal, Tarig; Al-Naffouri, Tareq Y.; Ahmed, Syed

    2015-01-01

    This paper addresses the problem of channel impulse response estimation for cluster-sparse channels under the Bayesian estimation framework. We develop a novel low-complexity minimum mean squared error (MMSE) estimator by exploiting the sparsity of the received signal profile and the structure of the measurement matrix. It is shown that due to the banded Toeplitz/circulant structure of the measurement matrix, a channel impulse response, such as underwater acoustic channel impulse responses, can be partitioned into a number of orthogonal or approximately orthogonal clusters. The orthogonal clusters, the sparsity of the channel impulse response and the structure of the measurement matrix, all combined, result in a computationally superior realization of the MMSE channel estimator. The MMSE estimator calculations boil down to simpler in-cluster calculations that can be reused in different clusters. The reduction in computational complexity allows for a more accurate implementation of the MMSE estimator. The proposed approach is tested using synthetic Gaussian channels, as well as simulated underwater acoustic channels. Symbol-error-rate performance and computation time confirm the superiority of the proposed method compared to selected benchmark methods in systems with preamble-based training signals transmitted over clustersparse channels.

  7. Low-Complexity Bayesian Estimation of Cluster-Sparse Channels

    KAUST Repository

    Ballal, Tarig

    2015-09-18

    This paper addresses the problem of channel impulse response estimation for cluster-sparse channels under the Bayesian estimation framework. We develop a novel low-complexity minimum mean squared error (MMSE) estimator by exploiting the sparsity of the received signal profile and the structure of the measurement matrix. It is shown that due to the banded Toeplitz/circulant structure of the measurement matrix, a channel impulse response, such as underwater acoustic channel impulse responses, can be partitioned into a number of orthogonal or approximately orthogonal clusters. The orthogonal clusters, the sparsity of the channel impulse response and the structure of the measurement matrix, all combined, result in a computationally superior realization of the MMSE channel estimator. The MMSE estimator calculations boil down to simpler in-cluster calculations that can be reused in different clusters. The reduction in computational complexity allows for a more accurate implementation of the MMSE estimator. The proposed approach is tested using synthetic Gaussian channels, as well as simulated underwater acoustic channels. Symbol-error-rate performance and computation time confirm the superiority of the proposed method compared to selected benchmark methods in systems with preamble-based training signals transmitted over clustersparse channels.

  8. Partitional clustering algorithms

    CERN Document Server

    2015-01-01

    This book summarizes the state-of-the-art in partitional clustering. Clustering, the unsupervised classification of patterns into groups, is one of the most important tasks in exploratory data analysis. Primary goals of clustering include gaining insight into, classifying, and compressing data. Clustering has a long and rich history that spans a variety of scientific disciplines including anthropology, biology, medicine, psychology, statistics, mathematics, engineering, and computer science. As a result, numerous clustering algorithms have been proposed since the early 1950s. Among these algorithms, partitional (nonhierarchical) ones have found many applications, especially in engineering and computer science. This book provides coverage of consensus clustering, constrained clustering, large scale and/or high dimensional clustering, cluster validity, cluster visualization, and applications of clustering. Examines clustering as it applies to large and/or high-dimensional data sets commonly encountered in reali...

  9. Why partition nuclear waste

    International Nuclear Information System (INIS)

    Cohen, J.J.

    1976-01-01

    A cursory review of literature dealing with various separatory processes involved in the handling of high-level liquid nuclear waste discloses that, for the most part, discussion centers on separation procedures and methodology for handling the resulting fractions, particularly the actinide wastes. There appears to be relatively little discussion on the incentives or motivations for performing these separations in the first place. Discussion is often limited to the assumption that we must separate out ''long-term'' from our ''short-term'' management problems. This paper deals with that assumption and devotes primary attention to the question of ''why partition waste'' rather than the question of ''how to partition waste'' or ''what to do with the segregated waste.''

  10. An Association-Oriented Partitioning Approach for Streaming Graph Query

    Directory of Open Access Journals (Sweden)

    Yun Hao

    2017-01-01

    Full Text Available The volumes of real-world graphs like knowledge graph are increasing rapidly, which makes streaming graph processing a hot research area. Processing graphs in streaming setting poses significant challenges from different perspectives, among which graph partitioning method plays a key role. Regarding graph query, a well-designed partitioning method is essential for achieving better performance. Existing offline graph partitioning methods often require full knowledge of the graph, which is not possible during streaming graph processing. In order to handle this problem, we propose an association-oriented streaming graph partitioning method named Assc. This approach first computes the rank values of vertices with a hybrid approximate PageRank algorithm. After splitting these vertices with an adapted variant affinity propagation algorithm, the process order on vertices in the sliding window can be determined. Finally, according to the level of these vertices and their association, the partition where the vertices should be distributed is decided. We compare its performance with a set of streaming graph partition methods and METIS, a widely adopted offline approach. The results show that our solution can partition graphs with hundreds of millions of vertices in streaming setting on a large collection of graph datasets and our approach outperforms other graph partitioning methods.

  11. BKP plane partitions

    International Nuclear Information System (INIS)

    Foda, Omar; Wheeler, Michael

    2007-01-01

    Using BKP neutral fermions, we derive a product expression for the generating function of volume-weighted plane partitions that satisfy two conditions. If we call a set of adjacent equal height-h columns, h > 0, an h-path, then 1. Every h-path can assume one of two possible colours. 2. There is a unique way to move along an h-path from any column to another

  12. BKP plane partitions

    Energy Technology Data Exchange (ETDEWEB)

    Foda, Omar; Wheeler, Michael [Department of Mathematics and Statistics, University of Melbourne, Parkville, Victoria 3010 (Australia)

    2007-01-15

    Using BKP neutral fermions, we derive a product expression for the generating function of volume-weighted plane partitions that satisfy two conditions. If we call a set of adjacent equal height-h columns, h > 0, an h-path, then 1. Every h-path can assume one of two possible colours. 2. There is a unique way to move along an h-path from any column to another.

  13. Generalised twisted partition functions

    CERN Document Server

    Petkova, V B

    2001-01-01

    We consider the set of partition functions that result from the insertion of twist operators compatible with conformal invariance in a given 2D Conformal Field Theory (CFT). A consistency equation, which gives a classification of twists, is written and solved in particular cases. This generalises old results on twisted torus boundary conditions, gives a physical interpretation of Ocneanu's algebraic construction, and might offer a new route to the study of properties of CFT.

  14. Bayesian calibration of thermodynamic parameters for geochemical speciation modeling of cementitious materials

    International Nuclear Information System (INIS)

    Sarkar, S.; Kosson, D.S.; Mahadevan, S.; Meeussen, J.C.L.; Sloot, H. van der; Arnold, J.R.; Brown, K.G.

    2012-01-01

    Chemical equilibrium modeling of cementitious materials requires aqueous–solid equilibrium constants of the controlling mineral phases (K sp ) and the available concentrations of primary components. Inherent randomness of the input and model parameters, experimental measurement error, the assumptions and approximations required for numerical simulation, and inadequate knowledge of the chemical process contribute to uncertainty in model prediction. A numerical simulation framework is developed in this paper to assess uncertainty in K sp values used in geochemical speciation models. A Bayesian statistical method is used in combination with an efficient, adaptive Metropolis sampling technique to develop probability density functions for K sp values. One set of leaching experimental observations is used for calibration and another set is used for comparison to evaluate the applicability of the approach. The estimated probability distributions of K sp values can be used in Monte Carlo simulation to assess uncertainty in the behavior of aqueous–solid partitioning of constituents in cement-based materials.

  15. Bayesian Nonparametric Hidden Markov Models with application to the analysis of copy-number-variation in mammalian genomes.

    Science.gov (United States)

    Yau, C; Papaspiliopoulos, O; Roberts, G O; Holmes, C

    2011-01-01

    We consider the development of Bayesian Nonparametric methods for product partition models such as Hidden Markov Models and change point models. Our approach uses a Mixture of Dirichlet Process (MDP) model for the unknown sampling distribution (likelihood) for the observations arising in each state and a computationally efficient data augmentation scheme to aid inference. The method uses novel MCMC methodology which combines recent retrospective sampling methods with the use of slice sampler variables. The methodology is computationally efficient, both in terms of MCMC mixing properties, and robustness to the length of the time series being investigated. Moreover, the method is easy to implement requiring little or no user-interaction. We apply our methodology to the analysis of genomic copy number variation.

  16. Bayesian networks with examples in R

    CERN Document Server

    Scutari, Marco

    2014-01-01

    Introduction. The Discrete Case: Multinomial Bayesian Networks. The Continuous Case: Gaussian Bayesian Networks. More Complex Cases. Theory and Algorithms for Bayesian Networks. Real-World Applications of Bayesian Networks. Appendices. Bibliography.

  17. Bayesian seismic AVO inversion

    Energy Technology Data Exchange (ETDEWEB)

    Buland, Arild

    2002-07-01

    A new linearized AVO inversion technique is developed in a Bayesian framework. The objective is to obtain posterior distributions for P-wave velocity, S-wave velocity and density. Distributions for other elastic parameters can also be assessed, for example acoustic impedance, shear impedance and P-wave to S-wave velocity ratio. The inversion algorithm is based on the convolutional model and a linearized weak contrast approximation of the Zoeppritz equation. The solution is represented by a Gaussian posterior distribution with explicit expressions for the posterior expectation and covariance, hence exact prediction intervals for the inverted parameters can be computed under the specified model. The explicit analytical form of the posterior distribution provides a computationally fast inversion method. Tests on synthetic data show that all inverted parameters were almost perfectly retrieved when the noise approached zero. With realistic noise levels, acoustic impedance was the best determined parameter, while the inversion provided practically no information about the density. The inversion algorithm has also been tested on a real 3-D dataset from the Sleipner Field. The results show good agreement with well logs but the uncertainty is high. The stochastic model includes uncertainties of both the elastic parameters, the wavelet and the seismic and well log data. The posterior distribution is explored by Markov chain Monte Carlo simulation using the Gibbs sampler algorithm. The inversion algorithm has been tested on a seismic line from the Heidrun Field with two wells located on the line. The uncertainty of the estimated wavelet is low. In the Heidrun examples the effect of including uncertainty of the wavelet and the noise level was marginal with respect to the AVO inversion results. We have developed a 3-D linearized AVO inversion method with spatially coupled model parameters where the objective is to obtain posterior distributions for P-wave velocity, S

  18. Determination of descriptors for polycyclic aromatic hydrocarbons and related compounds by chromatographic methods and liquid-liquid partition in totally organic biphasic systems.

    Science.gov (United States)

    Ariyasena, Thiloka C; Poole, Colin F

    2014-09-26

    Retention factors on several columns and at various temperatures using gas chromatography and from reversed-phase liquid chromatography on a SunFire C18 column with various mobile phase compositions containing acetonitrile, methanol and tetrahydrofuran as strength adjusting solvents are combined with liquid-liquid partition coefficients in totally organic biphasic systems to calculate descriptors for 23 polycyclic aromatic hydrocarbons and eighteen related compounds of environmental interest. The use of a consistent protocol for the above measurements provides descriptors that are more self consistent for the estimation of physicochemical properties (octanol-water, air-octanol, air-water, aqueous solubility, and subcooled liquid vapor pressure). The descriptor in this report tend to have smaller values for the L and E descriptors and random differences in the B and S descriptors compared with literature sources. A simple atom fragment constant model is proposed for the estimation of descriptors from structure for polycyclic aromatic hydrocarbons. The new descriptors show no bias in the prediction of the air-water partition coefficient for polycyclic aromatic hydrocarbons unlike the literature values. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Bayesian estimation and tracking a practical guide

    CERN Document Server

    Haug, Anton J

    2012-01-01

    A practical approach to estimating and tracking dynamic systems in real-worl applications Much of the literature on performing estimation for non-Gaussian systems is short on practical methodology, while Gaussian methods often lack a cohesive derivation. Bayesian Estimation and Tracking addresses the gap in the field on both accounts, providing readers with a comprehensive overview of methods for estimating both linear and nonlinear dynamic systems driven by Gaussian and non-Gaussian noices. Featuring a unified approach to Bayesian estimation and tracking, the book emphasizes the derivation

  20. Classifying emotion in Twitter using Bayesian network

    Science.gov (United States)

    Surya Asriadie, Muhammad; Syahrul Mubarok, Mohamad; Adiwijaya

    2018-03-01

    Language is used to express not only facts, but also emotions. Emotions are noticeable from behavior up to the social media statuses written by a person. Analysis of emotions in a text is done in a variety of media such as Twitter. This paper studies classification of emotions on twitter using Bayesian network because of its ability to model uncertainty and relationships between features. The result is two models based on Bayesian network which are Full Bayesian Network (FBN) and Bayesian Network with Mood Indicator (BNM). FBN is a massive Bayesian network where each word is treated as a node. The study shows the method used to train FBN is not very effective to create the best model and performs worse compared to Naive Bayes. F1-score for FBN is 53.71%, while for Naive Bayes is 54.07%. BNM is proposed as an alternative method which is based on the improvement of Multinomial Naive Bayes and has much lower computational complexity compared to FBN. Even though it’s not better compared to FBN, the resulting model successfully improves the performance of Multinomial Naive Bayes. F1-Score for Multinomial Naive Bayes model is 51.49%, while for BNM is 52.14%.