WorldWideScience

Sample records for highly inaccurate bayesian

  1. Distinguishing highly confident accurate and inaccurate memory: insights about relevant and irrelevant influences on memory confidence.

    Science.gov (United States)

    Chua, Elizabeth F; Hannula, Deborah E; Ranganath, Charan

    2012-01-01

    It is generally believed that accuracy and confidence in one's memory are related, but there are many instances when they diverge. Accordingly it is important to disentangle the factors that contribute to memory accuracy and confidence, especially those factors that contribute to confidence, but not accuracy. We used eye movements to separately measure fluent cue processing, the target recognition experience, and relative evidence assessment on recognition confidence and accuracy. Eye movements were monitored during a face-scene associative recognition task, in which participants first saw a scene cue, followed by a forced-choice recognition test for the associated face, with confidence ratings. Eye movement indices of the target recognition experience were largely indicative of accuracy, and showed a relationship to confidence for accurate decisions. In contrast, eye movements during the scene cue raised the possibility that more fluent cue processing was related to higher confidence for both accurate and inaccurate recognition decisions. In a second experiment we manipulated cue familiarity, and therefore cue fluency. Participants showed higher confidence for cue-target associations for when the cue was more familiar, especially for incorrect responses. These results suggest that over-reliance on cue familiarity and under-reliance on the target recognition experience may lead to erroneous confidence.

  2. A Public Relations Nightmare: ACLU Class Action Lawsuit Exposes Inaccurate and Inequitable High School Graduation Rates

    Science.gov (United States)

    Watson, Terri N.; Brown, Kathleen M.

    2010-01-01

    Florida's decision to equate a GED to a high school diploma undermines the attempt of No Child Left Behind to close the achievement gap, while infringing on the public's trust. Public trust fosters a culture of systemic equity and social justice, which are necessary for academic excellence (Byrk & Schneider, 2003). Florida's code of ethics for…

  3. Wing pattern morphology of three closely related Melitaea (Lepidoptera, Nymphalidae species reveals highly inaccurate external morphology-based species identification

    Directory of Open Access Journals (Sweden)

    Jure Jugovic

    2014-06-01

    Full Text Available Wing morphology of the three closely related species of Melitaea – M. athalia (Rottemburg, 1775, M. aurelia (Nickerl, 1850 and M. britomartis Assmann, 1847 – co-occurring in the Balkans (SE Europe was investigated in detail through visual inspection, morphometric analysis and multivariate statistical analysis. Results are compared to recent phylogenetic studies, searching for concordant patterns and discrepancies between the two approaches. The morphology of the genitalic structures is also compared with the results of the other two approaches. The main conclusions are as follows: (1 small albeit significant differences in wing morphology exist among the three species and (2 while the structure of male genitalia and phylogenetic position of the three species are concordant, they are (3 in discordance with the wing morphology. The present study represents another example where identification based on external morphology would lead to highly unreliable determinations, hence identification based on phylogenetic studies and/or genitalia is strongly recommended not only for the three studied species but also more broadly within the genus. Furthermore, we show that some of the characters generally used in the identification of these three Melitaea species should be avoided in future.

  4. Bayesian Peptide Peak Detection for High Resolution TOF Mass Spectrometry.

    Science.gov (United States)

    Zhang, Jianqiu; Zhou, Xiaobo; Wang, Honghui; Suffredini, Anthony; Zhang, Lin; Huang, Yufei; Wong, Stephen

    2010-11-01

    In this paper, we address the issue of peptide ion peak detection for high resolution time-of-flight (TOF) mass spectrometry (MS) data. A novel Bayesian peptide ion peak detection method is proposed for TOF data with resolution of 10 000-15 000 full width at half-maximum (FWHW). MS spectra exhibit distinct characteristics at this resolution, which are captured in a novel parametric model. Based on the proposed parametric model, a Bayesian peak detection algorithm based on Markov chain Monte Carlo (MCMC) sampling is developed. The proposed algorithm is tested on both simulated and real datasets. The results show a significant improvement in detection performance over a commonly employed method. The results also agree with expert's visual inspection. Moreover, better detection consistency is achieved across MS datasets from patients with identical pathological condition.

  5. Bayesian Inference of High-Dimensional Dynamical Ocean Models

    Science.gov (United States)

    Lin, J.; Lermusiaux, P. F. J.; Lolla, S. V. T.; Gupta, A.; Haley, P. J., Jr.

    2015-12-01

    This presentation addresses a holistic set of challenges in high-dimension ocean Bayesian nonlinear estimation: i) predict the probability distribution functions (pdfs) of large nonlinear dynamical systems using stochastic partial differential equations (PDEs); ii) assimilate data using Bayes' law with these pdfs; iii) predict the future data that optimally reduce uncertainties; and (iv) rank the known and learn the new model formulations themselves. Overall, we allow the joint inference of the state, equations, geometry, boundary conditions and initial conditions of dynamical models. Examples are provided for time-dependent fluid and ocean flows, including cavity, double-gyre and Strait flows with jets and eddies. The Bayesian model inference, based on limited observations, is illustrated first by the estimation of obstacle shapes and positions in fluid flows. Next, the Bayesian inference of biogeochemical reaction equations and of their states and parameters is presented, illustrating how PDE-based machine learning can rigorously guide the selection and discovery of complex ecosystem models. Finally, the inference of multiscale bottom gravity current dynamics is illustrated, motivated in part by classic overflows and dense water formation sites and their relevance to climate monitoring and dynamics. This is joint work with our MSEAS group at MIT.

  6. Assessing high reliability via Bayesian approach and accelerated tests

    International Nuclear Information System (INIS)

    Erto, Pasquale; Giorgio, Massimiliano

    2002-01-01

    Sometimes the assessment of very high reliability levels is difficult for the following main reasons: - the high reliability level of each item makes it impossible to obtain, in a reasonably short time, a sufficient number of failures; - the high cost of the high reliability items to submit to life tests makes it unfeasible to collect enough data for 'classical' statistical analyses. In the above context, this paper presents a Bayesian solution to the problem of estimation of the parameters of the Weibull-inverse power law model, on the basis of a limited number (say six) of life tests, carried out at different stress levels, all higher than the normal one. The over-stressed (i.e. accelerated) tests allow the use of experimental data obtained in a reasonably short time. The Bayesian approach enables one to reduce the required number of failures adding to the failure information the available a priori engineers' knowledge. This engineers' involvement conforms to the most advanced management policy that aims at involving everyone's commitment in order to obtain total quality. A Monte Carlo study of the non-asymptotic properties of the proposed estimators and a comparison with the properties of maximum likelihood estimators closes the work

  7. Bayesian Subset Modeling for High-Dimensional Generalized Linear Models

    KAUST Repository

    Liang, Faming

    2013-06-01

    This article presents a new prior setting for high-dimensional generalized linear models, which leads to a Bayesian subset regression (BSR) with the maximum a posteriori model approximately equivalent to the minimum extended Bayesian information criterion model. The consistency of the resulting posterior is established under mild conditions. Further, a variable screening procedure is proposed based on the marginal inclusion probability, which shares the same properties of sure screening and consistency with the existing sure independence screening (SIS) and iterative sure independence screening (ISIS) procedures. However, since the proposed procedure makes use of joint information from all predictors, it generally outperforms SIS and ISIS in real applications. This article also makes extensive comparisons of BSR with the popular penalized likelihood methods, including Lasso, elastic net, SIS, and ISIS. The numerical results indicate that BSR can generally outperform the penalized likelihood methods. The models selected by BSR tend to be sparser and, more importantly, of higher prediction ability. In addition, the performance of the penalized likelihood methods tends to deteriorate as the number of predictors increases, while this is not significant for BSR. Supplementary materials for this article are available online. © 2013 American Statistical Association.

  8. Bayesian Optimization in High Dimensions via Random Embeddings

    NARCIS (Netherlands)

    Wang, Z.; Zoghi, M.; Hutter, F.; Matheson, D.; de Freitas, N.; Rossi, F.

    2013-01-01

    Bayesian optimization techniques have been successfully applied to robotics, planning, sensor placement, recommendation, advertising, intelligent user interfaces and automatic algorithm configuration. Despite these successes, the approach is restricted to problems of moderate dimension, and several

  9. INLA goes extreme: Bayesian tail regression for the estimation of high spatio-temporal quantiles

    KAUST Repository

    Opitz, Thomas; Huser, Raphaë l; Bakka, Haakon; Rue, Haavard

    2018-01-01

    approach is based on a Bayesian generalized additive modeling framework that is designed to estimate complex trends in marginal extremes over space and time. First, we estimate a high non-stationary threshold using a gamma distribution for precipitation

  10. Adjusting case mix payment amounts for inaccurately reported comorbidity data.

    Science.gov (United States)

    Sutherland, Jason M; Hamm, Jeremy; Hatcher, Jeff

    2010-03-01

    Case mix methods such as diagnosis related groups have become a basis of payment for inpatient hospitalizations in many countries. Specifying cost weight values for case mix system payment has important consequences; recent evidence suggests case mix cost weight inaccuracies influence the supply of some hospital-based services. To begin to address the question of case mix cost weight accuracy, this paper is motivated by the objective of improving the accuracy of cost weight values due to inaccurate or incomplete comorbidity data. The methods are suitable to case mix methods that incorporate disease severity or comorbidity adjustments. The methods are based on the availability of detailed clinical and cost information linked at the patient level and leverage recent results from clinical data audits. A Bayesian framework is used to synthesize clinical data audit information regarding misclassification probabilities into cost weight value calculations. The models are implemented through Markov chain Monte Carlo methods. An example used to demonstrate the methods finds that inaccurate comorbidity data affects cost weight values by biasing cost weight values (and payments) downward. The implications for hospital payments are discussed and the generalizability of the approach is explored.

  11. Partial Deconvolution with Inaccurate Blur Kernel.

    Science.gov (United States)

    Ren, Dongwei; Zuo, Wangmeng; Zhang, David; Xu, Jun; Zhang, Lei

    2017-10-17

    Most non-blind deconvolution methods are developed under the error-free kernel assumption, and are not robust to inaccurate blur kernel. Unfortunately, despite the great progress in blind deconvolution, estimation error remains inevitable during blur kernel estimation. Consequently, severe artifacts such as ringing effects and distortions are likely to be introduced in the non-blind deconvolution stage. In this paper, we tackle this issue by suggesting: (i) a partial map in the Fourier domain for modeling kernel estimation error, and (ii) a partial deconvolution model for robust deblurring with inaccurate blur kernel. The partial map is constructed by detecting the reliable Fourier entries of estimated blur kernel. And partial deconvolution is applied to wavelet-based and learning-based models to suppress the adverse effect of kernel estimation error. Furthermore, an E-M algorithm is developed for estimating the partial map and recovering the latent sharp image alternatively. Experimental results show that our partial deconvolution model is effective in relieving artifacts caused by inaccurate blur kernel, and can achieve favorable deblurring quality on synthetic and real blurry images.Most non-blind deconvolution methods are developed under the error-free kernel assumption, and are not robust to inaccurate blur kernel. Unfortunately, despite the great progress in blind deconvolution, estimation error remains inevitable during blur kernel estimation. Consequently, severe artifacts such as ringing effects and distortions are likely to be introduced in the non-blind deconvolution stage. In this paper, we tackle this issue by suggesting: (i) a partial map in the Fourier domain for modeling kernel estimation error, and (ii) a partial deconvolution model for robust deblurring with inaccurate blur kernel. The partial map is constructed by detecting the reliable Fourier entries of estimated blur kernel. And partial deconvolution is applied to wavelet-based and learning

  12. Optimal execution in high-frequency trading with Bayesian learning

    Science.gov (United States)

    Du, Bian; Zhu, Hongliang; Zhao, Jingdong

    2016-11-01

    We consider optimal trading strategies in which traders submit bid and ask quotes to maximize the expected quadratic utility of total terminal wealth in a limit order book. The trader's bid and ask quotes will be changed by the Poisson arrival of market orders. Meanwhile, the trader may update his estimate of other traders' target sizes and directions by Bayesian learning. The solution of optimal execution in the limit order book is a two-step procedure. First, we model an inactive trading with no limit order in the market. The dealer simply holds dollars and shares of stocks until terminal time. Second, he calibrates his bid and ask quotes to the limit order book. The optimal solutions are given by dynamic programming and in fact they are globally optimal. We also give numerical simulation to the value function and optimal quotes at the last part of the article.

  13. Bayesian reasoning in high-energy physics. Principles and applications

    International Nuclear Information System (INIS)

    D'Agostini, G.

    1999-01-01

    Bayesian statistics is based on the intuitive idea that probability quantifies the degree of belief in the occurrence of an event. The choice of name is due to the key role played by Bayes' theorem, as a logical tool to update probability in the light of new pieces of information. This approach is very close to the intuitive reasoning of experienced physicists, and it allows all kinds of uncertainties to be handled in a consistent way. Many cases of evaluation of measurement uncertainty are considered in detail in this report, including uncertainty arising from systematic errors, upper/lower limits and unfolding. Approximate methods, very useful in routine applications, are provided and several standard methods are recovered for cases in which the (often hidden) assumptions on which they are based hold. (orig.)

  14. Bayesian reasoning in high-energy physics. Principles and applications

    Energy Technology Data Exchange (ETDEWEB)

    D' Agostini, G [Rome Univ. (Italy). Dipt. di Fisica; [European Organization for Nuclear Research, Geneva (Switzerland)

    1999-07-19

    Bayesian statistics is based on the intuitive idea that probability quantifies the degree of belief in the occurrence of an event. The choice of name is due to the key role played by Bayes' theorem, as a logical tool to update probability in the light of new pieces of information. This approach is very close to the intuitive reasoning of experienced physicists, and it allows all kinds of uncertainties to be handled in a consistent way. Many cases of evaluation of measurement uncertainty are considered in detail in this report, including uncertainty arising from systematic errors, upper/lower limits and unfolding. Approximate methods, very useful in routine applications, are provided and several standard methods are recovered for cases in which the (often hidden) assumptions on which they are based hold. (orig.)

  15. Bayesian approach to peak deconvolution and library search for high resolution gas chromatography - Mass spectrometry

    NARCIS (Netherlands)

    Barcaru, A.; Mol, H.G.J.; Tienstra, M.; Vivó-Truyols, G.

    2017-01-01

    A novel probabilistic Bayesian strategy is proposed to resolve highly coeluting peaks in high-resolution GC-MS (Orbitrap) data. Opposed to a deterministic approach, we propose to solve the problem probabilistically, using a complete pipeline. First, the retention time(s) for a (probabilistic) number

  16. High-resolution elastic recoil detection utilizing Bayesian probability theory

    International Nuclear Information System (INIS)

    Neumaier, P.; Dollinger, G.; Bergmaier, A.; Genchev, I.; Goergens, L.; Fischer, R.; Ronning, C.; Hofsaess, H.

    2001-01-01

    Elastic recoil detection (ERD) analysis is improved in view of depth resolution and the reliability of the measured spectra. Good statistics at even low ion fluences is obtained utilizing a large solid angle of 5 msr at the Munich Q3D magnetic spectrograph and using a 40 MeV 197 Au beam. In this way the elemental depth profiles are not essentially altered during analysis even if distributions with area densities below 1x10 14 atoms/cm 2 are measured. As the energy spread due to the angular acceptance is fully eliminated by ion-optical and numerical corrections, an accurate and reliable apparatus function is derived. It allows to deconvolute the measured spectra using the adaptive kernel method, a maximum entropy concept in the framework of Bayesian probability theory. In addition, the uncertainty of the reconstructed spectra is quantified. The concepts are demonstrated at 13 C depth profiles measured at ultra-thin films of tetrahedral amorphous carbon (ta-C). Depth scales of those profiles are given with an accuracy of 1.4x10 15 atoms/cm 2

  17. Structure Learning of Linear Bayesian Networks in High-Dimensions

    OpenAIRE

    Aragam, Nikhyl Bryon

    2015-01-01

    Research into graphical models is a rapidly developing enterprise, garnering significant interest from both the statistics and machine learning communities. A parallel thread in both communities has been the study of low-dimensional structures in high-dimensional models where $p\\gg n$. Recently, there has been a surge of interest in connecting these threads in order to understand the behaviour of graphical models in high-dimensions. Due to their relative simplicity, undirected models such as ...

  18. Hierarchy Bayesian model based services awareness of high-speed optical access networks

    Science.gov (United States)

    Bai, Hui-feng

    2018-03-01

    As the speed of optical access networks soars with ever increasing multiple services, the service-supporting ability of optical access networks suffers greatly from the shortage of service awareness. Aiming to solve this problem, a hierarchy Bayesian model based services awareness mechanism is proposed for high-speed optical access networks. This approach builds a so-called hierarchy Bayesian model, according to the structure of typical optical access networks. Moreover, the proposed scheme is able to conduct simple services awareness operation in each optical network unit (ONU) and to perform complex services awareness from the whole view of system in optical line terminal (OLT). Simulation results show that the proposed scheme is able to achieve better quality of services (QoS), in terms of packet loss rate and time delay.

  19. Bayesian Modeling of ChIP-chip Data Through a High-Order Ising Model

    KAUST Repository

    Mo, Qianxing

    2010-01-29

    ChIP-chip experiments are procedures that combine chromatin immunoprecipitation (ChIP) and DNA microarray (chip) technology to study a variety of biological problems, including protein-DNA interaction, histone modification, and DNA methylation. The most important feature of ChIP-chip data is that the intensity measurements of probes are spatially correlated because the DNA fragments are hybridized to neighboring probes in the experiments. We propose a simple, but powerful Bayesian hierarchical approach to ChIP-chip data through an Ising model with high-order interactions. The proposed method naturally takes into account the intrinsic spatial structure of the data and can be used to analyze data from multiple platforms with different genomic resolutions. The model parameters are estimated using the Gibbs sampler. The proposed method is illustrated using two publicly available data sets from Affymetrix and Agilent platforms, and compared with three alternative Bayesian methods, namely, Bayesian hierarchical model, hierarchical gamma mixture model, and Tilemap hidden Markov model. The numerical results indicate that the proposed method performs as well as the other three methods for the data from Affymetrix tiling arrays, but significantly outperforms the other three methods for the data from Agilent promoter arrays. In addition, we find that the proposed method has better operating characteristics in terms of sensitivities and false discovery rates under various scenarios. © 2010, The International Biometric Society.

  20. Small-signal analysis in high-energy physics: A Bayesian approach

    International Nuclear Information System (INIS)

    Prosper, H.B.

    1988-01-01

    The statistics of small signals masked by a background of imprecisely known magnitude is addressed from a Bayesian viewpoint using a simple statistical model which may be derived from the principle of maximum entropy. The issue of the correct assignment of prior probabilities is resolved by invoking an invariance principle proposed by Jaynes. We calculate the posterior probability and use it to calculate point estimates and upper limits for the magnitude of the signal. The results are applicable to high-energy physics experiments searching for new phenomena. We illustrate this by reanalyzing some published data from a few experiments

  1. Automated high resolution mapping of coffee in Rwanda using an expert Bayesian network

    Science.gov (United States)

    Mukashema, A.; Veldkamp, A.; Vrieling, A.

    2014-12-01

    African highland agro-ecosystems are dominated by small-scale agricultural fields that often contain a mix of annual and perennial crops. This makes such systems difficult to map by remote sensing. We developed an expert Bayesian network model to extract the small-scale coffee fields of Rwanda from very high resolution data. The model was subsequently applied to aerial orthophotos covering more than 99% of Rwanda and on one QuickBird image for the remaining part. The method consists of a stepwise adjustment of pixel probabilities, which incorporates expert knowledge on size of coffee trees and fields, and on their location. The initial naive Bayesian network, which is a spectral-based classification, yielded a coffee map with an overall accuracy of around 50%. This confirms that standard spectral variables alone cannot accurately identify coffee fields from high resolution images. The combination of spectral and ancillary data (DEM and a forest map) allowed mapping of coffee fields and associated uncertainties with an overall accuracy of 87%. Aggregated to district units, the mapped coffee areas demonstrated a high correlation with the coffee areas reported in the detailed national coffee census of 2009 (R2 = 0.92). Unlike the census data our map provides high spatial resolution of coffee area patterns of Rwanda. The proposed method has potential for mapping other perennial small scale cropping systems in the East African Highlands and elsewhere.

  2. Bayesian approach to peak deconvolution and library search for high resolution gas chromatography - Mass spectrometry.

    Science.gov (United States)

    Barcaru, A; Mol, H G J; Tienstra, M; Vivó-Truyols, G

    2017-08-29

    A novel probabilistic Bayesian strategy is proposed to resolve highly coeluting peaks in high-resolution GC-MS (Orbitrap) data. Opposed to a deterministic approach, we propose to solve the problem probabilistically, using a complete pipeline. First, the retention time(s) for a (probabilistic) number of compounds for each mass channel are estimated. The statistical dependency between m/z channels was implied by including penalties in the model objective function. Second, Bayesian Information Criterion (BIC) is used as Occam's razor for the probabilistic assessment of the number of components. Third, a probabilistic set of resolved spectra, and their associated retention times are estimated. Finally, a probabilistic library search is proposed, computing the spectral match with a high resolution library. More specifically, a correlative measure was used that included the uncertainties in the least square fitting, as well as the probability for different proposals for the number of compounds in the mixture. The method was tested on simulated high resolution data, as well as on a set of pesticides injected in a GC-Orbitrap with high coelution. The proposed pipeline was able to detect accurately the retention times and the spectra of the peaks. For our case, with extremely high coelution situation, 5 out of the 7 existing compounds under the selected region of interest, were correctly assessed. Finally, the comparison with the classical methods of deconvolution (i.e., MCR and AMDIS) indicates a better performance of the proposed algorithm in terms of the number of correctly resolved compounds. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Association between inaccurate estimation of body size and obesity in schoolchildren

    Directory of Open Access Journals (Sweden)

    Larissa da Cunha Feio Costa

    2015-12-01

    Full Text Available Objectives: To investigate the prevalence of inaccurate estimation of own body size among Brazilian schoolchildren of both sexes aged 7-10 years, and to test whether overweight/obesity; excess body fat and central obesity are associated with inaccuracy. Methods: Accuracy of body size estimation was assessed using the Figure Rating Scale for Brazilian Children. Multinomial logistic regression was used to analyze associations. Results: The overall prevalence of inaccurate body size estimation was 76%, with 34% of the children underestimating their body size and 42% overestimating their body size. Obesity measured by body mass index was associated with underestimation of body size in both sexes, while central obesity was only associated with overestimation of body size among girls. Conclusions: The results of this study suggest there is a high prevalence of inaccurate body size estimation and that inaccurate estimation is associated with obesity. Accurate estimation of own body size is important among obese schoolchildren because it may be the first step towards adopting healthy lifestyle behaviors.

  4. Dissecting high-dimensional phenotypes with bayesian sparse factor analysis of genetic covariance matrices.

    Science.gov (United States)

    Runcie, Daniel E; Mukherjee, Sayan

    2013-07-01

    Quantitative genetic studies that model complex, multivariate phenotypes are important for both evolutionary prediction and artificial selection. For example, changes in gene expression can provide insight into developmental and physiological mechanisms that link genotype and phenotype. However, classical analytical techniques are poorly suited to quantitative genetic studies of gene expression where the number of traits assayed per individual can reach many thousand. Here, we derive a Bayesian genetic sparse factor model for estimating the genetic covariance matrix (G-matrix) of high-dimensional traits, such as gene expression, in a mixed-effects model. The key idea of our model is that we need consider only G-matrices that are biologically plausible. An organism's entire phenotype is the result of processes that are modular and have limited complexity. This implies that the G-matrix will be highly structured. In particular, we assume that a limited number of intermediate traits (or factors, e.g., variations in development or physiology) control the variation in the high-dimensional phenotype, and that each of these intermediate traits is sparse - affecting only a few observed traits. The advantages of this approach are twofold. First, sparse factors are interpretable and provide biological insight into mechanisms underlying the genetic architecture. Second, enforcing sparsity helps prevent sampling errors from swamping out the true signal in high-dimensional data. We demonstrate the advantages of our model on simulated data and in an analysis of a published Drosophila melanogaster gene expression data set.

  5. Bayesian Multiresolution Variable Selection for Ultra-High Dimensional Neuroimaging Data.

    Science.gov (United States)

    Zhao, Yize; Kang, Jian; Long, Qi

    2018-01-01

    Ultra-high dimensional variable selection has become increasingly important in analysis of neuroimaging data. For example, in the Autism Brain Imaging Data Exchange (ABIDE) study, neuroscientists are interested in identifying important biomarkers for early detection of the autism spectrum disorder (ASD) using high resolution brain images that include hundreds of thousands voxels. However, most existing methods are not feasible for solving this problem due to their extensive computational costs. In this work, we propose a novel multiresolution variable selection procedure under a Bayesian probit regression framework. It recursively uses posterior samples for coarser-scale variable selection to guide the posterior inference on finer-scale variable selection, leading to very efficient Markov chain Monte Carlo (MCMC) algorithms. The proposed algorithms are computationally feasible for ultra-high dimensional data. Also, our model incorporates two levels of structural information into variable selection using Ising priors: the spatial dependence between voxels and the functional connectivity between anatomical brain regions. Applied to the resting state functional magnetic resonance imaging (R-fMRI) data in the ABIDE study, our methods identify voxel-level imaging biomarkers highly predictive of the ASD, which are biologically meaningful and interpretable. Extensive simulations also show that our methods achieve better performance in variable selection compared to existing methods.

  6. Approaches in highly parameterized inversion: bgaPEST, a Bayesian geostatistical approach implementation with PEST: documentation and instructions

    Science.gov (United States)

    Fienen, Michael N.; D'Oria, Marco; Doherty, John E.; Hunt, Randall J.

    2013-01-01

    The application bgaPEST is a highly parameterized inversion software package implementing the Bayesian Geostatistical Approach in a framework compatible with the parameter estimation suite PEST. Highly parameterized inversion refers to cases in which parameters are distributed in space or time and are correlated with one another. The Bayesian aspect of bgaPEST is related to Bayesian probability theory in which prior information about parameters is formally revised on the basis of the calibration dataset used for the inversion. Conceptually, this approach formalizes the conditionality of estimated parameters on the specific data and model available. The geostatistical component of the method refers to the way in which prior information about the parameters is used. A geostatistical autocorrelation function is used to enforce structure on the parameters to avoid overfitting and unrealistic results. Bayesian Geostatistical Approach is designed to provide the smoothest solution that is consistent with the data. Optionally, users can specify a level of fit or estimate a balance between fit and model complexity informed by the data. Groundwater and surface-water applications are used as examples in this text, but the possible uses of bgaPEST extend to any distributed parameter applications.

  7. 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

  8. Single molecule force spectroscopy at high data acquisition: A Bayesian nonparametric analysis

    Science.gov (United States)

    Sgouralis, Ioannis; Whitmore, Miles; Lapidus, Lisa; Comstock, Matthew J.; Pressé, Steve

    2018-03-01

    Bayesian nonparametrics (BNPs) are poised to have a deep impact in the analysis of single molecule data as they provide posterior probabilities over entire models consistent with the supplied data, not just model parameters of one preferred model. Thus they provide an elegant and rigorous solution to the difficult problem encountered when selecting an appropriate candidate model. Nevertheless, BNPs' flexibility to learn models and their associated parameters from experimental data is a double-edged sword. Most importantly, BNPs are prone to increasing the complexity of the estimated models due to artifactual features present in time traces. Thus, because of experimental challenges unique to single molecule methods, naive application of available BNP tools is not possible. Here we consider traces with time correlations and, as a specific example, we deal with force spectroscopy traces collected at high acquisition rates. While high acquisition rates are required in order to capture dwells in short-lived molecular states, in this setup, a slow response of the optical trap instrumentation (i.e., trapped beads, ambient fluid, and tethering handles) distorts the molecular signals introducing time correlations into the data that may be misinterpreted as true states by naive BNPs. Our adaptation of BNP tools explicitly takes into consideration these response dynamics, in addition to drift and noise, and makes unsupervised time series analysis of correlated single molecule force spectroscopy measurements possible, even at acquisition rates similar to or below the trap's response times.

  9. Bayesian reconstruction of photon interaction sequences for high-resolution PET detectors

    Energy Technology Data Exchange (ETDEWEB)

    Pratx, Guillem; Levin, Craig S [Molecular Imaging Program at Stanford, Department of Radiology, Stanford, CA (United States)], E-mail: cslevin@stanford.edu

    2009-09-07

    Realizing the full potential of high-resolution positron emission tomography (PET) systems involves accurately positioning events in which the annihilation photon deposits all its energy across multiple detector elements. Reconstructing the complete sequence of interactions of each photon provides a reliable way to select the earliest interaction because it ensures that all the interactions are consistent with one another. Bayesian estimation forms a natural framework to maximize the consistency of the sequence with the measurements while taking into account the physics of {gamma}-ray transport. An inherently statistical method, it accounts for the uncertainty in the measured energy and position of each interaction. An algorithm based on maximum a posteriori (MAP) was evaluated for computer simulations. For a high-resolution PET system based on cadmium zinc telluride detectors, 93.8% of the recorded coincidences involved at least one photon multiple-interactions event (PMIE). The MAP estimate of the first interaction was accurate for 85.2% of the single photons. This represents a two-fold reduction in the number of mispositioned events compared to minimum pair distance, a simpler yet efficient positioning method. The point-spread function of the system presented lower tails and higher peak value when MAP was used. This translated into improved image quality, which we quantified by studying contrast and spatial resolution gains.

  10. Introducing Bayesian thinking to high-throughput screening for false-negative rate estimation.

    Science.gov (United States)

    Wei, Xin; Gao, Lin; Zhang, Xiaolei; Qian, Hong; Rowan, Karen; Mark, David; Peng, Zhengwei; Huang, Kuo-Sen

    2013-10-01

    High-throughput screening (HTS) has been widely used to identify active compounds (hits) that bind to biological targets. Because of cost concerns, the comprehensive screening of millions of compounds is typically conducted without replication. Real hits that fail to exhibit measurable activity in the primary screen due to random experimental errors will be lost as false-negatives. Conceivably, the projected false-negative rate is a parameter that reflects screening quality. Furthermore, it can be used to guide the selection of optimal numbers of compounds for hit confirmation. Therefore, a method that predicts false-negative rates from the primary screening data is extremely valuable. In this article, we describe the implementation of a pilot screen on a representative fraction (1%) of the screening library in order to obtain information about assay variability as well as a preliminary hit activity distribution profile. Using this training data set, we then developed an algorithm based on Bayesian logic and Monte Carlo simulation to estimate the number of true active compounds and potential missed hits from the full library screen. We have applied this strategy to five screening projects. The results demonstrate that this method produces useful predictions on the numbers of false negatives.

  11. Robust Learning of High-dimensional Biological Networks with Bayesian Networks

    Science.gov (United States)

    Nägele, Andreas; Dejori, Mathäus; Stetter, Martin

    Structure learning of Bayesian networks applied to gene expression data has become a potentially useful method to estimate interactions between genes. However, the NP-hardness of Bayesian network structure learning renders the reconstruction of the full genetic network with thousands of genes unfeasible. Consequently, the maximal network size is usually restricted dramatically to a small set of genes (corresponding with variables in the Bayesian network). Although this feature reduction step makes structure learning computationally tractable, on the downside, the learned structure might be adversely affected due to the introduction of missing genes. Additionally, gene expression data are usually very sparse with respect to the number of samples, i.e., the number of genes is much greater than the number of different observations. Given these problems, learning robust network features from microarray data is a challenging task. This chapter presents several approaches tackling the robustness issue in order to obtain a more reliable estimation of learned network features.

  12. Recent developments in Bayesian inference of tokamak plasma equilibria and high-dimensional stochastic quadratures

    International Nuclear Information System (INIS)

    Von Nessi, G T; Hole, M J

    2014-01-01

    We present recent results and technical breakthroughs for the Bayesian inference of tokamak equilibria using force-balance as a prior constraint. Issues surrounding model parameter representation and posterior analysis are discussed and addressed. These points motivate the recent advancements embodied in the Bayesian Equilibrium Analysis and Simulation Tool (BEAST) software being presently utilized to study equilibria on the Mega-Ampere Spherical Tokamak (MAST) experiment in the UK (von Nessi et al 2012 J. Phys. A 46 185501). State-of-the-art results of using BEAST to study MAST equilibria are reviewed, with recent code advancements being systematically presented though out the manuscript. (paper)

  13. INLA goes extreme: Bayesian tail regression for the estimation of high spatio-temporal quantiles

    KAUST Repository

    Opitz, Thomas

    2018-05-25

    This work is motivated by the challenge organized for the 10th International Conference on Extreme-Value Analysis (EVA2017) to predict daily precipitation quantiles at the 99.8% level for each month at observed and unobserved locations. Our approach is based on a Bayesian generalized additive modeling framework that is designed to estimate complex trends in marginal extremes over space and time. First, we estimate a high non-stationary threshold using a gamma distribution for precipitation intensities that incorporates spatial and temporal random effects. Then, we use the Bernoulli and generalized Pareto (GP) distributions to model the rate and size of threshold exceedances, respectively, which we also assume to vary in space and time. The latent random effects are modeled additively using Gaussian process priors, which provide high flexibility and interpretability. We develop a penalized complexity (PC) prior specification for the tail index that shrinks the GP model towards the exponential distribution, thus preventing unrealistically heavy tails. Fast and accurate estimation of the posterior distributions is performed thanks to the integrated nested Laplace approximation (INLA). We illustrate this methodology by modeling the daily precipitation data provided by the EVA2017 challenge, which consist of observations from 40 stations in the Netherlands recorded during the period 1972–2016. Capitalizing on INLA’s fast computational capacity and powerful distributed computing resources, we conduct an extensive cross-validation study to select the model parameters that govern the smoothness of trends. Our results clearly outperform simple benchmarks and are comparable to the best-scoring approaches of the other teams.

  14. A non-parametric Bayesian approach to decompounding from high frequency data

    NARCIS (Netherlands)

    Gugushvili, Shota; van der Meulen, F.H.; Spreij, Peter

    2016-01-01

    Given a sample from a discretely observed compound Poisson process, we consider non-parametric estimation of the density f0 of its jump sizes, as well as of its intensity λ0. We take a Bayesian approach to the problem and specify the prior on f0 as the Dirichlet location mixture of normal densities.

  15. 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

  16. Bayesian Multiscale Analysis of X-Ray Jet Features in High Redshift Quasars

    Science.gov (United States)

    McKeough, Kathryn; Siemiginowska, A.; Kashyap, V.; Stein, N.

    2014-01-01

    X-ray emission of powerful quasar jets may be a result of the inverse Compton (IC) process in which the Cosmic Microwave Background (CMB) photons gain energy by interactions with the jet’s relativistic electrons. However, there is no definite evidence that IC/CMB process is responsible for the observed X-ray emission of large scale jets. A step toward understanding the X-ray emission process is to study the Radio and X-ray morphologies of the jet. We implement a sophisticated Bayesian image analysis program, Low-count Image Reconstruction and Analysis (LIRA) (Esch et al. 2004; Conners & van Dyk 2007), to analyze jet features in 11 Chandra images of high redshift quasars (z ~ 2 - 4.8). Out of the 36 regions where knots are visible in the radio jets, nine showed detectable X-ray emission. We measured the ratios of the X-ray and radio luminosities of the detected features and found that they are consistent with the CMB radiation relationship. We derived a range of the bulk lorentz factor (Γ) for detected jet features under the CMB jet emission model. There is no discernible trend of Γ with redshift within the sample. The efficiency of the X-ray emission between the detected jet feature and the corresponding quasar also shows no correlation with redshift. This work is supported in part by the National Science Foundation REU and the Department of Defense ASSURE programs under NSF Grant no.1262851 and by the Smithsonian Institution, and by NASA Contract NAS8-39073 to the Chandra X-ray Center (CXC). This research has made use of data obtained from the Chandra Data Archive and Chandra Source Catalog, and software provided by the CXC in the application packages CIAO, ChIPS, and Sherpa. We thank Teddy Cheung for providing the VLA radio images. Connors, A., & van Dyk, D. A. 2007, Statistical Challenges in Modern Astronomy IV, 371, 101 Esch, D. N., Connors, A., Karovska, M., & van Dyk, D. A. 2004, ApJ, 610, 1213

  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. 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

  19. A Practical pedestrian approach to parsimonious regression with inaccurate inputs

    Directory of Open Access Journals (Sweden)

    Seppo Karrila

    2014-04-01

    Full Text Available A measurement result often dictates an interval containing the correct value. Interval data is also created by roundoff, truncation, and binning. We focus on such common interval uncertainty in data. Inaccuracy in model inputs is typically ignored on model fitting. We provide a practical approach for regression with inaccurate data: the mathematics is easy, and the linear programming formulations simple to use even in a spreadsheet. This self-contained elementary presentation introduces interval linear systems and requires only basic knowledge of algebra. Feature selection is automatic; but can be controlled to find only a few most relevant inputs; and joint feature selection is enabled for multiple modeled outputs. With more features than cases, a novel connection to compressed sensing emerges: robustness against interval errors-in-variables implies model parsimony, and the input inaccuracies determine the regularization term. A small numerical example highlights counterintuitive results and a dramatic difference to total least squares.

  20. Endoscopic Localization of Colon Cancer Is Frequently Inaccurate.

    Science.gov (United States)

    Nayor, Jennifer; Rotman, Stephen R; Chan, Walter W; Goldberg, Joel E; Saltzman, John R

    2017-08-01

    Colonoscopic location of a tumor can influence both the surgical procedure choice and overall treatment strategy. To determine the accuracy of colonoscopy in determining the location of colon cancer compared to surgical localization and to elucidate factors that predict discordant colon cancer localization. We conducted a retrospective cross-sectional study of colon cancers diagnosed on colonoscopy at two academic tertiary-care hospitals and two affiliated community hospitals from 2012 to 2014. Colon cancer location was obtained from the endoscopic and surgical pathology reports and characterized by colon segment. We collected data on patient demographics, tumor characteristics, endoscopic procedure characteristics, surgery planned, and surgery performed. Univariate analyses using Chi-squared test and multivariate analysis using forward stepwise logistic regression were performed to determine factors that predict discordant colon cancer localization. There were 110 colon cancer cases identified during the study period. Inaccurate endoscopic colon cancer localization was found in 29% (32/110) of cases. These included 14 cases (12.7%) that were discordant by more than one colonic segment and three cases where the presurgical planned procedure was significantly changed at the time of surgery. On univariate analyses, right-sided colon lesions were associated with increased inaccuracy (43.8 vs 24.4%, p = 0.04). On multivariate analysis, right-sided colon lesions remained independently associated with inaccuracy (OR 1.74, 95% CI 1.03-2.93, p = 0.04). Colon cancer location as determined by colonoscopy is often inaccurate, which can result in intraoperative changes to surgical management, particularly in the right colon.

  1. Joint High-Dimensional Bayesian Variable and Covariance Selection with an Application to eQTL Analysis

    KAUST Repository

    Bhadra, Anindya

    2013-04-22

    We describe a Bayesian technique to (a) perform a sparse joint selection of significant predictor variables and significant inverse covariance matrix elements of the response variables in a high-dimensional linear Gaussian sparse seemingly unrelated regression (SSUR) setting and (b) perform an association analysis between the high-dimensional sets of predictors and responses in such a setting. To search the high-dimensional model space, where both the number of predictors and the number of possibly correlated responses can be larger than the sample size, we demonstrate that a marginalization-based collapsed Gibbs sampler, in combination with spike and slab type of priors, offers a computationally feasible and efficient solution. As an example, we apply our method to an expression quantitative trait loci (eQTL) analysis on publicly available single nucleotide polymorphism (SNP) and gene expression data for humans where the primary interest lies in finding the significant associations between the sets of SNPs and possibly correlated genetic transcripts. Our method also allows for inference on the sparse interaction network of the transcripts (response variables) after accounting for the effect of the SNPs (predictor variables). We exploit properties of Gaussian graphical models to make statements concerning conditional independence of the responses. Our method compares favorably to existing Bayesian approaches developed for this purpose. © 2013, The International Biometric Society.

  2. Probabilistic Safety Analysis of High Speed and Conventional Lines Using Bayesian Networks

    Energy Technology Data Exchange (ETDEWEB)

    Grande Andrade, Z.; Castillo Ron, E.; O' Connor, A.; Nogal, M.

    2016-07-01

    A Bayesian network approach is presented for probabilistic safety analysis (PSA) of railway lines. The idea consists of identifying and reproducing all the elements that the train encounters when circulating along a railway line, such as light and speed limit signals, tunnel or viaduct entries or exits, cuttings and embankments, acoustic sounds received in the cabin, curves, switches, etc. In addition, since the human error is very relevant for safety evaluation, the automatic train protection (ATP) systems and the driver behavior and its time evolution are modelled and taken into account to determine the probabilities of human errors. The nodes of the Bayesian network, their links and the associated probability tables are automatically constructed based on the line data that need to be carefully given. The conditional probability tables are reproduced by closed formulas, which facilitate the modelling and the sensitivity analysis. A sorted list of the most dangerous elements in the line is obtained, which permits making decisions about the line safety and programming maintenance operations in order to optimize them and reduce the maintenance costs substantially. The proposed methodology is illustrated by its application to several cases that include real lines such as the Palencia-Santander and the Dublin-Belfast lines. (Author)

  3. Π4U: A high performance computing framework for Bayesian uncertainty quantification of complex models

    Science.gov (United States)

    Hadjidoukas, P. E.; Angelikopoulos, P.; Papadimitriou, C.; Koumoutsakos, P.

    2015-03-01

    We present Π4U, an extensible framework, for non-intrusive Bayesian Uncertainty Quantification and Propagation (UQ+P) of complex and computationally demanding physical models, that can exploit massively parallel computer architectures. The framework incorporates Laplace asymptotic approximations as well as stochastic algorithms, along with distributed numerical differentiation and task-based parallelism for heterogeneous clusters. Sampling is based on the Transitional Markov Chain Monte Carlo (TMCMC) algorithm and its variants. The optimization tasks associated with the asymptotic approximations are treated via the Covariance Matrix Adaptation Evolution Strategy (CMA-ES). A modified subset simulation method is used for posterior reliability measurements of rare events. The framework accommodates scheduling of multiple physical model evaluations based on an adaptive load balancing library and shows excellent scalability. In addition to the software framework, we also provide guidelines as to the applicability and efficiency of Bayesian tools when applied to computationally demanding physical models. Theoretical and computational developments are demonstrated with applications drawn from molecular dynamics, structural dynamics and granular flow.

  4. Π4U: A high performance computing framework for Bayesian uncertainty quantification of complex models

    International Nuclear Information System (INIS)

    Hadjidoukas, P.E.; Angelikopoulos, P.; Papadimitriou, C.; Koumoutsakos, P.

    2015-01-01

    We present Π4U, 1 an extensible framework, for non-intrusive Bayesian Uncertainty Quantification and Propagation (UQ+P) of complex and computationally demanding physical models, that can exploit massively parallel computer architectures. The framework incorporates Laplace asymptotic approximations as well as stochastic algorithms, along with distributed numerical differentiation and task-based parallelism for heterogeneous clusters. Sampling is based on the Transitional Markov Chain Monte Carlo (TMCMC) algorithm and its variants. The optimization tasks associated with the asymptotic approximations are treated via the Covariance Matrix Adaptation Evolution Strategy (CMA-ES). A modified subset simulation method is used for posterior reliability measurements of rare events. The framework accommodates scheduling of multiple physical model evaluations based on an adaptive load balancing library and shows excellent scalability. In addition to the software framework, we also provide guidelines as to the applicability and efficiency of Bayesian tools when applied to computationally demanding physical models. Theoretical and computational developments are demonstrated with applications drawn from molecular dynamics, structural dynamics and granular flow

  5. Π4U: A high performance computing framework for Bayesian uncertainty quantification of complex models

    Energy Technology Data Exchange (ETDEWEB)

    Hadjidoukas, P.E.; Angelikopoulos, P. [Computational Science and Engineering Laboratory, ETH Zürich, CH-8092 (Switzerland); Papadimitriou, C. [Department of Mechanical Engineering, University of Thessaly, GR-38334 Volos (Greece); Koumoutsakos, P., E-mail: petros@ethz.ch [Computational Science and Engineering Laboratory, ETH Zürich, CH-8092 (Switzerland)

    2015-03-01

    We present Π4U,{sup 1} an extensible framework, for non-intrusive Bayesian Uncertainty Quantification and Propagation (UQ+P) of complex and computationally demanding physical models, that can exploit massively parallel computer architectures. The framework incorporates Laplace asymptotic approximations as well as stochastic algorithms, along with distributed numerical differentiation and task-based parallelism for heterogeneous clusters. Sampling is based on the Transitional Markov Chain Monte Carlo (TMCMC) algorithm and its variants. The optimization tasks associated with the asymptotic approximations are treated via the Covariance Matrix Adaptation Evolution Strategy (CMA-ES). A modified subset simulation method is used for posterior reliability measurements of rare events. The framework accommodates scheduling of multiple physical model evaluations based on an adaptive load balancing library and shows excellent scalability. In addition to the software framework, we also provide guidelines as to the applicability and efficiency of Bayesian tools when applied to computationally demanding physical models. Theoretical and computational developments are demonstrated with applications drawn from molecular dynamics, structural dynamics and granular flow.

  6. Lip-reading aids word recognition most in moderate noise: a Bayesian explanation using high-dimensional feature space.

    Science.gov (United States)

    Ma, Wei Ji; Zhou, Xiang; Ross, Lars A; Foxe, John J; Parra, Lucas C

    2009-01-01

    Watching a speaker's facial movements can dramatically enhance our ability to comprehend words, especially in noisy environments. From a general doctrine of combining information from different sensory modalities (the principle of inverse effectiveness), one would expect that the visual signals would be most effective at the highest levels of auditory noise. In contrast, we find, in accord with a recent paper, that visual information improves performance more at intermediate levels of auditory noise than at the highest levels, and we show that a novel visual stimulus containing only temporal information does the same. We present a Bayesian model of optimal cue integration that can explain these conflicts. In this model, words are regarded as points in a multidimensional space and word recognition is a probabilistic inference process. When the dimensionality of the feature space is low, the Bayesian model predicts inverse effectiveness; when the dimensionality is high, the enhancement is maximal at intermediate auditory noise levels. When the auditory and visual stimuli differ slightly in high noise, the model makes a counterintuitive prediction: as sound quality increases, the proportion of reported words corresponding to the visual stimulus should first increase and then decrease. We confirm this prediction in a behavioral experiment. We conclude that auditory-visual speech perception obeys the same notion of optimality previously observed only for simple multisensory stimuli.

  7. Lip-reading aids word recognition most in moderate noise: a Bayesian explanation using high-dimensional feature space.

    Directory of Open Access Journals (Sweden)

    Wei Ji Ma

    Full Text Available Watching a speaker's facial movements can dramatically enhance our ability to comprehend words, especially in noisy environments. From a general doctrine of combining information from different sensory modalities (the principle of inverse effectiveness, one would expect that the visual signals would be most effective at the highest levels of auditory noise. In contrast, we find, in accord with a recent paper, that visual information improves performance more at intermediate levels of auditory noise than at the highest levels, and we show that a novel visual stimulus containing only temporal information does the same. We present a Bayesian model of optimal cue integration that can explain these conflicts. In this model, words are regarded as points in a multidimensional space and word recognition is a probabilistic inference process. When the dimensionality of the feature space is low, the Bayesian model predicts inverse effectiveness; when the dimensionality is high, the enhancement is maximal at intermediate auditory noise levels. When the auditory and visual stimuli differ slightly in high noise, the model makes a counterintuitive prediction: as sound quality increases, the proportion of reported words corresponding to the visual stimulus should first increase and then decrease. We confirm this prediction in a behavioral experiment. We conclude that auditory-visual speech perception obeys the same notion of optimality previously observed only for simple multisensory stimuli.

  8. Machine health prognostics using the Bayesian-inference-based probabilistic indication and high-order particle filtering framework

    Science.gov (United States)

    Yu, Jianbo

    2015-12-01

    Prognostics is much efficient to achieve zero-downtime performance, maximum productivity and proactive maintenance of machines. Prognostics intends to assess and predict the time evolution of machine health degradation so that machine failures can be predicted and prevented. A novel prognostics system is developed based on the data-model-fusion scheme using the Bayesian inference-based self-organizing map (SOM) and an integration of logistic regression (LR) and high-order particle filtering (HOPF). In this prognostics system, a baseline SOM is constructed to model the data distribution space of healthy machine under an assumption that predictable fault patterns are not available. Bayesian inference-based probability (BIP) derived from the baseline SOM is developed as a quantification indication of machine health degradation. BIP is capable of offering failure probability for the monitored machine, which has intuitionist explanation related to health degradation state. Based on those historic BIPs, the constructed LR and its modeling noise constitute a high-order Markov process (HOMP) to describe machine health propagation. HOPF is used to solve the HOMP estimation to predict the evolution of the machine health in the form of a probability density function (PDF). An on-line model update scheme is developed to adapt the Markov process changes to machine health dynamics quickly. The experimental results on a bearing test-bed illustrate the potential applications of the proposed system as an effective and simple tool for machine health prognostics.

  9. Inaccurate preoperative imaging assessment on biliary anatomy not increases biliary complications after living donor liver transplantation

    International Nuclear Information System (INIS)

    Xu Xiao; Wei Xuyong; Ling Qi; Wang Kai; Bao Haiwei; Xie Haiyang; Zhou Lin; Zheng Shusen

    2012-01-01

    Backgrounds and aims: Accurate assessment of graft bile duct is important to plan surgical procedure. Magnetic resonance cholangiopancreatography (MRCP) has become an important diagnostic procedure in evaluation of pancreaticobiliary ductal abnormalities and has been reported as highly accurate. We aim to estimate the efficacy of preoperative MRCP on depicting biliary anatomy in living donor liver transplantation (LDLT), and to determine whether inaccurate preoperative imaging assessment would increase the biliary complications after LDLT. Methods: The data of 118 cases LDLT were recorded. Information from preoperative MRCP was assessed using intraoperative cholangiography (IOC) as the gold standard. The possible risk factors of recipient biliary complications were analyzed. Results: Of 118 donors, 84 had normal anatomy (type A) and 34 had anatomic variants (19 cases of type B, 9 cases of type C, 1 case of type E, 2 cases of type F and 3 cases of type I) confirmed by IOC. MRCP correctly predicted all 84 normal cases and 17 of 34 variant cases, and showed an accuracy of 85.6% (101/118). The incidence of biliary complications was comparable between cases with accurate and inaccurate classification of biliary tree from MRCP, and between cases with normal and variant anatomy of bile duct. While cases with graft duct opening ≤5 mm showed a significant higher incidence of total biliary complications (21.1% vs. 6.6%, P = 0.028) and biliary stricture (10.5% vs. 1.6%, P = 0.041) compared with cases with large duct opening >5 mm. Conclusion: MRCP could correctly predict normal but not variant biliary anatomy. Inaccurate assessment of biliary anatomy from MRCP not increases the rate of biliary complications, while small-sized graft duct may cause an increase in biliary complications particularly biliary stricture after LDLT.

  10. Entanglement-fidelity relations for inaccurate ancilla-driven quantum computation

    International Nuclear Information System (INIS)

    Morimae, Tomoyuki; Kahn, Jonas

    2010-01-01

    It was shown by T. Morimae [Phys. Rev. A 81, 060307(R) (2010)] that the gate fidelity of an inaccurate one-way quantum computation is upper bounded by a decreasing function of the amount of entanglement in the register. This means that a strong entanglement causes the low gate fidelity in the one-way quantum computation with inaccurate measurements. In this paper, we derive similar entanglement-fidelity relations for the inaccurate ancilla-driven quantum computation. These relations again imply that a strong entanglement in the register causes the low gate fidelity in the ancilla-driven quantum computation if the measurements on the ancilla are inaccurate.

  11. Compressive Sensing Based Bayesian Sparse Channel Estimation for OFDM Communication Systems: High Performance and Low Complexity

    Science.gov (United States)

    Xu, Li; Shan, Lin; Adachi, Fumiyuki

    2014-01-01

    In orthogonal frequency division modulation (OFDM) communication systems, channel state information (CSI) is required at receiver due to the fact that frequency-selective fading channel leads to disgusting intersymbol interference (ISI) over data transmission. Broadband channel model is often described by very few dominant channel taps and they can be probed by compressive sensing based sparse channel estimation (SCE) methods, for example, orthogonal matching pursuit algorithm, which can take the advantage of sparse structure effectively in the channel as for prior information. However, these developed methods are vulnerable to both noise interference and column coherence of training signal matrix. In other words, the primary objective of these conventional methods is to catch the dominant channel taps without a report of posterior channel uncertainty. To improve the estimation performance, we proposed a compressive sensing based Bayesian sparse channel estimation (BSCE) method which cannot only exploit the channel sparsity but also mitigate the unexpected channel uncertainty without scarifying any computational complexity. The proposed method can reveal potential ambiguity among multiple channel estimators that are ambiguous due to observation noise or correlation interference among columns in the training matrix. Computer simulations show that proposed method can improve the estimation performance when comparing with conventional SCE methods. PMID:24983012

  12. Fast Markov chain Monte Carlo sampling for sparse Bayesian inference in high-dimensional inverse problems using L1-type priors

    International Nuclear Information System (INIS)

    Lucka, Felix

    2012-01-01

    Sparsity has become a key concept for solving of high-dimensional inverse problems using variational regularization techniques. Recently, using similar sparsity-constraints in the Bayesian framework for inverse problems by encoding them in the prior distribution has attracted attention. Important questions about the relation between regularization theory and Bayesian inference still need to be addressed when using sparsity promoting inversion. A practical obstacle for these examinations is the lack of fast posterior sampling algorithms for sparse, high-dimensional Bayesian inversion. Accessing the full range of Bayesian inference methods requires being able to draw samples from the posterior probability distribution in a fast and efficient way. This is usually done using Markov chain Monte Carlo (MCMC) sampling algorithms. In this paper, we develop and examine a new implementation of a single component Gibbs MCMC sampler for sparse priors relying on L1-norms. We demonstrate that the efficiency of our Gibbs sampler increases when the level of sparsity or the dimension of the unknowns is increased. This property is contrary to the properties of the most commonly applied Metropolis–Hastings (MH) sampling schemes. We demonstrate that the efficiency of MH schemes for L1-type priors dramatically decreases when the level of sparsity or the dimension of the unknowns is increased. Practically, Bayesian inversion for L1-type priors using MH samplers is not feasible at all. As this is commonly believed to be an intrinsic feature of MCMC sampling, the performance of our Gibbs sampler also challenges common beliefs about the applicability of sample based Bayesian inference. (paper)

  13. Bayesian energy landscape tilting: towards concordant models of molecular ensembles.

    Science.gov (United States)

    Beauchamp, Kyle A; Pande, Vijay S; Das, Rhiju

    2014-03-18

    Predicting biological structure has remained challenging for systems such as disordered proteins that take on myriad conformations. Hybrid simulation/experiment strategies have been undermined by difficulties in evaluating errors from computational model inaccuracies and data uncertainties. Building on recent proposals from maximum entropy theory and nonequilibrium thermodynamics, we address these issues through a Bayesian energy landscape tilting (BELT) scheme for computing Bayesian hyperensembles over conformational ensembles. BELT uses Markov chain Monte Carlo to directly sample maximum-entropy conformational ensembles consistent with a set of input experimental observables. To test this framework, we apply BELT to model trialanine, starting from disagreeing simulations with the force fields ff96, ff99, ff99sbnmr-ildn, CHARMM27, and OPLS-AA. BELT incorporation of limited chemical shift and (3)J measurements gives convergent values of the peptide's α, β, and PPII conformational populations in all cases. As a test of predictive power, all five BELT hyperensembles recover set-aside measurements not used in the fitting and report accurate errors, even when starting from highly inaccurate simulations. BELT's principled framework thus enables practical predictions for complex biomolecular systems from discordant simulations and sparse data. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  14. Label-Driven Learning Framework: Towards More Accurate Bayesian Network Classifiers through Discrimination of High-Confidence Labels

    Directory of Open Access Journals (Sweden)

    Yi Sun

    2017-12-01

    Full Text Available Bayesian network classifiers (BNCs have demonstrated competitive classification accuracy in a variety of real-world applications. However, it is error-prone for BNCs to discriminate among high-confidence labels. To address this issue, we propose the label-driven learning framework, which incorporates instance-based learning and ensemble learning. For each testing instance, high-confidence labels are first selected by a generalist classifier, e.g., the tree-augmented naive Bayes (TAN classifier. Then, by focusing on these labels, conditional mutual information is redefined to more precisely measure mutual dependence between attributes, thus leading to a refined generalist with a more reasonable network structure. To enable finer discrimination, an expert classifier is tailored for each high-confidence label. Finally, the predictions of the refined generalist and the experts are aggregated. We extend TAN to LTAN (Label-driven TAN by applying the proposed framework. Extensive experimental results demonstrate that LTAN delivers superior classification accuracy to not only several state-of-the-art single-structure BNCs but also some established ensemble BNCs at the expense of reasonable computation overhead.

  15. Inaccurate DNA synthesis in cell extracts of yeast producing active human DNA polymerase iota.

    Science.gov (United States)

    Makarova, Alena V; Grabow, Corinn; Gening, Leonid V; Tarantul, Vyacheslav Z; Tahirov, Tahir H; Bessho, Tadayoshi; Pavlov, Youri I

    2011-01-31

    Mammalian Pol ι has an unusual combination of properties: it is stimulated by Mn(2+) ions, can bypass some DNA lesions and misincorporates "G" opposite template "T" more frequently than incorporates the correct "A." We recently proposed a method of detection of Pol ι activity in animal cell extracts, based on primer extension opposite the template T with a high concentration of only two nucleotides, dGTP and dATP (incorporation of "G" versus "A" method of Gening, abbreviated as "misGvA"). We provide unambiguous proof of the "misGvA" approach concept and extend the applicability of the method for the studies of variants of Pol ι in the yeast model system with different cation cofactors. We produced human Pol ι in baker's yeast, which do not have a POLI ortholog. The "misGvA" activity is absent in cell extracts containing an empty vector, or producing catalytically dead Pol ι, or Pol ι lacking exon 2, but is robust in the strain producing wild-type Pol ι or its catalytic core, or protein with the active center L62I mutant. The signature pattern of primer extension products resulting from inaccurate DNA synthesis by extracts of cells producing either Pol ι or human Pol η is different. The DNA sequence of the template is critical for the detection of the infidelity of DNA synthesis attributed to DNA Pol ι. The primer/template and composition of the exogenous DNA precursor pool can be adapted to monitor replication fidelity in cell extracts expressing various error-prone Pols or mutator variants of accurate Pols. Finally, we demonstrate that the mutation rates in yeast strains producing human DNA Pols ι and η are not elevated over the control strain, despite highly inaccurate DNA synthesis by their extracts.

  16. Inaccurate DNA synthesis in cell extracts of yeast producing active human DNA polymerase iota.

    Directory of Open Access Journals (Sweden)

    Alena V Makarova

    2011-01-01

    Full Text Available Mammalian Pol ι has an unusual combination of properties: it is stimulated by Mn(2+ ions, can bypass some DNA lesions and misincorporates "G" opposite template "T" more frequently than incorporates the correct "A." We recently proposed a method of detection of Pol ι activity in animal cell extracts, based on primer extension opposite the template T with a high concentration of only two nucleotides, dGTP and dATP (incorporation of "G" versus "A" method of Gening, abbreviated as "misGvA". We provide unambiguous proof of the "misGvA" approach concept and extend the applicability of the method for the studies of variants of Pol ι in the yeast model system with different cation cofactors. We produced human Pol ι in baker's yeast, which do not have a POLI ortholog. The "misGvA" activity is absent in cell extracts containing an empty vector, or producing catalytically dead Pol ι, or Pol ι lacking exon 2, but is robust in the strain producing wild-type Pol ι or its catalytic core, or protein with the active center L62I mutant. The signature pattern of primer extension products resulting from inaccurate DNA synthesis by extracts of cells producing either Pol ι or human Pol η is different. The DNA sequence of the template is critical for the detection of the infidelity of DNA synthesis attributed to DNA Pol ι. The primer/template and composition of the exogenous DNA precursor pool can be adapted to monitor replication fidelity in cell extracts expressing various error-prone Pols or mutator variants of accurate Pols. Finally, we demonstrate that the mutation rates in yeast strains producing human DNA Pols ι and η are not elevated over the control strain, despite highly inaccurate DNA synthesis by their extracts.

  17. 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

  18. 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

  19. Estimation of post-test probabilities by residents: Bayesian reasoning versus heuristics?

    Science.gov (United States)

    Hall, Stacey; Phang, Sen Han; Schaefer, Jeffrey P; Ghali, William; Wright, Bruce; McLaughlin, Kevin

    2014-08-01

    Although the process of diagnosing invariably begins with a heuristic, we encourage our learners to support their diagnoses by analytical cognitive processes, such as Bayesian reasoning, in an attempt to mitigate the effects of heuristics on diagnosing. There are, however, limited data on the use ± impact of Bayesian reasoning on the accuracy of disease probability estimates. In this study our objective was to explore whether Internal Medicine residents use a Bayesian process to estimate disease probabilities by comparing their disease probability estimates to literature-derived Bayesian post-test probabilities. We gave 35 Internal Medicine residents four clinical vignettes in the form of a referral letter and asked them to estimate the post-test probability of the target condition in each case. We then compared these to literature-derived probabilities. For each vignette the estimated probability was significantly different from the literature-derived probability. For the two cases with low literature-derived probability our participants significantly overestimated the probability of these target conditions being the correct diagnosis, whereas for the two cases with high literature-derived probability the estimated probability was significantly lower than the calculated value. Our results suggest that residents generate inaccurate post-test probability estimates. Possible explanations for this include ineffective application of Bayesian reasoning, attribute substitution whereby a complex cognitive task is replaced by an easier one (e.g., a heuristic), or systematic rater bias, such as central tendency bias. Further studies are needed to identify the reasons for inaccuracy of disease probability estimates and to explore ways of improving accuracy.

  20. 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.

  1. 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

  2. Inverting reflections using full-waveform inversion with inaccurate starting models

    KAUST Repository

    AlTheyab, Abdullah; Schuster, Gerard T.

    2015-01-01

    We present a method for inverting seismic reflections using full-waveform inversion (FWI) with inaccurate starting models. For a layered medium, near-offset reflections (with zero angle of incidence) are unlikely to be cycle-skipped regardless

  3. 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...

  4. Bayesian Modeling of ChIP-chip Data Through a High-Order Ising Model

    KAUST Repository

    Mo, Qianxing; Liang, Faming

    2010-01-01

    approach to ChIP-chip data through an Ising model with high-order interactions. The proposed method naturally takes into account the intrinsic spatial structure of the data and can be used to analyze data from multiple platforms with different genomic

  5. Bayesian estimation and use of high-throughput remote sensing indices for quantitative genetic analyses of leaf growth.

    Science.gov (United States)

    Baker, Robert L; Leong, Wen Fung; An, Nan; Brock, Marcus T; Rubin, Matthew J; Welch, Stephen; Weinig, Cynthia

    2018-02-01

    We develop Bayesian function-valued trait models that mathematically isolate genetic mechanisms underlying leaf growth trajectories by factoring out genotype-specific differences in photosynthesis. Remote sensing data can be used instead of leaf-level physiological measurements. Characterizing the genetic basis of traits that vary during ontogeny and affect plant performance is a major goal in evolutionary biology and agronomy. Describing genetic programs that specifically regulate morphological traits can be complicated by genotypic differences in physiological traits. We describe the growth trajectories of leaves using novel Bayesian function-valued trait (FVT) modeling approaches in Brassica rapa recombinant inbred lines raised in heterogeneous field settings. While frequentist approaches estimate parameter values by treating each experimental replicate discretely, Bayesian models can utilize information in the global dataset, potentially leading to more robust trait estimation. We illustrate this principle by estimating growth asymptotes in the face of missing data and comparing heritabilities of growth trajectory parameters estimated by Bayesian and frequentist approaches. Using pseudo-Bayes factors, we compare the performance of an initial Bayesian logistic growth model and a model that incorporates carbon assimilation (A max ) as a cofactor, thus statistically accounting for genotypic differences in carbon resources. We further evaluate two remotely sensed spectroradiometric indices, photochemical reflectance (pri2) and MERIS Terrestrial Chlorophyll Index (mtci) as covariates in lieu of A max , because these two indices were genetically correlated with A max across years and treatments yet allow much higher throughput compared to direct leaf-level gas-exchange measurements. For leaf lengths in uncrowded settings, including A max improves model fit over the initial model. The mtci and pri2 indices also outperform direct A max measurements. Of particular

  6. Visual perception as retrospective Bayesian decoding from high- to low-level features.

    Science.gov (United States)

    Ding, Stephanie; Cueva, Christopher J; Tsodyks, Misha; Qian, Ning

    2017-10-24

    When a stimulus is presented, its encoding is known to progress from low- to high-level features. How these features are decoded to produce perception is less clear, and most models assume that decoding follows the same low- to high-level hierarchy of encoding. There are also theories arguing for global precedence, reversed hierarchy, or bidirectional processing, but they are descriptive without quantitative comparison with human perception. Moreover, observers often inspect different parts of a scene sequentially to form overall perception, suggesting that perceptual decoding requires working memory, yet few models consider how working-memory properties may affect decoding hierarchy. We probed decoding hierarchy by comparing absolute judgments of single orientations and relative/ordinal judgments between two sequentially presented orientations. We found that lower-level, absolute judgments failed to account for higher-level, relative/ordinal judgments. However, when ordinal judgment was used to retrospectively decode memory representations of absolute orientations, striking aspects of absolute judgments, including the correlation and forward/backward aftereffects between two reported orientations in a trial, were explained. We propose that the brain prioritizes decoding of higher-level features because they are more behaviorally relevant, and more invariant and categorical, and thus easier to specify and maintain in noisy working memory, and that more reliable higher-level decoding constrains less reliable lower-level decoding. Published under the PNAS license.

  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. Sparse Bayesian classification and feature selection for biological expression data with high correlations.

    Directory of Open Access Journals (Sweden)

    Xian Yang

    Full Text Available Classification models built on biological expression data are increasingly used to predict distinct disease subtypes. Selected features that separate sample groups can be the candidates of biomarkers, helping us to discover biological functions/pathways. However, three challenges are associated with building a robust classification and feature selection model: 1 the number of significant biomarkers is much smaller than that of measured features for which the search will be exhaustive; 2 current biological expression data are big in both sample size and feature size which will worsen the scalability of any search algorithms; and 3 expression profiles of certain features are typically highly correlated which may prevent to distinguish the predominant features. Unfortunately, most of the existing algorithms are partially addressing part of these challenges but not as a whole. In this paper, we propose a unified framework to address the above challenges. The classification and feature selection problem is first formulated as a nonconvex optimisation problem. Then the problem is relaxed and solved iteratively by a sequence of convex optimisation procedures which can be distributed computed and therefore allows the efficient implementation on advanced infrastructures. To illustrate the competence of our method over others, we first analyse a randomly generated simulation dataset under various conditions. We then analyse a real gene expression dataset on embryonal tumour. Further downstream analysis, such as functional annotation and pathway analysis, are performed on the selected features which elucidate several biological findings.

  9. 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

  10. Bayesian screening for active compounds in high-dimensional chemical spaces combining property descriptors and molecular fingerprints.

    Science.gov (United States)

    Vogt, Martin; Bajorath, Jürgen

    2008-01-01

    Bayesian classifiers are increasingly being used to distinguish active from inactive compounds and search large databases for novel active molecules. We introduce an approach to directly combine the contributions of property descriptors and molecular fingerprints in the search for active compounds that is based on a Bayesian framework. Conventionally, property descriptors and fingerprints are used as alternative features for virtual screening methods. Following the approach introduced here, probability distributions of descriptor values and fingerprint bit settings are calculated for active and database molecules and the divergence between the resulting combined distributions is determined as a measure of biological activity. In test calculations on a large number of compound activity classes, this methodology was found to consistently perform better than similarity searching using fingerprints and multiple reference compounds or Bayesian screening calculations using probability distributions calculated only from property descriptors. These findings demonstrate that there is considerable synergy between different types of property descriptors and fingerprints in recognizing diverse structure-activity relationships, at least in the context of Bayesian modeling.

  11. 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...

  12. Borderline features are associated with inaccurate trait self-estimations.

    Science.gov (United States)

    Morey, Leslie C

    2014-01-01

    Many treatments for Borderline Personality Disorder (BPD) are based upon the hypothesis that gross distortion in perceptions and attributions related to self and others represent a core mechanism for the enduring difficulties displayed by such patients. However, available experimental evidence of such distortions provides equivocal results, with some studies suggesting that BPD is related to inaccuracy in such perceptions and others indicative of enhanced accuracy in some judgments. The current study uses a novel methodology to explore whether individuals with BPD features are less accurate in estimating their levels of universal personality characteristics as compared to community norms. One hundred and four students received course instruction on the Five Factor Model of personality, and then were asked to estimate their levels of these five traits relative to community norms. They then completed the NEO-Five Factor Inventory and the Personality Assessment Inventory-Borderline Features scale (PAI-BOR). Accuracy of estimates was calculated by computing squared differences between self-estimated trait levels and norm-referenced standardized scores in the NEO-FFI. There was a moderately strong relationship between PAI-BOR score and inaccuracy of trait level estimates. In particular, high BOR individuals dramatically overestimated their levels of Agreeableness and Conscientiousness, estimating themselves to be slightly above average on each of these characteristics but actually scoring well below average on both. The accuracy of estimates of levels of Neuroticism were unrelated to BOR scores, despite the fact that BOR scores were highly correlated with Neuroticism. These findings support the hypothesis that a key feature of BPD involves marked perceptual distortions of various aspects of self in relationship to others. However, the results also indicate that this is not a global perceptual deficit, as high BOR scorers accurately estimated that their emotional

  13. Patient Self-Assessment of Surgical Site Infection is Inaccurate.

    Science.gov (United States)

    Richter, Vered; Cohen, Matan J; Benenson, Shmuel; Almogy, Gideon; Brezis, Mayer

    2017-08-01

    Availability of surgical site infection (SSI) surveillance rates challenges clinicians, healthcare administrators and leaders and the public. The purpose of this report is to demonstrate the consequences patient self-assessment strategies have on SSI reporting rates. We performed SSI surveillance among patients undergoing general surgery procedures, including telephone follow-up 30 days after surgery. Additionally we undertook a separate validation study in which we compared patient self-assessments of SSI with surgeon assessment. Finally, we performed a meta-analysis of similar validation studies of patient self-assessment strategies. There were 22/266 in-hospital SSIs diagnosed (8.3%), and additional 16 cases were detected through the 30-day follow-up. In total, the SSI rate was 16.8% (95% CI 10.1-18.5). In the validation survey, we found patient telephone surveillance to have a sensitivity of 66% (95% CI 40-93%) and a specificity of 90% (95% CI 86-94%). The meta-analysis included five additional studies. The overall sensitivity was 83.3% (95% CI 79-88%), and the overall specificity was 97.4% (95% CI 97-98%). Simulation of the meta-analysis results divulged that when the true infection rate is 1%, reported rates would be 4%; a true rate of 50%, the reported rates would be 43%. Patient self-assessment strategies in order to fulfill 30-day SSI surveillance misestimate SSI rates and lead to an erroneous overall appreciation of inter-institutional variation. Self-assessment strategies overestimate SSIs rate of institutions with high-quality performance and underestimate rates of poor performance. We propose such strategies be abandoned. Alternative strategies of patient follow-up strategies should be evaluated in order to provide valid and reliable information regarding institutional performance in preventing patient harm.

  14. 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

  15. 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.

  16. Kernel Bayesian ART and ARTMAP.

    Science.gov (United States)

    Masuyama, Naoki; Loo, Chu Kiong; Dawood, Farhan

    2018-02-01

    Adaptive Resonance Theory (ART) is one of the successful approaches to resolving "the plasticity-stability dilemma" in neural networks, and its supervised learning model called ARTMAP is a powerful tool for classification. Among several improvements, such as Fuzzy or Gaussian based models, the state of art model is Bayesian based one, while solving the drawbacks of others. However, it is known that the Bayesian approach for the high dimensional and a large number of data requires high computational cost, and the covariance matrix in likelihood becomes unstable. This paper introduces Kernel Bayesian ART (KBA) and ARTMAP (KBAM) by integrating Kernel Bayes' Rule (KBR) and Correntropy Induced Metric (CIM) to Bayesian ART (BA) and ARTMAP (BAM), respectively, while maintaining the properties of BA and BAM. The kernel frameworks in KBA and KBAM are able to avoid the curse of dimensionality. In addition, the covariance-free Bayesian computation by KBR provides the efficient and stable computational capability to KBA and KBAM. Furthermore, Correntropy-based similarity measurement allows improving the noise reduction ability even in the high dimensional space. The simulation experiments show that KBA performs an outstanding self-organizing capability than BA, and KBAM provides the superior classification ability than BAM, respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. 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...

  18. 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

  19. 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

  20. Precise age for the Permian-Triassic boundary in South China from high-precision U-Pb geochronology and Bayesian age-depth modeling

    Science.gov (United States)

    Baresel, Björn; Bucher, Hugo; Brosse, Morgane; Cordey, Fabrice; Guodun, Kuang; Schaltegger, Urs

    2017-03-01

    This study is based on zircon U-Pb ages of 12 volcanic ash layers and volcanogenic sandstones from two deep water sections with conformable and continuous formational Permian-Triassic boundaries (PTBs) in the Nanpanjiang Basin (South China). Our dates of single, thermally annealed and chemically abraded zircons bracket the PTB in Dongpan and Penglaitan and provide the basis for a first proof-of-concept study utilizing a Bayesian chronology model comparing the three sections of Dongpan, Penglaitan and the Global Stratotype Section and Point (GSSP) at Meishan. Our Bayesian modeling demonstrates that the formational boundaries in Dongpan (251.939 ± 0.030 Ma), Penglaitan (251.984 ± 0.031 Ma) and Meishan (251.956 ± 0.035 Ma) are synchronous within analytical uncertainty of ˜ 40 ka. It also provides quantitative evidence that the ages of the paleontologically defined boundaries, based on conodont unitary association zones in Meishan and on macrofaunas in Dongpan, are identical and coincide with the age of the formational boundaries. The age model also confirms the extreme condensation around the PTB in Meishan, which distorts the projection of any stratigraphic points or intervals onto other more expanded sections by means of Bayesian age-depth models. Dongpan and Penglaitan possess significantly higher sediment accumulation rates and thus offer a greater potential for high-resolution studies of environmental proxies and correlations around the PTB than Meishan. This study highlights the power of high-resolution radio-isotopic ages that allow a robust intercalibration of patterns of biotic changes and fluctuating environmental proxies and will help recognizing their global, regional or local significance.

  1. A Bayesian kriging model for estimating residential exposure to air pollution of children living in a high-risk area in Italy

    Directory of Open Access Journals (Sweden)

    Ana M. Vicedo-Cabrera

    2013-11-01

    Full Text Available A core challenge in epidemiological analysis of the impact of exposure to air pollution on health is assessment of the individual exposure for subjects at risk. Geographical information systems (GIS-based pollution mapping, such as kriging, has become one of the main tools for evaluating individual exposure to ambient pollutants. We applied universal Bayesian kriging to estimate the residential exposure to gaseous air pollutants for children living in a high-risk area (Milazzo- Valle del Mela in Sicily, Italy. Ad hoc air quality monitoring campaigns were carried out: 12 weekly measurements for sulphur dioxide (SO2 and nitrogen dioxide (NO2 were obtained from 21 passive dosimeters located at each school yard of the study area from November 2007 to April 2008. Universal Bayesian kriging was performed to predict individual exposure levels at each residential address for all 6- to 12-years-old children attending primary school at various locations in the study area. Land use, altitude, distance to main roads and population density were included as covariates in the models. A large geographical heterogeneity in air quality was recorded suggesting complex exposure patterns. We obtained a predicted mean level of 25.78 (±10.61 μg/m3 of NO2 and 4.10 (±2.71 μg/m3 of SO2 at 1,682 children’s residential addresses, with a normalised root mean squared error of 28% and 25%, respectively. We conclude that universal Bayesian kriging approach is a useful tool for the assessment of realistic exposure estimates with regard to ambient pollutants at home addresses. Its prediction uncertainty is highly informative and can be used for both designing subsequent campaigns and for improved modelling of epidemiological associations.

  2. 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...

  3. A non-convex variational approach to photometric stereo under inaccurate lighting

    DEFF Research Database (Denmark)

    Quéau, Yvain; Wu, Tao; Lauze, Francois Bernard

    2017-01-01

    This paper tackles the photometric stereo problem in the presence of inaccurate lighting, obtained either by calibration or by an uncalibrated photometric stereo method. Based on a precise modeling of noise and outliers, a robust variational approach is introduced. It explicitly accounts for self...

  4. Accurate and inaccurate HIV transmission beliefs, stigmatizing and HIV protection motivation in northern Thailand

    NARCIS (Netherlands)

    Boer, Hendrik; Emons, P.A.A.; Emons, P.A.A.

    2004-01-01

    We assessed the relation between accurate beliefs about HIV transmission and inaccurate beliefs about HIV transmission and emotional reactions to people with AIDS (PWA) and AIDS risk groups, stigmatizing attitudes and motivation to protect from HIV. In Chiang Rai, northern Thailand, 219 respondents

  5. Leg mass characteristics of accurate and inaccurate kickers--an Australian football perspective.

    Science.gov (United States)

    Hart, Nicolas H; Nimphius, Sophia; Cochrane, Jodie L; Newton, Robert U

    2013-01-01

    Athletic profiling provides valuable information to sport scientists, assisting in the optimal design of strength and conditioning programmes. Understanding the influence these physical characteristics may have on the generation of kicking accuracy is advantageous. The aim of this study was to profile and compare the lower limb mass characteristics of accurate and inaccurate Australian footballers. Thirty-one players were recruited from the Western Australian Football League to perform ten drop punt kicks over 20 metres to a player target. Players were separated into accurate (n = 15) and inaccurate (n = 16) groups, with leg mass characteristics assessed using whole body dual energy x-ray absorptiometry (DXA) scans. Accurate kickers demonstrated significantly greater relative lean mass (P ≤ 0.004) and significantly lower relative fat mass (P ≤ 0.024) across all segments of the kicking and support limbs, while also exhibiting significantly higher intra-limb lean-to-fat mass ratios for all segments across both limbs (P ≤ 0.009). Inaccurate kickers also produced significantly larger asymmetries between limbs than accurate kickers (P ≤ 0.028), showing considerably lower lean mass in their support leg. These results illustrate a difference in leg mass characteristics between accurate and inaccurate kickers, highlighting the potential influence these may have on technical proficiency of the drop punt.

  6. Inaccurate Citations in Biomedical Journalism: Effect on the Impact Factor of the American Journal of Roentgenology.

    Science.gov (United States)

    Karabulut, Nevzat

    2017-03-01

    The aim of this study is to investigate the frequency of incorrect citations and its effects on the impact factor of a specific biomedical journal: the American Journal of Roentgenology. The Cited Reference Search function of Thomson Reuters' Web of Science database (formerly the Institute for Scientific Information's Web of Knowledge database) was used to identify erroneous citations. This was done by entering the journal name into the Cited Work field and entering "2011-2012" into the Cited Year(s) field. The errors in any part of the inaccurately cited references (e.g., author names, title, year, volume, issue, and page numbers) were recorded, and the types of errors (i.e., absent, deficient, or mistyped) were analyzed. Erroneous citations were corrected using the Suggest a Correction function of the Web of Science database. The effect of inaccurate citations on the impact factor of the AJR was calculated. Overall, 183 of 1055 citable articles published in 2011-2012 were inaccurately cited 423 times (mean [± SD], 2.31 ± 4.67 times; range, 1-44 times). Of these 183 articles, 110 (60.1%) were web-only articles and 44 (24.0%) were print articles. The most commonly identified errors were page number errors (44.8%) and misspelling of an author's name (20.2%). Incorrect citations adversely affected the impact factor of the AJR by 0.065 in 2012 and by 0.123 in 2013. Inaccurate citations are not infrequent in biomedical journals, yet they can be detected and corrected using the Web of Science database. Although the accuracy of references is primarily the responsibility of authors, the journal editorial office should also define a periodic inaccurate citation check task and correct erroneous citations to reclaim unnecessarily lost credit.

  7. 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.

  8. Toward improved prediction of the bedrock depth underneath hillslopes: Bayesian inference of the bottom-up control hypothesis using high-resolution topographic data

    Science.gov (United States)

    Gomes, Guilherme J. C.; Vrugt, Jasper A.; Vargas, Eurípedes A.

    2016-04-01

    The depth to bedrock controls a myriad of processes by influencing subsurface flow paths, erosion rates, soil moisture, and water uptake by plant roots. As hillslope interiors are very difficult and costly to illuminate and access, the topography of the bedrock surface is largely unknown. This essay is concerned with the prediction of spatial patterns in the depth to bedrock (DTB) using high-resolution topographic data, numerical modeling, and Bayesian analysis. Our DTB model builds on the bottom-up control on fresh-bedrock topography hypothesis of Rempe and Dietrich (2014) and includes a mass movement and bedrock-valley morphology term to extent the usefulness and general applicability of the model. We reconcile the DTB model with field observations using Bayesian analysis with the DREAM algorithm. We investigate explicitly the benefits of using spatially distributed parameter values to account implicitly, and in a relatively simple way, for rock mass heterogeneities that are very difficult, if not impossible, to characterize adequately in the field. We illustrate our method using an artificial data set of bedrock depth observations and then evaluate our DTB model with real-world data collected at the Papagaio river basin in Rio de Janeiro, Brazil. Our results demonstrate that the DTB model predicts accurately the observed bedrock depth data. The posterior mean DTB simulation is shown to be in good agreement with the measured data. The posterior prediction uncertainty of the DTB model can be propagated forward through hydromechanical models to derive probabilistic estimates of factors of safety.

  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. 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

  11. Bayesian network learning for natural hazard assessments

    Science.gov (United States)

    Vogel, Kristin

    2016-04-01

    Even though quite different in occurrence and consequences, from a modelling perspective many natural hazards share similar properties and challenges. Their complex nature as well as lacking knowledge about their driving forces and potential effects make their analysis demanding. On top of the uncertainty about the modelling framework, inaccurate or incomplete event observations and the intrinsic randomness of the natural phenomenon add up to different interacting layers of uncertainty, which require a careful handling. Thus, for reliable natural hazard assessments it is crucial not only to capture and quantify involved uncertainties, but also to express and communicate uncertainties in an intuitive way. Decision-makers, who often find it difficult to deal with uncertainties, might otherwise return to familiar (mostly deterministic) proceedings. In the scope of the DFG research training group „NatRiskChange" we apply the probabilistic framework of Bayesian networks for diverse natural hazard and vulnerability studies. The great potential of Bayesian networks was already shown in previous natural hazard assessments. Treating each model component as random variable, Bayesian networks aim at capturing the joint distribution of all considered variables. Hence, each conditional distribution of interest (e.g. the effect of precautionary measures on damage reduction) can be inferred. The (in-)dependencies between the considered variables can be learned purely data driven or be given by experts. Even a combination of both is possible. By translating the (in-)dependences into a graph structure, Bayesian networks provide direct insights into the workings of the system and allow to learn about the underlying processes. Besides numerous studies on the topic, learning Bayesian networks from real-world data remains challenging. In previous studies, e.g. on earthquake induced ground motion and flood damage assessments, we tackled the problems arising with continuous variables

  12. Predicting the heat of vaporization of iron at high temperatures using time-resolved laser-induced incandescence and Bayesian model selection

    Science.gov (United States)

    Sipkens, Timothy A.; Hadwin, Paul J.; Grauer, Samuel J.; Daun, Kyle J.

    2018-03-01

    Competing theories have been proposed to account for how the latent heat of vaporization of liquid iron varies with temperature, but experimental confirmation remains elusive, particularly at high temperatures. We propose time-resolved laser-induced incandescence measurements on iron nanoparticles combined with Bayesian model plausibility, as a novel method for evaluating these relationships. Our approach scores the explanatory power of candidate models, accounting for parameter uncertainty, model complexity, measurement noise, and goodness-of-fit. The approach is first validated with simulated data and then applied to experimental data for iron nanoparticles in argon. Our results justify the use of Román's equation to account for the temperature dependence of the latent heat of vaporization of liquid iron.

  13. 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…

  14. 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

  15. 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.

  16. 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.

  17. Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments.

    Directory of Open Access Journals (Sweden)

    Hahnbeom Park

    Full Text Available Protein loop modeling is a tool for predicting protein local structures of particular interest, providing opportunities for applications involving protein structure prediction and de novo protein design. Until recently, the majority of loop modeling methods have been developed and tested by reconstructing loops in frameworks of experimentally resolved structures. In many practical applications, however, the protein loops to be modeled are located in inaccurate structural environments. These include loops in model structures, low-resolution experimental structures, or experimental structures of different functional forms. Accordingly, discrepancies in the accuracy of the structural environment assumed in development of the method and that in practical applications present additional challenges to modern loop modeling methods. This study demonstrates a new strategy for employing a hybrid energy function combining physics-based and knowledge-based components to help tackle this challenge. The hybrid energy function is designed to combine the strengths of each energy component, simultaneously maintaining accurate loop structure prediction in a high-resolution framework structure and tolerating minor environmental errors in low-resolution structures. A loop modeling method based on global optimization of this new energy function is tested on loop targets situated in different levels of environmental errors, ranging from experimental structures to structures perturbed in backbone as well as side chains and template-based model structures. The new method performs comparably to force field-based approaches in loop reconstruction in crystal structures and better in loop prediction in inaccurate framework structures. This result suggests that higher-accuracy predictions would be possible for a broader range of applications. The web server for this method is available at http://galaxy.seoklab.org/loop with the PS2 option for the scoring function.

  18. Near-Nash equilibrium strategies for LQ differential games with inaccurate state information

    Directory of Open Access Journals (Sweden)

    2006-01-01

    Full Text Available ε -Nash equilibrium or “near equilibrium” for a linear quadratic cost game is considered. Due to inaccurate state information, the standard solution for feedback Nash equilibrium cannot be applied. Instead, an estimation of the players' states is substituted into the optimal control strategies equation obtained for perfect state information. The magnitude of the ε in the ε -Nash equilibrium will depend on the quality of the estimation process. To illustrate this approach, a Luenberger-type observer is used in the numerical example to generate the players' state estimates in a two-player non-zero-sum LQ differential game.

  19. 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

  20. 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.

  1. Data in support of a central role of plasminogen activator inhibitor-2 polymorphism in recurrent cardiovascular disease risk in the setting of high HDL cholesterol and C-reactive protein using Bayesian network modeling

    Directory of Open Access Journals (Sweden)

    James P. Corsetti

    2016-09-01

    Full Text Available Data is presented that was utilized as the basis for Bayesian network modeling of influence pathways focusing on the central role of a polymorphism of plasminogen activator inhibitor-2 (PAI-2 on recurrent cardiovascular disease risk in patients with high levels of HDL cholesterol and C-reactive protein (CRP as a marker of inflammation, “Influences on Plasminogen Activator Inhibitor-2 Polymorphism-Associated Recurrent Cardiovascular Disease Risk in Patients with High HDL Cholesterol and Inflammation” (Corsetti et al., 2016; [1]. The data consist of occurrence of recurrent coronary events in 166 post myocardial infarction patients along with 1. clinical data on gender, race, age, and body mass index; 2. blood level data on 17 biomarkers; and 3. genotype data on 53 presumptive CVD-related single nucleotide polymorphisms. Additionally, a flow diagram of the Bayesian modeling procedure is presented along with Bayesian network subgraphs (root nodes to outcome events utilized as the data from which PAI-2 associated influence pathways were derived (Corsetti et al., 2016; [1]. Keywords: Recurrent cardiovascular disease risk, Pathophysiology, Plasminogen activator inhibitor-2, Bayesian network

  2. Inverting reflections using full-waveform inversion with inaccurate starting models

    KAUST Repository

    AlTheyab, Abdullah

    2015-08-19

    We present a method for inverting seismic reflections using full-waveform inversion (FWI) with inaccurate starting models. For a layered medium, near-offset reflections (with zero angle of incidence) are unlikely to be cycle-skipped regardless of the low-wavenumber velocity error in the initial models. Therefore, we use them as a starting point for FWI, and the subsurface velocity model is then updated during the FWI iterations using reflection wavepaths from varying offsets that are not cycle-skipped. To enhance low-wavenumber updates and accelerate the convergence, we take several passes through the non-linear Gauss-Seidel iterations, where we invert traces from a narrow range of near offsets and finally end at the far offsets. Every pass is followed by applying smoothing to the cumulative slowness update. The smoothing is strong at the early stages and relaxed at later iterations to allow for a gradual reconstruction of the subsurface model in a multiscale manner. Applications to synthetic and field data, starting from inaccurate models, show significant low-wavenumber updates and flattening of common-image gathers after many iterations.

  3. 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

  4. 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...

  5. 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...

  6. 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

  7. 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

  8. 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.

  9. Distinguishing highly confident accurate and inaccurate memory: insights about relevant and irrelevant influences on memory confidence

    OpenAIRE

    Chua, Elizabeth F.; Hannula, Deborah E.; Ranganath, Charan

    2012-01-01

    It is generally believed that accuracy and confidence in one’s memory are related, but there are many instances when they diverge. Accordingly, it is important to disentangle the factors which contribute to memory accuracy and confidence, especially those factors that contribute to confidence, but not accuracy. We used eye movements to separately measure fluent cue processing, the target recognition experience, and relative evidence assessment on recognition confidence and accuracy. Eye movem...

  10. 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.

  11. Space Shuttle RTOS Bayesian Network

    Science.gov (United States)

    Morris, A. Terry; Beling, Peter A.

    2001-01-01

    With shrinking budgets and the requirements to increase reliability and operational life of the existing orbiter fleet, NASA has proposed various upgrades for the Space Shuttle that are consistent with national space policy. The cockpit avionics upgrade (CAU), a high priority item, has been selected as the next major upgrade. The primary functions of cockpit avionics include flight control, guidance and navigation, communication, and orbiter landing support. Secondary functions include the provision of operational services for non-avionics systems such as data handling for the payloads and caution and warning alerts to the crew. Recently, a process to selection the optimal commercial-off-the-shelf (COTS) real-time operating system (RTOS) for the CAU was conducted by United Space Alliance (USA) Corporation, which is a joint venture between Boeing and Lockheed Martin, the prime contractor for space shuttle operations. In order to independently assess the RTOS selection, NASA has used the Bayesian network-based scoring methodology described in this paper. Our two-stage methodology addresses the issue of RTOS acceptability by incorporating functional, performance and non-functional software measures related to reliability, interoperability, certifiability, efficiency, correctness, business, legal, product history, cost and life cycle. The first stage of the methodology involves obtaining scores for the various measures using a Bayesian network. The Bayesian network incorporates the causal relationships between the various and often competing measures of interest while also assisting the inherently complex decision analysis process with its ability to reason under uncertainty. The structure and selection of prior probabilities for the network is extracted from experts in the field of real-time operating systems. Scores for the various measures are computed using Bayesian probability. In the second stage, multi-criteria trade-off analyses are performed between the scores

  12. Orbits of massive satellite galaxies - II. Bayesian estimates of the Milky Way and Andromeda masses using high-precision astrometry and cosmological simulations

    Science.gov (United States)

    Patel, Ekta; Besla, Gurtina; Mandel, Kaisey

    2017-07-01

    In the era of high-precision astrometry, space observatories like the Hubble Space Telescope (HST) and Gaia are providing unprecedented 6D phase-space information of satellite galaxies. Such measurements can shed light on the structure and assembly history of the Local Group, but improved statistical methods are needed to use them efficiently. Here we illustrate such a method using analogues of the Local Group's two most massive satellite galaxies, the Large Magellanic Cloud (LMC) and Triangulum (M33), from the Illustris dark-matter-only cosmological simulation. We use a Bayesian inference scheme combining measurements of positions, velocities and specific orbital angular momenta (j) of the LMC/M33 with importance sampling of their simulated analogues to compute posterior estimates of the Milky Way (MW) and Andromeda's (M31) halo masses. We conclude that the resulting host halo mass is more susceptible to bias when using measurements of the current position and velocity of satellites, especially when satellites are at short-lived phases of their orbits (I.e. at pericentre). Instead, the j value of a satellite is well conserved over time and provides a more reliable constraint on host mass. The inferred virial mass of the MW (M31) using j of the LMC (M33) is {{M}}_{vir, MW} = 1.02^{+0.77}_{-0.55} × 10^{12} M⊙ ({{M}}_{vir, M31} = 1.37^{+1.39}_{-0.75} × 10^{12} M⊙). Choosing simulated analogues whose j values are consistent with the conventional picture of a previous (<3 Gyr ago), close encounter (<100 kpc) of M33 about M31 results in a very low virial mass for M31 (˜1012 M⊙). This supports the new scenario put forth in Patel, Besla & Sohn, wherein M33 is on its first passage about M31 or on a long-period orbit. We conclude that this Bayesian inference scheme, utilizing satellite j, is a promising method to reduce the current factor of 2 spread in the mass range of the MW and M31. This method is easily adaptable to include additional satellites as new 6D

  13. The Test of Inaccurate Position of Renography Detector to Relative UptakeFigure and Individual Excretion

    International Nuclear Information System (INIS)

    Bambang-Supardiyono; Prayitno

    2000-01-01

    Accuracy of detector position toward the kidney location (preciseposition) in renography will resulting the maximum count figure, detectorposition change from the precise point (inaccurate) will decreasing the countrate. Therefore for it had been simulated the influence of count figure ofright kidney (fixed left kidney count) ± 5 % to ± 20 % to relativeuptake figure and individual excretion. Based on the calculation it was foundthat the relation of detector position ± 0.5 cm to ± 2 cm from theprecise point will have effect to relative uptake figure ± (1.25 % to 5.00%), the fixed individual excretion figure. The change is still can beaccepted because the qualitative information with 10 % accuracy is stillacceptable. (author)

  14. The Development of Bayesian Theory and Its Applications in Business and Bioinformatics

    Science.gov (United States)

    Zhang, Yifei

    2018-03-01

    Bayesian Theory originated from an Essay of a British mathematician named Thomas Bayes in 1763, and after its development in 20th century, Bayesian Statistics has been taking a significant part in statistical study of all fields. Due to the recent breakthrough of high-dimensional integral, Bayesian Statistics has been improved and perfected, and now it can be used to solve problems that Classical Statistics failed to solve. This paper summarizes Bayesian Statistics’ history, concepts and applications, which are illustrated in five parts: the history of Bayesian Statistics, the weakness of Classical Statistics, Bayesian Theory and its development and applications. The first two parts make a comparison between Bayesian Statistics and Classical Statistics in a macroscopic aspect. And the last three parts focus on Bayesian Theory in specific -- from introducing some particular Bayesian Statistics’ concepts to listing their development and finally their applications.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. Bayesian policy reuse

    CSIR Research Space (South Africa)

    Rosman, Benjamin

    2016-02-01

    Full Text Available Keywords Policy Reuse · Reinforcement Learning · Online Learning · Online Bandits · Transfer Learning · Bayesian Optimisation · Bayesian Decision Theory. 1 Introduction As robots and software agents are becoming more ubiquitous in many applications.... The agent has access to a library of policies (pi1, pi2 and pi3), and has previously experienced a set of task instances (τ1, τ2, τ3, τ4), as well as samples of the utilities of the library policies on these instances (the black dots indicate the means...

  20. Estimating the true accuracy of diagnostic tests for dengue infection using bayesian latent class models.

    Directory of Open Access Journals (Sweden)

    Wirichada Pan-ngum

    Full Text Available Accuracy of rapid diagnostic tests for dengue infection has been repeatedly estimated by comparing those tests with reference assays. We hypothesized that those estimates might be inaccurate if the accuracy of the reference assays is not perfect. Here, we investigated this using statistical modeling.Data from a cohort study of 549 patients suspected of dengue infection presenting at Colombo North Teaching Hospital, Ragama, Sri Lanka, that described the application of our reference assay (a combination of Dengue IgM antibody capture ELISA and IgG antibody capture ELISA and of three rapid diagnostic tests (Panbio NS1 antigen, IgM antibody and IgG antibody rapid immunochromatographic cassette tests were re-evaluated using bayesian latent class models (LCMs. The estimated sensitivity and specificity of the reference assay were 62.0% and 99.6%, respectively. Prevalence of dengue infection (24.3%, and sensitivities and specificities of the Panbio NS1 (45.9% and 97.9%, IgM (54.5% and 95.5% and IgG (62.1% and 84.5% estimated by bayesian LCMs were significantly different from those estimated by assuming that the reference assay was perfect. Sensitivity, specificity, PPV and NPV for a combination of NS1, IgM and IgG cassette tests on admission samples were 87.0%, 82.8%, 62.0% and 95.2%, respectively.Our reference assay is an imperfect gold standard. In our setting, the combination of NS1, IgM and IgG rapid diagnostic tests could be used on admission to rule out dengue infection with a high level of accuracy (NPV 95.2%. Further evaluation of rapid diagnostic tests for dengue infection should include the use of appropriate statistical models.

  1. The dynamic programming high-order Dynamic Bayesian Networks learning for identifying effective connectivity in human brain from fMRI.

    Science.gov (United States)

    Dang, Shilpa; Chaudhury, Santanu; Lall, Brejesh; Roy, Prasun Kumar

    2017-06-15

    Determination of effective connectivity (EC) among brain regions using fMRI is helpful in understanding the underlying neural mechanisms. Dynamic Bayesian Networks (DBNs) are an appropriate class of probabilistic graphical temporal-models that have been used in past to model EC from fMRI, specifically order-one. High-order DBNs (HO-DBNs) have still not been explored for fMRI data. A fundamental problem faced in the structure-learning of HO-DBN is high computational-burden and low accuracy by the existing heuristic search techniques used for EC detection from fMRI. In this paper, we propose using dynamic programming (DP) principle along with integration of properties of scoring-function in a way to reduce search space for structure-learning of HO-DBNs and finally, for identifying EC from fMRI which has not been done yet to the best of our knowledge. The proposed exact search-&-score learning approach HO-DBN-DP is an extension of the technique which was originally devised for learning a BN's structure from static data (Singh and Moore, 2005). The effectiveness in structure-learning is shown on synthetic fMRI dataset. The algorithm reaches globally-optimal solution in appreciably reduced time-complexity than the static counterpart due to integration of properties. The proof of optimality is provided. The results demonstrate that HO-DBN-DP is comparably more accurate and faster than currently used structure-learning algorithms used for identifying EC from fMRI. The real data EC from HO-DBN-DP shows consistency with previous literature than the classical Granger Causality method. Hence, the DP algorithm can be employed for reliable EC estimates from experimental fMRI data. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Bayesian estimation of dose rate effectiveness

    International Nuclear Information System (INIS)

    Arnish, J.J.; Groer, P.G.

    2000-01-01

    A Bayesian statistical method was used to quantify the effectiveness of high dose rate 137 Cs gamma radiation at inducing fatal mammary tumours and increasing the overall mortality rate in BALB/c female mice. The Bayesian approach considers both the temporal and dose dependence of radiation carcinogenesis and total mortality. This paper provides the first direct estimation of dose rate effectiveness using Bayesian statistics. This statistical approach provides a quantitative description of the uncertainty of the factor characterising the dose rate in terms of a probability density function. The results show that a fixed dose from 137 Cs gamma radiation delivered at a high dose rate is more effective at inducing fatal mammary tumours and increasing the overall mortality rate in BALB/c female mice than the same dose delivered at a low dose rate. (author)

  3. Numeracy, frequency, and Bayesian reasoning

    Directory of Open Access Journals (Sweden)

    Gretchen B. Chapman

    2009-02-01

    Full Text Available Previous research has demonstrated that Bayesian reasoning performance is improved if uncertainty information is presented as natural frequencies rather than single-event probabilities. A questionnaire study of 342 college students replicated this effect but also found that the performance-boosting benefits of the natural frequency presentation occurred primarily for participants who scored high in numeracy. This finding suggests that even comprehension and manipulation of natural frequencies requires a certain threshold of numeracy abilities, and that the beneficial effects of natural frequency presentation may not be as general as previously believed.

  4. 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...

  5. Bayesian logistic regression analysis

    NARCIS (Netherlands)

    Van Erp, H.R.N.; Van Gelder, P.H.A.J.M.

    2012-01-01

    In this paper we present a Bayesian logistic regression analysis. It is found that if one wishes to derive the posterior distribution of the probability of some event, then, together with the traditional Bayes Theorem and the integrating out of nuissance parameters, the Jacobian transformation is an

  6. Bayesian Dark Knowledge

    NARCIS (Netherlands)

    Korattikara, A.; Rathod, V.; Murphy, K.; Welling, M.; Cortes, C.; Lawrence, N.D.; Lee, D.D.; Sugiyama, M.; Garnett, R.

    2015-01-01

    We consider the problem of Bayesian parameter estimation for deep neural networks, which is important in problem settings where we may have little data, and/ or where we need accurate posterior predictive densities p(y|x, D), e.g., for applications involving bandits or active learning. One simple

  7. Bayesian Geostatistical Design

    DEFF Research Database (Denmark)

    Diggle, Peter; Lophaven, Søren Nymand

    2006-01-01

    locations to, or deletion of locations from, an existing design, and prospective design, which consists of choosing positions for a new set of sampling locations. We propose a Bayesian design criterion which focuses on the goal of efficient spatial prediction whilst allowing for the fact that model...

  8. Bayesian statistical inference

    Directory of Open Access Journals (Sweden)

    Bruno De Finetti

    2017-04-01

    Full Text Available This work was translated into English and published in the volume: Bruno De Finetti, Induction and Probability, Biblioteca di Statistica, eds. P. Monari, D. Cocchi, Clueb, Bologna, 1993.Bayesian statistical Inference is one of the last fundamental philosophical papers in which we can find the essential De Finetti's approach to the statistical inference.

  9. 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...

  10. Bayesian Independent Component Analysis

    DEFF Research Database (Denmark)

    Winther, Ole; Petersen, Kaare Brandt

    2007-01-01

    In this paper we present an empirical Bayesian framework for independent component analysis. The framework provides estimates of the sources, the mixing matrix and the noise parameters, and is flexible with respect to choice of source prior and the number of sources and sensors. Inside the engine...

  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. 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.

  13. Monte Carlo Bayesian inference on a statistical model of sub-gridcolumn moisture variability using high-resolution cloud observations. Part 2: Sensitivity tests and results

    Science.gov (United States)

    Norris, Peter M.; da Silva, Arlindo M.

    2018-01-01

    Part 1 of this series presented a Monte Carlo Bayesian method for constraining a complex statistical model of global circulation model (GCM) sub-gridcolumn moisture variability using high-resolution Moderate Resolution Imaging Spectroradiometer (MODIS) cloud data, thereby permitting parameter estimation and cloud data assimilation for large-scale models. This article performs some basic testing of this new approach, verifying that it does indeed reduce mean and standard deviation biases significantly with respect to the assimilated MODIS cloud optical depth, brightness temperature and cloud-top pressure and that it also improves the simulated rotational–Raman scattering cloud optical centroid pressure (OCP) against independent (non-assimilated) retrievals from the Ozone Monitoring Instrument (OMI). Of particular interest, the Monte Carlo method does show skill in the especially difficult case 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 allows non-gradient-based jumps into regions of non-zero cloud probability. In the example provided, the method is able to restore marine stratocumulus near the Californian coast, where the background state has a clear swath. This article also examines a number of algorithmic and physical sensitivities of the new method and provides guidance for its cost-effective implementation. One obvious difficulty for the method, and other cloud data assimilation methods as well, is the lack of information content in passive-radiometer-retrieved cloud observables on cloud vertical structure, beyond cloud-top pressure and optical thickness, thus necessitating strong dependence on the background vertical moisture structure. It is found that a simple flow-dependent correlation modification from Riishojgaard provides some help in this respect, by

  14. Monte Carlo Bayesian Inference on a Statistical Model of Sub-gridcolumn Moisture Variability Using High-resolution Cloud Observations . Part II; Sensitivity Tests and Results

    Science.gov (United States)

    da Silva, Arlindo M.; Norris, Peter M.

    2013-01-01

    Part I presented a Monte Carlo Bayesian method for constraining a complex statistical model of GCM sub-gridcolumn moisture variability using high-resolution MODIS cloud data, thereby permitting large-scale model parameter estimation and cloud data assimilation. This part performs some basic testing of this new approach, verifying that it does indeed significantly reduce mean and standard deviation biases with respect to the assimilated MODIS cloud optical depth, brightness temperature and cloud top pressure, and that it also improves the simulated rotational-Ramman scattering cloud optical centroid pressure (OCP) against independent (non-assimilated) retrievals from the OMI instrument. Of particular interest, the Monte Carlo method does show skill in the especially difficult case 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 allows finite jumps into regions of non-zero cloud probability. In the example provided, the method is able to restore marine stratocumulus near the Californian coast where the background state has a clear swath. This paper also examines a number of algorithmic and physical sensitivities of the new method and provides guidance for its cost-effective implementation. One obvious difficulty for the method, and other cloud data assimilation methods as well, is the lack of information content in the cloud observables on cloud vertical structure, beyond cloud top pressure and optical thickness, thus necessitating strong dependence on the background vertical moisture structure. It is found that a simple flow-dependent correlation modification due to Riishojgaard (1998) provides some help in this respect, by better honoring inversion structures in the background state.

  15. Monte Carlo Bayesian Inference on a Statistical Model of Sub-Gridcolumn Moisture Variability Using High-Resolution Cloud Observations. Part 2: Sensitivity Tests and Results

    Science.gov (United States)

    Norris, Peter M.; da Silva, Arlindo M.

    2016-01-01

    Part 1 of this series presented a Monte Carlo Bayesian method for constraining a complex statistical model of global circulation model (GCM) sub-gridcolumn moisture variability using high-resolution Moderate Resolution Imaging Spectroradiometer (MODIS) cloud data, thereby permitting parameter estimation and cloud data assimilation for large-scale models. This article performs some basic testing of this new approach, verifying that it does indeed reduce mean and standard deviation biases significantly with respect to the assimilated MODIS cloud optical depth, brightness temperature and cloud-top pressure and that it also improves the simulated rotational-Raman scattering cloud optical centroid pressure (OCP) against independent (non-assimilated) retrievals from the Ozone Monitoring Instrument (OMI). Of particular interest, the Monte Carlo method does show skill in the especially difficult case 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 allows non-gradient-based jumps into regions of non-zero cloud probability. In the example provided, the method is able to restore marine stratocumulus near the Californian coast, where the background state has a clear swath. This article also examines a number of algorithmic and physical sensitivities of the new method and provides guidance for its cost-effective implementation. One obvious difficulty for the method, and other cloud data assimilation methods as well, is the lack of information content in passive-radiometer-retrieved cloud observables on cloud vertical structure, beyond cloud-top pressure and optical thickness, thus necessitating strong dependence on the background vertical moisture structure. It is found that a simple flow-dependent correlation modification from Riishojgaard provides some help in this respect, by

  16. High throughput assessment of cells and tissues: Bayesian classification of spectral metrics from infrared vibrational spectroscopic imaging data.

    Science.gov (United States)

    Bhargava, Rohit; Fernandez, Daniel C; Hewitt, Stephen M; Levin, Ira W

    2006-07-01

    Vibrational spectroscopy allows a visualization of tissue constituents based on intrinsic chemical composition and provides a potential route to obtaining diagnostic markers of diseases. Characterizations utilizing infrared vibrational spectroscopy, in particular, are conventionally low throughput in data acquisition, generally lacking in spatial resolution with the resulting data requiring intensive numerical computations to extract information. These factors impair the ability of infrared spectroscopic measurements to represent accurately the spatial heterogeneity in tissue, to incorporate robustly the diversity introduced by patient cohorts or preparative artifacts and to validate developed protocols in large population studies. In this manuscript, we demonstrate a combination of Fourier transform infrared (FTIR) spectroscopic imaging, tissue microarrays (TMAs) and fast numerical analysis as a paradigm for the rapid analysis, development and validation of high throughput spectroscopic characterization protocols. We provide an extended description of the data treatment algorithm and a discussion of various factors that may influence decision-making using this approach. Finally, a number of prostate tissue biopsies, arranged in an array modality, are employed to examine the efficacy of this approach in histologic recognition of epithelial cell polarization in patients displaying a variety of normal, malignant and hyperplastic conditions. An index of epithelial cell polarization, derived from a combined spectral and morphological analysis, is determined to be a potentially useful diagnostic marker.

  17. Inaccurate Dental Charting in an Audit of 1128 General Dental Practice Records.

    Science.gov (United States)

    Brown, Nathan L; Jephcote, Victoria E L

    2017-03-01

    Fourteen dentists at different practices in the UK assessed the dental charts of 1128 patients who were new to the dentist but not new to the practice; 44% of the dental charts were found to be inaccurate. Inaccuracy of the individual practice-based charts ranged between 16% for the best performing practices to 83% for the worst: 5% of dental charts had too many teeth charted and 5% had too few teeth charted; 13% of charts had missed amalgam restorations and 18% had missed tooth-coloured restorations; 5% of charts had amalgam restorations recorded but with the surfaces incorrect (eg an MO restoration charted but a DO restoration actually present); 9% of charts had tooth-coloured restoration surfaces incorrectly recorded. For 7.5% of charts, amalgams were charted but not actually present. Other inaccuracies were also noted. The authors reinforce the requirements of the GDC, the advice of defence organizations, and the forensic importance of accurate dental charts. Clinical relevance: Dental charting forms part of the patient’s dental records, and the GDC requires dentists to maintain complete and accurate dental records.

  18. Location-based Mobile Relay Selection and Impact of Inaccurate Path Loss Model Parameters

    DEFF Research Database (Denmark)

    Nielsen, Jimmy Jessen; Madsen, Tatiana Kozlova; Schwefel, Hans-Peter

    2010-01-01

    In this paper we propose a relay selection scheme which uses collected location information together with a path loss model for relay selection, and analyze the performance impact of mobility and different error causes on this scheme. Performance is evaluated in terms of bit error rate...... by simulations. The SNR measurement based relay selection scheme proposed previously is unsuitable for use with fast moving users in e.g. vehicular scenarios due to a large signaling overhead. The proposed location based scheme is shown to work well with fast moving users due to a lower signaling overhead...... in these situations. As the location-based scheme relies on a path loss model to estimate link qualities and select relays, the sensitivity with respect to inaccurate estimates of the unknown path loss model parameters is investigated. The parameter ranges that result in useful performance were found...

  19. Clinical models are inaccurate in predicting bile duct stones in situ for patients with gallbladder.

    Science.gov (United States)

    Topal, B; Fieuws, S; Tomczyk, K; Aerts, R; Van Steenbergen, W; Verslype, C; Penninckx, F

    2009-01-01

    The probability that a patient has common bile duct stones (CBDS) is a key factor in determining diagnostic and treatment strategies. This prospective cohort study evaluated the accuracy of clinical models in predicting CBDS for patients who will undergo cholecystectomy for lithiasis. From October 2005 until September 2006, 335 consecutive patients with symptoms of gallstone disease underwent cholecystectomy. Statistical analysis was performed on prospective patient data obtained at the time of first presentation to the hospital. Demonstrable CBDS at the time of endoscopic retrograde cholangiopancreatography (ERCP) or intraoperative cholangiography (IOC) was considered the gold standard for the presence of CBDS. Common bile duct stones were demonstrated in 53 patients. For 35 patients, ERCP was performed, with successful stone clearance in 24 of 30 patients who had proven CBDS. In 29 patients, IOC showed CBDS, which were managed successfully via laparoscopic common bile duct exploration, with stone extraction at the time of cholecystectomy. Prospective validation of the existing model for CBDS resulted in a predictive accuracy rate of 73%. The new model showed a predictive accuracy rate of 79%. Clinical models are inaccurate in predicting CBDS in patients with cholelithiasis. Management strategies should be based on the local availability of therapeutic expertise.

  20. Methods for detecting and correcting inaccurate results in inductively coupled plasma-atomic emission spectrometry

    Science.gov (United States)

    Chan, George C. Y. [Bloomington, IN; Hieftje, Gary M [Bloomington, IN

    2010-08-03

    A method for detecting and correcting inaccurate results in inductively coupled plasma-atomic emission spectrometry (ICP-AES). ICP-AES analysis is performed across a plurality of selected locations in the plasma on an unknown sample, collecting the light intensity at one or more selected wavelengths of one or more sought-for analytes, creating a first dataset. The first dataset is then calibrated with a calibration dataset creating a calibrated first dataset curve. If the calibrated first dataset curve has a variability along the location within the plasma for a selected wavelength, errors are present. Plasma-related errors are then corrected by diluting the unknown sample and performing the same ICP-AES analysis on the diluted unknown sample creating a calibrated second dataset curve (accounting for the dilution) for the one or more sought-for analytes. The cross-over point of the calibrated dataset curves yields the corrected value (free from plasma related errors) for each sought-for analyte.

  1. Inaccurate pulse CO-oximetry of carboxyhemoglobin due to digital clubbing: case report.

    Science.gov (United States)

    Harlan, Nicole; Weaver, Lindell K; Deru, Kayla

    2016-01-01

    Newer pulse CO-oximeters provide a non-invasive and quick means of measuring oxyhemoglobin, carboxyhemoglobin and methemoglobin. Clubbing has been reported to cause inaccuracy in pulse oximeters. We present a case of inaccurate carboxy-hemoglobin measurement by pulse CO-oximetry due to digital clubbing. An 18-year-old man with a history of cystic fibrosis presented after a suicide attempt by inhalation of exhaust. At the initial emergency department evaluation, his blood carboxyhemoglobin was 33%. He was intubated, placed on 100% oxygen and transferred to our facility. Upon arrival, we placed three different pulse CO-oximeters on different fingers and toes. Carboxyhemoglobin levels measured by these meters ranged from 9%-11%. A venous blood gas drawn on arrival showed a carboxyhemoglobin level of 2.3% after four hours on 100% oxygen by endotracheal tube. Thirty minutes later, we checked arterial blood gas, which revealed a COHb level of 0.9%. Again, non-invasive carboxyhemoglobin measurements read 10%. The patient was treated with hyperbaric oxygen for carbon monoxide poisoning. This case suggests that non-invasive measurements of carboxyhemoglobin should be correlated with the clinic history and with an arterial or venous blood gas oximetry analysis.

  2. 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

  3. 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...

  4. Bayesian optimization for materials science

    CERN Document Server

    Packwood, Daniel

    2017-01-01

    This book provides a short and concise introduction to Bayesian optimization specifically for experimental and computational materials scientists. After explaining the basic idea behind Bayesian optimization and some applications to materials science in Chapter 1, the mathematical theory of Bayesian optimization is outlined in Chapter 2. Finally, Chapter 3 discusses an application of Bayesian optimization to a complicated structure optimization problem in computational surface science. Bayesian optimization is a promising global optimization technique that originates in the field of machine learning and is starting to gain attention in materials science. For the purpose of materials design, Bayesian optimization can be used to predict new materials with novel properties without extensive screening of candidate materials. For the purpose of computational materials science, Bayesian optimization can be incorporated into first-principles calculations to perform efficient, global structure optimizations. While re...

  5. Motion Learning Based on Bayesian Program Learning

    Directory of Open Access Journals (Sweden)

    Cheng Meng-Zhen

    2017-01-01

    Full Text Available The concept of virtual human has been highly anticipated since the 1980s. By using computer technology, Human motion simulation could generate authentic visual effect, which could cheat human eyes visually. Bayesian Program Learning train one or few motion data, generate new motion data by decomposing and combining. And the generated motion will be more realistic and natural than the traditional one.In this paper, Motion learning based on Bayesian program learning allows us to quickly generate new motion data, reduce workload, improve work efficiency, reduce the cost of motion capture, and improve the reusability of data.

  6. Length Scales in Bayesian Automatic Adaptive Quadrature

    Directory of Open Access Journals (Sweden)

    Adam Gh.

    2016-01-01

    Full Text Available Two conceptual developments in the Bayesian automatic adaptive quadrature approach to the numerical solution of one-dimensional Riemann integrals [Gh. Adam, S. Adam, Springer LNCS 7125, 1–16 (2012] are reported. First, it is shown that the numerical quadrature which avoids the overcomputing and minimizes the hidden floating point loss of precision asks for the consideration of three classes of integration domain lengths endowed with specific quadrature sums: microscopic (trapezoidal rule, mesoscopic (Simpson rule, and macroscopic (quadrature sums of high algebraic degrees of precision. Second, sensitive diagnostic tools for the Bayesian inference on macroscopic ranges, coming from the use of Clenshaw-Curtis quadrature, are derived.

  7. An Alternative Flight Software Trigger Paradigm: Applying Multivariate Logistic Regression to Sense Trigger Conditions Using Inaccurate or Scarce Information

    Science.gov (United States)

    Smith, Kelly M.; Gay, Robert S.; Stachowiak, Susan J.

    2013-01-01

    In late 2014, NASA will fly the Orion capsule on a Delta IV-Heavy rocket for the Exploration Flight Test-1 (EFT-1) mission. For EFT-1, the Orion capsule will be flying with a new GPS receiver and new navigation software. Given the experimental nature of the flight, the flight software must be robust to the loss of GPS measurements. Once the high-speed entry is complete, the drogue parachutes must be deployed within the proper conditions to stabilize the vehicle prior to deploying the main parachutes. When GPS is available in nominal operations, the vehicle will deploy the drogue parachutes based on an altitude trigger. However, when GPS is unavailable, the navigated altitude errors become excessively large, driving the need for a backup barometric altimeter to improve altitude knowledge. In order to increase overall robustness, the vehicle also has an alternate method of triggering the parachute deployment sequence based on planet-relative velocity if both the GPS and the barometric altimeter fail. However, this backup trigger results in large altitude errors relative to the targeted altitude. Motivated by this challenge, this paper demonstrates how logistic regression may be employed to semi-automatically generate robust triggers based on statistical analysis. Logistic regression is used as a ground processor pre-flight to develop a statistical classifier. The classifier would then be implemented in flight software and executed in real-time. This technique offers improved performance even in the face of highly inaccurate measurements. Although the logistic regression-based trigger approach will not be implemented within EFT-1 flight software, the methodology can be carried forward for future missions and vehicles.

  8. An Alternative Flight Software Paradigm: Applying Multivariate Logistic Regression to Sense Trigger Conditions using Inaccurate or Scarce Information

    Science.gov (United States)

    Smith, Kelly; Gay, Robert; Stachowiak, Susan

    2013-01-01

    In late 2014, NASA will fly the Orion capsule on a Delta IV-Heavy rocket for the Exploration Flight Test-1 (EFT-1) mission. For EFT-1, the Orion capsule will be flying with a new GPS receiver and new navigation software. Given the experimental nature of the flight, the flight software must be robust to the loss of GPS measurements. Once the high-speed entry is complete, the drogue parachutes must be deployed within the proper conditions to stabilize the vehicle prior to deploying the main parachutes. When GPS is available in nominal operations, the vehicle will deploy the drogue parachutes based on an altitude trigger. However, when GPS is unavailable, the navigated altitude errors become excessively large, driving the need for a backup barometric altimeter to improve altitude knowledge. In order to increase overall robustness, the vehicle also has an alternate method of triggering the parachute deployment sequence based on planet-relative velocity if both the GPS and the barometric altimeter fail. However, this backup trigger results in large altitude errors relative to the targeted altitude. Motivated by this challenge, this paper demonstrates how logistic regression may be employed to semi-automatically generate robust triggers based on statistical analysis. Logistic regression is used as a ground processor pre-flight to develop a statistical classifier. The classifier would then be implemented in flight software and executed in real-time. This technique offers improved performance even in the face of highly inaccurate measurements. Although the logistic regression-based trigger approach will not be implemented within EFT-1 flight software, the methodology can be carried forward for future missions and vehicles

  9. Heritability of slow and/or inaccurate reading ability in 33,000 adult twins with self-reported data

    DEFF Research Database (Denmark)

    Fibiger-Dagnæs, Steen; von Bornemann Hjelmborg, Jacob; Erbs, Lena

    2012-01-01

    Genetic influence for adult slow and/or inaccurate reading ability was studied from selfreported answers, using a dichotomous question on having difficulties in reading the Danish subtitles on foreign TV programs. The data from 33,424 twins were population based and were used for biometric analys...

  10. BELM: Bayesian extreme learning machine.

    Science.gov (United States)

    Soria-Olivas, Emilio; Gómez-Sanchis, Juan; Martín, José D; Vila-Francés, Joan; Martínez, Marcelino; Magdalena, José R; Serrano, Antonio J

    2011-03-01

    The theory of extreme learning machine (ELM) has become very popular on the last few years. ELM is a new approach for learning the parameters of the hidden layers of a multilayer neural network (as the multilayer perceptron or the radial basis function neural network). Its main advantage is the lower computational cost, which is especially relevant when dealing with many patterns defined in a high-dimensional space. This brief proposes a bayesian approach to ELM, which presents some advantages over other approaches: it allows the introduction of a priori knowledge; obtains the confidence intervals (CIs) without the need of applying methods that are computationally intensive, e.g., bootstrap; and presents high generalization capabilities. Bayesian ELM is benchmarked against classical ELM in several artificial and real datasets that are widely used for the evaluation of machine learning algorithms. Achieved results show that the proposed approach produces a competitive accuracy with some additional advantages, namely, automatic production of CIs, reduction of probability of model overfitting, and use of a priori knowledge.

  11. Bayesian decision theory : A simple toy problem

    NARCIS (Netherlands)

    van Erp, H.R.N.; Linger, R.O.; van Gelder, P.H.A.J.M.

    2016-01-01

    We give here a comparison of the expected outcome theory, the expected utility theory, and the Bayesian decision theory, by way of a simple numerical toy problem in which we look at the investment willingness to avert a high impact low probability event. It will be found that for this toy problem

  12. Probability and Bayesian statistics

    CERN Document Server

    1987-01-01

    This book contains selected and refereed contributions to the "Inter­ national Symposium on Probability and Bayesian Statistics" which was orga­ nized to celebrate the 80th birthday of Professor Bruno de Finetti at his birthplace Innsbruck in Austria. Since Professor de Finetti died in 1985 the symposium was dedicated to the memory of Bruno de Finetti and took place at Igls near Innsbruck from 23 to 26 September 1986. Some of the pa­ pers are published especially by the relationship to Bruno de Finetti's scientific work. The evolution of stochastics shows growing importance of probability as coherent assessment of numerical values as degrees of believe in certain events. This is the basis for Bayesian inference in the sense of modern statistics. The contributions in this volume cover a broad spectrum ranging from foundations of probability across psychological aspects of formulating sub­ jective probability statements, abstract measure theoretical considerations, contributions to theoretical statistics an...

  13. Bayesian community detection

    DEFF Research Database (Denmark)

    Mørup, Morten; Schmidt, Mikkel N

    2012-01-01

    Many networks of scientific interest naturally decompose into clusters or communities with comparatively fewer external than internal links; however, current Bayesian models of network communities do not exert this intuitive notion of communities. We formulate a nonparametric Bayesian model...... for community detection consistent with an intuitive definition of communities and present a Markov chain Monte Carlo procedure for inferring the community structure. A Matlab toolbox with the proposed inference procedure is available for download. On synthetic and real networks, our model detects communities...... consistent with ground truth, and on real networks, it outperforms existing approaches in predicting missing links. This suggests that community structure is an important structural property of networks that should be explicitly modeled....

  14. Approximate Bayesian recursive estimation

    Czech Academy of Sciences Publication Activity Database

    Kárný, Miroslav

    2014-01-01

    Roč. 285, č. 1 (2014), s. 100-111 ISSN 0020-0255 R&D Projects: GA ČR GA13-13502S Institutional support: RVO:67985556 Keywords : Approximate parameter estimation * Bayesian recursive estimation * Kullback–Leibler divergence * Forgetting Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 4.038, year: 2014 http://library.utia.cas.cz/separaty/2014/AS/karny-0425539.pdf

  15. 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....

  16. Bayesian Hypothesis Testing

    Energy Technology Data Exchange (ETDEWEB)

    Andrews, Stephen A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Sigeti, David E. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-11-15

    These are a set of slides about Bayesian hypothesis testing, where many hypotheses are tested. The conclusions are the following: The value of the Bayes factor obtained when using the median of the posterior marginal is almost the minimum value of the Bayes factor. The value of τ2 which minimizes the Bayes factor is a reasonable choice for this parameter. This allows a likelihood ratio to be computed with is the least favorable to H0.

  17. 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.

  18. Bayesian ARTMAP for regression.

    Science.gov (United States)

    Sasu, L M; Andonie, R

    2013-10-01

    Bayesian ARTMAP (BA) is a recently introduced neural architecture which uses a combination of Fuzzy ARTMAP competitive learning and Bayesian learning. Training is generally performed online, in a single-epoch. During training, BA creates input data clusters as Gaussian categories, and also infers the conditional probabilities between input patterns and categories, and between categories and classes. During prediction, BA uses Bayesian posterior probability estimation. So far, BA was used only for classification. The goal of this paper is to analyze the efficiency of BA for regression problems. Our contributions are: (i) we generalize the BA algorithm using the clustering functionality of both ART modules, and name it BA for Regression (BAR); (ii) we prove that BAR is a universal approximator with the best approximation property. In other words, BAR approximates arbitrarily well any continuous function (universal approximation) and, for every given continuous function, there is one in the set of BAR approximators situated at minimum distance (best approximation); (iii) we experimentally compare the online trained BAR with several neural models, on the following standard regression benchmarks: CPU Computer Hardware, Boston Housing, Wisconsin Breast Cancer, and Communities and Crime. Our results show that BAR is an appropriate tool for regression tasks, both for theoretical and practical reasons. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. 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...

  20. A Robust Obstacle Avoidance for Service Robot Using Bayesian Approach

    Directory of Open Access Journals (Sweden)

    Widodo Budiharto

    2011-03-01

    Full Text Available The objective of this paper is to propose a robust obstacle avoidance method for service robot in indoor environment. The method for obstacles avoidance uses information about static obstacles on the landmark using edge detection. Speed and direction of people that walks as moving obstacle obtained by single camera using tracking and recognition system and distance measurement using 3 ultrasonic sensors. A new geometrical model and maneuvering method for moving obstacle avoidance introduced and combined with Bayesian approach for state estimation. The obstacle avoidance problem is formulated using decision theory, prior and posterior distribution and loss function to determine an optimal response based on inaccurate sensor data. Algorithms for moving obstacles avoidance method proposed and experiment results implemented to service robot also presented. Various experiments show that our proposed method very fast, robust and successfully implemented to service robot called Srikandi II that equipped with 4 DOF arm robot developed in our laboratory.

  1. Bayesian Correlation Analysis for Sequence Count Data.

    Directory of Open Access Journals (Sweden)

    Daniel Sánchez-Taltavull

    Full Text Available Evaluating the similarity of different measured variables is a fundamental task of statistics, and a key part of many bioinformatics algorithms. Here we propose a Bayesian scheme for estimating the correlation between different entities' measurements based on high-throughput sequencing data. These entities could be different genes or miRNAs whose expression is measured by RNA-seq, different transcription factors or histone marks whose expression is measured by ChIP-seq, or even combinations of different types of entities. Our Bayesian formulation accounts for both measured signal levels and uncertainty in those levels, due to varying sequencing depth in different experiments and to varying absolute levels of individual entities, both of which affect the precision of the measurements. In comparison with a traditional Pearson correlation analysis, we show that our Bayesian correlation analysis retains high correlations when measurement confidence is high, but suppresses correlations when measurement confidence is low-especially for entities with low signal levels. In addition, we consider the influence of priors on the Bayesian correlation estimate. Perhaps surprisingly, we show that naive, uniform priors on entities' signal levels can lead to highly biased correlation estimates, particularly when different experiments have widely varying sequencing depths. However, we propose two alternative priors that provably mitigate this problem. We also prove that, like traditional Pearson correlation, our Bayesian correlation calculation constitutes a kernel in the machine learning sense, and thus can be used as a similarity measure in any kernel-based machine learning algorithm. We demonstrate our approach on two RNA-seq datasets and one miRNA-seq dataset.

  2. 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.

  3. Comprehension and computation in Bayesian problem solving

    Directory of Open Access Journals (Sweden)

    Eric D. Johnson

    2015-07-01

    Full Text Available Humans have long been characterized as poor probabilistic reasoners when presented with explicit numerical information. Bayesian word problems provide a well-known example of this, where even highly educated and cognitively skilled individuals fail to adhere to mathematical norms. It is widely agreed that natural frequencies can facilitate Bayesian reasoning relative to normalized formats (e.g. probabilities, percentages, both by clarifying logical set-subset relations and by simplifying numerical calculations. Nevertheless, between-study performance on transparent Bayesian problems varies widely, and generally remains rather unimpressive. We suggest there has been an over-focus on this representational facilitator (i.e. transparent problem structures at the expense of the specific logical and numerical processing requirements and the corresponding individual abilities and skills necessary for providing Bayesian-like output given specific verbal and numerical input. We further suggest that understanding this task-individual pair could benefit from considerations from the literature on mathematical cognition, which emphasizes text comprehension and problem solving, along with contributions of online executive working memory, metacognitive regulation, and relevant stored knowledge and skills. We conclude by offering avenues for future research aimed at identifying the stages in problem solving at which correct versus incorrect reasoners depart, and how individual difference might influence this time point.

  4. 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.

  5. Applied Bayesian modelling

    CERN Document Server

    Congdon, Peter

    2014-01-01

    This book provides an accessible approach to Bayesian computing and data analysis, with an emphasis on the interpretation of real data sets. Following in the tradition of the successful first edition, this book aims to make a wide range of statistical modeling applications accessible using tested code that can be readily adapted to the reader's own applications. The second edition has been thoroughly reworked and updated to take account of advances in the field. A new set of worked examples is included. The novel aspect of the first edition was the coverage of statistical modeling using WinBU

  6. Inverse Tasks In The Tsunami Problem: Nonlinear Regression With Inaccurate Input Data

    Science.gov (United States)

    Lavrentiev, M.; Shchemel, A.; Simonov, K.

    A variant of modified training functional that allows considering inaccurate input data is suggested. A limiting case when a part of input data is completely undefined, and, therefore, a problem of reconstruction of hidden parameters should be solved, is also considered. Some numerical experiments are presented. It is assumed that a dependence of known output variables on known input ones should be found is the classic problem definition, which is widely used in the majority of neural nets algorithms. The quality of approximation is evaluated as a performance function. Often the error of the task is evaluated as squared distance between known input data and predicted data multiplied by weighed coefficients. These coefficients may be named "precision coefficients". When inputs are not known exactly, natural generalization of performance function is adding member that responsible for distance between known inputs and shifted inputs, which lessen model's error. It is desirable that the set of variable parameters is compact for training to be con- verging. In the above problem it is possible to choose variants of demands of a priori compactness, which allow meaningful interpretation in the smoothness of the model dependence. Two kinds of regularization was used, first limited squares of coefficients responsible for nonlinearity and second limited multiplication of the above coeffi- cients and linear coefficients. Asymptotic universality of neural net ability to approxi- mate various smooth functions with any accuracy by increase of the number of tunable parameters is often the base for selecting a type of neural net approximation. It is pos- sible to show that used neural net will approach to Fourier integral transform, which approximate abilities are known, with increasing of the number of tunable parameters. In the limiting case, when input data is set with zero precision, the problem of recon- struction of hidden parameters with observed output data appears. The

  7. Inference in hybrid Bayesian networks

    DEFF Research Database (Denmark)

    Lanseth, Helge; Nielsen, Thomas Dyhre; Rumí, Rafael

    2009-01-01

    Since the 1980s, Bayesian Networks (BNs) have become increasingly popular for building statistical models of complex systems. This is particularly true for boolean systems, where BNs often prove to be a more efficient modelling framework than traditional reliability-techniques (like fault trees...... decade's research on inference in hybrid Bayesian networks. The discussions are linked to an example model for estimating human reliability....

  8. Searching Algorithm Using Bayesian Updates

    Science.gov (United States)

    Caudle, Kyle

    2010-01-01

    In late October 1967, the USS Scorpion was lost at sea, somewhere between the Azores and Norfolk Virginia. Dr. Craven of the U.S. Navy's Special Projects Division is credited with using Bayesian Search Theory to locate the submarine. Bayesian Search Theory is a straightforward and interesting application of Bayes' theorem which involves searching…

  9. Bayesian Data Analysis (lecture 2)

    CERN Multimedia

    CERN. Geneva

    2018-01-01

    framework but we will also go into more detail and discuss for example the role of the prior. The second part of the lecture will cover further examples and applications that heavily rely on the bayesian approach, as well as some computational tools needed to perform a bayesian analysis.

  10. Bayesian Data Analysis (lecture 1)

    CERN Multimedia

    CERN. Geneva

    2018-01-01

    framework but we will also go into more detail and discuss for example the role of the prior. The second part of the lecture will cover further examples and applications that heavily rely on the bayesian approach, as well as some computational tools needed to perform a bayesian analysis.

  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 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...

  14. 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.

  15. How to practise Bayesian statistics outside the Bayesian church: What philosophy for Bayesian statistical modelling?

    NARCIS (Netherlands)

    Borsboom, D.; Haig, B.D.

    2013-01-01

    Unlike most other statistical frameworks, Bayesian statistical inference is wedded to a particular approach in the philosophy of science (see Howson & Urbach, 2006); this approach is called Bayesianism. Rather than being concerned with model fitting, this position in the philosophy of science

  16. Bayesian network modelling of upper gastrointestinal bleeding

    Science.gov (United States)

    Aisha, Nazziwa; Shohaimi, Shamarina; Adam, Mohd Bakri

    2013-09-01

    Bayesian networks are graphical probabilistic models that represent causal and other relationships between domain variables. In the context of medical decision making, these models have been explored to help in medical diagnosis and prognosis. In this paper, we discuss the Bayesian network formalism in building medical support systems and we learn a tree augmented naive Bayes Network (TAN) from gastrointestinal bleeding data. The accuracy of the TAN in classifying the source of gastrointestinal bleeding into upper or lower source is obtained. The TAN achieves a high classification accuracy of 86% and an area under curve of 92%. A sensitivity analysis of the model shows relatively high levels of entropy reduction for color of the stool, history of gastrointestinal bleeding, consistency and the ratio of blood urea nitrogen to creatinine. The TAN facilitates the identification of the source of GIB and requires further validation.

  17. 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.

  18. 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.

  19. Book review: Bayesian analysis for population ecology

    Science.gov (United States)

    Link, William A.

    2011-01-01

    Brian Dennis described the field of ecology as “fertile, uncolonized ground for Bayesian ideas.” He continued: “The Bayesian propagule has arrived at the shore. Ecologists need to think long and hard about the consequences of a Bayesian ecology. The Bayesian outlook is a successful competitor, but is it a weed? I think so.” (Dennis 2004)

  20. A Bayesian approach to particle identification in ALICE

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    Among the LHC experiments, ALICE has unique particle identification (PID) capabilities exploiting different types of detectors. During Run 1, a Bayesian approach to PID was developed and intensively tested. It facilitates the combination of information from different sub-systems. The adopted methodology and formalism as well as the performance of the Bayesian PID approach for charged pions, kaons and protons in the central barrel of ALICE will be reviewed. Results are presented with PID performed via measurements of specific energy loss (dE/dx) and time-of-flight using information from the TPC and TOF detectors, respectively. Methods to extract priors from data and to compare PID efficiencies and misidentification probabilities in data and Monte Carlo using high-purity samples of identified particles will be presented. Bayesian PID results were found consistent with previous measurements published by ALICE. The Bayesian PID approach gives a higher signal-to-background ratio and a similar or larger statist...

  1. The NIFTY way of Bayesian signal inference

    International Nuclear Information System (INIS)

    Selig, Marco

    2014-01-01

    We introduce NIFTY, 'Numerical Information Field Theory', a software package for the development of Bayesian signal inference algorithms that operate independently from any underlying spatial grid and its resolution. A large number of Bayesian and Maximum Entropy methods for 1D signal reconstruction, 2D imaging, as well as 3D tomography, appear formally similar, but one often finds individualized implementations that are neither flexible nor easily transferable. Signal inference in the framework of NIFTY can be done in an abstract way, such that algorithms, prototyped in 1D, can be applied to real world problems in higher-dimensional settings. NIFTY as a versatile library is applicable and already has been applied in 1D, 2D, 3D and spherical settings. A recent application is the D 3 PO algorithm targeting the non-trivial task of denoising, deconvolving, and decomposing photon observations in high energy astronomy

  2. The NIFTy way of Bayesian signal inference

    Science.gov (United States)

    Selig, Marco

    2014-12-01

    We introduce NIFTy, "Numerical Information Field Theory", a software package for the development of Bayesian signal inference algorithms that operate independently from any underlying spatial grid and its resolution. A large number of Bayesian and Maximum Entropy methods for 1D signal reconstruction, 2D imaging, as well as 3D tomography, appear formally similar, but one often finds individualized implementations that are neither flexible nor easily transferable. Signal inference in the framework of NIFTy can be done in an abstract way, such that algorithms, prototyped in 1D, can be applied to real world problems in higher-dimensional settings. NIFTy as a versatile library is applicable and already has been applied in 1D, 2D, 3D and spherical settings. A recent application is the D3PO algorithm targeting the non-trivial task of denoising, deconvolving, and decomposing photon observations in high energy astronomy.

  3. Modelling dependable systems using hybrid Bayesian networks

    International Nuclear Information System (INIS)

    Neil, Martin; Tailor, Manesh; Marquez, David; Fenton, Norman; Hearty, Peter

    2008-01-01

    A hybrid Bayesian network (BN) is one that incorporates both discrete and continuous nodes. In our extensive applications of BNs for system dependability assessment, the models are invariably hybrid and the need for efficient and accurate computation is paramount. We apply a new iterative algorithm that efficiently combines dynamic discretisation with robust propagation algorithms on junction tree structures to perform inference in hybrid BNs. We illustrate its use in the field of dependability with two example of reliability estimation. Firstly we estimate the reliability of a simple single system and next we implement a hierarchical Bayesian model. In the hierarchical model we compute the reliability of two unknown subsystems from data collected on historically similar subsystems and then input the result into a reliability block model to compute system level reliability. We conclude that dynamic discretisation can be used as an alternative to analytical or Monte Carlo methods with high precision and can be applied to a wide range of dependability problems

  4. Bayesian component separation: The Planck experience

    Science.gov (United States)

    Wehus, Ingunn Kathrine; Eriksen, Hans Kristian

    2018-05-01

    Bayesian component separation techniques have played a central role in the data reduction process of Planck. The most important strength of this approach is its global nature, in which a parametric and physical model is fitted to the data. Such physical modeling allows the user to constrain very general data models, and jointly probe cosmological, astrophysical and instrumental parameters. This approach also supports statistically robust goodness-of-fit tests in terms of data-minus-model residual maps, which are essential for identifying residual systematic effects in the data. The main challenges are high code complexity and computational cost. Whether or not these costs are justified for a given experiment depends on its final uncertainty budget. We therefore predict that the importance of Bayesian component separation techniques is likely to increase with time for intensity mapping experiments, similar to what has happened in the CMB field, as observational techniques mature, and their overall sensitivity improves.

  5. Bayesian image restoration, using configurations

    OpenAIRE

    Thorarinsdottir, Thordis

    2006-01-01

    In this paper, we develop a Bayesian procedure for removing noise from images that can be viewed as noisy realisations of random sets in the plane. The procedure utilises recent advances in configuration theory for noise free random sets, where the probabilities of observing the different boundary configurations are expressed in terms of the mean normal measure of the random set. These probabilities are used as prior probabilities in a Bayesian image restoration approach. Estimation of the re...

  6. 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...

  7. The image recognition based on neural network and Bayesian decision

    Science.gov (United States)

    Wang, Chugege

    2018-04-01

    The artificial neural network began in 1940, which is an important part of artificial intelligence. At present, it has become a hot topic in the fields of neuroscience, computer science, brain science, mathematics, and psychology. Thomas Bayes firstly reported the Bayesian theory in 1763. After the development in the twentieth century, it has been widespread in all areas of statistics. In recent years, due to the solution of the problem of high-dimensional integral calculation, Bayesian Statistics has been improved theoretically, which solved many problems that cannot be solved by classical statistics and is also applied to the interdisciplinary fields. In this paper, the related concepts and principles of the artificial neural network are introduced. It also summarizes the basic content and principle of Bayesian Statistics, and combines the artificial neural network technology and Bayesian decision theory and implement them in all aspects of image recognition, such as enhanced face detection method based on neural network and Bayesian decision, as well as the image classification based on the Bayesian decision. It can be seen that the combination of artificial intelligence and statistical algorithms has always been the hot research topic.

  8. Bayesian Recurrent Neural Network for Language Modeling.

    Science.gov (United States)

    Chien, Jen-Tzung; Ku, Yuan-Chu

    2016-02-01

    A language model (LM) is calculated as the probability of a word sequence that provides the solution to word prediction for a variety of information systems. A recurrent neural network (RNN) is powerful to learn the large-span dynamics of a word sequence in the continuous space. However, the training of the RNN-LM is an ill-posed problem because of too many parameters from a large dictionary size and a high-dimensional hidden layer. This paper presents a Bayesian approach to regularize the RNN-LM and apply it for continuous speech recognition. We aim to penalize the too complicated RNN-LM by compensating for the uncertainty of the estimated model parameters, which is represented by a Gaussian prior. The objective function in a Bayesian classification network is formed as the regularized cross-entropy error function. The regularized model is constructed not only by calculating the regularized parameters according to the maximum a posteriori criterion but also by estimating the Gaussian hyperparameter by maximizing the marginal likelihood. A rapid approximation to a Hessian matrix is developed to implement the Bayesian RNN-LM (BRNN-LM) by selecting a small set of salient outer-products. The proposed BRNN-LM achieves a sparser model than the RNN-LM. Experiments on different corpora show the robustness of system performance by applying the rapid BRNN-LM under different conditions.

  9. Particle identification in ALICE: a Bayesian approach

    CERN Document Server

    Adam, Jaroslav; Aggarwal, Madan Mohan; Aglieri Rinella, Gianluca; Agnello, Michelangelo; Agrawal, Neelima; Ahammed, Zubayer; Ahmad, Shakeel; Ahn, Sang Un; Aiola, Salvatore; Akindinov, Alexander; Alam, Sk Noor; Silva De Albuquerque, Danilo; Aleksandrov, Dmitry; Alessandro, Bruno; Alexandre, Didier; Alfaro Molina, Jose Ruben; Alici, Andrea; Alkin, Anton; Millan Almaraz, Jesus Roberto; Alme, Johan; Alt, Torsten; Altinpinar, Sedat; Altsybeev, Igor; Alves Garcia Prado, Caio; Andrei, Cristian; Andronic, Anton; Anguelov, Venelin; Anticic, Tome; Antinori, Federico; Antonioli, Pietro; Aphecetche, Laurent Bernard; Appelshaeuser, Harald; Arcelli, Silvia; Arnaldi, Roberta; Arnold, Oliver Werner; Arsene, Ionut Cristian; Arslandok, Mesut; Audurier, Benjamin; Augustinus, Andre; Averbeck, Ralf Peter; Azmi, Mohd Danish; Badala, Angela; Baek, Yong Wook; Bagnasco, Stefano; Bailhache, Raphaelle Marie; Bala, Renu; Balasubramanian, Supraja; Baldisseri, Alberto; Baral, Rama Chandra; Barbano, Anastasia Maria; Barbera, Roberto; Barile, Francesco; Barnafoldi, Gergely Gabor; Barnby, Lee Stuart; Ramillien Barret, Valerie; Bartalini, Paolo; Barth, Klaus; Bartke, Jerzy Gustaw; Bartsch, Esther; Basile, Maurizio; Bastid, Nicole; Basu, Sumit; Bathen, Bastian; Batigne, Guillaume; Batista Camejo, Arianna; Batyunya, Boris; Batzing, Paul Christoph; Bearden, Ian Gardner; Beck, Hans; Bedda, Cristina; Behera, Nirbhay Kumar; Belikov, Iouri; Bellini, Francesca; Bello Martinez, Hector; Bellwied, Rene; Belmont Iii, Ronald John; Belmont Moreno, Ernesto; Belyaev, Vladimir; Benacek, Pavel; Bencedi, Gyula; Beole, Stefania; Berceanu, Ionela; Bercuci, Alexandru; Berdnikov, Yaroslav; Berenyi, Daniel; Bertens, Redmer Alexander; Berzano, Dario; Betev, Latchezar; Bhasin, Anju; Bhat, Inayat Rasool; Bhati, Ashok Kumar; Bhattacharjee, Buddhadeb; Bhom, Jihyun; Bianchi, Livio; Bianchi, Nicola; Bianchin, Chiara; Bielcik, Jaroslav; Bielcikova, Jana; Bilandzic, Ante; Biro, Gabor; Biswas, Rathijit; Biswas, Saikat; Bjelogrlic, Sandro; Blair, Justin Thomas; Blau, Dmitry; Blume, Christoph; Bock, Friederike; Bogdanov, Alexey; Boggild, Hans; Boldizsar, Laszlo; Bombara, Marek; Book, Julian Heinz; Borel, Herve; Borissov, Alexander; Borri, Marcello; Bossu, Francesco; Botta, Elena; Bourjau, Christian; Braun-Munzinger, Peter; Bregant, Marco; Breitner, Timo Gunther; Broker, Theo Alexander; Browning, Tyler Allen; Broz, Michal; Brucken, Erik Jens; Bruna, Elena; Bruno, Giuseppe Eugenio; Budnikov, Dmitry; Buesching, Henner; Bufalino, Stefania; Buncic, Predrag; Busch, Oliver; Buthelezi, Edith Zinhle; Bashir Butt, Jamila; Buxton, Jesse Thomas; Cabala, Jan; Caffarri, Davide; Cai, Xu; Caines, Helen Louise; Calero Diaz, Liliet; Caliva, Alberto; Calvo Villar, Ernesto; Camerini, Paolo; Carena, Francesco; Carena, Wisla; Carnesecchi, Francesca; Castillo Castellanos, Javier Ernesto; Castro, Andrew John; Casula, Ester Anna Rita; Ceballos Sanchez, Cesar; Cepila, Jan; Cerello, Piergiorgio; Cerkala, Jakub; Chang, Beomsu; Chapeland, Sylvain; Chartier, Marielle; Charvet, Jean-Luc Fernand; Chattopadhyay, Subhasis; Chattopadhyay, Sukalyan; Chauvin, Alex; Chelnokov, Volodymyr; Cherney, Michael Gerard; Cheshkov, Cvetan Valeriev; Cheynis, Brigitte; Chibante Barroso, Vasco Miguel; Dobrigkeit Chinellato, David; Cho, Soyeon; Chochula, Peter; Choi, Kyungeon; Chojnacki, Marek; Choudhury, Subikash; Christakoglou, Panagiotis; Christensen, Christian Holm; Christiansen, Peter; Chujo, Tatsuya; Chung, Suh-Urk; Cicalo, Corrado; Cifarelli, Luisa; Cindolo, Federico; Cleymans, Jean Willy Andre; Colamaria, Fabio Filippo; Colella, Domenico; Collu, Alberto; Colocci, Manuel; Conesa Balbastre, Gustavo; Conesa Del Valle, Zaida; Connors, Megan Elizabeth; Contreras Nuno, Jesus Guillermo; Cormier, Thomas Michael; Corrales Morales, Yasser; Cortes Maldonado, Ismael; Cortese, Pietro; Cosentino, Mauro Rogerio; Costa, Filippo; Crochet, Philippe; Cruz Albino, Rigoberto; Cuautle Flores, Eleazar; Cunqueiro Mendez, Leticia; Dahms, Torsten; Dainese, Andrea; Danisch, Meike Charlotte; Danu, Andrea; Das, Debasish; Das, Indranil; Das, Supriya; Dash, Ajay Kumar; Dash, Sadhana; De, Sudipan; De Caro, Annalisa; De Cataldo, Giacinto; De Conti, Camila; De Cuveland, Jan; De Falco, Alessandro; De Gruttola, Daniele; De Marco, Nora; De Pasquale, Salvatore; Deisting, Alexander; Deloff, Andrzej; Denes, Ervin Sandor; Deplano, Caterina; Dhankher, Preeti; Di Bari, Domenico; Di Mauro, Antonio; Di Nezza, Pasquale; Diaz Corchero, Miguel Angel; Dietel, Thomas; Dillenseger, Pascal; Divia, Roberto; Djuvsland, Oeystein; Dobrin, Alexandru Florin; Domenicis Gimenez, Diogenes; Donigus, Benjamin; Dordic, Olja; Drozhzhova, Tatiana; Dubey, Anand Kumar; Dubla, Andrea; Ducroux, Laurent; Dupieux, Pascal; Ehlers Iii, Raymond James; Elia, Domenico; Endress, Eric; Engel, Heiko; Epple, Eliane; Erazmus, Barbara Ewa; Erdemir, Irem; Erhardt, Filip; Espagnon, Bruno; Estienne, Magali Danielle; Esumi, Shinichi; Eum, Jongsik; Evans, David; Evdokimov, Sergey; Eyyubova, Gyulnara; Fabbietti, Laura; Fabris, Daniela; Faivre, Julien; Fantoni, Alessandra; Fasel, Markus; Feldkamp, Linus; Feliciello, Alessandro; Feofilov, Grigorii; Ferencei, Jozef; Fernandez Tellez, Arturo; Gonzalez Ferreiro, Elena; Ferretti, Alessandro; Festanti, Andrea; Feuillard, Victor Jose Gaston; Figiel, Jan; Araujo Silva Figueredo, Marcel; Filchagin, Sergey; Finogeev, Dmitry; Fionda, Fiorella; Fiore, Enrichetta Maria; Fleck, Martin Gabriel; Floris, Michele; Foertsch, Siegfried Valentin; Foka, Panagiota; Fokin, Sergey; Fragiacomo, Enrico; Francescon, Andrea; Frankenfeld, Ulrich Michael; Fronze, Gabriele Gaetano; Fuchs, Ulrich; Furget, Christophe; Furs, Artur; Fusco Girard, Mario; Gaardhoeje, Jens Joergen; Gagliardi, Martino; Gago Medina, Alberto Martin; Gallio, Mauro; Gangadharan, Dhevan Raja; Ganoti, Paraskevi; Gao, Chaosong; Garabatos Cuadrado, Jose; Garcia-Solis, Edmundo Javier; Gargiulo, Corrado; Gasik, Piotr Jan; Gauger, Erin Frances; Germain, Marie; Gheata, Andrei George; Gheata, Mihaela; Ghosh, Premomoy; Ghosh, Sanjay Kumar; Gianotti, Paola; Giubellino, Paolo; Giubilato, Piero; Gladysz-Dziadus, Ewa; Glassel, Peter; Gomez Coral, Diego Mauricio; Gomez Ramirez, Andres; Sanchez Gonzalez, Andres; Gonzalez, Victor; Gonzalez Zamora, Pedro; Gorbunov, Sergey; Gorlich, Lidia Maria; Gotovac, Sven; Grabski, Varlen; Grachov, Oleg Anatolievich; Graczykowski, Lukasz Kamil; Graham, Katie Leanne; Grelli, Alessandro; Grigoras, Alina Gabriela; Grigoras, Costin; Grigoryev, Vladislav; Grigoryan, Ara; Grigoryan, Smbat; Grynyov, Borys; Grion, Nevio; Gronefeld, Julius Maximilian; Grosse-Oetringhaus, Jan Fiete; Grosso, Raffaele; Guber, Fedor; Guernane, Rachid; Guerzoni, Barbara; Gulbrandsen, Kristjan Herlache; Gunji, Taku; Gupta, Anik; Gupta, Ramni; Haake, Rudiger; Haaland, Oystein Senneset; Hadjidakis, Cynthia Marie; Haiduc, Maria; Hamagaki, Hideki; Hamar, Gergoe; Hamon, Julien Charles; Harris, John William; Harton, Austin Vincent; Hatzifotiadou, Despina; Hayashi, Shinichi; Heckel, Stefan Thomas; Hellbar, Ernst; Helstrup, Haavard; Herghelegiu, Andrei Ionut; Herrera Corral, Gerardo Antonio; Hess, Benjamin Andreas; Hetland, Kristin Fanebust; Hillemanns, Hartmut; Hippolyte, Boris; Horak, David; Hosokawa, Ritsuya; Hristov, Peter Zahariev; Humanic, Thomas; Hussain, Nur; Hussain, Tahir; Hutter, Dirk; Hwang, Dae Sung; Ilkaev, Radiy; Inaba, Motoi; Incani, Elisa; Ippolitov, Mikhail; Irfan, Muhammad; Ivanov, Marian; Ivanov, Vladimir; Izucheev, Vladimir; Jacazio, Nicolo; Jacobs, Peter Martin; Jadhav, Manoj Bhanudas; Jadlovska, Slavka; Jadlovsky, Jan; Jahnke, Cristiane; Jakubowska, Monika Joanna; Jang, Haeng Jin; Janik, Malgorzata Anna; Pahula Hewage, Sandun; Jena, Chitrasen; Jena, Satyajit; Jimenez Bustamante, Raul Tonatiuh; Jones, Peter Graham; Jusko, Anton; Kalinak, Peter; Kalweit, Alexander Philipp; Kamin, Jason Adrian; Kang, Ju Hwan; Kaplin, Vladimir; Kar, Somnath; Karasu Uysal, Ayben; Karavichev, Oleg; Karavicheva, Tatiana; Karayan, Lilit; Karpechev, Evgeny; Kebschull, Udo Wolfgang; Keidel, Ralf; Keijdener, Darius Laurens; Keil, Markus; Khan, Mohammed Mohisin; Khan, Palash; Khan, Shuaib Ahmad; Khanzadeev, Alexei; Kharlov, Yury; Kileng, Bjarte; Kim, Do Won; Kim, Dong Jo; Kim, Daehyeok; Kim, Hyeonjoong; Kim, Jinsook; Kim, Minwoo; Kim, Se Yong; Kim, Taesoo; Kirsch, Stefan; Kisel, Ivan; Kiselev, Sergey; Kisiel, Adam Ryszard; Kiss, Gabor; Klay, Jennifer Lynn; Klein, Carsten; Klein, Jochen; Klein-Boesing, Christian; Klewin, Sebastian; Kluge, Alexander; Knichel, Michael Linus; Knospe, Anders Garritt; Kobdaj, Chinorat; Kofarago, Monika; Kollegger, Thorsten; Kolozhvari, Anatoly; Kondratev, Valerii; Kondratyeva, Natalia; Kondratyuk, Evgeny; Konevskikh, Artem; Kopcik, Michal; Kostarakis, Panagiotis; Kour, Mandeep; Kouzinopoulos, Charalampos; Kovalenko, Oleksandr; Kovalenko, Vladimir; Kowalski, Marek; Koyithatta Meethaleveedu, Greeshma; Kralik, Ivan; Kravcakova, Adela; Krivda, Marian; Krizek, Filip; Kryshen, Evgeny; Krzewicki, Mikolaj; Kubera, Andrew Michael; Kucera, Vit; Kuhn, Christian Claude; Kuijer, Paulus Gerardus; Kumar, Ajay; Kumar, Jitendra; Kumar, Lokesh; Kumar, Shyam; Kurashvili, Podist; Kurepin, Alexander; Kurepin, Alexey; Kuryakin, Alexey; Kweon, Min Jung; Kwon, Youngil; La Pointe, Sarah Louise; La Rocca, Paola; Ladron De Guevara, Pedro; Lagana Fernandes, Caio; Lakomov, Igor; Langoy, Rune; Lara Martinez, Camilo Ernesto; Lardeux, Antoine Xavier; Lattuca, Alessandra; Laudi, Elisa; Lea, Ramona; Leardini, Lucia; Lee, Graham Richard; Lee, Seongjoo; Lehas, Fatiha; Lemmon, Roy Crawford; Lenti, Vito; Leogrande, Emilia; Leon Monzon, Ildefonso; Leon Vargas, Hermes; Leoncino, Marco; Levai, Peter; Li, Shuang; Li, Xiaomei; Lien, Jorgen Andre; Lietava, Roman; Lindal, Svein; Lindenstruth, Volker; Lippmann, Christian; Lisa, Michael Annan; Ljunggren, Hans Martin; Lodato, Davide Francesco; Lonne, Per-Ivar; Loginov, Vitaly; Loizides, Constantinos; Lopez, Xavier Bernard; Lopez Torres, Ernesto; Lowe, Andrew John; Luettig, Philipp Johannes; Lunardon, Marcello; Luparello, Grazia; Lutz, Tyler Harrison; Maevskaya, Alla; Mager, Magnus; Mahajan, Sanjay; Mahmood, Sohail Musa; Maire, Antonin; Majka, Richard Daniel; Malaev, Mikhail; Maldonado Cervantes, Ivonne Alicia; Malinina, Liudmila; Mal'Kevich, Dmitry; Malzacher, Peter; Mamonov, Alexander; Manko, Vladislav; Manso, Franck; Manzari, Vito; Marchisone, Massimiliano; Mares, Jiri; Margagliotti, Giacomo Vito; Margotti, Anselmo; Margutti, Jacopo; Marin, Ana Maria; Markert, Christina; Marquard, Marco; Martin, Nicole Alice; Martin Blanco, Javier; Martinengo, Paolo; Martinez Hernandez, Mario Ivan; Martinez-Garcia, Gines; Martinez Pedreira, Miguel; Mas, Alexis Jean-Michel; Masciocchi, Silvia; Masera, Massimo; Masoni, Alberto; Mastroserio, Annalisa; Matyja, Adam Tomasz; Mayer, Christoph; Mazer, Joel Anthony; Mazzoni, Alessandra Maria; Mcdonald, Daniel; Meddi, Franco; Melikyan, Yuri; Menchaca-Rocha, Arturo Alejandro; Meninno, Elisa; Mercado-Perez, Jorge; Meres, Michal; Miake, Yasuo; Mieskolainen, Matti Mikael; Mikhaylov, Konstantin; Milano, Leonardo; Milosevic, Jovan; Mischke, Andre; Mishra, Aditya Nath; Miskowiec, Dariusz Czeslaw; Mitra, Jubin; Mitu, Ciprian Mihai; Mohammadi, Naghmeh; Mohanty, Bedangadas; Molnar, Levente; Montano Zetina, Luis Manuel; Montes Prado, Esther; Moreira De Godoy, Denise Aparecida; Perez Moreno, Luis Alberto; Moretto, Sandra; Morreale, Astrid; Morsch, Andreas; Muccifora, Valeria; Mudnic, Eugen; Muhlheim, Daniel Michael; Muhuri, Sanjib; Mukherjee, Maitreyee; Mulligan, James Declan; Gameiro Munhoz, Marcelo; Munzer, Robert Helmut; Murakami, Hikari; Murray, Sean; Musa, Luciano; Musinsky, Jan; Naik, Bharati; Nair, Rahul; Nandi, Basanta Kumar; Nania, Rosario; Nappi, Eugenio; Naru, Muhammad Umair; Ferreira Natal Da Luz, Pedro Hugo; Nattrass, Christine; Rosado Navarro, Sebastian; Nayak, Kishora; Nayak, Ranjit; Nayak, Tapan Kumar; Nazarenko, Sergey; Nedosekin, Alexander; Nellen, Lukas; Ng, Fabian; Nicassio, Maria; Niculescu, Mihai; Niedziela, Jeremi; Nielsen, Borge Svane; Nikolaev, Sergey; Nikulin, Sergey; Nikulin, Vladimir; Noferini, Francesco; Nomokonov, Petr; Nooren, Gerardus; Cabanillas Noris, Juan Carlos; Norman, Jaime; Nyanin, Alexander; Nystrand, Joakim Ingemar; Oeschler, Helmut Oskar; Oh, Saehanseul; Oh, Sun Kun; Ohlson, Alice Elisabeth; Okatan, Ali; Okubo, Tsubasa; Olah, Laszlo; Oleniacz, Janusz; Oliveira Da Silva, Antonio Carlos; Oliver, Michael Henry; Onderwaater, Jacobus; Oppedisano, Chiara; Orava, Risto; Oravec, Matej; Ortiz Velasquez, Antonio; Oskarsson, Anders Nils Erik; Otwinowski, Jacek Tomasz; Oyama, Ken; Ozdemir, Mahmut; Pachmayer, Yvonne Chiara; Pagano, Davide; Pagano, Paola; Paic, Guy; Pal, Susanta Kumar; Pan, Jinjin; Pandey, Ashutosh Kumar; Papikyan, Vardanush; Pappalardo, Giuseppe; Pareek, Pooja; Park, Woojin; Parmar, Sonia; Passfeld, Annika; Paticchio, Vincenzo; Patra, Rajendra Nath; Paul, Biswarup; Pei, Hua; Peitzmann, Thomas; Pereira Da Costa, Hugo Denis Antonio; Peresunko, Dmitry Yurevich; Perez Lara, Carlos Eugenio; Perez Lezama, Edgar; Peskov, Vladimir; Pestov, Yury; Petracek, Vojtech; Petrov, Viacheslav; Petrovici, Mihai; Petta, Catia; Piano, Stefano; Pikna, Miroslav; Pillot, Philippe; Ozelin De Lima Pimentel, Lais; Pinazza, Ombretta; Pinsky, Lawrence; Piyarathna, Danthasinghe; Ploskon, Mateusz Andrzej; Planinic, Mirko; Pluta, Jan Marian; Pochybova, Sona; Podesta Lerma, Pedro Luis Manuel; Poghosyan, Martin; Polishchuk, Boris; Poljak, Nikola; Poonsawat, Wanchaloem; Pop, Amalia; Porteboeuf, Sarah Julie; Porter, R Jefferson; Pospisil, Jan; Prasad, Sidharth Kumar; Preghenella, Roberto; Prino, Francesco; Pruneau, Claude Andre; Pshenichnov, Igor; Puccio, Maximiliano; Puddu, Giovanna; Pujahari, Prabhat Ranjan; Punin, Valery; Putschke, Jorn Henning; Qvigstad, Henrik; Rachevski, Alexandre; Raha, Sibaji; Rajput, Sonia; Rak, Jan; Rakotozafindrabe, Andry Malala; Ramello, Luciano; Rami, Fouad; Raniwala, Rashmi; Raniwala, Sudhir; Rasanen, Sami Sakari; Rascanu, Bogdan Theodor; Rathee, Deepika; Read, Kenneth Francis; Redlich, Krzysztof; Reed, Rosi Jan; Rehman, Attiq Ur; Reichelt, Patrick Simon; Reidt, Felix; Ren, Xiaowen; Renfordt, Rainer Arno Ernst; Reolon, Anna Rita; Reshetin, Andrey; Reygers, Klaus Johannes; Riabov, Viktor; Ricci, Renato Angelo; Richert, Tuva Ora Herenui; Richter, Matthias Rudolph; Riedler, Petra; Riegler, Werner; Riggi, Francesco; Ristea, Catalin-Lucian; Rocco, Elena; Rodriguez Cahuantzi, Mario; Rodriguez Manso, Alis; Roeed, Ketil; Rogochaya, Elena; Rohr, David Michael; Roehrich, Dieter; Ronchetti, Federico; Ronflette, Lucile; Rosnet, Philippe; Rossi, Andrea; Roukoutakis, Filimon; Roy, Ankhi; Roy, Christelle Sophie; Roy, Pradip Kumar; Rubio Montero, Antonio Juan; Rui, Rinaldo; Russo, Riccardo; Ryabinkin, Evgeny; Ryabov, Yury; Rybicki, Andrzej; Saarinen, Sampo; Sadhu, Samrangy; Sadovskiy, Sergey; Safarik, Karel; Sahlmuller, Baldo; Sahoo, Pragati; Sahoo, Raghunath; Sahoo, Sarita; Sahu, Pradip Kumar; Saini, Jogender; Sakai, Shingo; Saleh, Mohammad Ahmad; Salzwedel, Jai Samuel Nielsen; Sambyal, Sanjeev Singh; Samsonov, Vladimir; Sandor, Ladislav; Sandoval, Andres; Sano, Masato; Sarkar, Debojit; Sarkar, Nachiketa; Sarma, Pranjal; Scapparone, Eugenio; Scarlassara, Fernando; Schiaua, Claudiu Cornel; Schicker, Rainer Martin; Schmidt, Christian Joachim; Schmidt, Hans Rudolf; Schuchmann, Simone; Schukraft, Jurgen; Schulc, Martin; Schutz, Yves Roland; Schwarz, Kilian Eberhard; Schweda, Kai Oliver; Scioli, Gilda; Scomparin, Enrico; Scott, Rebecca Michelle; Sefcik, Michal; Seger, Janet Elizabeth; Sekiguchi, Yuko; Sekihata, Daiki; Selyuzhenkov, Ilya; Senosi, Kgotlaesele; Senyukov, Serhiy; Serradilla Rodriguez, Eulogio; Sevcenco, Adrian; Shabanov, Arseniy; Shabetai, Alexandre; Shadura, Oksana; Shahoyan, Ruben; Shahzad, Muhammed Ikram; Shangaraev, Artem; Sharma, Ankita; Sharma, Mona; Sharma, Monika; Sharma, Natasha; Sheikh, Ashik Ikbal; Shigaki, Kenta; Shou, Qiye; Shtejer Diaz, Katherin; Sibiryak, Yury; Siddhanta, Sabyasachi; Sielewicz, Krzysztof Marek; Siemiarczuk, Teodor; Silvermyr, David Olle Rickard; Silvestre, Catherine Micaela; Simatovic, Goran; Simonetti, Giuseppe; Singaraju, Rama Narayana; Singh, Ranbir; Singha, Subhash; Singhal, Vikas; Sinha, Bikash; Sarkar - Sinha, Tinku; Sitar, Branislav; Sitta, Mario; Skaali, Bernhard; Slupecki, Maciej; Smirnov, Nikolai; Snellings, Raimond; Snellman, Tomas Wilhelm; Song, Jihye; Song, Myunggeun; Song, Zixuan; Soramel, Francesca; Sorensen, Soren Pontoppidan; Derradi De Souza, Rafael; Sozzi, Federica; Spacek, Michal; Spiriti, Eleuterio; Sputowska, Iwona Anna; Spyropoulou-Stassinaki, Martha; Stachel, Johanna; Stan, Ionel; Stankus, Paul; Stenlund, Evert Anders; Steyn, Gideon Francois; Stiller, Johannes Hendrik; Stocco, Diego; Strmen, Peter; Alarcon Do Passo Suaide, Alexandre; Sugitate, Toru; Suire, Christophe Pierre; Suleymanov, Mais Kazim Oglu; Suljic, Miljenko; Sultanov, Rishat; Sumbera, Michal; Sumowidagdo, Suharyo; Szabo, Alexander; Szanto De Toledo, Alejandro; Szarka, Imrich; Szczepankiewicz, Adam; Szymanski, Maciej Pawel; Tabassam, Uzma; Takahashi, Jun; Tambave, Ganesh Jagannath; Tanaka, Naoto; Tarhini, Mohamad; Tariq, Mohammad; Tarzila, Madalina-Gabriela; Tauro, Arturo; Tejeda Munoz, Guillermo; Telesca, Adriana; Terasaki, Kohei; Terrevoli, Cristina; Teyssier, Boris; Thaeder, Jochen Mathias; Thakur, Dhananjaya; Thomas, Deepa; Tieulent, Raphael Noel; Timmins, Anthony Robert; Toia, Alberica; Trogolo, Stefano; Trombetta, Giuseppe; Trubnikov, Victor; Trzaska, Wladyslaw Henryk; Tsuji, Tomoya; Tumkin, Alexandr; Turrisi, Rosario; Tveter, Trine Spedstad; Ullaland, Kjetil; Uras, Antonio; Usai, Gianluca; Utrobicic, Antonija; Vala, Martin; Valencia Palomo, Lizardo; Vallero, Sara; Van Der Maarel, Jasper; Van Hoorne, Jacobus Willem; Van Leeuwen, Marco; Vanat, Tomas; Vande Vyvre, Pierre; Varga, Dezso; Diozcora Vargas Trevino, Aurora; Vargyas, Marton; Varma, Raghava; Vasileiou, Maria; Vasiliev, Andrey; Vauthier, Astrid; Vechernin, Vladimir; Veen, Annelies Marianne; Veldhoen, Misha; Velure, Arild; Vercellin, Ermanno; Vergara Limon, Sergio; Vernet, Renaud; Verweij, Marta; Vickovic, Linda; Viesti, Giuseppe; Viinikainen, Jussi Samuli; Vilakazi, Zabulon; Villalobos Baillie, Orlando; Villatoro Tello, Abraham; Vinogradov, Alexander; Vinogradov, Leonid; Vinogradov, Yury; Virgili, Tiziano; Vislavicius, Vytautas; Viyogi, Yogendra; Vodopyanov, Alexander; Volkl, Martin Andreas; Voloshin, Kirill; Voloshin, Sergey; Volpe, Giacomo; Von Haller, Barthelemy; Vorobyev, Ivan; Vranic, Danilo; Vrlakova, Janka; Vulpescu, Bogdan; Wagner, Boris; Wagner, Jan; Wang, Hongkai; Wang, Mengliang; Watanabe, Daisuke; Watanabe, Yosuke; Weber, Michael; Weber, Steffen Georg; Weiser, Dennis Franz; Wessels, Johannes Peter; Westerhoff, Uwe; Whitehead, Andile Mothegi; Wiechula, Jens; Wikne, Jon; Wilk, Grzegorz Andrzej; Wilkinson, Jeremy John; Williams, Crispin; Windelband, Bernd Stefan; Winn, Michael Andreas; Yang, Hongyan; Yang, Ping; Yano, Satoshi; Yasin, Zafar; Yin, Zhongbao; Yokoyama, Hiroki; Yoo, In-Kwon; Yoon, Jin Hee; Yurchenko, Volodymyr; Yushmanov, Igor; Zaborowska, Anna; Zaccolo, Valentina; Zaman, Ali; Zampolli, Chiara; Correia Zanoli, Henrique Jose; Zaporozhets, Sergey; Zardoshti, Nima; Zarochentsev, Andrey; Zavada, Petr; Zavyalov, Nikolay; Zbroszczyk, Hanna Paulina; Zgura, Sorin Ion; Zhalov, Mikhail; Zhang, Haitao; Zhang, Xiaoming; Zhang, Yonghong; Chunhui, Zhang; Zhang, Zuman; Zhao, Chengxin; Zhigareva, Natalia; Zhou, Daicui; Zhou, You; Zhou, Zhuo; Zhu, Hongsheng; Zhu, Jianhui; Zichichi, Antonino; Zimmermann, Alice; Zimmermann, Markus Bernhard; Zinovjev, Gennady; Zyzak, Maksym

    2016-05-25

    We present a Bayesian approach to particle identification (PID) within the ALICE experiment. The aim is to more effectively combine the particle identification capabilities of its various detectors. After a brief explanation of the adopted methodology and formalism, the performance of the Bayesian PID approach for charged pions, kaons and protons in the central barrel of ALICE is studied. PID is performed via measurements of specific energy loss (dE/dx) and time-of-flight. PID efficiencies and misidentification probabilities are extracted and compared with Monte Carlo simulations using high purity samples of identified particles in the decay channels ${\\rm K}_{\\rm S}^{\\rm 0}\\rightarrow \\pi^+\\pi^-$, $\\phi\\rightarrow {\\rm K}^-{\\rm K}^+$ and $\\Lambda\\rightarrow{\\rm p}\\pi^-$ in p–Pb collisions at $\\sqrt{s_{\\rm NN}}= 5.02$TeV. In order to thoroughly assess the validity of the Bayesian approach, this methodology was used to obtain corrected $p_{\\rm T}$ spectra of pions, kaons, protons, and D$^0$ mesons in pp coll...

  10. Bayesian Inference of a Multivariate Regression Model

    Directory of Open Access Journals (Sweden)

    Marick S. Sinay

    2014-01-01

    Full Text Available We explore Bayesian inference of a multivariate linear regression model with use of a flexible prior for the covariance structure. The commonly adopted Bayesian setup involves the conjugate prior, multivariate normal distribution for the regression coefficients and inverse Wishart specification for the covariance matrix. Here we depart from this approach and propose a novel Bayesian estimator for the covariance. A multivariate normal prior for the unique elements of the matrix logarithm of the covariance matrix is considered. Such structure allows for a richer class of prior distributions for the covariance, with respect to strength of beliefs in prior location hyperparameters, as well as the added ability, to model potential correlation amongst the covariance structure. The posterior moments of all relevant parameters of interest are calculated based upon numerical results via a Markov chain Monte Carlo procedure. The Metropolis-Hastings-within-Gibbs algorithm is invoked to account for the construction of a proposal density that closely matches the shape of the target posterior distribution. As an application of the proposed technique, we investigate a multiple regression based upon the 1980 High School and Beyond Survey.

  11. Risk-sensitivity in Bayesian sensorimotor integration.

    Directory of Open Access Journals (Sweden)

    Jordi Grau-Moya

    Full Text Available Information processing in the nervous system during sensorimotor tasks with inherent uncertainty has been shown to be consistent with Bayesian integration. Bayes optimal decision-makers are, however, risk-neutral in the sense that they weigh all possibilities based on prior expectation and sensory evidence when they choose the action with highest expected value. In contrast, risk-sensitive decision-makers are sensitive to model uncertainty and bias their decision-making processes when they do inference over unobserved variables. In particular, they allow deviations from their probabilistic model in cases where this model makes imprecise predictions. Here we test for risk-sensitivity in a sensorimotor integration task where subjects exhibit Bayesian information integration when they infer the position of a target from noisy sensory feedback. When introducing a cost associated with subjects' response, we found that subjects exhibited a characteristic bias towards low cost responses when their uncertainty was high. This result is in accordance with risk-sensitive decision-making processes that allow for deviations from Bayes optimal decision-making in the face of uncertainty. Our results suggest that both Bayesian integration and risk-sensitivity are important factors to understand sensorimotor integration in a quantitative fashion.

  12. 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

  13. Bayesian Estimation and Inference using Stochastic Hardware

    Directory of Open Access Journals (Sweden)

    Chetan Singh Thakur

    2016-03-01

    Full Text Available In this paper, we present the implementation of two types of Bayesian inference problems to demonstrate the potential of building probabilistic algorithms in hardware using single set of building blocks with the ability to perform these computations in real time. The first implementation, referred to as the BEAST (Bayesian Estimation and Stochastic Tracker, demonstrates a simple problem where an observer uses an underlying Hidden Markov Model (HMM to track a target in one dimension. In this implementation, sensors make noisy observations of the target position at discrete time steps. The tracker learns the transition model for target movement, and the observation model for the noisy sensors, and uses these to estimate the target position by solving the Bayesian recursive equation online. We show the tracking performance of the system and demonstrate how it can learn the observation model, the transition model, and the external distractor (noise probability interfering with the observations. In the second implementation, referred to as the Bayesian INference in DAG (BIND, we show how inference can be performed in a Directed Acyclic Graph (DAG using stochastic circuits. We show how these building blocks can be easily implemented using simple digital logic gates. An advantage of the stochastic electronic implementation is that it is robust to certain types of noise, which may become an issue in integrated circuit (IC technology with feature sizes in the order of tens of nanometers due to their low noise margin, the effect of high-energy cosmic rays and the low supply voltage. In our framework, the flipping of random individual bits would not affect the system performance because information is encoded in a bit stream.

  14. Bayesian Estimation and Inference Using Stochastic Electronics.

    Science.gov (United States)

    Thakur, Chetan Singh; Afshar, Saeed; Wang, Runchun M; Hamilton, Tara J; Tapson, Jonathan; van Schaik, André

    2016-01-01

    In this paper, we present the implementation of two types of Bayesian inference problems to demonstrate the potential of building probabilistic algorithms in hardware using single set of building blocks with the ability to perform these computations in real time. The first implementation, referred to as the BEAST (Bayesian Estimation and Stochastic Tracker), demonstrates a simple problem where an observer uses an underlying Hidden Markov Model (HMM) to track a target in one dimension. In this implementation, sensors make noisy observations of the target position at discrete time steps. The tracker learns the transition model for target movement, and the observation model for the noisy sensors, and uses these to estimate the target position by solving the Bayesian recursive equation online. We show the tracking performance of the system and demonstrate how it can learn the observation model, the transition model, and the external distractor (noise) probability interfering with the observations. In the second implementation, referred to as the Bayesian INference in DAG (BIND), we show how inference can be performed in a Directed Acyclic Graph (DAG) using stochastic circuits. We show how these building blocks can be easily implemented using simple digital logic gates. An advantage of the stochastic electronic implementation is that it is robust to certain types of noise, which may become an issue in integrated circuit (IC) technology with feature sizes in the order of tens of nanometers due to their low noise margin, the effect of high-energy cosmic rays and the low supply voltage. In our framework, the flipping of random individual bits would not affect the system performance because information is encoded in a bit stream.

  15. Improving medical decisions for incapacitated persons: does focusing on "accurate predictions" lead to an inaccurate picture?

    Science.gov (United States)

    Kim, Scott Y H

    2014-04-01

    The Patient Preference Predictor (PPP) proposal places a high priority on the accuracy of predicting patients' preferences and finds the performance of surrogates inadequate. However, the quest to develop a highly accurate, individualized statistical model has significant obstacles. First, it will be impossible to validate the PPP beyond the limit imposed by 60%-80% reliability of people's preferences for future medical decisions--a figure no better than the known average accuracy of surrogates. Second, evidence supports the view that a sizable minority of persons may not even have preferences to predict. Third, many, perhaps most, people express their autonomy just as much by entrusting their loved ones to exercise their judgment than by desiring to specifically control future decisions. Surrogate decision making faces none of these issues and, in fact, it may be more efficient, accurate, and authoritative than is commonly assumed.

  16. Social intelligence, empathy, and aggressive behavior: Is a stereotype of aggressive individual as socially incompetent inaccurate?

    OpenAIRE

    Marina Vidmar; Andreja Avsec

    2012-01-01

    In the present research, which was carried out on 187 high school students (86 girls and 101 boys), we examined to what extent different aspects of social intelligence contribute to indirect and direct aggression and to what extent empathy can act as a mitigator of aggression. We used The Aggression Questionnaire to measure physical aggression, IAS-A (which includes Social Exclusion, Use of Malicious Humour and Guilt Induction sub-scales) to measure indirect aggression, TSIS (which includes S...

  17. Fifty Psychological and Psychiatric Terms to Avoid: A List of Inaccurate, Misleading, Misused, Ambiguous, and Logically Confused Words and Phrases

    Directory of Open Access Journals (Sweden)

    Scott O Lilienfeld

    2015-08-01

    Full Text Available The goal of this article is to promote clear thinking and clear writing among students and teachers of psychological science by curbing terminological misinformation and confusion. To this end, we present a provisional list of 50 commonly used terms in psychology, psychiatry, and allied fields that should be avoided, or at most used sparingly and with explicit caveats. We provide corrective information for students, instructors, and researchers regarding these terms, which we organize for expository purposes into five categories: inaccurate or misleading terms, frequently misused terms, ambiguous terms, oxymorons, and pleonasms. For each term, we (a explain why it is problematic, (b delineate one or more examples of its misuse, and (c when pertinent, offer recommendations for preferable terms. By being more judicious in their use of terminology, psychologists and psychiatrists can foster clearer thinking in their students and the field at large regarding mental phenomena.

  18. Fifty psychological and psychiatric terms to avoid: a list of inaccurate, misleading, misused, ambiguous, and logically confused words and phrases.

    Science.gov (United States)

    Lilienfeld, Scott O; Sauvigné, Katheryn C; Lynn, Steven Jay; Cautin, Robin L; Latzman, Robert D; Waldman, Irwin D

    2015-01-01

    The goal of this article is to promote clear thinking and clear writing among students and teachers of psychological science by curbing terminological misinformation and confusion. To this end, we present a provisional list of 50 commonly used terms in psychology, psychiatry, and allied fields that should be avoided, or at most used sparingly and with explicit caveats. We provide corrective information for students, instructors, and researchers regarding these terms, which we organize for expository purposes into five categories: inaccurate or misleading terms, frequently misused terms, ambiguous terms, oxymorons, and pleonasms. For each term, we (a) explain why it is problematic, (b) delineate one or more examples of its misuse, and (c) when pertinent, offer recommendations for preferable terms. By being more judicious in their use of terminology, psychologists and psychiatrists can foster clearer thinking in their students and the field at large regarding mental phenomena.

  19. Bayesian networks improve causal environmental ...

    Science.gov (United States)

    Rule-based weight of evidence approaches to ecological risk assessment may not account for uncertainties and generally lack probabilistic integration of lines of evidence. Bayesian networks allow causal inferences to be made from evidence by including causal knowledge about the problem, using this knowledge with probabilistic calculus to combine multiple lines of evidence, and minimizing biases in predicting or diagnosing causal relationships. Too often, sources of uncertainty in conventional weight of evidence approaches are ignored that can be accounted for with Bayesian networks. Specifying and propagating uncertainties improve the ability of models to incorporate strength of the evidence in the risk management phase of an assessment. Probabilistic inference from a Bayesian network allows evaluation of changes in uncertainty for variables from the evidence. The network structure and probabilistic framework of a Bayesian approach provide advantages over qualitative approaches in weight of evidence for capturing the impacts of multiple sources of quantifiable uncertainty on predictions of ecological risk. Bayesian networks can facilitate the development of evidence-based policy under conditions of uncertainty by incorporating analytical inaccuracies or the implications of imperfect information, structuring and communicating causal issues through qualitative directed graph formulations, and quantitatively comparing the causal power of multiple stressors on value

  20. Bayesian Latent Class Analysis Tutorial.

    Science.gov (United States)

    Li, Yuelin; Lord-Bessen, Jennifer; Shiyko, Mariya; Loeb, Rebecca

    2018-01-01

    This article is a how-to guide on Bayesian computation using Gibbs sampling, demonstrated in the context of Latent Class Analysis (LCA). It is written for students in quantitative psychology or related fields who have a working knowledge of Bayes Theorem and conditional probability and have experience in writing computer programs in the statistical language R . The overall goals are to provide an accessible and self-contained tutorial, along with a practical computation tool. We begin with how Bayesian computation is typically described in academic articles. Technical difficulties are addressed by a hypothetical, worked-out example. We show how Bayesian computation can be broken down into a series of simpler calculations, which can then be assembled together to complete a computationally more complex model. The details are described much more explicitly than what is typically available in elementary introductions to Bayesian modeling so that readers are not overwhelmed by the mathematics. Moreover, the provided computer program shows how Bayesian LCA can be implemented with relative ease. The computer program is then applied in a large, real-world data set and explained line-by-line. We outline the general steps in how to extend these considerations to other methodological applications. We conclude with suggestions for further readings.

  1. Social intelligence, empathy, and aggressive behavior: Is a stereotype of aggressive individual as socially incompetent inaccurate?

    Directory of Open Access Journals (Sweden)

    Marina Vidmar

    2012-03-01

    Full Text Available In the present research, which was carried out on 187 high school students (86 girls and 101 boys, we examined to what extent different aspects of social intelligence contribute to indirect and direct aggression and to what extent empathy can act as a mitigator of aggression. We used The Aggression Questionnaire to measure physical aggression, IAS-A (which includes Social Exclusion, Use of Malicious Humour and Guilt Induction sub-scales to measure indirect aggression, TSIS (which includes Social Information Processing, Social Skills and Social Awareness sub-scales to measure social intelligence and IRI (Perspective Taking and Empathic Concern sub-scales. The results confirmed our expectations that the cognitive aspect of empathy acts as an inhibitor of both direct and indirect aggression. The relationship between the ability of processing social information and indirect aggresssion was positive, whereas the relationship between social awareness and indirect aggression was negative, which shows that the relationships between various aspects of social intelligence and aggression are complex. People who have a high degree of social intelligence but do not have the tendency to take the other's perspective can use their abilities (especially social information processing to performn less evident and less prosecuted forms of aggressive behaviour which still have deleterious effects on interpersonal relationships.

  2. MATRIX-VECTOR ALGORITHMS OF LOCAL POSTERIORI INFERENCE IN ALGEBRAIC BAYESIAN NETWORKS ON QUANTA PROPOSITIONS

    Directory of Open Access Journals (Sweden)

    A. A. Zolotin

    2015-07-01

    Full Text Available Posteriori inference is one of the three kinds of probabilistic-logic inferences in the probabilistic graphical models theory and the base for processing of knowledge patterns with probabilistic uncertainty using Bayesian networks. The paper deals with a task of local posteriori inference description in algebraic Bayesian networks that represent a class of probabilistic graphical models by means of matrix-vector equations. The latter are essentially based on the use of tensor product of matrices, Kronecker degree and Hadamard product. Matrix equations for calculating posteriori probabilities vectors within posteriori inference in knowledge patterns with quanta propositions are obtained. Similar equations of the same type have already been discussed within the confines of the theory of algebraic Bayesian networks, but they were built only for the case of posteriori inference in the knowledge patterns on the ideals of conjuncts. During synthesis and development of matrix-vector equations on quanta propositions probability vectors, a number of earlier results concerning normalizing factors in posteriori inference and assignment of linear projective operator with a selector vector was adapted. We consider all three types of incoming evidences - deterministic, stochastic and inaccurate - combined with scalar and interval estimation of probability truth of propositional formulas in the knowledge patterns. Linear programming problems are formed. Their solution gives the desired interval values of posterior probabilities in the case of inaccurate evidence or interval estimates in a knowledge pattern. That sort of description of a posteriori inference gives the possibility to extend the set of knowledge pattern types that we can use in the local and global posteriori inference, as well as simplify complex software implementation by use of existing third-party libraries, effectively supporting submission and processing of matrices and vectors when

  3. Interactive Instruction in Bayesian Inference

    DEFF Research Database (Denmark)

    Khan, Azam; Breslav, Simon; Hornbæk, Kasper

    2018-01-01

    An instructional approach is presented to improve human performance in solving Bayesian inference problems. Starting from the original text of the classic Mammography Problem, the textual expression is modified and visualizations are added according to Mayer’s principles of instruction. These pri......An instructional approach is presented to improve human performance in solving Bayesian inference problems. Starting from the original text of the classic Mammography Problem, the textual expression is modified and visualizations are added according to Mayer’s principles of instruction....... These principles concern coherence, personalization, signaling, segmenting, multimedia, spatial contiguity, and pretraining. Principles of self-explanation and interactivity are also applied. Four experiments on the Mammography Problem showed that these principles help participants answer the questions...... that an instructional approach to improving human performance in Bayesian inference is a promising direction....

  4. 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.

  5. 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.

  6. 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.

  7. Wing pattern morphology of three closely related Melitaea (Lepidoptera, Nymphalidae) species reveals highly inaccurate external morphology-based species identification

    OpenAIRE

    Jugovic,Jure; Koren,Toni

    2014-01-01

    Wing morphology of the three closely related species of Melitaea – M. athalia (Rottemburg, 1775), M. aurelia (Nickerl, 1850) and M. britomartis Assmann, 1847 – co-occurring in the Balkans (SE Europe) was investigated in detail through visual inspection, morphometric analysis and multivariate statistical analysis. Results are compared to recent phylogenetic studies, searching for concordant patterns and discrepancies between the two approaches. The morphology of the genitalic structures is als...

  8. Learning Bayesian networks for discrete data

    KAUST Repository

    Liang, Faming; Zhang, Jian

    2009-01-01

    Bayesian networks have received much attention in the recent literature. In this article, we propose an approach to learn Bayesian networks using the stochastic approximation Monte Carlo (SAMC) algorithm. Our approach has two nice features. Firstly

  9. Bayesian Network Induction via Local Neighborhoods

    National Research Council Canada - National Science Library

    Margaritis, Dimitris

    1999-01-01

    .... We present an efficient algorithm for learning Bayesian networks from data. Our approach constructs Bayesian networks by first identifying each node's Markov blankets, then connecting nodes in a consistent way...

  10. Can a significance test be genuinely Bayesian?

    OpenAIRE

    Pereira, Carlos A. de B.; Stern, Julio Michael; Wechsler, Sergio

    2008-01-01

    The Full Bayesian Significance Test, FBST, is extensively reviewed. Its test statistic, a genuine Bayesian measure of evidence, is discussed in detail. Its behavior in some problems of statistical inference like testing for independence in contingency tables is discussed.

  11. Bayesian modeling using WinBUGS

    CERN Document Server

    Ntzoufras, Ioannis

    2009-01-01

    A hands-on introduction to the principles of Bayesian modeling using WinBUGS Bayesian Modeling Using WinBUGS provides an easily accessible introduction to the use of WinBUGS programming techniques in a variety of Bayesian modeling settings. The author provides an accessible treatment of the topic, offering readers a smooth introduction to the principles of Bayesian modeling with detailed guidance on the practical implementation of key principles. The book begins with a basic introduction to Bayesian inference and the WinBUGS software and goes on to cover key topics, including: Markov Chain Monte Carlo algorithms in Bayesian inference Generalized linear models Bayesian hierarchical models Predictive distribution and model checking Bayesian model and variable evaluation Computational notes and screen captures illustrate the use of both WinBUGS as well as R software to apply the discussed techniques. Exercises at the end of each chapter allow readers to test their understanding of the presented concepts and all ...

  12. Inference in hybrid Bayesian networks

    International Nuclear Information System (INIS)

    Langseth, Helge; Nielsen, Thomas D.; Rumi, Rafael; Salmeron, Antonio

    2009-01-01

    Since the 1980s, Bayesian networks (BNs) have become increasingly popular for building statistical models of complex systems. This is particularly true for boolean systems, where BNs often prove to be a more efficient modelling framework than traditional reliability techniques (like fault trees and reliability block diagrams). However, limitations in the BNs' calculation engine have prevented BNs from becoming equally popular for domains containing mixtures of both discrete and continuous variables (the so-called hybrid domains). In this paper we focus on these difficulties, and summarize some of the last decade's research on inference in hybrid Bayesian networks. The discussions are linked to an example model for estimating human reliability.

  13. 3D Bayesian contextual classifiers

    DEFF Research Database (Denmark)

    Larsen, Rasmus

    2000-01-01

    We extend a series of multivariate Bayesian 2-D contextual classifiers to 3-D by specifying a simultaneous Gaussian distribution for the feature vectors as well as a prior distribution of the class variables of a pixel and its 6 nearest 3-D neighbours.......We extend a series of multivariate Bayesian 2-D contextual classifiers to 3-D by specifying a simultaneous Gaussian distribution for the feature vectors as well as a prior distribution of the class variables of a pixel and its 6 nearest 3-D neighbours....

  14. Embedding the results of focussed Bayesian fusion into a global context

    Science.gov (United States)

    Sander, Jennifer; Heizmann, Michael

    2014-05-01

    Bayesian statistics offers a well-founded and powerful fusion methodology also for the fusion of heterogeneous information sources. However, except in special cases, the needed posterior distribution is not analytically derivable. As consequence, Bayesian fusion may cause unacceptably high computational and storage costs in practice. Local Bayesian fusion approaches aim at reducing the complexity of the Bayesian fusion methodology significantly. This is done by concentrating the actual Bayesian fusion on the potentially most task relevant parts of the domain of the Properties of Interest. Our research on these approaches is motivated by an analogy to criminal investigations where criminalists pursue clues also only locally. This publication follows previous publications on a special local Bayesian fusion technique called focussed Bayesian fusion. Here, the actual calculation of the posterior distribution gets completely restricted to a suitably chosen local context. By this, the global posterior distribution is not completely determined. Strategies for using the results of a focussed Bayesian analysis appropriately are needed. In this publication, we primarily contrast different ways of embedding the results of focussed Bayesian fusion explicitly into a global context. To obtain a unique global posterior distribution, we analyze the application of the Maximum Entropy Principle that has been shown to be successfully applicable in metrology and in different other areas. To address the special need for making further decisions subsequently to the actual fusion task, we further analyze criteria for decision making under partial information.

  15. Superior Rhythm Discrimination With the SmartShock Technology Algorithm - Results of the Implantable Defibrillator With Enhanced Features and Settings for Reduction of Inaccurate Detection (DEFENSE) Trial.

    Science.gov (United States)

    Oginosawa, Yasushi; Kohno, Ritsuko; Honda, Toshihiro; Kikuchi, Kan; Nozoe, Masatsugu; Uchida, Takayuki; Minamiguchi, Hitoshi; Sonoda, Koichiro; Ogawa, Masahiro; Ideguchi, Takeshi; Kizaki, Yoshihisa; Nakamura, Toshihiro; Oba, Kageyuki; Higa, Satoshi; Yoshida, Keiki; Tsunoda, Soichi; Fujino, Yoshihisa; Abe, Haruhiko

    2017-08-25

    Shocks delivered by implanted anti-tachyarrhythmia devices, even when appropriate, lower the quality of life and survival. The new SmartShock Technology ® (SST) discrimination algorithm was developed to prevent the delivery of inappropriate shock. This prospective, multicenter, observational study compared the rate of inaccurate detection of ventricular tachyarrhythmia using the SST vs. a conventional discrimination algorithm.Methods and Results:Recipients of implantable cardioverter defibrillators (ICD) or cardiac resynchronization therapy defibrillators (CRT-D) equipped with the SST algorithm were enrolled and followed up every 6 months. The tachycardia detection rate was set at ≥150 beats/min with the SST algorithm. The primary endpoint was the time to first inaccurate detection of ventricular tachycardia (VT) with conventional vs. the SST discrimination algorithm, up to 2 years of follow-up. Between March 2012 and September 2013, 185 patients (mean age, 64.0±14.9 years; men, 74%; secondary prevention indication, 49.5%) were enrolled at 14 Japanese medical centers. Inaccurate detection was observed in 32 patients (17.6%) with the conventional, vs. in 19 patients (10.4%) with the SST algorithm. SST significantly lowered the rate of inaccurate detection by dual chamber devices (HR, 0.50; 95% CI: 0.263-0.950; P=0.034). Compared with previous algorithms, the SST discrimination algorithm significantly lowered the rate of inaccurate detection of VT in recipients of dual-chamber ICD or CRT-D.

  16. 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.

  17. Large-Scale Distributed Bayesian Matrix Factorization using Stochastic Gradient MCMC

    NARCIS (Netherlands)

    Ahn, S.; Korattikara, A.; Liu, N.; Rajan, S.; Welling, M.

    2015-01-01

    Despite having various attractive qualities such as high prediction accuracy and the ability to quantify uncertainty and avoid ovrfitting, Bayesian Matrix Factorization has not been widely adopted because of the prohibitive cost of inference. In this paper, we propose a scalable distributed Bayesian

  18. Bayesian networks and food security - An introduction

    NARCIS (Netherlands)

    Stein, A.

    2004-01-01

    This paper gives an introduction to Bayesian networks. Networks are defined and put into a Bayesian context. Directed acyclical graphs play a crucial role here. Two simple examples from food security are addressed. Possible uses of Bayesian networks for implementation and further use in decision

  19. Plug & Play object oriented Bayesian networks

    DEFF Research Database (Denmark)

    Bangsø, Olav; Flores, J.; Jensen, Finn Verner

    2003-01-01

    been shown to be quite suitable for dynamic domains as well. However, processing object oriented Bayesian networks in practice does not take advantage of their modular structure. Normally the object oriented Bayesian network is transformed into a Bayesian network and, inference is performed...... dynamic domains. The communication needed between instances is achieved by means of a fill-in propagation scheme....

  20. A Bayesian framework for risk perception

    NARCIS (Netherlands)

    van Erp, H.R.N.

    2017-01-01

    We present here a Bayesian framework of risk perception. This framework encompasses plausibility judgments, decision making, and question asking. Plausibility judgments are modeled by way of Bayesian probability theory, decision making is modeled by way of a Bayesian decision theory, and relevancy

  1. 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)

  2. Structure-based bayesian sparse reconstruction

    KAUST Repository

    Quadeer, Ahmed Abdul

    2012-12-01

    Sparse signal reconstruction algorithms have attracted research attention due to their wide applications in various fields. In this paper, we present a simple Bayesian approach that utilizes the sparsity constraint and a priori statistical information (Gaussian or otherwise) to obtain near optimal estimates. In addition, we make use of the rich structure of the sensing matrix encountered in many signal processing applications to develop a fast sparse recovery algorithm. The computational complexity of the proposed algorithm is very low compared with the widely used convex relaxation methods as well as greedy matching pursuit techniques, especially at high sparsity. © 1991-2012 IEEE.

  3. Bayesian analogy with relational transformations.

    Science.gov (United States)

    Lu, Hongjing; Chen, Dawn; Holyoak, Keith J

    2012-07-01

    How can humans acquire relational representations that enable analogical inference and other forms of high-level reasoning? Using comparative relations as a model domain, we explore the possibility that bottom-up learning mechanisms applied to objects coded as feature vectors can yield representations of relations sufficient to solve analogy problems. We introduce Bayesian analogy with relational transformations (BART) and apply the model to the task of learning first-order comparative relations (e.g., larger, smaller, fiercer, meeker) from a set of animal pairs. Inputs are coded by vectors of continuous-valued features, based either on human magnitude ratings, normed feature ratings (De Deyne et al., 2008), or outputs of the topics model (Griffiths, Steyvers, & Tenenbaum, 2007). Bootstrapping from empirical priors, the model is able to induce first-order relations represented as probabilistic weight distributions, even when given positive examples only. These learned representations allow classification of novel instantiations of the relations and yield a symbolic distance effect of the sort obtained with both humans and other primates. BART then transforms its learned weight distributions by importance-guided mapping, thereby placing distinct dimensions into correspondence. These transformed representations allow BART to reliably solve 4-term analogies (e.g., larger:smaller::fiercer:meeker), a type of reasoning that is arguably specific to humans. Our results provide a proof-of-concept that structured analogies can be solved with representations induced from unstructured feature vectors by mechanisms that operate in a largely bottom-up fashion. We discuss potential implications for algorithmic and neural models of relational thinking, as well as for the evolution of abstract thought. Copyright 2012 APA, all rights reserved.

  4. Bayesian tomographic reconstruction of microsystems

    International Nuclear Information System (INIS)

    Salem, Sofia Fekih; Vabre, Alexandre; Mohammad-Djafari, Ali

    2007-01-01

    The microtomography by X ray transmission plays an increasingly dominating role in the study and the understanding of microsystems. Within this framework, an experimental setup of high resolution X ray microtomography was developed at CEA-List to quantify the physical parameters related to the fluids flow in microsystems. Several difficulties rise from the nature of experimental data collected on this setup: enhanced error measurements due to various physical phenomena occurring during the image formation (diffusion, beam hardening), and specificities of the setup (limited angle, partial view of the object, weak contrast).To reconstruct the object we must solve an inverse problem. This inverse problem is known to be ill-posed. It therefore needs to be regularized by introducing prior information. The main prior information we account for is that the object is composed of a finite known number of different materials distributed in compact regions. This a priori information is introduced via a Gauss-Markov field for the contrast distributions with a hidden Potts-Markov field for the class materials in the Bayesian estimation framework. The computations are done by using an appropriate Markov Chain Monte Carlo (MCMC) technique.In this paper, we present first the basic steps of the proposed algorithms. Then we focus on one of the main steps in any iterative reconstruction method which is the computation of forward and adjoint operators (projection and backprojection). A fast implementation of these two operators is crucial for the real application of the method. We give some details on the fast computation of these steps and show some preliminary results of simulations

  5. Inferring the most probable maps of underground utilities using Bayesian mapping model

    Science.gov (United States)

    Bilal, Muhammad; Khan, Wasiq; Muggleton, Jennifer; Rustighi, Emiliano; Jenks, Hugo; Pennock, Steve R.; Atkins, Phil R.; Cohn, Anthony

    2018-03-01

    Mapping the Underworld (MTU), a major initiative in the UK, is focused on addressing social, environmental and economic consequences raised from the inability to locate buried underground utilities (such as pipes and cables) by developing a multi-sensor mobile device. The aim of MTU device is to locate different types of buried assets in real time with the use of automated data processing techniques and statutory records. The statutory records, even though typically being inaccurate and incomplete, provide useful prior information on what is buried under the ground and where. However, the integration of information from multiple sensors (raw data) with these qualitative maps and their visualization is challenging and requires the implementation of robust machine learning/data fusion approaches. An approach for automated creation of revised maps was developed as a Bayesian Mapping model in this paper by integrating the knowledge extracted from sensors raw data and available statutory records. The combination of statutory records with the hypotheses from sensors was for initial estimation of what might be found underground and roughly where. The maps were (re)constructed using automated image segmentation techniques for hypotheses extraction and Bayesian classification techniques for segment-manhole connections. The model consisting of image segmentation algorithm and various Bayesian classification techniques (segment recognition and expectation maximization (EM) algorithm) provided robust performance on various simulated as well as real sites in terms of predicting linear/non-linear segments and constructing refined 2D/3D maps.

  6. Bayesian image restoration, using configurations

    DEFF Research Database (Denmark)

    Thorarinsdottir, Thordis

    configurations are expressed in terms of the mean normal measure of the random set. These probabilities are used as prior probabilities in a Bayesian image restoration approach. Estimation of the remaining parameters in the model is outlined for salt and pepper noise. The inference in the model is discussed...

  7. Bayesian image restoration, using configurations

    DEFF Research Database (Denmark)

    Thorarinsdottir, Thordis Linda

    2006-01-01

    configurations are expressed in terms of the mean normal measure of the random set. These probabilities are used as prior probabilities in a Bayesian image restoration approach. Estimation of the remaining parameters in the model is outlined for the salt and pepper noise. The inference in the model is discussed...

  8. Differentiated Bayesian Conjoint Choice Designs

    NARCIS (Netherlands)

    Z. Sándor (Zsolt); M. Wedel (Michel)

    2003-01-01

    textabstractPrevious conjoint choice design construction procedures have produced a single design that is administered to all subjects. This paper proposes to construct a limited set of different designs. The designs are constructed in a Bayesian fashion, taking into account prior uncertainty about

  9. Bayesian Networks and Influence Diagrams

    DEFF Research Database (Denmark)

    Kjærulff, Uffe Bro; Madsen, Anders Læsø

    Bayesian Networks and Influence Diagrams: A Guide to Construction and Analysis, Second Edition, provides a comprehensive guide for practitioners who wish to understand, construct, and analyze intelligent systems for decision support based on probabilistic networks. This new edition contains six new...

  10. Bayesian Sampling using Condition Indicators

    DEFF Research Database (Denmark)

    Faber, Michael H.; Sørensen, John Dalsgaard

    2002-01-01

    of condition indicators introduced by Benjamin and Cornell (1970) a Bayesian approach to quality control is formulated. The formulation is then extended to the case where the quality control is based on sampling of indirect information about the condition of the components, i.e. condition indicators...

  11. Bayesian Classification of Image Structures

    DEFF Research Database (Denmark)

    Goswami, Dibyendu; Kalkan, Sinan; Krüger, Norbert

    2009-01-01

    In this paper, we describe work on Bayesian classi ers for distinguishing between homogeneous structures, textures, edges and junctions. We build semi-local classiers from hand-labeled images to distinguish between these four different kinds of structures based on the concept of intrinsic dimensi...

  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. 3-D contextual Bayesian classifiers

    DEFF Research Database (Denmark)

    Larsen, Rasmus

    In this paper we will consider extensions of a series of Bayesian 2-D contextual classification pocedures proposed by Owen (1984) Hjort & Mohn (1984) and Welch & Salter (1971) and Haslett (1985) to 3 spatial dimensions. It is evident that compared to classical pixelwise classification further...

  14. Bayesian Alternation During Tactile Augmentation

    Directory of Open Access Journals (Sweden)

    Caspar Mathias Goeke

    2016-10-01

    Full Text Available A large number of studies suggest that the integration of multisensory signals by humans is well described by Bayesian principles. However, there are very few reports about cue combination between a native and an augmented sense. In particular, we asked the question whether adult participants are able to integrate an augmented sensory cue with existing native sensory information. Hence for the purpose of this study we build a tactile augmentation device. Consequently, we compared different hypotheses of how untrained adult participants combine information from a native and an augmented sense. In a two-interval forced choice (2 IFC task, while subjects were blindfolded and seated on a rotating platform, our sensory augmentation device translated information on whole body yaw rotation to tactile stimulation. Three conditions were realized: tactile stimulation only (augmented condition, rotation only (native condition, and both augmented and native information (bimodal condition. Participants had to choose one out of two consecutive rotations with higher angular rotation. For the analysis, we fitted the participants’ responses with a probit model and calculated the just notable difference (JND. Then we compared several models for predicting bimodal from unimodal responses. An objective Bayesian alternation model yielded a better prediction (χred2 = 1.67 than the Bayesian integration model (χred2= 4.34. Slightly higher accuracy showed a non-Bayesian winner takes all model (χred2= 1.64, which either used only native or only augmented values per subject for prediction. However the performance of the Bayesian alternation model could be substantially improved (χred2= 1.09 utilizing subjective weights obtained by a questionnaire. As a result, the subjective Bayesian alternation model predicted bimodal performance most accurately among all tested models. These results suggest that information from augmented and existing sensory modalities in

  15. SU-E-T-377: Inaccurate Positioning Might Introduce Significant MapCheck Calibration Error in Flatten Filter Free Beams

    International Nuclear Information System (INIS)

    Wang, S; Chao, C; Chang, J

    2014-01-01

    Purpose: This study investigates the calibration error of detector sensitivity for MapCheck due to inaccurate positioning of the device, which is not taken into account by the current commercial iterative calibration algorithm. We hypothesize the calibration is more vulnerable to the positioning error for the flatten filter free (FFF) beams than the conventional flatten filter flattened beams. Methods: MapCheck2 was calibrated with 10MV conventional and FFF beams, with careful alignment and with 1cm positioning error during calibration, respectively. Open fields of 37cmx37cm were delivered to gauge the impact of resultant calibration errors. The local calibration error was modeled as a detector independent multiplication factor, with which propagation error was estimated with positioning error from 1mm to 1cm. The calibrated sensitivities, without positioning error, were compared between the conventional and FFF beams to evaluate the dependence on the beam type. Results: The 1cm positioning error leads to 0.39% and 5.24% local calibration error in the conventional and FFF beams respectively. After propagating to the edges of MapCheck, the calibration errors become 6.5% and 57.7%, respectively. The propagation error increases almost linearly with respect to the positioning error. The difference of sensitivities between the conventional and FFF beams was small (0.11 ± 0.49%). Conclusion: The results demonstrate that the positioning error is not handled by the current commercial calibration algorithm of MapCheck. Particularly, the calibration errors for the FFF beams are ~9 times greater than those for the conventional beams with identical positioning error, and a small 1mm positioning error might lead to up to 8% calibration error. Since the sensitivities are only slightly dependent of the beam type and the conventional beam is less affected by the positioning error, it is advisable to cross-check the sensitivities between the conventional and FFF beams to detect

  16. 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)

  17. Bayesian cost-effectiveness analysis with the R package BCEA

    CERN Document Server

    Baio, Gianluca; Heath, Anna

    2017-01-01

    The book provides a description of the process of health economic evaluation and modelling for cost-effectiveness analysis, particularly from the perspective of a Bayesian statistical approach. Some relevant theory and introductory concepts are presented using practical examples and two running case studies. The book also describes in detail how to perform health economic evaluations using the R package BCEA (Bayesian Cost-Effectiveness Analysis). BCEA can be used to post-process the results of a Bayesian cost-effectiveness model and perform advanced analyses producing standardised and highly customisable outputs. It presents all the features of the package, including its many functions and their practical application, as well as its user-friendly web interface. The book is a valuable resource for statisticians and practitioners working in the field of health economics wanting to simplify and standardise their workflow, for example in the preparation of dossiers in support of marketing authorisation, or acade...

  18. Kaolin Quality Prediction from Samples: A Bayesian Network Approach

    International Nuclear Information System (INIS)

    Rivas, T.; Taboada, J.; Ordonez, C.; Matias, J. M.

    2009-01-01

    We describe the results of an expert system applied to the evaluation of samples of kaolin for industrial use in paper or ceramic manufacture. Different machine learning techniques - classification trees, support vector machines and Bayesian networks - were applied with the aim of evaluating and comparing their interpretability and prediction capacities. The predictive capacity of these models for the samples analyzed was highly satisfactory, both for ceramic quality and paper quality. However, Bayesian networks generally proved to be the most useful technique for our study, as this approach combines good predictive capacity with excellent interpretability of the kaolin quality structure, as it graphically represents relationships between variables and facilitates what-if analyses.

  19. Bayesian linkage and segregation analysis: factoring the problem.

    Science.gov (United States)

    Matthysse, S

    2000-01-01

    Complex segregation analysis and linkage methods are mathematical techniques for the genetic dissection of complex diseases. They are used to delineate complex modes of familial transmission and to localize putative disease susceptibility loci to specific chromosomal locations. The computational problem of Bayesian linkage and segregation analysis is one of integration in high-dimensional spaces. In this paper, three available techniques for Bayesian linkage and segregation analysis are discussed: Markov Chain Monte Carlo (MCMC), importance sampling, and exact calculation. The contribution of each to the overall integration will be explicitly discussed.

  20. 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.

  1. Sample Size Calculation: Inaccurate A Priori Assumptions for Nuisance Parameters Can Greatly Affect the Power of a Randomized Controlled Trial.

    Directory of Open Access Journals (Sweden)

    Elsa Tavernier

    Full Text Available We aimed to examine the extent to which inaccurate assumptions for nuisance parameters used to calculate sample size can affect the power of a randomized controlled trial (RCT. In a simulation study, we separately considered an RCT with continuous, dichotomous or time-to-event outcomes, with associated nuisance parameters of standard deviation, success rate in the control group and survival rate in the control group at some time point, respectively. For each type of outcome, we calculated a required sample size N for a hypothesized treatment effect, an assumed nuisance parameter and a nominal power of 80%. We then assumed a nuisance parameter associated with a relative error at the design stage. For each type of outcome, we randomly drew 10,000 relative errors of the associated nuisance parameter (from empirical distributions derived from a previously published review. Then, retro-fitting the sample size formula, we derived, for the pre-calculated sample size N, the real power of the RCT, taking into account the relative error for the nuisance parameter. In total, 23%, 0% and 18% of RCTs with continuous, binary and time-to-event outcomes, respectively, were underpowered (i.e., the real power was 90%. Even with proper calculation of sample size, a substantial number of trials are underpowered or overpowered because of imprecise knowledge of nuisance parameters. Such findings raise questions about how sample size for RCTs should be determined.

  2. 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

  3. 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.

  4. 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.

  5. BAYESIAN IMAGE RESTORATION, USING CONFIGURATIONS

    Directory of Open Access Journals (Sweden)

    Thordis Linda Thorarinsdottir

    2011-05-01

    Full Text Available In this paper, we develop a Bayesian procedure for removing noise from images that can be viewed as noisy realisations of random sets in the plane. The procedure utilises recent advances in configuration theory for noise free random sets, where the probabilities of observing the different boundary configurations are expressed in terms of the mean normal measure of the random set. These probabilities are used as prior probabilities in a Bayesian image restoration approach. Estimation of the remaining parameters in the model is outlined for salt and pepper noise. The inference in the model is discussed in detail for 3 X 3 and 5 X 5 configurations and examples of the performance of the procedure are given.

  6. Bayesian analysis of ion beam diagnostics

    International Nuclear Information System (INIS)

    Toussaint, U. von; Fischer, R.; Dose, V.

    2001-01-01

    Ion beam diagnostics are routinely used for quantitative analysis of the surface composition of mixture materials up to a depth of a few μm. Unfortunately, advantageous properties of the diagnostics, like high depth resolution in combination with a large penetration depth, no destruction of the surface, high sensitivity for large as well as for small atomic numbers, and high sensitivity are mutually exclusive. Among other things, this is due to the ill-conditioned inverse problem of reconstructing depth distributions of the composition elements. Robust results for depth distributions are obtained with adaptive methods in the framework of Bayesian probability theory. The method of adaptive kernels allows for distributions which contain only the significant information of the data while noise fitting is avoided. This is achieved by adaptively reducing the degrees of freedom supporting the distribution. As applications for ion beam diagnostics Rutherford backscattering spectroscopy and particle induced X-ray emission are shown

  7. Multiview Bayesian Correlated Component Analysis

    DEFF Research Database (Denmark)

    Kamronn, Simon Due; Poulsen, Andreas Trier; Hansen, Lars Kai

    2015-01-01

    are identical. Here we propose a hierarchical probabilistic model that can infer the level of universality in such multiview data, from completely unrelated representations, corresponding to canonical correlation analysis, to identical representations as in correlated component analysis. This new model, which...... we denote Bayesian correlated component analysis, evaluates favorably against three relevant algorithms in simulated data. A well-established benchmark EEG data set is used to further validate the new model and infer the variability of spatial representations across multiple subjects....

  8. Polynomial Chaos Surrogates for Bayesian Inference

    KAUST Repository

    Le Maitre, Olivier

    2016-01-06

    The Bayesian inference is a popular probabilistic method to solve inverse problems, such as the identification of field parameter in a PDE model. The inference rely on the Bayes rule to update the prior density of the sought field, from observations, and derive its posterior distribution. In most cases the posterior distribution has no explicit form and has to be sampled, for instance using a Markov-Chain Monte Carlo method. In practice the prior field parameter is decomposed and truncated (e.g. by means of Karhunen- Lo´eve decomposition) to recast the inference problem into the inference of a finite number of coordinates. Although proved effective in many situations, the Bayesian inference as sketched above faces several difficulties requiring improvements. First, sampling the posterior can be a extremely costly task as it requires multiple resolutions of the PDE model for different values of the field parameter. Second, when the observations are not very much informative, the inferred parameter field can highly depends on its prior which can be somehow arbitrary. These issues have motivated the introduction of reduced modeling or surrogates for the (approximate) determination of the parametrized PDE solution and hyperparameters in the description of the prior field. Our contribution focuses on recent developments in these two directions: the acceleration of the posterior sampling by means of Polynomial Chaos expansions and the efficient treatment of parametrized covariance functions for the prior field. We also discuss the possibility of making such approach adaptive to further improve its efficiency.

  9. 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

  10. American Gastroenterological Association guidelines are inaccurate in detecting pancreatic cysts with advanced neoplasia: a clinicopathologic study of 225 patients with supporting molecular data.

    Science.gov (United States)

    Singhi, Aatur D; Zeh, Herbert J; Brand, Randall E; Nikiforova, Marina N; Chennat, Jennifer S; Fasanella, Kenneth E; Khalid, Asif; Papachristou, Georgios I; Slivka, Adam; Hogg, Melissa; Lee, Kenneth K; Tsung, Allan; Zureikat, Amer H; McGrath, Kevin

    2016-06-01

    The American Gastroenterological Association (AGA) recently reported evidence-based guidelines for the management of asymptomatic neoplastic pancreatic cysts. These guidelines advocate a higher threshold for surgical resection than prior guidelines and imaging surveillance for a considerable number of patients with pancreatic cysts. The aims of this study were to assess the accuracy of the AGA guidelines in detecting advanced neoplasia and present an alternative approach to pancreatic cysts. The study population consisted of 225 patients who underwent EUS-guided FNA for pancreatic cysts between January 2014 and May 2015. For each patient, clinical findings, EUS features, cytopathology results, carcinoembryonic antigen analysis, and molecular testing of pancreatic cyst fluid were reviewed. Molecular testing included the assessment of hotspot mutations and deletions for KRAS, GNAS, VHL, TP53, PIK3CA, and PTEN. Diagnostic pathology results were available for 41 patients (18%), with 13 (6%) harboring advanced neoplasia. Among these cases, the AGA guidelines identified advanced neoplasia with 62% sensitivity, 79% specificity, 57% positive predictive value, and 82% negative predictive value. Moreover, the AGA guidelines missed 45% of intraductal papillary mucinous neoplasms with adenocarcinoma or high-grade dysplasia. For cases without confirmatory pathology, 27 of 184 patients (15%) with serous cystadenomas (SCAs) based on EUS findings and/or VHL alterations would continue magnetic resonance imaging (MRI) surveillance. In comparison, a novel algorithmic pathway using molecular testing of pancreatic cyst fluid detected advanced neoplasias with 100% sensitivity, 90% specificity, 79% positive predictive value, and 100% negative predictive value. The AGA guidelines were inaccurate in detecting pancreatic cysts with advanced neoplasia. Furthermore, because the AGA guidelines manage all neoplastic cysts similarly, patients with SCAs will continue to undergo unnecessary MRI

  11. Prediction and assimilation of surf-zone processes using a Bayesian network: Part I: Forward models

    Science.gov (United States)

    Plant, Nathaniel G.; Holland, K. Todd

    2011-01-01

    Prediction of coastal processes, including waves, currents, and sediment transport, can be obtained from a variety of detailed geophysical-process models with many simulations showing significant skill. This capability supports a wide range of research and applied efforts that can benefit from accurate numerical predictions. However, the predictions are only as accurate as the data used to drive the models and, given the large temporal and spatial variability of the surf zone, inaccuracies in data are unavoidable such that useful predictions require corresponding estimates of uncertainty. We demonstrate how a Bayesian-network model can be used to provide accurate predictions of wave-height evolution in the surf zone given very sparse and/or inaccurate boundary-condition data. The approach is based on a formal treatment of a data-assimilation problem that takes advantage of significant reduction of the dimensionality of the model system. We demonstrate that predictions of a detailed geophysical model of the wave evolution are reproduced accurately using a Bayesian approach. In this surf-zone application, forward prediction skill was 83%, and uncertainties in the model inputs were accurately transferred to uncertainty in output variables. We also demonstrate that if modeling uncertainties were not conveyed to the Bayesian network (i.e., perfect data or model were assumed), then overly optimistic prediction uncertainties were computed. More consistent predictions and uncertainties were obtained by including model-parameter errors as a source of input uncertainty. Improved predictions (skill of 90%) were achieved because the Bayesian network simultaneously estimated optimal parameters while predicting wave heights.

  12. 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...

  13. A Bayesian model for binary Markov chains

    Directory of Open Access Journals (Sweden)

    Belkheir Essebbar

    2004-02-01

    Full Text Available This note is concerned with Bayesian estimation of the transition probabilities of a binary Markov chain observed from heterogeneous individuals. The model is founded on the Jeffreys' prior which allows for transition probabilities to be correlated. The Bayesian estimator is approximated by means of Monte Carlo Markov chain (MCMC techniques. The performance of the Bayesian estimates is illustrated by analyzing a small simulated data set.

  14. Development of a data-processing method based on Bayesian k-means clustering to discriminate aneugens and clastogens in a high-content micronucleus assay.

    Science.gov (United States)

    Huang, Z H; Li, N; Rao, K F; Liu, C T; Huang, Y; Ma, M; Wang, Z J

    2018-03-01

    Genotoxicants can be identified as aneugens and clastogens through a micronucleus (MN) assay. The current high-content screening-based MN assays usually discriminate an aneugen from a clastogen based on only one parameter, such as the MN size, intensity, or morphology, which yields low accuracies (70-84%) because each of these parameters may contribute to the results. Therefore, the development of an algorithm that can synthesize high-dimensionality data to attain comparative results is important. To improve the automation and accuracy of detection using the current parameter-based mode of action (MoA), the MN MoA signatures of 20 chemicals were systematically recruited in this study to develop an algorithm. The results of the algorithm showed very good agreement (93.58%) between the prediction and reality, indicating that the proposed algorithm is a validated analytical platform for the rapid and objective acquisition of genotoxic MoA messages.

  15. 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).

  16. 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.

  17. Bayesian phylogeography finds its roots.

    Directory of Open Access Journals (Sweden)

    Philippe Lemey

    2009-09-01

    Full Text Available As a key factor in endemic and epidemic dynamics, the geographical distribution of viruses has been frequently interpreted in the light of their genetic histories. Unfortunately, inference of historical dispersal or migration patterns of viruses has mainly been restricted to model-free heuristic approaches that provide little insight into the temporal setting of the spatial dynamics. The introduction of probabilistic models of evolution, however, offers unique opportunities to engage in this statistical endeavor. Here we introduce a Bayesian framework for inference, visualization and hypothesis testing of phylogeographic history. By implementing character mapping in a Bayesian software that samples time-scaled phylogenies, we enable the reconstruction of timed viral dispersal patterns while accommodating phylogenetic uncertainty. Standard Markov model inference is extended with a stochastic search variable selection procedure that identifies the parsimonious descriptions of the diffusion process. In addition, we propose priors that can incorporate geographical sampling distributions or characterize alternative hypotheses about the spatial dynamics. To visualize the spatial and temporal information, we summarize inferences using virtual globe software. We describe how Bayesian phylogeography compares with previous parsimony analysis in the investigation of the influenza A H5N1 origin and H5N1 epidemiological linkage among sampling localities. Analysis of rabies in West African dog populations reveals how virus diffusion may enable endemic maintenance through continuous epidemic cycles. From these analyses, we conclude that our phylogeographic framework will make an important asset in molecular epidemiology that can be easily generalized to infer biogeogeography from genetic data for many organisms.

  18. Development of dynamic Bayesian models for web application test management

    Science.gov (United States)

    Azarnova, T. V.; Polukhin, P. V.; Bondarenko, Yu V.; Kashirina, I. L.

    2018-03-01

    The mathematical apparatus of dynamic Bayesian networks is an effective and technically proven tool that can be used to model complex stochastic dynamic processes. According to the results of the research, mathematical models and methods of dynamic Bayesian networks provide a high coverage of stochastic tasks associated with error testing in multiuser software products operated in a dynamically changing environment. Formalized representation of the discrete test process as a dynamic Bayesian model allows us to organize the logical connection between individual test assets for multiple time slices. This approach gives an opportunity to present testing as a discrete process with set structural components responsible for the generation of test assets. Dynamic Bayesian network-based models allow us to combine in one management area individual units and testing components with different functionalities and a direct influence on each other in the process of comprehensive testing of various groups of computer bugs. The application of the proposed models provides an opportunity to use a consistent approach to formalize test principles and procedures, methods used to treat situational error signs, and methods used to produce analytical conclusions based on test results.

  19. 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

  20. Bayesian inference for Hawkes processes

    DEFF Research Database (Denmark)

    Rasmussen, Jakob Gulddahl

    The Hawkes process is a practically and theoretically important class of point processes, but parameter-estimation for such a process can pose various problems. In this paper we explore and compare two approaches to Bayesian inference. The first approach is based on the so-called conditional...... intensity function, while the second approach is based on an underlying clustering and branching structure in the Hawkes process. For practical use, MCMC (Markov chain Monte Carlo) methods are employed. The two approaches are compared numerically using three examples of the Hawkes process....

  1. Bayesian inference for Hawkes processes

    DEFF Research Database (Denmark)

    Rasmussen, Jakob Gulddahl

    2013-01-01

    The Hawkes process is a practically and theoretically important class of point processes, but parameter-estimation for such a process can pose various problems. In this paper we explore and compare two approaches to Bayesian inference. The first approach is based on the so-called conditional...... intensity function, while the second approach is based on an underlying clustering and branching structure in the Hawkes process. For practical use, MCMC (Markov chain Monte Carlo) methods are employed. The two approaches are compared numerically using three examples of the Hawkes process....

  2. Whole-body FDG PET-MR oncologic imaging: pitfalls in clinical interpretation related to inaccurate MR-based attenuation correction.

    Science.gov (United States)

    Attenberger, Ulrike; Catana, Ciprian; Chandarana, Hersh; Catalano, Onofrio A; Friedman, Kent; Schonberg, Stefan A; Thrall, James; Salvatore, Marco; Rosen, Bruce R; Guimaraes, Alexander R

    2015-08-01

    Simultaneous data collection for positron emission tomography and magnetic resonance imaging (PET/MR) is now a reality. While the full benefits of concurrently acquiring PET and MR data and the potential added clinical value are still being evaluated, initial studies have identified several important potential pitfalls in the interpretation of fluorodeoxyglucose (FDG) PET/MRI in oncologic whole-body imaging, the majority of which being related to the errors in the attenuation maps created from the MR data. The purpose of this article was to present such pitfalls and artifacts using case examples, describe their etiology, and discuss strategies to overcome them. Using a case-based approach, we will illustrate artifacts related to (1) Inaccurate bone tissue segmentation; (2) Inaccurate air cavities segmentation; (3) Motion-induced misregistration; (4) RF coils in the PET field of view; (5) B0 field inhomogeneity; (6) B1 field inhomogeneity; (7) Metallic implants; (8) MR contrast agents.

  3. Bayesian phylogenetic estimation of fossil ages.

    Science.gov (United States)

    Drummond, Alexei J; Stadler, Tanja

    2016-07-19

    Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth-death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the 'morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.This article is part of the themed issue 'Dating species divergences using

  4. Bayesian analysis of magnetic island dynamics

    International Nuclear Information System (INIS)

    Preuss, R.; Maraschek, M.; Zohm, H.; Dose, V.

    2003-01-01

    We examine a first order differential equation with respect to time used to describe magnetic islands in magnetically confined plasmas. The free parameters of this equation are obtained by employing Bayesian probability theory. Additionally, a typical Bayesian change point is solved in the process of obtaining the data

  5. Learning dynamic Bayesian networks with mixed variables

    DEFF Research Database (Denmark)

    Bøttcher, Susanne Gammelgaard

    This paper considers dynamic Bayesian networks for discrete and continuous variables. We only treat the case, where the distribution of the variables is conditional Gaussian. We show how to learn the parameters and structure of a dynamic Bayesian network and also how the Markov order can be learned...

  6. Using Bayesian Networks to Improve Knowledge Assessment

    Science.gov (United States)

    Millan, Eva; Descalco, Luis; Castillo, Gladys; Oliveira, Paula; Diogo, Sandra

    2013-01-01

    In this paper, we describe the integration and evaluation of an existing generic Bayesian student model (GBSM) into an existing computerized testing system within the Mathematics Education Project (PmatE--Projecto Matematica Ensino) of the University of Aveiro. This generic Bayesian student model had been previously evaluated with simulated…

  7. 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...

  8. Bayesian Decision Theoretical Framework for Clustering

    Science.gov (United States)

    Chen, Mo

    2011-01-01

    In this thesis, we establish a novel probabilistic framework for the data clustering problem from the perspective of Bayesian decision theory. The Bayesian decision theory view justifies the important questions: what is a cluster and what a clustering algorithm should optimize. We prove that the spectral clustering (to be specific, the…

  9. 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

  10. Bayesian models: A statistical primer for ecologists

    Science.gov (United States)

    Hobbs, N. Thompson; Hooten, Mevin B.

    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 probability and develops a step-by-step sequence of connected ideas, including basic distribution theory, network diagrams, hierarchical models, Markov chain Monte Carlo, and inference from single and multiple models. This unique book places less emphasis on computer coding, favoring instead a concise presentation of the mathematical statistics needed to understand how and why Bayesian analysis works. It also explains how to write out properly formulated hierarchical Bayesian models and use them in computing, research papers, and proposals.This primer enables ecologists to understand the statistical principles behind Bayesian modeling and apply them to research, teaching, policy, and management.Presents the mathematical and statistical foundations of Bayesian modeling in language accessible to non-statisticiansCovers basic distribution theory, network diagrams, hierarchical models, Markov chain Monte Carlo, and moreDeemphasizes computer coding in favor of basic principlesExplains how to write out properly factored statistical expressions representing Bayesian models

  11. Particle identification in ALICE: a Bayesian approach

    NARCIS (Netherlands)

    Adam, J.; Adamova, D.; Aggarwal, M. M.; Rinella, G. Aglieri; Agnello, M.; Agrawal, N.; Ahammed, Z.; Ahn, S. U.; Aiola, S.; Akindinov, A.; Alam, S. N.; Albuquerque, D. S. D.; Aleksandrov, D.; Alessandro, B.; Alexandre, D.; Alfaro Molina, R.; Alici, A.; Alkin, A.; Almaraz, J. R. M.; Alme, J.; Alt, T.; Altinpinar, S.; Altsybeev, I.; Alves Garcia Prado, C.; Andrei, C.; Andronic, A.; Anguelov, V.; Anticic, T.; Antinori, F.; Antonioli, P.; Aphecetche, L.; Appelshaeuser, H.; Arcelli, S.; Arnaldi, R.; Arnold, O. W.; Arsene, I. C.; Arslandok, M.; Audurier, B.; Augustinus, A.; Averbeck, R.; Azmi, M. D.; Badala, A.; Baek, Y. W.; Bagnasco, S.; Bailhache, R.; Bala, R.; Balasubramanian, S.; Baldisseri, A.; Baral, R. C.; Barbano, A. M.; Barbera, R.; Barile, F.; Barnafoeldi, G. G.; Barnby, L. S.; Barret, V.; Bartalini, P.; Barth, K.; Bartke, J.; Bartsch, E.; Basile, M.; Bastid, N.; Bathen, B.; Batigne, G.; Camejo, A. Batista; Batyunya, B.; Batzing, P. C.; Bearden, I. G.; Beck, H.; Bedda, C.; Behera, N. K.; Belikov, I.; Bellini, F.; Bello Martinez, H.; Bellwied, R.; Belmont, R.; Belmont-Moreno, E.; Belyaev, V.; Benacek, P.; Bencedi, G.; Beole, S.; Berceanu, I.; Bercuci, A.; Berdnikov, Y.; Berenyi, D.; Bertens, R. A.; Berzano, D.; Betev, L.; Bhasin, A.; Bhat, I. R.; Bhati, A. K.; Bhattacharjee, B.; Bhom, J.; Bianchi, L.; Bianchi, N.; Bianchin, C.; Bielcik, J.; Bielcikova, J.; Bilandzic, A.; Biro, G.; Biswas, R.; Biswas, S.; Bjelogrlic, S.; Blair, J. T.; Blau, D.; Blume, C.; Bock, F.; Bogdanov, A.; Boggild, H.; Boldizsar, L.; Bombara, M.; Book, J.; Borel, H.; Borissov, A.; Borri, M.; Bossu, F.; Botta, E.; Bourjau, C.; Braun-Munzinger, P.; Bregant, M.; Breitner, T.; Broker, T. A.; Browning, T. A.; Broz, M.; Brucken, E. J.; Bruna, E.; Bruno, G. E.; Budnikov, D.; Buesching, H.; Bufalino, S.; Buncic, P.; Busch, O.; Buthelezi, Z.; Butt, J. B.; Buxton, J. T.; Cabala, J.; Caffarri, D.; Cai, X.; Caines, H.; Diaz, L. Calero; Caliva, A.; Calvo Villar, E.; Camerini, P.; Carena, F.; Carena, W.; Carnesecchi, F.; Castellanos, J. Castillo; Castro, A. J.; Casula, E. A. R.; Sanchez, C. Ceballos; Cepila, J.; Cerello, P.; Cerkala, J.; Chang, B.; Chapeland, S.; Chartier, M.; Charvet, J. L.; Chattopadhyay, S.; Chattopadhyay, S.; Chauvin, A.; Chelnokov, V.; Cherney, M.; Cheshkov, C.; Cheynis, B.; Barroso, V. Chibante; Chinellato, D. D.; Cho, S.; Chochula, P.; Choi, K.; Chojnacki, M.; Choudhury, S.; Christakoglou, P.; Christensen, C. H.; Christiansen, P.; Chujo, T.; Cicalo, C.; Cifarelli, L.; Cindolo, F.; Cleymans, J.; Colamaria, F.; Colella, D.; Collu, A.; Colocci, M.; Balbastre, G. Conesa; del Valle, Z. Conesa; Connors, M. E.; Contreras, J. G.; Cormier, T. M.; Morales, Y. Corrales; Cortes Maldonado, I.; Cortese, P.; Cosentino, M. R.; Costa, F.; Crochet, P.; Cruz Albino, R.; Cuautle, E.; Cunqueiro, L.; Dahms, T.; Dainese, A.; Danisch, M. C.; Danu, A.; Das, I.; Das, S.; Dash, A.; Dash, S.; De, S.; De Caro, A.; de Cataldo, G.; de Conti, C.; de Cuveland, J.; De Falco, A.; De Gruttola, D.; De Marco, N.; De Pasquale, S.; Deisting, A.; Deloff, A.; Denes, E.; Deplano, C.; Dhankher, P.; Di Bari, D.; Di Mauro, A.; Di Nezza, P.; Corchero, M. A. Diaz; Dietel, T.; Dillenseger, P.; Divia, R.; Djuvsland, O.; Dobrin, A.; Gimenez, D. Domenicis; Doenigus, B.; Dordic, O.; Drozhzhova, T.; Dubey, A. K.; Dubla, A.; Ducroux, L.; Dupieux, P.; Ehlers, R. J.; Elia, D.; Endress, E.; Engel, H.; Epple, E.; Erazmus, B.; Erdemir, I.; Erhardt, F.; Espagnon, B.; Estienne, M.; Esumi, S.; Eum, J.; Evans, D.; Evdokimov, S.; Eyyubova, G.; Fabbietti, L.; Fabris, D.; Faivre, J.; Fantoni, A.; Fasel, M.; Feldkamp, L.; Feliciello, A.; Feofilov, G.; Ferencei, J.; Fernandez Tellez, A.; Ferreiro, E. G.; Ferretti, A.; Festanti, A.; Feuillard, V. J. G.; Figiel, J.; Figueredo, M. A. S.; Filchagin, S.; Finogeev, D.; Fionda, F. M.; Fiore, E. M.; Fleck, M. G.; Floris, M.; Foertsch, S.; Foka, P.; Fokin, S.; Fragiacomo, E.; Francescon, A.; Frankenfeld, U.; Fronze, G. G.; Fuchs, U.; Furget, C.; Furs, A.; Girard, M. Fusco; Gaardhoje, J. J.; Gagliardi, M.; Gago, A. M.; Gallio, M.; Gangadharan, D. R.; Ganoti, P.; Gao, C.; Garabatos, C.; Garcia-Solis, E.; Gargiulo, C.; Gasik, P.; Gauger, E. F.; Germain, M.; Gheata, A.; Gheata, M.; Gianotti, P.; Giubellino, P.; Giubilato, P.; Gladysz-Dziadus, E.; Glaessel, P.; Gomez Coral, D. M.; Ramirez, A. Gomez; Gonzalez, A. S.; Gonzalez, V.; Gonzalez-Zamora, P.; Gorbunov, S.; Goerlich, L.; Gotovac, S.; Grabski, V.; Grachov, O. A.; Graczykowski, L. K.; Graham, K. L.; Grelli, A.; Grigoras, A.; Grigoras, C.; Grigoriev, V.; Grigoryan, A.; Grigoryan, S.; Grinyov, B.; Grion, N.; Gronefeld, J. M.; Grosse-Oetringhaus, J. F.; Grosso, R.; Guber, F.; Guernane, R.; Guerzoni, B.; Gulbrandsen, K.; Gunji, T.; Gupta, A.; Haake, R.; Haaland, O.; Hadjidakis, C.; Haiduc, M.; Hamagaki, H.; Hamar, G.; Hamon, J. C.; Harris, J. W.; Harton, A.; Hatzifotiadou, D.; Hayashi, S.; Heckel, S. T.; Hellbaer, E.; Helstrup, H.; Herghelegiu, A.; Herrera Corral, G.; Hess, B. A.; Hetland, K. F.; Hillemanns, H.; Hippolyte, B.; Horak, D.; Hosokawa, R.; Hristov, P.; Humanic, T. J.; Hussain, N.; Hussain, T.; Hutter, D.; Hwang, D. S.; Ilkaev, R.; Inaba, M.; Incani, E.; Ippolitov, M.; Irfan, M.; Ivanov, M.; Ivanov, V.; Izucheev, V.; Jacazio, N.; Jadhav, M. B.; Jadlovska, S.; Jadlovsky, J.; Jahnke, C.; Jakubowska, M. J.; Jang, H. J.; Janik, M. A.; Jayarathna, P. H. S. Y.; Jena, C.; Jena, S.; Bustamante, R. T. Jimenez; Jones, P. G.; Jusko, A.; Kalinak, P.; Kalweit, A.; Kamin, J.; Kaplin, V.; Kar, S.; Uysal, A. Karasu; Karavichev, O.; Karavicheva, T.; Karayan, L.; Karpechev, E.; Kebschull, U.; Keidel, R.; Keijdener, D. L. D.; Keil, M.; Khan, M. Mohisin; Khan, P.; Khan, S. A.; Khanzadeev, A.; Kharlov, Y.; Kileng, B.; Kim, D. W.; Kim, D. J.; Kim, D.; Kim, J. S.; Kim, M.; Kim, T.; Kirsch, S.; Kisel, I.; Kiselev, S.; Kisiel, A.; Kiss, G.; Klay, J. L.; Klein, C.; Klein-Boesing, C.; Klewin, S.; Kluge, A.; Knichel, M. L.; Knospe, A. G.; Kobdaj, C.; Kofarago, M.; Kollegger, T.; Kolojvari, A.; Kondratiev, V.; Kondratyeva, N.; Kondratyuk, E.; Konevskikh, A.; Kopcik, M.; Kostarakis, P.; Kour, M.; Kouzinopoulos, C.; Kovalenko, O.; Kovalenko, V.; Kowalski, M.; Meethaleveedu, G. Koyithatta; Kralik, I.; Kravcakova, A.; Krivda, M.; Krizek, F.; Kryshen, E.; Krzewicki, M.; Kubera, A. M.; Kucera, V.; Kuijer, P. G.; Kumar, J.; Kumar, L.; Kumar, S.; Kurashvili, P.; Kurepin, A.; Kurepin, A. B.; Kuryakin, A.; Kweon, M. J.; Kwon, Y.; La Pointe, S. L.; La Rocca, P.; Ladron de Guevara, P.; Lagana Fernandes, C.; Lakomov, I.; Langoy, R.; Lara, C.; Lardeux, A.; Lattuca, A.; Laudi, E.; Lea, R.; Leardini, L.; Lee, G. R.; Lee, S.; Lehas, F.; Lemmon, R. C.; Lenti, V.; Leogrande, E.; Monzon, I. Leon; Leon Vargas, H.; Leoncino, M.; Levai, P.; Lien, J.; Lietava, R.; Lindal, S.; Lindenstruth, V.; Lippmann, C.; Lisa, M. A.; Ljunggren, H. M.; Lodato, D. F.; Loenne, P. I.; Loginov, V.; Loizides, C.; Lopez, X.; Torres, E. Lopez; Lowe, A.; Luettig, P.; Lunardon, M.; Luparello, G.; Lutz, T. H.; Maevskaya, A.; Mager, M.; Mahajan, S.; Mahmood, S. M.; Maire, A.; Majka, R. D.; Malaev, M.; Maldonado Cervantes, I.; Malinina, L.; Mal'Kevich, D.; Malzacher, P.; Mamonov, A.; Manko, V.; Manso, F.; Manzari, V.; Marchisone, M.; Mares, J.; Margagliotti, G. V.; Margotti, A.; Margutti, J.; Marin, A.; Markert, C.; Marquard, M.; Martin, N. A.; Blanco, J. Martin; Martinengo, P.; Martinez, M. I.; Garcia, G. Martinez; Pedreira, M. Martinez; Mas, A.; Masciocchi, S.; Masera, M.; Masoni, A.; Mastroserio, A.; Matyja, A.; Mayer, C.; Mazer, J.; Mazzoni, M. A.; Mcdonald, D.; Meddi, F.; Melikyan, Y.; Menchaca-Rocha, A.; Meninno, E.; Perez, J. Mercado; Meres, M.; Miake, Y.; Mieskolainen, M. M.; Mikhaylov, K.; Milano, L.; Milosevic, J.; Mischke, A.; Mishra, A. N.; Miskowiec, D.; Mitra, J.; Mitu, C. M.; Mohammadi, N.; Mohanty, B.; Molnar, L.; Montano Zetina, L.; Montes, E.; De Godoy, D. A. Moreira; Moreno, L. A. P.; Moretto, S.; Morreale, A.; Morsch, A.; Muccifora, V.; Mudnic, E.; Muehlheim, D.; Muhuri, S.; Mukherjee, M.; Mulligan, J. D.; Munhoz, M. G.; Munzer, R. H.; Murakami, H.; Murray, S.; Musa, L.; Musinsky, J.; Naik, B.; Nair, R.; Nandi, B. K.; Nania, R.; Nappi, E.; Naru, M. U.; Natal da Luz, H.; Nattrass, C.; Navarro, S. R.; Nayak, K.; Nayak, R.; Nayak, T. K.; Nazarenko, S.; Nedosekin, A.; Nellen, L.; Ng, F.; Nicassio, M.; Niculescu, M.; Niedziela, J.; Nielsen, B. S.; Nikolaev, S.; Nikulin, S.; Nikulin, V.; Noferini, F.; Nomokonov, P.; Nooren, G.; Noris, J. C. C.; Norman, J.; Nyanin, A.; Nystrand, J.; Oeschler, H.; Oh, S.; Oh, S. K.; Ohlson, A.; Okatan, A.; Okubo, T.; Olah, L.; Oleniacz, J.; Oliveira Da Silva, A. C.; Oliver, M. H.; Onderwaater, J.; Oppedisano, C.; Orava, R.; Oravec, M.; Ortiz Velasquez, A.; Oskarsson, A.; Otwinowski, J.; Oyama, K.; Ozdemir, M.; Pachmayer, Y.; Pagano, D.; Pagano, P.; Paic, G.; Pal, S. K.; Pan, J.; Papikyan, V.; Pappalardo, G. S.; Pareek, P.; Park, W. J.; Parmar, S.; Passfeld, A.; Paticchio, V.; Patra, R. N.; Paul, B.; Pei, H.; Peitzmann, T.; Da Costa, H. Pereira; Peresunko, D.; Lara, C. E. Perez; Lezama, E. Perez; Peskov, V.; Pestov, Y.; Petracek, V.; Petrov, V.; Petrovici, M.; Petta, C.; Piano, S.; Pikna, M.; Pillot, P.; Pimentel, L. O. D. L.; Pinazza, O.; Pinsky, L.; Piyarathna, D. B.; Ploskon, M.; Planinic, M.; Pluta, J.; Pochybova, S.; Podesta-Lerma, P. L. M.; Poghosyan, M. G.; Polichtchouk, B.; Poljak, N.; Poonsawat, W.; Pop, A.; Porteboeuf-Houssais, S.; Porter, J.; Pospisil, J.; Prasad, S. K.; Preghenella, R.; Prino, F.; Pruneau, C. A.; Pshenichnov, I.; Puccio, M.; Puddu, G.; Pujahari, P.; Punin, V.; Putschke, J.; Qvigstad, H.; Rachevski, A.; Raha, S.; Rajput, S.; Rak, J.; Rakotozafindrabe, A.; Ramello, L.; Rami, F.; Raniwala, R.; Raniwala, S.; Raesaenen, S. S.; Rascanu, B. T.; Rathee, D.; Read, K. F.; Redlich, K.; Reed, R. J.; Reichelt, P.; Reidt, F.; Ren, X.; Renfordt, R.; Reolon, A. R.; Reshetin, A.; Reygers, K.; Riabov, V.; Ricci, R. A.; Richert, T.; Richter, M.; Riedler, P.; Riegler, W.; Riggi, F.; Ristea, C.; Rocco, E.; Rodriguez Cahuantzi, M.; Manso, A. Rodriguez; Roed, K.; Rogochaya, E.; Rohr, D.; Roehrich, D.; Ronchetti, F.; Ronflette, L.; Rosnet, P.; Rossi, A.; Roukoutakis, F.; Roy, A.; Roy, C.; Roy, P.; Montero, A. J. Rubio; Rui, R.; Russo, R.; Ryabinkin, E.; Ryabov, Y.; Rybicki, A.; Saarinen, S.; Sadhu, S.; Sadovsky, S.; Safarik, K.; Sahlmuller, B.; Sahoo, P.; Sahoo, R.; Sahoo, S.; Sahu, P. K.; Saini, J.; Sakai, S.; Saleh, M. A.; Salzwedel, J.; Sambyal, S.; Samsonov, V.; Sandor, L.; Sandoval, A.; Sano, M.; Sarkar, D.; Sarkar, N.; Sarma, P.; Scapparone, E.; Scarlassara, F.; Schiaua, C.; Schicker, R.; Schmidt, C.; Schmidt, H. R.; Schuchmann, S.; Schukraft, J.; Schulc, M.; Schutz, Y.; Schwarz, K.; Schweda, K.; Scioli, G.; Scomparin, E.; Scott, R.; Sefcik, M.; Seger, J. E.; Sekiguchi, Y.; Sekihata, D.; Selyuzhenkov, I.; Senosi, K.; Senyukov, S.; Serradilla, E.; Sevcenco, A.; Shabanov, A.; Shabetai, A.; Shadura, O.; Shahoyan, R.; Shahzad, M. I.; Shangaraev, A.; Sharma, M.; Sharma, M.; Sharma, N.; Sheikh, A. I.; Shigaki, K.; Shou, Q.; Shtejer, K.; Sibiriak, Y.; Siddhanta, S.; Sielewicz, K. M.; Siemiarczuk, T.; Silvermyr, D.; Silvestre, C.; Simatovic, G.; Simonetti, G.; Singaraju, R.; Singh, R.; Singha, S.; Singhal, V.; Sinha, B. C.; Sinha, T.; Sitar, B.; Sitta, M.; Skaali, T. B.; Slupecki, M.; Smirnov, N.; Snellings, R. J. M.; Snellman, T. W.; Song, J.; Song, M.; Song, Z.; Soramel, F.; Sorensen, S.; de Souza, R. D.; Sozzi, F.; Spacek, M.; Spiriti, E.; Sputowska, I.; Spyropoulou-Stassinaki, M.; Stachel, J.; Stan, I.; Stankus, P.; Stenlund, E.; Steyn, G.; Stiller, J. H.; Stocco, D.; Strmen, P.; Suaide, A. A. P.; Sugitate, T.; Suire, C.; Suleymanov, M.; Suljic, M.; Sultanov, R.; Sumbera, M.; Sumowidagdo, S.; Szabo, A.; Szanto de Toledo, A.; Szarka, I.; Szczepankiewicz, A.; Szymanski, M.; Tabassam, U.; Takahashi, J.; Tambave, G. J.; Tanaka, N.; Tarhini, M.; Tariq, M.; Tarzila, M. G.; Tauro, A.; Tejeda Munoz, G.; Telesca, A.; Terasaki, K.; Terrevoli, C.; Teyssier, B.; Thaeder, J.; Thakur, D.; Thomas, D.; Tieulent, R.; Timmins, A. R.; Toia, A.; Trogolo, S.; Trombetta, G.; Trubnikov, V.; Trzaska, W. H.; Tsuji, T.; Tumkin, A.; Turrisi, R.; Tveter, T. S.; Ullaland, K.; Uras, A.; Usai, G. L.; Utrobicic, A.; Vala, M.; Palomo, L. Valencia; Vallero, S.; Van Der Maarel, J.; Van Hoorne, J. W.; van Leeuwen, M.; Vanat, T.; Vyvre, P. Vande; Varga, D.; Vargas, A.; Vargyas, M.; Varma, R.; Vasileiou, M.; Vasiliev, A.; Vauthier, A.; Vechernin, V.; Veen, A. M.; Veldhoen, M.; Velure, A.; Vercellin, E.; Vergara Limon, S.; Vernet, R.; Verweij, M.; Vickovic, L.; Viesti, G.; Viinikainen, J.; Vilakazi, Z.; Baillie, O. Villalobos; Villatoro Tello, A.; Vinogradov, A.; Vinogradov, L.; Vinogradov, Y.; Virgili, T.; Vislavicius, V.; Viyogi, Y. P.; Vodopyanov, A.; Voelkl, M. A.; Voloshin, K.; Voloshin, S. A.; Volpe, G.; von Haller, B.; Vorobyev, I.; Vranic, D.; Vrlakova, J.; Vulpescu, B.; Wagner, B.; Wagner, J.; Wang, H.; Watanabe, D.; Watanabe, Y.; Weiser, D. F.; Westerhoff, U.; Whitehead, A. M.; Wiechula, J.; Wikne, J.; Wilk, G.; Wilkinson, J.; Williams, M. C. S.; Windelband, B.; Winn, M.; Yang, H.; Yano, S.; Yasin, Z.; Yokoyama, H.; Yoo, I. -K.; Yoon, J. H.; Yurchenko, V.; Yushmanov, I.; Zaborowska, A.; Zaccolo, V.; Zaman, A.; Zampolli, C.; Zanoli, H. J. C.; Zaporozhets, S.; Zardoshti, N.; Zarochentsev, A.; Zavada, P.; Zaviyalov, N.; Zbroszczyk, H.; Zgura, I. S.; Zhalov, M.; Zhang, C.; Zhao, C.; Zhigareva, N.; Zhou, Y.; Zhou, Z.; Zhu, H.; Zichichi, A.; Zimmermann, A.; Zimmermann, M. B.; Zinovjev, G.; Zyzak, M.

    2016-01-01

    We present a Bayesian approach to particle identification (PID) within the ALICE experiment. The aim is to more effectively combine the particle identification capabilities of its various detectors. After a brief explanation of the adopted methodology and formalism, the performance of the Bayesian

  12. Advances in Bayesian Modeling in Educational Research

    Science.gov (United States)

    Levy, Roy

    2016-01-01

    In this article, I provide a conceptually oriented overview of Bayesian approaches to statistical inference and contrast them with frequentist approaches that currently dominate conventional practice in educational research. The features and advantages of Bayesian approaches are illustrated with examples spanning several statistical modeling…

  13. Compiling Relational Bayesian Networks for Exact Inference

    DEFF Research Database (Denmark)

    Jaeger, Manfred; Darwiche, Adnan; Chavira, Mark

    2006-01-01

    We describe in this paper a system for exact inference with relational Bayesian networks as defined in the publicly available PRIMULA tool. The system is based on compiling propositional instances of relational Bayesian networks into arithmetic circuits and then performing online inference...

  14. Compiling Relational Bayesian Networks for Exact Inference

    DEFF Research Database (Denmark)

    Jaeger, Manfred; Chavira, Mark; Darwiche, Adnan

    2004-01-01

    We describe a system for exact inference with relational Bayesian networks as defined in the publicly available \\primula\\ tool. The system is based on compiling propositional instances of relational Bayesian networks into arithmetic circuits and then performing online inference by evaluating...

  15. 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.

  16. Bayesian Nonparametric Longitudinal Data Analysis.

    Science.gov (United States)

    Quintana, Fernando A; Johnson, Wesley O; Waetjen, Elaine; Gold, Ellen

    2016-01-01

    Practical Bayesian nonparametric methods have been developed across a wide variety of contexts. Here, we develop a novel statistical model that generalizes standard mixed models for longitudinal data that include flexible mean functions as well as combined compound symmetry (CS) and autoregressive (AR) covariance structures. AR structure is often specified through the use of a Gaussian process (GP) with covariance functions that allow longitudinal data to be more correlated if they are observed closer in time than if they are observed farther apart. We allow for AR structure by considering a broader class of models that incorporates a Dirichlet Process Mixture (DPM) over the covariance parameters of the GP. We are able to take advantage of modern Bayesian statistical methods in making full predictive inferences and about characteristics of longitudinal profiles and their differences across covariate combinations. We also take advantage of the generality of our model, which provides for estimation of a variety of covariance structures. We observe that models that fail to incorporate CS or AR structure can result in very poor estimation of a covariance or correlation matrix. In our illustration using hormone data observed on women through the menopausal transition, biology dictates the use of a generalized family of sigmoid functions as a model for time trends across subpopulation categories.

  17. 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 ...

  18. 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.

  19. Bayesian calibration of simultaneity in audiovisual temporal order judgments.

    Directory of Open Access Journals (Sweden)

    Shinya Yamamoto

    Full Text Available After repeated exposures to two successive audiovisual stimuli presented in one frequent order, participants eventually perceive a pair separated by some lag time in the same order as occurring simultaneously (lag adaptation. In contrast, we previously found that perceptual changes occurred in the opposite direction in response to tactile stimuli, conforming to bayesian integration theory (bayesian calibration. We further showed, in theory, that the effect of bayesian calibration cannot be observed when the lag adaptation was fully operational. This led to the hypothesis that bayesian calibration affects judgments regarding the order of audiovisual stimuli, but that this effect is concealed behind the lag adaptation mechanism. In the present study, we showed that lag adaptation is pitch-insensitive using two sounds at 1046 and 1480 Hz. This enabled us to cancel lag adaptation by associating one pitch with sound-first stimuli and the other with light-first stimuli. When we presented each type of stimulus (high- or low-tone in a different block, the point of simultaneity shifted to "sound-first" for the pitch associated with sound-first stimuli, and to "light-first" for the pitch associated with light-first stimuli. These results are consistent with lag adaptation. In contrast, when we delivered each type of stimulus in a randomized order, the point of simultaneity shifted to "light-first" for the pitch associated with sound-first stimuli, and to "sound-first" for the pitch associated with light-first stimuli. The results clearly show that bayesian calibration is pitch-specific and is at work behind pitch-insensitive lag adaptation during temporal order judgment of audiovisual stimuli.

  20. Merging Digital Surface Models Implementing Bayesian Approaches

    Science.gov (United States)

    Sadeq, H.; Drummond, J.; Li, Z.

    2016-06-01

    In this research different DSMs from different sources have been merged. The merging is based on a probabilistic model using a Bayesian Approach. The implemented data have been sourced from very high resolution satellite imagery sensors (e.g. WorldView-1 and Pleiades). It is deemed preferable to use a Bayesian Approach when the data obtained from the sensors are limited and it is difficult to obtain many measurements or it would be very costly, thus the problem of the lack of data can be solved by introducing a priori estimations of data. To infer the prior data, it is assumed that the roofs of the buildings are specified as smooth, and for that purpose local entropy has been implemented. In addition to the a priori estimations, GNSS RTK measurements have been collected in the field which are used as check points to assess the quality of the DSMs and to validate the merging result. The model has been applied in the West-End of Glasgow containing different kinds of buildings, such as flat roofed and hipped roofed buildings. Both quantitative and qualitative methods have been employed to validate the merged DSM. The validation results have shown that the model was successfully able to improve the quality of the DSMs and improving some characteristics such as the roof surfaces, which consequently led to better representations. In addition to that, the developed model has been compared with the well established Maximum Likelihood model and showed similar quantitative statistical results and better qualitative results. Although the proposed model has been applied on DSMs that were derived from satellite imagery, it can be applied to any other sourced DSMs.

  1. MERGING DIGITAL SURFACE MODELS IMPLEMENTING BAYESIAN APPROACHES

    Directory of Open Access Journals (Sweden)

    H. Sadeq

    2016-06-01

    Full Text Available In this research different DSMs from different sources have been merged. The merging is based on a probabilistic model using a Bayesian Approach. The implemented data have been sourced from very high resolution satellite imagery sensors (e.g. WorldView-1 and Pleiades. It is deemed preferable to use a Bayesian Approach when the data obtained from the sensors are limited and it is difficult to obtain many measurements or it would be very costly, thus the problem of the lack of data can be solved by introducing a priori estimations of data. To infer the prior data, it is assumed that the roofs of the buildings are specified as smooth, and for that purpose local entropy has been implemented. In addition to the a priori estimations, GNSS RTK measurements have been collected in the field which are used as check points to assess the quality of the DSMs and to validate the merging result. The model has been applied in the West-End of Glasgow containing different kinds of buildings, such as flat roofed and hipped roofed buildings. Both quantitative and qualitative methods have been employed to validate the merged DSM. The validation results have shown that the model was successfully able to improve the quality of the DSMs and improving some characteristics such as the roof surfaces, which consequently led to better representations. In addition to that, the developed model has been compared with the well established Maximum Likelihood model and showed similar quantitative statistical results and better qualitative results. Although the proposed model has been applied on DSMs that were derived from satellite imagery, it can be applied to any other sourced DSMs.

  2. Efficient Bayesian hierarchical functional data analysis with basis function approximations using Gaussian-Wishart processes.

    Science.gov (United States)

    Yang, Jingjing; Cox, Dennis D; Lee, Jong Soo; Ren, Peng; Choi, Taeryon

    2017-12-01

    Functional data are defined as realizations of random functions (mostly smooth functions) varying over a continuum, which are usually collected on discretized grids with measurement errors. In order to accurately smooth noisy functional observations and deal with the issue of high-dimensional observation grids, we propose a novel Bayesian method based on the Bayesian hierarchical model with a Gaussian-Wishart process prior and basis function representations. We first derive an induced model for the basis-function coefficients of the functional data, and then use this model to conduct posterior inference through Markov chain Monte Carlo methods. Compared to the standard Bayesian inference that suffers serious computational burden and instability in analyzing high-dimensional functional data, our method greatly improves the computational scalability and stability, while inheriting the advantage of simultaneously smoothing raw observations and estimating the mean-covariance functions in a nonparametric way. In addition, our method can naturally handle functional data observed on random or uncommon grids. Simulation and real studies demonstrate that our method produces similar results to those obtainable by the standard Bayesian inference with low-dimensional common grids, while efficiently smoothing and estimating functional data with random and high-dimensional observation grids when the standard Bayesian inference fails. In conclusion, our method can efficiently smooth and estimate high-dimensional functional data, providing one way to resolve the curse of dimensionality for Bayesian functional data analysis with Gaussian-Wishart processes. © 2017, The International Biometric Society.

  3. National evaluation of Chinese coastal erosion to sea level rise using a Bayesian approach

    International Nuclear Information System (INIS)

    Zhan, Q; Fan, X; Du, X; Zhu, J

    2014-01-01

    In this paper a Causal Bayesian network is developed to predict decadal-scale shoreline evolution of China to sea-level rise. The Bayesian model defines relationships between 6 factors of Chinese coastal system such as coastal geomorphology, mean tide range, mean wave height, coastal slope, relative sea-level rise rate and shoreline erosion rate. Using the Bayesian probabilistic model, we make quantitative assessment of china's shoreline evolution in response to different future sea level rise rates. Results indicate that the probability of coastal erosion with high and very high rates increases from 28% to 32.3% when relative sea-level rise rates is 4∼6mm/a, and to 44.9% when relative sea-level rise rates is more than 6mm/a. A hindcast evaluation of the Bayesian model shows that the model correctly predicts 79.3% of the cases. Model test indicates that the Bayesian model shows higher predictive capabilities for stable coasts and very highly eroding coasts than moderately and highly eroding coasts. This study demonstrates that the Bayesian model is adapted to predicting decadal-scale Chinese coastal erosion associated with sea-level rise

  4. Bus Route Design with a Bayesian Network Analysis of Bus Service Revenues

    OpenAIRE

    Liu, Yi; Jia, Yuanhua; Feng, Xuesong; Wu, Jiang

    2018-01-01

    A Bayesian network is used to estimate revenues of bus services in consideration of the effect of bus travel demands, passenger transport distances, and so on. In this research, the area X in Beijing has been selected as the study area because of its relatively high bus travel demand and, on the contrary, unsatisfactory bus services. It is suggested that the proposed Bayesian network approach is able to rationally predict the probabilities of different revenues of various route services, from...

  5. Bayesian image reconstruction for improving detection performance of muon tomography.

    Science.gov (United States)

    Wang, Guobao; Schultz, Larry J; Qi, Jinyi

    2009-05-01

    Muon tomography is a novel technology that is being developed for detecting high-Z materials in vehicles or cargo containers. Maximum likelihood methods have been developed for reconstructing the scattering density image from muon measurements. However, the instability of maximum likelihood estimation often results in noisy images and low detectability of high-Z targets. In this paper, we propose using regularization to improve the image quality of muon tomography. We formulate the muon reconstruction problem in a Bayesian framework by introducing a prior distribution on scattering density images. An iterative shrinkage algorithm is derived to maximize the log posterior distribution. At each iteration, the algorithm obtains the maximum a posteriori update by shrinking an unregularized maximum likelihood update. Inverse quadratic shrinkage functions are derived for generalized Laplacian priors and inverse cubic shrinkage functions are derived for generalized Gaussian priors. Receiver operating characteristic studies using simulated data demonstrate that the Bayesian reconstruction can greatly improve the detection performance of muon tomography.

  6. A Bayesian Reflection on Surfaces

    Directory of Open Access Journals (Sweden)

    David R. Wolf

    1999-10-01

    Full Text Available Abstract: The topic of this paper is a novel Bayesian continuous-basis field representation and inference framework. Within this paper several problems are solved: The maximally informative inference of continuous-basis fields, that is where the basis for the field is itself a continuous object and not representable in a finite manner; the tradeoff between accuracy of representation in terms of information learned, and memory or storage capacity in bits; the approximation of probability distributions so that a maximal amount of information about the object being inferred is preserved; an information theoretic justification for multigrid methodology. The maximally informative field inference framework is described in full generality and denoted the Generalized Kalman Filter. The Generalized Kalman Filter allows the update of field knowledge from previous knowledge at any scale, and new data, to new knowledge at any other scale. An application example instance, the inference of continuous surfaces from measurements (for example, camera image data, is presented.

  7. Attention in a bayesian framework

    DEFF Research Database (Denmark)

    Whiteley, Louise Emma; Sahani, Maneesh

    2012-01-01

    , and include both selective phenomena, where attention is invoked by cues that point to particular stimuli, and integrative phenomena, where attention is invoked dynamically by endogenous processing. However, most previous Bayesian accounts of attention have focused on describing relatively simple experimental...... selective and integrative roles, and thus cannot be easily extended to complex environments. We suggest that the resource bottleneck stems from the computational intractability of exact perceptual inference in complex settings, and that attention reflects an evolved mechanism for approximate inference which...... can be shaped to refine the local accuracy of perception. We show that this approach extends the simple picture of attention as prior, so as to provide a unified and computationally driven account of both selective and integrative attentional phenomena....

  8. On Bayesian System Reliability Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Soerensen Ringi, M

    1995-05-01

    The view taken in this thesis is that reliability, the probability that a system will perform a required function for a stated period of time, depends on a person`s state of knowledge. Reliability changes as this state of knowledge changes, i.e. when new relevant information becomes available. Most existing models for system reliability prediction are developed in a classical framework of probability theory and they overlook some information that is always present. Probability is just an analytical tool to handle uncertainty, based on judgement and subjective opinions. It is argued that the Bayesian approach gives a much more comprehensive understanding of the foundations of probability than the so called frequentistic school. A new model for system reliability prediction is given in two papers. The model encloses the fact that component failures are dependent because of a shared operational environment. The suggested model also naturally permits learning from failure data of similar components in non identical environments. 85 refs.

  9. 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...

  10. On Bayesian System Reliability Analysis

    International Nuclear Information System (INIS)

    Soerensen Ringi, M.

    1995-01-01

    The view taken in this thesis is that reliability, the probability that a system will perform a required function for a stated period of time, depends on a person's state of knowledge. Reliability changes as this state of knowledge changes, i.e. when new relevant information becomes available. Most existing models for system reliability prediction are developed in a classical framework of probability theory and they overlook some information that is always present. Probability is just an analytical tool to handle uncertainty, based on judgement and subjective opinions. It is argued that the Bayesian approach gives a much more comprehensive understanding of the foundations of probability than the so called frequentistic school. A new model for system reliability prediction is given in two papers. The model encloses the fact that component failures are dependent because of a shared operational environment. The suggested model also naturally permits learning from failure data of similar components in non identical environments. 85 refs

  11. Bayesian estimation in homodyne interferometry

    International Nuclear Information System (INIS)

    Olivares, Stefano; Paris, Matteo G A

    2009-01-01

    We address phase-shift estimation by means of squeezed vacuum probe and homodyne detection. We analyse Bayesian estimator, which is known to asymptotically saturate the classical Cramer-Rao bound to the variance, and discuss convergence looking at the a posteriori distribution as the number of measurements increases. We also suggest two feasible adaptive methods, acting on the squeezing parameter and/or the homodyne local oscillator phase, which allow us to optimize homodyne detection and approach the ultimate bound to precision imposed by the quantum Cramer-Rao theorem. The performances of our two-step methods are investigated by means of Monte Carlo simulated experiments with a small number of homodyne data, thus giving a quantitative meaning to the notion of asymptotic optimality.

  12. Bayesian Kernel Mixtures for Counts.

    Science.gov (United States)

    Canale, Antonio; Dunson, David B

    2011-12-01

    Although Bayesian nonparametric mixture models for continuous data are well developed, there is a limited literature on related approaches for count data. A common strategy is to use a mixture of Poissons, which unfortunately is quite restrictive in not accounting for distributions having variance less than the mean. Other approaches include mixing multinomials, which requires finite support, and using a Dirichlet process prior with a Poisson base measure, which does not allow smooth deviations from the Poisson. As a broad class of alternative models, we propose to use nonparametric mixtures of rounded continuous kernels. An efficient Gibbs sampler is developed for posterior computation, and a simulation study is performed to assess performance. Focusing on the rounded Gaussian case, we generalize the modeling framework to account for multivariate count data, joint modeling with continuous and categorical variables, and other complications. The methods are illustrated through applications to a developmental toxicity study and marketing data. This article has supplementary material online.

  13. Bayesian networks in educational assessment

    CERN Document Server

    Almond, Russell G; Steinberg, Linda S; Yan, Duanli; Williamson, David M

    2015-01-01

    Bayesian inference networks, a synthesis of statistics and expert systems, have advanced reasoning under uncertainty in medicine, business, and social sciences. This innovative volume is the first comprehensive treatment exploring how they can be applied to design and analyze innovative educational assessments. Part I develops Bayes nets’ foundations in assessment, statistics, and graph theory, and works through the real-time updating algorithm. Part II addresses parametric forms for use with assessment, model-checking techniques, and estimation with the EM algorithm and Markov chain Monte Carlo (MCMC). A unique feature is the volume’s grounding in Evidence-Centered Design (ECD) framework for assessment design. This “design forward” approach enables designers to take full advantage of Bayes nets’ modularity and ability to model complex evidentiary relationships that arise from performance in interactive, technology-rich assessments such as simulations. Part III describes ECD, situates Bayes nets as ...

  14. Bayesian hierarchical model for large-scale covariance matrix estimation.

    Science.gov (United States)

    Zhu, Dongxiao; Hero, Alfred O

    2007-12-01

    Many bioinformatics problems implicitly depend on estimating large-scale covariance matrix. The traditional approaches tend to give rise to high variance and low accuracy due to "overfitting." We cast the large-scale covariance matrix estimation problem into the Bayesian hierarchical model framework, and introduce dependency between covariance parameters. We demonstrate the advantages of our approaches over the traditional approaches using simulations and OMICS data analysis.

  15. Why 1D electrical resistivity techniques can result in inaccurate siting of boreholes in hard rock aquifers and why electrical resistivity tomography must be preferred: the example of Benin, West Africa

    Science.gov (United States)

    Alle, Iboukoun Christian; Descloitres, Marc; Vouillamoz, Jean-Michel; Yalo, Nicaise; Lawson, Fabrice Messan Amen; Adihou, Akonfa Consolas

    2018-03-01

    Hard rock aquifers are of particular importance for supplying people with drinking water in Africa and in the world. Although the common use of one-dimensional (1D) electrical resistivity techniques to locate drilling site, the failure rate of boreholes is usually high. For instance, about 40% of boreholes drilled in hard rock aquifers in Benin are unsuccessful. This study investigates why the current use of 1D techniques (e.g. electrical profiling and electrical sounding) can result in inaccurate siting of boreholes, and checks the interest and the limitations of the use of two-dimensional (2D) Electrical Resistivity Tomography (ERT). Geophysical numerical modeling and comprehensive 1D and 2D resistivity surveys were carried out in hard rock aquifers in Benin. The experiments carried out at 7 sites located in different hard rock groups confirmed the results of the numerical modeling: the current use of 1D techniques can frequently leads to inaccurate siting, and ERT better reveals hydrogeological targets such as thick weathered zone (e.g. stratiform fractured layer and preferential weathering associated with subvertical fractured zone). Moreover, a cost analysis demonstrates that the use of ERT can save money at the scale of a drilling programme if ERT improves the success rate by only 5% as compared to the success rate obtained with 1D techniques. Finally, this study demonstrates, using the example of Benin, that the use of electrical resistivity profiling and sounding for siting boreholes in weathered hard rocks of western Africa should be discarded and replaced by the use of ERT technique, more efficient.

  16. Robust bayesian analysis of an autoregressive model with ...

    African Journals Online (AJOL)

    In this work, robust Bayesian analysis of the Bayesian estimation of an autoregressive model with exponential innovations is performed. Using a Bayesian robustness methodology, we show that, using a suitable generalized quadratic loss, we obtain optimal Bayesian estimators of the parameters corresponding to the ...

  17. 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

  18. A Probability-based Evolutionary Algorithm with Mutations to Learn Bayesian Networks

    Directory of Open Access Journals (Sweden)

    Sho Fukuda

    2014-12-01

    Full Text Available Bayesian networks are regarded as one of the essential tools to analyze causal relationship between events from data. To learn the structure of highly-reliable Bayesian networks from data as quickly as possible is one of the important problems that several studies have been tried to achieve. In recent years, probability-based evolutionary algorithms have been proposed as a new efficient approach to learn Bayesian networks. In this paper, we target on one of the probability-based evolutionary algorithms called PBIL (Probability-Based Incremental Learning, and propose a new mutation operator. Through performance evaluation, we found that the proposed mutation operator has a good performance in learning Bayesian networks

  19. 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.

  20. Bayesian selection of misspecified models is overconfident and may cause spurious posterior probabilities for phylogenetic trees.

    Science.gov (United States)

    Yang, Ziheng; Zhu, Tianqi

    2018-02-20

    The Bayesian method is noted to produce spuriously high posterior probabilities for phylogenetic trees in analysis of large datasets, but the precise reasons for this overconfidence are unknown. In general, the performance of Bayesian selection of misspecified models is poorly understood, even though this is of great scientific interest since models are never true in real data analysis. Here we characterize the asymptotic behavior of Bayesian model selection and show that when the competing models are equally wrong, Bayesian model selection exhibits surprising and polarized behaviors in large datasets, supporting one model with full force while rejecting the others. If one model is slightly less wrong than the other, the less wrong model will eventually win when the amount of data increases, but the method may become overconfident before it becomes reliable. We suggest that this extreme behavior may be a major factor for the spuriously high posterior probabilities for evolutionary trees. The philosophical implications of our results to the application of Bayesian model selection to evaluate opposing scientific hypotheses are yet to be explored, as are the behaviors of non-Bayesian methods in similar situations.

  1. Protein construct storage: Bayesian variable selection and prediction with mixtures.

    Science.gov (United States)

    Clyde, M A; Parmigiani, G

    1998-07-01

    Determining optimal conditions for protein storage while maintaining a high level of protein activity is an important question in pharmaceutical research. A designed experiment based on a space-filling design was conducted to understand the effects of factors affecting protein storage and to establish optimal storage conditions. Different model-selection strategies to identify important factors may lead to very different answers about optimal conditions. Uncertainty about which factors are important, or model uncertainty, can be a critical issue in decision-making. We use Bayesian variable selection methods for linear models to identify important variables in the protein storage data, while accounting for model uncertainty. We also use the Bayesian framework to build predictions based on a large family of models, rather than an individual model, and to evaluate the probability that certain candidate storage conditions are optimal.

  2. Towards port sustainability through probabilistic models: Bayesian networks

    Directory of Open Access Journals (Sweden)

    B. Molina

    2018-04-01

    Full Text Available It is necessary that a manager of an infrastructure knows relations between variables. Using Bayesian networks, variables can be classified, predicted and diagnosed, being able to estimate posterior probability of the unknown ones based on known ones. The proposed methodology has generated a database with port variables, which have been classified as economic, social, environmental and institutional, as addressed in of smart ports studies made in all Spanish Port System. Network has been developed using an acyclic directed graph, which have let us know relationships in terms of parents and sons. In probabilistic terms, it can be concluded from the constructed network that the most decisive variables for port sustainability are those that are part of the institutional dimension. It has been concluded that Bayesian networks allow modeling uncertainty probabilistically even when the number of variables is high as it occurs in port planning and exploitation.

  3. Statistical assignment of DNA sequences using Bayesian phylogenetics

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Huelsenbeck, John P.

    2008-01-01

    We provide a new automated statistical method for DNA barcoding based on a Bayesian phylogenetic analysis. The method is based on automated database sequence retrieval, alignment, and phylogenetic analysis using a custom-built program for Bayesian phylogenetic analysis. We show on real data...... that the method outperforms Blast searches as a measure of confidence and can help eliminate 80% of all false assignment based on best Blast hit. However, the most important advance of the method is that it provides statistically meaningful measures of confidence. We apply the method to a re......-analysis of previously published ancient DNA data and show that, with high statistical confidence, most of the published sequences are in fact of Neanderthal origin. However, there are several cases of chimeric sequences that are comprised of a combination of both Neanderthal and modern human DNA....

  4. Predicting Software Suitability Using a Bayesian Belief Network

    Science.gov (United States)

    Beaver, Justin M.; Schiavone, Guy A.; Berrios, Joseph S.

    2005-01-01

    The ability to reliably predict the end quality of software under development presents a significant advantage for a development team. It provides an opportunity to address high risk components earlier in the development life cycle, when their impact is minimized. This research proposes a model that captures the evolution of the quality of a software product, and provides reliable forecasts of the end quality of the software being developed in terms of product suitability. Development team skill, software process maturity, and software problem complexity are hypothesized as driving factors of software product quality. The cause-effect relationships between these factors and the elements of software suitability are modeled using Bayesian Belief Networks, a machine learning method. This research presents a Bayesian Network for software quality, and the techniques used to quantify the factors that influence and represent software quality. The developed model is found to be effective in predicting the end product quality of small-scale software development efforts.

  5. 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...

  6. 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

  7. Structure-based bayesian sparse reconstruction

    KAUST Repository

    Quadeer, Ahmed Abdul; Al-Naffouri, Tareq Y.

    2012-01-01

    Sparse signal reconstruction algorithms have attracted research attention due to their wide applications in various fields. In this paper, we present a simple Bayesian approach that utilizes the sparsity constraint and a priori statistical

  8. An Intuitive Dashboard for Bayesian Network Inference

    International Nuclear Information System (INIS)

    Reddy, Vikas; Farr, Anna Charisse; Wu, Paul; Mengersen, Kerrie; Yarlagadda, Prasad K D V

    2014-01-01

    Current Bayesian network software packages provide good graphical interface for users who design and develop Bayesian networks for various applications. However, the intended end-users of these networks may not necessarily find such an interface appealing and at times it could be overwhelming, particularly when the number of nodes in the network is large. To circumvent this problem, this paper presents an intuitive dashboard, which provides an additional layer of abstraction, enabling the end-users to easily perform inferences over the Bayesian networks. Unlike most software packages, which display the nodes and arcs of the network, the developed tool organises the nodes based on the cause-and-effect relationship, making the user-interaction more intuitive and friendly. In addition to performing various types of inferences, the users can conveniently use the tool to verify the behaviour of the developed Bayesian network. The tool has been developed using QT and SMILE libraries in C++

  9. Learning Bayesian networks for discrete data

    KAUST Repository

    Liang, Faming

    2009-02-01

    Bayesian networks have received much attention in the recent literature. In this article, we propose an approach to learn Bayesian networks using the stochastic approximation Monte Carlo (SAMC) algorithm. Our approach has two nice features. Firstly, it possesses the self-adjusting mechanism and thus avoids essentially the local-trap problem suffered by conventional MCMC simulation-based approaches in learning Bayesian networks. Secondly, it falls into the class of dynamic importance sampling algorithms; the network features can be inferred by dynamically weighted averaging the samples generated in the learning process, and the resulting estimates can have much lower variation than the single model-based estimates. The numerical results indicate that our approach can mix much faster over the space of Bayesian networks than the conventional MCMC simulation-based approaches. © 2008 Elsevier B.V. All rights reserved.

  10. An Intuitive Dashboard for Bayesian Network Inference

    Science.gov (United States)

    Reddy, Vikas; Charisse Farr, Anna; Wu, Paul; Mengersen, Kerrie; Yarlagadda, Prasad K. D. V.

    2014-03-01

    Current Bayesian network software packages provide good graphical interface for users who design and develop Bayesian networks for various applications. However, the intended end-users of these networks may not necessarily find such an interface appealing and at times it could be overwhelming, particularly when the number of nodes in the network is large. To circumvent this problem, this paper presents an intuitive dashboard, which provides an additional layer of abstraction, enabling the end-users to easily perform inferences over the Bayesian networks. Unlike most software packages, which display the nodes and arcs of the network, the developed tool organises the nodes based on the cause-and-effect relationship, making the user-interaction more intuitive and friendly. In addition to performing various types of inferences, the users can conveniently use the tool to verify the behaviour of the developed Bayesian network. The tool has been developed using QT and SMILE libraries in C++.

  11. 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.

  12. 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.)

  13. 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

  14. 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.

  15. Application of a predictive Bayesian model to environmental accounting.

    Science.gov (United States)

    Anex, R P; Englehardt, J D

    2001-03-30

    Environmental accounting techniques are intended to capture important environmental costs and benefits that are often overlooked in standard accounting practices. Environmental accounting methods themselves often ignore or inadequately represent large but highly uncertain environmental costs and costs conditioned by specific prior events. Use of a predictive Bayesian model is demonstrated for the assessment of such highly uncertain environmental and contingent costs. The predictive Bayesian approach presented generates probability distributions for the quantity of interest (rather than parameters thereof). A spreadsheet implementation of a previously proposed predictive Bayesian model, extended to represent contingent costs, is described and used to evaluate whether a firm should undertake an accelerated phase-out of its PCB containing transformers. Variability and uncertainty (due to lack of information) in transformer accident frequency and severity are assessed simultaneously using a combination of historical accident data, engineering model-based cost estimates, and subjective judgement. Model results are compared using several different risk measures. Use of the model for incorporation of environmental risk management into a company's overall risk management strategy is discussed.

  16. Looking for Sustainable Urban Mobility through Bayesian Networks

    Directory of Open Access Journals (Sweden)

    Giovanni Fusco

    2004-11-01

    Full Text Available There is no formalised theory of sustainable urban mobility systems. Observed patterns of urban mobility are often considered unsustainable. But we don’t know what a city with sustainable mobility should look like. It is nevertheless increasingly apparent that the urban mobility system plays an important role in the achievement of the city’s wider sustainability objectives.In this paper we explore the characteristics of sustainable urban mobility systems through the technique of Bayesian networks. At the frontier between multivariate statistics and artificial intelligence, Bayesian networks provide powerful models of causal knowledge in an uncertain context. Using data on urban structure, transportation offer, mobility demand, resource consumption and environmental externalities from seventy-five world cities, we developed a systemic model of the city-transportation-environment interaction in the form of a Bayesian network. The network could then be used to infer the features of the city with sustainable mobility.The Bayesian model indicates that the city with sustainable mobility is most probably a dense city with highly efficient transit and multimodal mobility. It produces high levels of accessibility without relying on a fast road network. The achievement of sustainability objectives for urban mobility is probably compatible with all socioeconomic contexts.By measuring the distance of world cities from the inferred sustainability profile, we finally derive a geography of sustainability for mobility systems. The cities closest to the sustainability profile are in Central Europe as well as in affluent countries of the Far East. Car-dependent American cities are the farthest from the desired sustainability profile.

  17. Seeded Bayesian Networks: Constructing genetic networks from microarray data

    Directory of Open Access Journals (Sweden)

    Quackenbush John

    2008-07-01

    Full Text Available Abstract Background DNA microarrays and other genomics-inspired technologies provide large datasets that often include hidden patterns of correlation between genes reflecting the complex processes that underlie cellular metabolism and physiology. The challenge in analyzing large-scale expression data has been to extract biologically meaningful inferences regarding these processes – often represented as networks – in an environment where the datasets are often imperfect and biological noise can obscure the actual signal. Although many techniques have been developed in an attempt to address these issues, to date their ability to extract meaningful and predictive network relationships has been limited. Here we describe a method that draws on prior information about gene-gene interactions to infer biologically relevant pathways from microarray data. Our approach consists of using preliminary networks derived from the literature and/or protein-protein interaction data as seeds for a Bayesian network analysis of microarray results. Results Through a bootstrap analysis of gene expression data derived from a number of leukemia studies, we demonstrate that seeded Bayesian Networks have the ability to identify high-confidence gene-gene interactions which can then be validated by comparison to other sources of pathway data. Conclusion The use of network seeds greatly improves the ability of Bayesian Network analysis to learn gene interaction networks from gene expression data. We demonstrate that the use of seeds derived from the biomedical literature or high-throughput protein-protein interaction data, or the combination, provides improvement over a standard Bayesian Network analysis, allowing networks involving dynamic processes to be deduced from the static snapshots of biological systems that represent the most common source of microarray data. Software implementing these methods has been included in the widely used TM4 microarray analysis package.

  18. Bayesian probability theory and inverse problems

    International Nuclear Information System (INIS)

    Kopec, S.

    1994-01-01

    Bayesian probability theory is applied to approximate solving of the inverse problems. In order to solve the moment problem with the noisy data, the entropic prior is used. The expressions for the solution and its error bounds are presented. When the noise level tends to zero, the Bayesian solution tends to the classic maximum entropy solution in the L 2 norm. The way of using spline prior is also shown. (author)

  19. 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...

  20. Bayesian Modeling of a Human MMORPG Player

    Science.gov (United States)

    Synnaeve, Gabriel; Bessière, Pierre

    2011-03-01

    This paper describes an application of Bayesian programming to the control of an autonomous avatar in a multiplayer role-playing game (the example is based on World of Warcraft). We model a particular task, which consists of choosing what to do and to select which target in a situation where allies and foes are present. We explain the model in Bayesian programming and show how we could learn the conditional probabilities from data gathered during human-played sessions.

  1. Variations on Bayesian Prediction and Inference

    Science.gov (United States)

    2016-05-09

    inference 2.2.1 Background There are a number of statistical inference problems that are not generally formulated via a full probability model...problem of inference about an unknown parameter, the Bayesian approach requires a full probability 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND...the problem of inference about an unknown parameter, the Bayesian approach requires a full probability model/likelihood which can be an obstacle

  2. 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.

  3. 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.

  4. Bayesian Networks for Modeling Dredging Decisions

    Science.gov (United States)

    2011-10-01

    years, that algorithms have been developed to solve these problems efficiently. Most modern Bayesian network software uses junction tree (a.k.a. join... software was used to develop the network . This is by no means an exhaustive list of Bayesian network applications, but it is representative of recent...characteristic node (SCN), state- defining node ( SDN ), effect node (EFN), or value node. The five types of nodes can be described as follows: ERDC/EL TR-11

  5. Fully probabilistic design of hierarchical Bayesian models

    Czech Academy of Sciences Publication Activity Database

    Quinn, A.; Kárný, Miroslav; Guy, Tatiana Valentine

    2016-01-01

    Roč. 369, č. 1 (2016), s. 532-547 ISSN 0020-0255 R&D Projects: GA ČR GA13-13502S Institutional support: RVO:67985556 Keywords : Fully probabilistic design * Ideal distribution * Minimum cross-entropy principle * Bayesian conditioning * Kullback-Leibler divergence * Bayesian nonparametric modelling Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 4.832, year: 2016 http://library.utia.cas.cz/separaty/2016/AS/karny-0463052.pdf

  6. 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...

  7. Philosophy and the practice of Bayesian statistics.

    Science.gov (United States)

    Gelman, Andrew; Shalizi, Cosma Rohilla

    2013-02-01

    A substantial school in the philosophy of science identifies Bayesian inference with inductive inference and even rationality as such, and seems to be strengthened by the rise and practical success of Bayesian statistics. We argue that the most successful forms of Bayesian statistics do not actually support that particular philosophy but rather accord much better with sophisticated forms of hypothetico-deductivism. We examine the actual role played by prior distributions in Bayesian models, and the crucial aspects of model checking and model revision, which fall outside the scope of Bayesian confirmation theory. We draw on the literature on the consistency of Bayesian updating and also on our experience of applied work in social science. Clarity about these matters should benefit not just philosophy of science, but also statistical practice. At best, the inductivist view has encouraged researchers to fit and compare models without checking them; at worst, theorists have actively discouraged practitioners from performing model checking because it does not fit into their framework. © 2012 The British Psychological Society.

  8. Fragment virtual screening based on Bayesian categorization for discovering novel VEGFR-2 scaffolds.

    Science.gov (United States)

    Zhang, Yanmin; Jiao, Yu; Xiong, Xiao; Liu, Haichun; Ran, Ting; Xu, Jinxing; Lu, Shuai; Xu, Anyang; Pan, Jing; Qiao, Xin; Shi, Zhihao; Lu, Tao; Chen, Yadong

    2015-11-01

    The discovery of novel scaffolds against a specific target has long been one of the most significant but challengeable goals in discovering lead compounds. A scaffold that binds in important regions of the active pocket is more favorable as a starting point because scaffolds generally possess greater optimization possibilities. However, due to the lack of sufficient chemical space diversity of the databases and the ineffectiveness of the screening methods, it still remains a great challenge to discover novel active scaffolds. Since the strengths and weaknesses of both fragment-based drug design and traditional virtual screening (VS), we proposed a fragment VS concept based on Bayesian categorization for the discovery of novel scaffolds. This work investigated the proposal through an application on VEGFR-2 target. Firstly, scaffold and structural diversity of chemical space for 10 compound databases were explicitly evaluated. Simultaneously, a robust Bayesian classification model was constructed for screening not only compound databases but also their corresponding fragment databases. Although analysis of the scaffold diversity demonstrated a very unevenly distribution of scaffolds over molecules, results showed that our Bayesian model behaved better in screening fragments than molecules. Through a literature retrospective research, several generated fragments with relatively high Bayesian scores indeed exhibit VEGFR-2 biological activity, which strongly proved the effectiveness of fragment VS based on Bayesian categorization models. This investigation of Bayesian-based fragment VS can further emphasize the necessity for enrichment of compound databases employed in lead discovery by amplifying the diversity of databases with novel structures.

  9. EXONEST: The Bayesian Exoplanetary Explorer

    Directory of Open Access Journals (Sweden)

    Kevin H. Knuth

    2017-10-01

    Full Text Available The fields of astronomy and astrophysics are currently engaged in an unprecedented era of discovery as recent missions have revealed thousands of exoplanets orbiting other stars. While the Kepler Space Telescope mission has enabled most of these exoplanets to be detected by identifying transiting events, exoplanets often exhibit additional photometric effects that can be used to improve the characterization of exoplanets. The EXONEST Exoplanetary Explorer is a Bayesian exoplanet inference engine based on nested sampling and originally designed to analyze archived Kepler Space Telescope and CoRoT (Convection Rotation et Transits planétaires exoplanet mission data. We discuss the EXONEST software package and describe how it accommodates plug-and-play models of exoplanet-associated photometric effects for the purpose of exoplanet detection, characterization and scientific hypothesis testing. The current suite of models allows for both circular and eccentric orbits in conjunction with photometric effects, such as the primary transit and secondary eclipse, reflected light, thermal emissions, ellipsoidal variations, Doppler beaming and superrotation. We discuss our new efforts to expand the capabilities of the software to include more subtle photometric effects involving reflected and refracted light. We discuss the EXONEST inference engine design and introduce our plans to port the current MATLAB-based EXONEST software package over to the next generation Exoplanetary Explorer, which will be a Python-based open source project with the capability to employ third-party plug-and-play models of exoplanet-related photometric effects.

  10. 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

  11. 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

  12. Remotely Sensed Monitoring of Small Reservoir Dynamics: A Bayesian Approach

    Directory of Open Access Journals (Sweden)

    Dirk Eilander

    2014-01-01

    Full Text Available Multipurpose small reservoirs are important for livelihoods in rural semi-arid regions. To manage and plan these reservoirs and to assess their hydrological impact at a river basin scale, it is important to monitor their water storage dynamics. This paper introduces a Bayesian approach for monitoring small reservoirs with radar satellite images. The newly developed growing Bayesian classifier has a high degree of automation, can readily be extended with auxiliary information and reduces the confusion error to the land-water boundary pixels. A case study has been performed in the Upper East Region of Ghana, based on Radarsat-2 data from November 2012 until April 2013. Results show that the growing Bayesian classifier can deal with the spatial and temporal variability in synthetic aperture radar (SAR backscatter intensities from small reservoirs. Due to its ability to incorporate auxiliary information, the algorithm is able to delineate open water from SAR imagery with a low land-water contrast in the case of wind-induced Bragg scattering or limited vegetation on the land surrounding a small reservoir.

  13. Bayesian geostatistical modeling of leishmaniasis incidence in Brazil.

    Directory of Open Access Journals (Sweden)

    Dimitrios-Alexios Karagiannis-Voules

    Full Text Available BACKGROUND: Leishmaniasis is endemic in 98 countries with an estimated 350 million people at risk and approximately 2 million cases annually. Brazil is one of the most severely affected countries. METHODOLOGY: We applied Bayesian geostatistical negative binomial models to analyze reported incidence data of cutaneous and visceral leishmaniasis in Brazil covering a 10-year period (2001-2010. Particular emphasis was placed on spatial and temporal patterns. The models were fitted using integrated nested Laplace approximations to perform fast approximate Bayesian inference. Bayesian variable selection was employed to determine the most important climatic, environmental, and socioeconomic predictors of cutaneous and visceral leishmaniasis. PRINCIPAL FINDINGS: For both types of leishmaniasis, precipitation and socioeconomic proxies were identified as important risk factors. The predicted number of cases in 2010 were 30,189 (standard deviation [SD]: 7,676 for cutaneous leishmaniasis and 4,889 (SD: 288 for visceral leishmaniasis. Our risk maps predicted the highest numbers of infected people in the states of Minas Gerais and Pará for visceral and cutaneous leishmaniasis, respectively. CONCLUSIONS/SIGNIFICANCE: Our spatially explicit, high-resolution incidence maps identified priority areas where leishmaniasis control efforts should be targeted with the ultimate goal to reduce disease incidence.

  14. Bayesian Estimation of Small Effects in Exercise and Sports Science.

    Directory of Open Access Journals (Sweden)

    Kerrie L Mengersen

    Full Text Available The aim of this paper is to provide a Bayesian formulation of the so-called magnitude-based inference approach to quantifying and interpreting effects, and in a case study example provide accurate probabilistic statements that correspond to the intended magnitude-based inferences. The model is described in the context of a published small-scale athlete study which employed a magnitude-based inference approach to compare the effect of two altitude training regimens (live high-train low (LHTL, and intermittent hypoxic exposure (IHE on running performance and blood measurements of elite triathletes. The posterior distributions, and corresponding point and interval estimates, for the parameters and associated effects and comparisons of interest, were estimated using Markov chain Monte Carlo simulations. The Bayesian analysis was shown to provide more direct probabilistic comparisons of treatments and able to identify small effects of interest. The approach avoided asymptotic assumptions and overcame issues such as multiple testing. Bayesian analysis of unscaled effects showed a probability of 0.96 that LHTL yields a substantially greater increase in hemoglobin mass than IHE, a 0.93 probability of a substantially greater improvement in running economy and a greater than 0.96 probability that both IHE and LHTL yield a substantially greater improvement in maximum blood lactate concentration compared to a Placebo. The conclusions are consistent with those obtained using a 'magnitude-based inference' approach that has been promoted in the field. The paper demonstrates that a fully Bayesian analysis is a simple and effective way of analysing small effects, providing a rich set of results that are straightforward to interpret in terms of probabilistic statements.

  15. Bayesian Estimation of Small Effects in Exercise and Sports Science.

    Science.gov (United States)

    Mengersen, Kerrie L; Drovandi, Christopher C; Robert, Christian P; Pyne, David B; Gore, Christopher J

    2016-01-01

    The aim of this paper is to provide a Bayesian formulation of the so-called magnitude-based inference approach to quantifying and interpreting effects, and in a case study example provide accurate probabilistic statements that correspond to the intended magnitude-based inferences. The model is described in the context of a published small-scale athlete study which employed a magnitude-based inference approach to compare the effect of two altitude training regimens (live high-train low (LHTL), and intermittent hypoxic exposure (IHE)) on running performance and blood measurements of elite triathletes. The posterior distributions, and corresponding point and interval estimates, for the parameters and associated effects and comparisons of interest, were estimated using Markov chain Monte Carlo simulations. The Bayesian analysis was shown to provide more direct probabilistic comparisons of treatments and able to identify small effects of interest. The approach avoided asymptotic assumptions and overcame issues such as multiple testing. Bayesian analysis of unscaled effects showed a probability of 0.96 that LHTL yields a substantially greater increase in hemoglobin mass than IHE, a 0.93 probability of a substantially greater improvement in running economy and a greater than 0.96 probability that both IHE and LHTL yield a substantially greater improvement in maximum blood lactate concentration compared to a Placebo. The conclusions are consistent with those obtained using a 'magnitude-based inference' approach that has been promoted in the field. The paper demonstrates that a fully Bayesian analysis is a simple and effective way of analysing small effects, providing a rich set of results that are straightforward to interpret in terms of probabilistic statements.

  16. Bayesian object classification of gold nanoparticles

    KAUST Repository

    Konomi, Bledar A.; Dhavala, Soma S.; Huang, Jianhua Z.; Kundu, Subrata; Huitink, David; Liang, Hong; Ding, Yu; Mallick, Bani K.

    2013-01-01

    The properties of materials synthesized with nanoparticles (NPs) are highly correlated to the sizes and shapes of the nanoparticles. The transmission electron microscopy (TEM) imaging technique can be used to measure the morphological characteristics of NPs, which can be simple circles or more complex irregular polygons with varying degrees of scales and sizes. A major difficulty in analyzing the TEM images is the overlapping of objects, having different morphological properties with no specific information about the number of objects present. Furthermore, the objects lying along the boundary render automated image analysis much more difficult. To overcome these challenges, we propose a Bayesian method based on the marked-point process representation of the objects. We derive models, both for the marks which parameterize the morphological aspects and the points which determine the location of the objects. The proposed model is an automatic image segmentation and classification procedure, which simultaneously detects the boundaries and classifies the NPs into one of the predetermined shape families. We execute the inference by sampling the posterior distribution using Markov chainMonte Carlo (MCMC) since the posterior is doubly intractable. We apply our novel method to several TEM imaging samples of gold NPs, producing the needed statistical characterization of their morphology. © Institute of Mathematical Statistics, 2013.

  17. BEAST: Bayesian evolutionary analysis by sampling trees

    Directory of Open Access Journals (Sweden)

    Drummond Alexei J

    2007-11-01

    Full Text Available Abstract Background The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. Results BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license. Conclusion BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.

  18. BAYESIAN INFERENCE OF CMB GRAVITATIONAL LENSING

    Energy Technology Data Exchange (ETDEWEB)

    Anderes, Ethan [Department of Statistics, University of California, Davis, CA 95616 (United States); Wandelt, Benjamin D.; Lavaux, Guilhem [Sorbonne Universités, UPMC Univ Paris 06 and CNRS, UMR7095, Institut d’Astrophysique de Paris, F-75014, Paris (France)

    2015-08-01

    The Planck satellite, along with several ground-based telescopes, has mapped the cosmic microwave background (CMB) at sufficient resolution and signal-to-noise so as to allow a detection of the subtle distortions due to the gravitational influence of the intervening matter distribution. A natural modeling approach is to write a Bayesian hierarchical model for the lensed CMB in terms of the unlensed CMB and the lensing potential. So far there has been no feasible algorithm for inferring the posterior distribution of the lensing potential from the lensed CMB map. We propose a solution that allows efficient Markov Chain Monte Carlo sampling from the joint posterior of the lensing potential and the unlensed CMB map using the Hamiltonian Monte Carlo technique. The main conceptual step in the solution is a re-parameterization of CMB lensing in terms of the lensed CMB and the “inverse lensing” potential. We demonstrate a fast implementation on simulated data, including noise and a sky cut, that uses a further acceleration based on a very mild approximation of the inverse lensing potential. We find that the resulting Markov Chain has short correlation lengths and excellent convergence properties, making it promising for applications to high-resolution CMB data sets in the future.

  19. Bayesian object classification of gold nanoparticles

    KAUST Repository

    Konomi, Bledar A.

    2013-06-01

    The properties of materials synthesized with nanoparticles (NPs) are highly correlated to the sizes and shapes of the nanoparticles. The transmission electron microscopy (TEM) imaging technique can be used to measure the morphological characteristics of NPs, which can be simple circles or more complex irregular polygons with varying degrees of scales and sizes. A major difficulty in analyzing the TEM images is the overlapping of objects, having different morphological properties with no specific information about the number of objects present. Furthermore, the objects lying along the boundary render automated image analysis much more difficult. To overcome these challenges, we propose a Bayesian method based on the marked-point process representation of the objects. We derive models, both for the marks which parameterize the morphological aspects and the points which determine the location of the objects. The proposed model is an automatic image segmentation and classification procedure, which simultaneously detects the boundaries and classifies the NPs into one of the predetermined shape families. We execute the inference by sampling the posterior distribution using Markov chainMonte Carlo (MCMC) since the posterior is doubly intractable. We apply our novel method to several TEM imaging samples of gold NPs, producing the needed statistical characterization of their morphology. © Institute of Mathematical Statistics, 2013.

  20. Bayesian data assimilation in shape registration

    KAUST Repository

    Cotter, C J

    2013-03-28

    In this paper we apply a Bayesian framework to the problem of geodesic curve matching. Given a template curve, the geodesic equations provide a mapping from initial conditions for the conjugate momentum onto topologically equivalent shapes. Here, we aim to recover the well-defined posterior distribution on the initial momentum which gives rise to observed points on the target curve; this is achieved by explicitly including a reparameterization in the formulation. Appropriate priors are chosen for the functions which together determine this field and the positions of the observation points, the initial momentum p0 and the reparameterization vector field ν, informed by regularity results about the forward model. Having done this, we illustrate how maximum likelihood estimators can be used to find regions of high posterior density, but also how we can apply recently developed Markov chain Monte Carlo methods on function spaces to characterize the whole of the posterior density. These illustrative examples also include scenarios where the posterior distribution is multimodal and irregular, leading us to the conclusion that knowledge of a state of global maximal posterior density does not always give us the whole picture, and full posterior sampling can give better quantification of likely states and the overall uncertainty inherent in the problem. © 2013 IOP Publishing Ltd.

  1. Objective Bayesianism and the Maximum Entropy Principle

    Directory of Open Access Journals (Sweden)

    Jon Williamson

    2013-09-01

    Full Text Available Objective Bayesian epistemology invokes three norms: the strengths of our beliefs should be probabilities; they should be calibrated to our evidence of physical probabilities; and they should otherwise equivocate sufficiently between the basic propositions that we can express. The three norms are sometimes explicated by appealing to the maximum entropy principle, which says that a belief function should be a probability function, from all those that are calibrated to evidence, that has maximum entropy. However, the three norms of objective Bayesianism are usually justified in different ways. In this paper, we show that the three norms can all be subsumed under a single justification in terms of minimising worst-case expected loss. This, in turn, is equivalent to maximising a generalised notion of entropy. We suggest that requiring language invariance, in addition to minimising worst-case expected loss, motivates maximisation of standard entropy as opposed to maximisation of other instances of generalised entropy. Our argument also provides a qualified justification for updating degrees of belief by Bayesian conditionalisation. However, conditional probabilities play a less central part in the objective Bayesian account than they do under the subjective view of Bayesianism, leading to a reduced role for Bayes’ Theorem.

  2. A default Bayesian hypothesis test for mediation.

    Science.gov (United States)

    Nuijten, Michèle B; Wetzels, Ruud; Matzke, Dora; Dolan, Conor V; Wagenmakers, Eric-Jan

    2015-03-01

    In order to quantify the relationship between multiple variables, researchers often carry out a mediation analysis. In such an analysis, a mediator (e.g., knowledge of a healthy diet) transmits the effect from an independent variable (e.g., classroom instruction on a healthy diet) to a dependent variable (e.g., consumption of fruits and vegetables). Almost all mediation analyses in psychology use frequentist estimation and hypothesis-testing techniques. A recent exception is Yuan and MacKinnon (Psychological Methods, 14, 301-322, 2009), who outlined a Bayesian parameter estimation procedure for mediation analysis. Here we complete the Bayesian alternative to frequentist mediation analysis by specifying a default Bayesian hypothesis test based on the Jeffreys-Zellner-Siow approach. We further extend this default Bayesian test by allowing a comparison to directional or one-sided alternatives, using Markov chain Monte Carlo techniques implemented in JAGS. All Bayesian tests are implemented in the R package BayesMed (Nuijten, Wetzels, Matzke, Dolan, & Wagenmakers, 2014).

  3. 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%.

  4. Empirical Bayesian inference and model uncertainty

    International Nuclear Information System (INIS)

    Poern, K.

    1994-01-01

    This paper presents a hierarchical or multistage empirical Bayesian approach for the estimation of uncertainty concerning the intensity of a homogeneous Poisson process. A class of contaminated gamma distributions is considered to describe the uncertainty concerning the intensity. These distributions in turn are defined through a set of secondary parameters, the knowledge of which is also described and updated via Bayes formula. This two-stage Bayesian approach is an example where the modeling uncertainty is treated in a comprehensive way. Each contaminated gamma distributions, represented by a point in the 3D space of secondary parameters, can be considered as a specific model of the uncertainty about the Poisson intensity. Then, by the empirical Bayesian method each individual model is assigned a posterior probability

  5. 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...

  6. A nonparametric Bayesian approach for genetic evaluation in ...

    African Journals Online (AJOL)

    South African Journal of Animal Science ... the Bayesian and Classical models, a Bayesian procedure is provided which allows these random ... data from the Elsenburg Dormer sheep stud and data from a simulation experiment are utilized. >

  7. 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...

  8. 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

  9. 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

  10. Justifying Objective Bayesianism on Predicate Languages

    Directory of Open Access Journals (Sweden)

    Jürgen Landes

    2015-04-01

    Full Text Available Objective Bayesianism says that the strengths of one’s beliefs ought to be probabilities, calibrated to physical probabilities insofar as one has evidence of them, and otherwise sufficiently equivocal. These norms of belief are often explicated using the maximum entropy principle. In this paper we investigate the extent to which one can provide a unified justification of the objective Bayesian norms in the case in which the background language is a first-order predicate language, with a view to applying the resulting formalism to inductive logic. We show that the maximum entropy principle can be motivated largely in terms of minimising worst-case expected loss.

  11. Nonparametric Bayesian Modeling of Complex Networks

    DEFF Research Database (Denmark)

    Schmidt, Mikkel Nørgaard; Mørup, Morten

    2013-01-01

    an infinite mixture model as running example, we go through the steps of deriving the model as an infinite limit of a finite parametric model, inferring the model parameters by Markov chain Monte Carlo, and checking the model?s fit and predictive performance. We explain how advanced nonparametric models......Modeling structure in complex networks using Bayesian nonparametrics makes it possible to specify flexible model structures and infer the adequate model complexity from the observed data. This article provides a gentle introduction to nonparametric Bayesian modeling of complex networks: Using...

  12. 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

  13. 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

  14. Case study on human α1-antitrypsin: Recombinant protein titers obtained by commercial ELISA kits are inaccurate

    DEFF Research Database (Denmark)

    Hansen, Henning Gram; Kildegaard, Helene Faustrup; Min Lee, Gyun

    2016-01-01

    Accurate titer determination of recombinant proteins is crucial for evaluating protein production cell lines and processes. Even though enzyme-linked immunosorbent assay (ELISA) is the most widely used assay for determining protein titer, little is known about the accuracy of commercially available...... ELISA kits. We observed that estimations of recombinant human ø1-antitrypsin (rø1AT) titer by Coomassie-stained SDS-PAGE gels did not correspond to previously obtained titers obtained by a commercially available ELISA kit. This prompted us to develop two independent quantification assays based...... on biolayer interferometry and reversed-phase high-performance liquid chromatography. We compared the rø1AT titer obtained by these assays with three different off-the-shelf ELISA kits and found that the ELISA kits led to inconsistent results. The data presented here show that recombinant protein titers...

  15. COBRA: a Bayesian approach to pulsar searching

    Science.gov (United States)

    Lentati, L.; Champion, D. J.; Kramer, M.; Barr, E.; Torne, P.

    2018-02-01

    We introduce COBRA, a GPU-accelerated Bayesian analysis package for performing pulsar searching, that uses candidates from traditional search techniques to set the prior used for the periodicity of the source, and performs a blind search in all remaining parameters. COBRA incorporates models for both isolated and accelerated systems, as well as both Keplerian and relativistic binaries, and exploits pulse phase information to combine search epochs coherently, over time, frequency or across multiple telescopes. We demonstrate the efficacy of our approach in a series of simulations that challenge typical search techniques, including highly aliased signals, and relativistic binary systems. In the most extreme case, we simulate an 8 h observation containing 24 orbits of a pulsar in a binary with a 30 M⊙ companion. Even in this scenario we show that we can build up from an initial low-significance candidate, to fully recovering the signal. We also apply the method to survey data of three pulsars from the globular cluster 47Tuc: PSRs J0024-7204D, J0023-7203J and J0024-7204R. This final pulsar is in a 1.6 h binary, the shortest of any pulsar in 47Tuc, and additionally shows significant scintillation. By allowing the amplitude of the source to vary as a function of time, however, we show that we are able to obtain optimal combinations of such noisy data. We also demonstrate the ability of COBRA to perform high-precision pulsar timing directly on the single pulse survey data, and obtain a 95 per cent upper limit on the eccentricity of PSR J0024-7204R of εb < 0.0007.

  16. Bayesian inversion of refraction seismic traveltime data

    Science.gov (United States)

    Ryberg, T.; Haberland, Ch

    2018-03-01

    We apply a Bayesian Markov chain Monte Carlo (McMC) formalism to the inversion of refraction seismic, traveltime data sets to derive 2-D velocity models below linear arrays (i.e. profiles) of sources and seismic receivers. Typical refraction data sets, especially when using the far-offset observations, are known as having experimental geometries which are very poor, highly ill-posed and far from being ideal. As a consequence, the structural resolution quickly degrades with depth. Conventional inversion techniques, based on regularization, potentially suffer from the choice of appropriate inversion parameters (i.e. number and distribution of cells, starting velocity models, damping and smoothing constraints, data noise level, etc.) and only local model space exploration. McMC techniques are used for exhaustive sampling of the model space without the need of prior knowledge (or assumptions) of inversion parameters, resulting in a large number of models fitting the observations. Statistical analysis of these models allows to derive an average (reference) solution and its standard deviation, thus providing uncertainty estimates of the inversion result. The highly non-linear character of the inversion problem, mainly caused by the experiment geometry, does not allow to derive a reference solution and error map by a simply averaging procedure. We present a modified averaging technique, which excludes parts of the prior distribution in the posterior values due to poor ray coverage, thus providing reliable estimates of inversion model properties even in those parts of the models. The model is discretized by a set of Voronoi polygons (with constant slowness cells) or a triangulated mesh (with interpolation within the triangles). Forward traveltime calculations are performed by a fast, finite-difference-based eikonal solver. The method is applied to a data set from a refraction seismic survey from Northern Namibia and compared to conventional tomography. An inversion test

  17. MRI performed on dedicated knee coils is inaccurate for the measurement of tibial tubercle trochlear groove distance

    International Nuclear Information System (INIS)

    Aarvold, A.; Pope, A.; Sakthivel, V.K.; Ayer, R.V.

    2014-01-01

    Tibial tubercle trochlear groove distance (TTD) is a significant factor in patello-femoral instability. Initially described on CT scans with the knee in full extension, the measurement has been validated on MR scans. Dedicated knee MRI coils have subsequently superseded both CT and MRI body coils for knee imaging. However, the knee rests in partial flexion within the dedicated knee coil. The objective of this study is to investigate whether images from dedicated knee MRI coils produce different TTD measurements from MR body coils. Thirty-two symptomatic knees (27 patients) had simultaneous knee MR scans performed in both a dedicated knee coil and a body coil. TTD measurements were independently compared to assess whether the coil type used affected TTD. Patients' ages ranged from 10 to 27 years (mean 15 years). Mean TTD in the dedicated knee coil (partially flexed knee) was 11.3 mm compared with 19.9 mm in the body coil (that permits full knee extension). The mean difference was 8.6 mm, which was highly significant (p < 0.0001, unpaired t test). Inter-rater correlation co-efficient was 96 %. Of the knees that recorded a ''normal'' TTD on the dedicated knee coil, 60-100 % recorded a ''pathological'' TTD on body coil images, depending on which diagnostic value for ''normal'' cut-off was used. This study has identified a highly significant difference in TTD measurement when knees are scanned in a dedicated knee coil with the knee partially flexed, compared with an MR body coil. It is critical for surgeons and radiologists managing patello-femoral instability to appreciate this profound difference. TTD measurement taken from knees scanned in dedicated knee coils may lead to patients being falsely re-assured or erroneously denied surgery. (orig.)

  18. Sparse-grid, reduced-basis Bayesian inversion: Nonaffine-parametric nonlinear equations

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Peng, E-mail: peng@ices.utexas.edu [The Institute for Computational Engineering and Sciences, The University of Texas at Austin, 201 East 24th Street, Stop C0200, Austin, TX 78712-1229 (United States); Schwab, Christoph, E-mail: christoph.schwab@sam.math.ethz.ch [Seminar für Angewandte Mathematik, Eidgenössische Technische Hochschule, Römistrasse 101, CH-8092 Zürich (Switzerland)

    2016-07-01

    We extend the reduced basis (RB) accelerated Bayesian inversion methods for affine-parametric, linear operator equations which are considered in [16,17] to non-affine, nonlinear parametric operator equations. We generalize the analysis of sparsity of parametric forward solution maps in [20] and of Bayesian inversion in [48,49] to the fully discrete setting, including Petrov–Galerkin high-fidelity (“HiFi”) discretization of the forward maps. We develop adaptive, stochastic collocation based reduction methods for the efficient computation of reduced bases on the parametric solution manifold. The nonaffinity and nonlinearity with respect to (w.r.t.) the distributed, uncertain parameters and the unknown solution is collocated; specifically, by the so-called Empirical Interpolation Method (EIM). For the corresponding Bayesian inversion problems, computational efficiency is enhanced in two ways: first, expectations w.r.t. the posterior are computed by adaptive quadratures with dimension-independent convergence rates proposed in [49]; the present work generalizes [49] to account for the impact of the PG discretization in the forward maps on the convergence rates of the Quantities of Interest (QoI for short). Second, we propose to perform the Bayesian estimation only w.r.t. a parsimonious, RB approximation of the posterior density. Based on the approximation results in [49], the infinite-dimensional parametric, deterministic forward map and operator admit N-term RB and EIM approximations which converge at rates which depend only on the sparsity of the parametric forward map. In several numerical experiments, the proposed algorithms exhibit dimension-independent convergence rates which equal, at least, the currently known rate estimates for N-term approximation. We propose to accelerate Bayesian estimation by first offline construction of reduced basis surrogates of the Bayesian posterior density. The parsimonious surrogates can then be employed for online data

  19. 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,

  20. 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,

  1. 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

  2. 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.

  3. Bayesian Software Health Management for Aircraft Guidance, Navigation, and Control

    Science.gov (United States)

    Schumann, Johann; Mbaya, Timmy; Menghoel, Ole

    2011-01-01

    Modern aircraft, both piloted fly-by-wire commercial aircraft as well as UAVs, more and more depend on highly complex safety critical software systems with many sensors and computer-controlled actuators. Despite careful design and V&V of the software, severe incidents have happened due to malfunctioning software. In this paper, we discuss the use of Bayesian networks (BNs) to monitor the health of the on-board software and sensor system, and to perform advanced on-board diagnostic reasoning. We will focus on the approach to develop reliable and robust health models for the combined software and sensor systems.

  4. Bayesian tomography by interacting Markov chains

    Science.gov (United States)

    Romary, T.

    2017-12-01

    In seismic tomography, we seek to determine the velocity of the undergound from noisy first arrival travel time observations. In most situations, this is an ill posed inverse problem that admits several unperfect solutions. Given an a priori distribution over the parameters of the velocity model, the Bayesian formulation allows to state this problem as a probabilistic one, with a solution under the form of a posterior distribution. The posterior distribution is generally high dimensional and may exhibit multimodality. Moreover, as it is known only up to a constant, the only sensible way to addressthis problem is to try to generate simulations from the posterior. The natural tools to perform these simulations are Monte Carlo Markov chains (MCMC). Classical implementations of MCMC algorithms generally suffer from slow mixing: the generated states are slow to enter the stationary regime, that is to fit the observations, and when one mode of the posterior is eventually identified, it may become difficult to visit others. Using a varying temperature parameter relaxing the constraint on the data may help to enter the stationary regime. Besides, the sequential nature of MCMC makes them ill fitted toparallel implementation. Running a large number of chains in parallel may be suboptimal as the information gathered by each chain is not mutualized. Parallel tempering (PT) can be seen as a first attempt to make parallel chains at different temperatures communicate but only exchange information between current states. In this talk, I will show that PT actually belongs to a general class of interacting Markov chains algorithm. I will also show that this class enables to design interacting schemes that can take advantage of the whole history of the chain, by authorizing exchanges toward already visited states. The algorithms will be illustrated with toy examples and an application to first arrival traveltime tomography.

  5. Bayesian Dose-Response Modeling in Sparse Data

    Science.gov (United States)

    Kim, Steven B.

    This book discusses Bayesian dose-response modeling in small samples applied to two different settings. The first setting is early phase clinical trials, and the second setting is toxicology studies in cancer risk assessment. In early phase clinical trials, experimental units are humans who are actual patients. Prior to a clinical trial, opinions from multiple subject area experts are generally more informative than the opinion of a single expert, but we may face a dilemma when they have disagreeing prior opinions. In this regard, we consider compromising the disagreement and compare two different approaches for making a decision. In addition to combining multiple opinions, we also address balancing two levels of ethics in early phase clinical trials. The first level is individual-level ethics which reflects the perspective of trial participants. The second level is population-level ethics which reflects the perspective of future patients. We extensively compare two existing statistical methods which focus on each perspective and propose a new method which balances the two conflicting perspectives. In toxicology studies, experimental units are living animals. Here we focus on a potential non-monotonic dose-response relationship which is known as hormesis. Briefly, hormesis is a phenomenon which can be characterized by a beneficial effect at low doses and a harmful effect at high doses. In cancer risk assessments, the estimation of a parameter, which is known as a benchmark dose, can be highly sensitive to a class of assumptions, monotonicity or hormesis. In this regard, we propose a robust approach which considers both monotonicity and hormesis as a possibility. In addition, We discuss statistical hypothesis testing for hormesis and consider various experimental designs for detecting hormesis based on Bayesian decision theory. Past experiments have not been optimally designed for testing for hormesis, and some Bayesian optimal designs may not be optimal under a

  6. Predicting coastal cliff erosion using a Bayesian probabilistic model

    Science.gov (United States)

    Hapke, Cheryl J.; Plant, Nathaniel G.

    2010-01-01

    Regional coastal cliff retreat is difficult to model due to the episodic nature of failures and the along-shore variability of retreat events. There is a growing demand, however, for predictive models that can be used to forecast areas vulnerable to coastal erosion hazards. Increasingly, probabilistic models are being employed that require data sets of high temporal density to define the joint probability density function that relates forcing variables (e.g. wave conditions) and initial conditions (e.g. cliff geometry) to erosion events. In this study we use a multi-parameter Bayesian network to investigate correlations between key variables that control and influence variations in cliff retreat processes. The network uses Bayesian statistical methods to estimate event probabilities using existing observations. Within this framework, we forecast the spatial distribution of cliff retreat along two stretches of cliffed coast in Southern California. The input parameters are the height and slope of the cliff, a descriptor of material strength based on the dominant cliff-forming lithology, and the long-term cliff erosion rate that represents prior behavior. The model is forced using predicted wave impact hours. Results demonstrate that the Bayesian approach is well-suited to the forward modeling of coastal cliff retreat, with the correct outcomes forecast in 70–90% of the modeled transects. The model also performs well in identifying specific locations of high cliff erosion, thus providing a foundation for hazard mapping. This approach can be employed to predict cliff erosion at time-scales ranging from storm events to the impacts of sea-level rise at the century-scale.

  7. Heavy-Particle Collisions Involving Many Active Electrons: How (In-)Accurate Are Our Calculated Cross Sections?

    International Nuclear Information System (INIS)

    Kirchner, Tom

    2014-01-01

    Full text: The theoretical description of ion-atom and ion-molecule collisions is a difficult task: one deals with a two-center or a multi-center problem, for which standard angular momentum expansions do not work very well, and one typically faces the problem that several processes, such as electron transfer and ionization into the continuum, compete with each other. If more than two electrons are present, the numerical solution of the full Schrödinger equation of the collision system is out of reach and assumptions and approximations have to be introduced at the outset. This is to say that one solves (at most) a model in order to describe the collision system and, as a consequence, has to deal with a two-fold problem when it comes to estimating the uncertainties and inaccuracies of the calculated data: (i) to assess the limitations of the model (which may be compared with quantifying systematic errors in an experiment); (ii) to perform careful convergence studies for the numerical procedures involved (which may be compared with narrowing statistical experimental errors). These two interrelated problems were illustrated by using a recent work on X-ray emission from a highly-charged ion after electron capture as an example. The calculations for this problem are based on the assumption that collisional capture and post-collisional de-excitation processes can be treated independently. This introduces a first systematic error, but probably a very small one, because capture and de-excitation take place on different time scales. Similarly, the assumption of a classical straight-line projectile trajectory is uncritical. Three sources of significant uncertainties are present in the collision calculation: (i) usage of the independent-electron model, (ii) usage of a finite basis set to solve the single-electron time-dependent Schrödinger equation, (iii) usage of multinomial statistics to calculate multiple (shell-specific) capture probabilities, which form the starting

  8. Bayesian Meta-Analysis of Coefficient Alpha

    Science.gov (United States)

    Brannick, Michael T.; Zhang, Nanhua

    2013-01-01

    The current paper describes and illustrates a Bayesian approach to the meta-analysis of coefficient alpha. Alpha is the most commonly used estimate of the reliability or consistency (freedom from measurement error) for educational and psychological measures. The conventional approach to meta-analysis uses inverse variance weights to combine…

  9. Optimal Detection under the Restricted Bayesian Criterion

    Directory of Open Access Journals (Sweden)

    Shujun Liu

    2017-07-01

    Full Text Available This paper aims to find a suitable decision rule for a binary composite hypothesis-testing problem with a partial or coarse prior distribution. To alleviate the negative impact of the information uncertainty, a constraint is considered that the maximum conditional risk cannot be greater than a predefined value. Therefore, the objective of this paper becomes to find the optimal decision rule to minimize the Bayes risk under the constraint. By applying the Lagrange duality, the constrained optimization problem is transformed to an unconstrained optimization problem. In doing so, the restricted Bayesian decision rule is obtained as a classical Bayesian decision rule corresponding to a modified prior distribution. Based on this transformation, the optimal restricted Bayesian decision rule is analyzed and the corresponding algorithm is developed. Furthermore, the relation between the Bayes risk and the predefined value of the constraint is also discussed. The Bayes risk obtained via the restricted Bayesian decision rule is a strictly decreasing and convex function of the constraint on the maximum conditional risk. Finally, the numerical results including a detection example are presented and agree with the theoretical results.

  10. Heuristics as Bayesian inference under extreme priors.

    Science.gov (United States)

    Parpart, Paula; Jones, Matt; Love, Bradley C

    2018-05-01

    Simple heuristics are often regarded as tractable decision strategies because they ignore a great deal of information in the input data. One puzzle is why heuristics can outperform full-information models, such as linear regression, which make full use of the available information. These "less-is-more" effects, in which a relatively simpler model outperforms a more complex model, are prevalent throughout cognitive science, and are frequently argued to demonstrate an inherent advantage of simplifying computation or ignoring information. In contrast, we show at the computational level (where algorithmic restrictions are set aside) that it is never optimal to discard information. Through a formal Bayesian analysis, we prove that popular heuristics, such as tallying and take-the-best, are formally equivalent to Bayesian inference under the limit of infinitely strong priors. Varying the strength of the prior yields a continuum of Bayesian models with the heuristics at one end and ordinary regression at the other. Critically, intermediate models perform better across all our simulations, suggesting that down-weighting information with the appropriate prior is preferable to entirely ignoring it. Rather than because of their simplicity, our analyses suggest heuristics perform well because they implement strong priors that approximate the actual structure of the environment. We end by considering how new heuristics could be derived by infinitely strengthening the priors of other Bayesian models. These formal results have implications for work in psychology, machine learning and economics. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  11. A strongly quasiconvex PAC-Bayesian bound

    DEFF Research Database (Denmark)

    Thiemann, Niklas; Igel, Christian; Wintenberger, Olivier

    2017-01-01

    We propose a new PAC-Bayesian bound and a way of constructing a hypothesis space, so that the bound is convex in the posterior distribution and also convex in a trade-off parameter between empirical performance of the posterior distribution and its complexity. The complexity is measured by the Ku...

  12. Multisnapshot Sparse Bayesian Learning for DOA

    DEFF Research Database (Denmark)

    Gerstoft, Peter; Mecklenbrauker, Christoph F.; Xenaki, Angeliki

    2016-01-01

    The directions of arrival (DOA) of plane waves are estimated from multisnapshot sensor array data using sparse Bayesian learning (SBL). The prior for the source amplitudes is assumed independent zero-mean complex Gaussian distributed with hyperparameters, the unknown variances (i.e., the source...

  13. Approximate Bayesian evaluations of measurement uncertainty

    Science.gov (United States)

    Possolo, Antonio; Bodnar, Olha

    2018-04-01

    The Guide to the Expression of Uncertainty in Measurement (GUM) includes formulas that produce an estimate of a scalar output quantity that is a function of several input quantities, and an approximate evaluation of the associated standard uncertainty. This contribution presents approximate, Bayesian counterparts of those formulas for the case where the output quantity is a parameter of the joint probability distribution of the input quantities, also taking into account any information about the value of the output quantity available prior to measurement expressed in the form of a probability distribution on the set of possible values for the measurand. The approximate Bayesian estimates and uncertainty evaluations that we present have a long history and illustrious pedigree, and provide sufficiently accurate approximations in many applications, yet are very easy to implement in practice. Differently from exact Bayesian estimates, which involve either (analytical or numerical) integrations, or Markov Chain Monte Carlo sampling, the approximations that we describe involve only numerical optimization and simple algebra. Therefore, they make Bayesian methods widely accessible to metrologists. We illustrate the application of the proposed techniques in several instances of measurement: isotopic ratio of silver in a commercial silver nitrate; odds of cryptosporidiosis in AIDS patients; height of a manometer column; mass fraction of chromium in a reference material; and potential-difference in a Zener voltage standard.

  14. Inverse Problems in a Bayesian Setting

    KAUST Repository

    Matthies, Hermann G.

    2016-02-13

    In a Bayesian setting, inverse problems and uncertainty quantification (UQ)—the propagation of uncertainty through a computational (forward) model—are strongly connected. In the form of conditional expectation the Bayesian update becomes computationally attractive. We give a detailed account of this approach via conditional approximation, various approximations, and the construction of filters. Together with a functional or spectral approach for the forward UQ there is no need for time-consuming and slowly convergent Monte Carlo sampling. The developed sampling-free non-linear Bayesian update in form of a filter is derived from the variational problem associated with conditional expectation. This formulation in general calls for further discretisation to make the computation possible, and we choose a polynomial approximation. After giving details on the actual computation in the framework of functional or spectral approximations, we demonstrate the workings of the algorithm on a number of examples of increasing complexity. At last, we compare the linear and nonlinear Bayesian update in form of a filter on some examples.

  15. Error probabilities in default Bayesian hypothesis testing

    NARCIS (Netherlands)

    Gu, Xin; Hoijtink, Herbert; Mulder, J,

    2016-01-01

    This paper investigates the classical type I and type II error probabilities of default Bayes factors for a Bayesian t test. Default Bayes factors quantify the relative evidence between the null hypothesis and the unrestricted alternative hypothesis without needing to specify prior distributions for

  16. Bayesian Averaging is Well-Temperated

    DEFF Research Database (Denmark)

    Hansen, Lars Kai

    2000-01-01

    Bayesian predictions are stochastic just like predictions of any other inference scheme that generalize from a finite sample. While a simple variational argument shows that Bayes averaging is generalization optimal given that the prior matches the teacher parameter distribution the situation is l...

  17. Robust bayesian inference of generalized Pareto distribution ...

    African Journals Online (AJOL)

    En utilisant une etude exhaustive de Monte Carlo, nous prouvons que, moyennant une fonction perte generalisee adequate, on peut construire un estimateur Bayesien robuste du modele. Key words: Bayesian estimation; Extreme value; Generalized Fisher information; Gener- alized Pareto distribution; Monte Carlo; ...

  18. 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

  19. Inverse Problems in a Bayesian Setting

    KAUST Repository

    Matthies, Hermann G.; Zander, Elmar; Rosić, Bojana V.; Litvinenko, Alexander; Pajonk, Oliver

    2016-01-01

    In a Bayesian setting, inverse problems and uncertainty quantification (UQ)—the propagation of uncertainty through a computational (forward) model—are strongly connected. In the form of conditional expectation the Bayesian update becomes computationally attractive. We give a detailed account of this approach via conditional approximation, various approximations, and the construction of filters. Together with a functional or spectral approach for the forward UQ there is no need for time-consuming and slowly convergent Monte Carlo sampling. The developed sampling-free non-linear Bayesian update in form of a filter is derived from the variational problem associated with conditional expectation. This formulation in general calls for further discretisation to make the computation possible, and we choose a polynomial approximation. After giving details on the actual computation in the framework of functional or spectral approximations, we demonstrate the workings of the algorithm on a number of examples of increasing complexity. At last, we compare the linear and nonlinear Bayesian update in form of a filter on some examples.

  20. A Bayesian perspective on some replacement strategies

    International Nuclear Information System (INIS)

    Mazzuchi, Thomas A.; Soyer, Refik

    1996-01-01

    In this paper we present a Bayesian decision theoretic approach for determining optimal replacement strategies. This approach enables us to formally incorporate, express, and update our uncertainty when determining optimal replacement strategies. We develop relevant expressions for both the block replacement protocol with minimal repair and the age replacement protocol and illustrate the use of our approach with real data

  1. Comparison between Fisherian and Bayesian approach to ...

    African Journals Online (AJOL)

    ... of its simplicity and optimality properties is normally used for two group cases. However, Bayesian approach is found to be better than Fisher's approach because of its low misclassification error rate. Keywords: variance-covariance matrices, centroids, prior probability, mahalanobis distance, probability of misclassification ...

  2. BAYESIAN ESTIMATION OF THERMONUCLEAR REACTION RATES

    Energy Technology Data Exchange (ETDEWEB)

    Iliadis, C.; Anderson, K. S. [Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3255 (United States); Coc, A. [Centre de Sciences Nucléaires et de Sciences de la Matière (CSNSM), CNRS/IN2P3, Univ. Paris-Sud, Université Paris–Saclay, Bâtiment 104, F-91405 Orsay Campus (France); Timmes, F. X.; Starrfield, S., E-mail: iliadis@unc.edu [School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287-1504 (United States)

    2016-11-01

    The problem of estimating non-resonant astrophysical S -factors and thermonuclear reaction rates, based on measured nuclear cross sections, is of major interest for nuclear energy generation, neutrino physics, and element synthesis. Many different methods have been applied to this problem in the past, almost all of them based on traditional statistics. Bayesian methods, on the other hand, are now in widespread use in the physical sciences. In astronomy, for example, Bayesian statistics is applied to the observation of extrasolar planets, gravitational waves, and Type Ia supernovae. However, nuclear physics, in particular, has been slow to adopt Bayesian methods. We present astrophysical S -factors and reaction rates based on Bayesian statistics. We develop a framework that incorporates robust parameter estimation, systematic effects, and non-Gaussian uncertainties in a consistent manner. The method is applied to the reactions d(p, γ ){sup 3}He, {sup 3}He({sup 3}He,2p){sup 4}He, and {sup 3}He( α , γ ){sup 7}Be, important for deuterium burning, solar neutrinos, and Big Bang nucleosynthesis.

  3. Non-Linear Approximation of Bayesian Update

    KAUST Repository

    Litvinenko, Alexander

    2016-01-01

    We develop a non-linear approximation of expensive Bayesian formula. This non-linear approximation is applied directly to Polynomial Chaos Coefficients. In this way, we avoid Monte Carlo sampling and sampling error. We can show that the famous Kalman Update formula is a particular case of this update.

  4. A Bayesian Approach to Interactive Retrieval

    Science.gov (United States)

    Tague, Jean M.

    1973-01-01

    A probabilistic model for interactive retrieval is presented. Bayesian statistical decision theory principles are applied: use of prior and sample information about the relationship of document descriptions to query relevance; maximization of expected value of a utility function, to the problem of optimally restructuring search strategies in an…

  5. Encoding dependence in Bayesian causal networks

    Science.gov (United States)

    Bayesian networks (BNs) represent complex, uncertain spatio-temporal dynamics by propagation of conditional probabilities between identifiable states with a testable causal interaction model. Typically, they assume random variables are discrete in time and space with a static network structure that ...

  6. Forecasting nuclear power supply with Bayesian autoregression

    International Nuclear Information System (INIS)

    Beck, R.; Solow, J.L.

    1994-01-01

    We explore the possibility of forecasting the quarterly US generation of electricity from nuclear power using a Bayesian autoregression model. In terms of forecasting accuracy, this approach compares favorably with both the Department of Energy's current forecasting methodology and their more recent efforts using ARIMA models, and it is extremely easy and inexpensive to implement. (author)

  7. A Bayesian Nonparametric Approach to Factor Analysis

    DEFF Research Database (Denmark)

    Piatek, Rémi; Papaspiliopoulos, Omiros

    2018-01-01

    This paper introduces a new approach for the inference of non-Gaussian factor models based on Bayesian nonparametric methods. It relaxes the usual normality assumption on the latent factors, widely used in practice, which is too restrictive in many settings. Our approach, on the contrary, does no...

  8. Hierarchical Bayesian Models of Subtask Learning

    Science.gov (United States)

    Anglim, Jeromy; Wynton, Sarah K. A.

    2015-01-01

    The current study used Bayesian hierarchical methods to challenge and extend previous work on subtask learning consistency. A general model of individual-level subtask learning was proposed focusing on power and exponential functions with constraints to test for inconsistency. To study subtask learning, we developed a novel computer-based booking…

  9. Non-Linear Approximation of Bayesian Update

    KAUST Repository

    Litvinenko, Alexander

    2016-06-23

    We develop a non-linear approximation of expensive Bayesian formula. This non-linear approximation is applied directly to Polynomial Chaos Coefficients. In this way, we avoid Monte Carlo sampling and sampling error. We can show that the famous Kalman Update formula is a particular case of this update.

  10. Bayesian approach and application to operation safety

    International Nuclear Information System (INIS)

    Procaccia, H.; Suhner, M.Ch.

    2003-01-01

    The management of industrial risks requires the development of statistical and probabilistic analyses which use all the available convenient information in order to compensate the insufficient experience feedback in a domain where accidents and incidents remain too scarce to perform a classical statistical frequency analysis. The Bayesian decision approach is well adapted to this problem because it integrates both the expertise and the experience feedback. The domain of knowledge is widen, the forecasting study becomes possible and the decisions-remedial actions are strengthen thanks to risk-cost-benefit optimization analyzes. This book presents the bases of the Bayesian approach and its concrete applications in various industrial domains. After a mathematical presentation of the industrial operation safety concepts and of the Bayesian approach principles, this book treats of some of the problems that can be solved thanks to this approach: softwares reliability, controls linked with the equipments warranty, dynamical updating of databases, expertise modeling and weighting, Bayesian optimization in the domains of maintenance, quality control, tests and design of new equipments. A synthesis of the mathematical formulae used in this approach is given in conclusion. (J.S.)

  11. Bayesian Fundamentalism or Enlightenment? On the explanatory status and theoretical contributions of Bayesian models of cognition.

    Science.gov (United States)

    Jones, Matt; Love, Bradley C

    2011-08-01

    The prominence of Bayesian modeling of cognition has increased recently largely because of mathematical advances in specifying and deriving predictions from complex probabilistic models. Much of this research aims to demonstrate that cognitive behavior can be explained from rational principles alone, without recourse to psychological or neurological processes and representations. We note commonalities between this rational approach and other movements in psychology - namely, Behaviorism and evolutionary psychology - that set aside mechanistic explanations or make use of optimality assumptions. Through these comparisons, we identify a number of challenges that limit the rational program's potential contribution to psychological theory. Specifically, rational Bayesian models are significantly unconstrained, both because they are uninformed by a wide range of process-level data and because their assumptions about the environment are generally not grounded in empirical measurement. The psychological implications of most Bayesian models are also unclear. Bayesian inference itself is conceptually trivial, but strong assumptions are often embedded in the hypothesis sets and the approximation algorithms used to derive model predictions, without a clear delineation between psychological commitments and implementational details. Comparing multiple Bayesian models of the same task is rare, as is the realization that many Bayesian models recapitulate existing (mechanistic level) theories. Despite the expressive power of current Bayesian models, we argue they must be developed in conjunction with mechanistic considerations to offer substantive explanations of cognition. We lay out several means for such an integration, which take into account the representations on which Bayesian inference operates, as well as the algorithms and heuristics that carry it out. We argue this unification will better facilitate lasting contributions to psychological theory, avoiding the pitfalls

  12. Developing Large-Scale Bayesian Networks by Composition: Fault Diagnosis of Electrical Power Systems in Aircraft and Spacecraft

    Science.gov (United States)

    Mengshoel, Ole Jakob; Poll, Scott; Kurtoglu, Tolga

    2009-01-01

    This CD contains files that support the talk (see CASI ID 20100021404). There are 24 models that relate to the ADAPT system and 1 Excel worksheet. In the paper an investigation into the use of Bayesian networks to construct large-scale diagnostic systems is described. The high-level specifications, Bayesian networks, clique trees, and arithmetic circuits representing 24 different electrical power systems are described in the talk. The data in the CD are the models of the 24 different power systems.

  13. Bayesian assignment of gene ontology terms to gene expression experiments.

    Science.gov (United States)

    Sykacek, P

    2012-09-15

    Gene expression assays allow for genome scale analyses of molecular biological mechanisms. State-of-the-art data analysis provides lists of involved genes, either by calculating significance levels of mRNA abundance or by Bayesian assessments of gene activity. A common problem of such approaches is the difficulty of interpreting the biological implication of the resulting gene lists. This lead to an increased interest in methods for inferring high-level biological information. A common approach for representing high level information is by inferring gene ontology (GO) terms which may be attributed to the expression data experiment. This article proposes a probabilistic model for GO term inference. Modelling assumes that gene annotations to GO terms are available and gene involvement in an experiment is represented by a posterior probabilities over gene-specific indicator variables. Such probability measures result from many Bayesian approaches for expression data analysis. The proposed model combines these indicator probabilities in a probabilistic fashion and provides a probabilistic GO term assignment as a result. Experiments on synthetic and microarray data suggest that advantages of the proposed probabilistic GO term inference over statistical test-based approaches are in particular evident for sparsely annotated GO terms and in situations of large uncertainty about gene activity. Provided that appropriate annotations exist, the proposed approach is easily applied to inferring other high level assignments like pathways. Source code under GPL license is available from the author. peter.sykacek@boku.ac.at.

  14. Bayesian assignment of gene ontology terms to gene expression experiments

    Science.gov (United States)

    Sykacek, P.

    2012-01-01

    Motivation: Gene expression assays allow for genome scale analyses of molecular biological mechanisms. State-of-the-art data analysis provides lists of involved genes, either by calculating significance levels of mRNA abundance or by Bayesian assessments of gene activity. A common problem of such approaches is the difficulty of interpreting the biological implication of the resulting gene lists. This lead to an increased interest in methods for inferring high-level biological information. A common approach for representing high level information is by inferring gene ontology (GO) terms which may be attributed to the expression data experiment. Results: This article proposes a probabilistic model for GO term inference. Modelling assumes that gene annotations to GO terms are available and gene involvement in an experiment is represented by a posterior probabilities over gene-specific indicator variables. Such probability measures result from many Bayesian approaches for expression data analysis. The proposed model combines these indicator probabilities in a probabilistic fashion and provides a probabilistic GO term assignment as a result. Experiments on synthetic and microarray data suggest that advantages of the proposed probabilistic GO term inference over statistical test-based approaches are in particular evident for sparsely annotated GO terms and in situations of large uncertainty about gene activity. Provided that appropriate annotations exist, the proposed approach is easily applied to inferring other high level assignments like pathways. Availability: Source code under GPL license is available from the author. Contact: peter.sykacek@boku.ac.at PMID:22962488

  15. Receiver-based recovery of clipped ofdm signals for papr reduction: A bayesian approach

    KAUST Repository

    Ali, Anum

    2014-01-01

    Clipping is one of the simplest peak-to-average power ratio reduction schemes for orthogonal frequency division multiplexing (OFDM). Deliberately clipping the transmission signal degrades system performance, and clipping mitigation is required at the receiver for information restoration. In this paper, we acknowledge the sparse nature of the clipping signal and propose a low-complexity Bayesian clipping estimation scheme. The proposed scheme utilizes a priori information about the sparsity rate and noise variance for enhanced recovery. At the same time, the proposed scheme is robust against inaccurate estimates of the clipping signal statistics. The undistorted phase property of the clipped signal, as well as the clipping likelihood, is utilized for enhanced reconstruction. Furthermore, motivated by the nature of modern OFDM-based communication systems, we extend our clipping reconstruction approach to multiple antenna receivers and multi-user OFDM.We also address the problem of channel estimation from pilots contaminated by the clipping distortion. Numerical findings are presented that depict favorable results for the proposed scheme compared to the established sparse reconstruction schemes.

  16. Forecasts: uncertain, inaccurate and biased?

    DEFF Research Database (Denmark)

    Nicolaisen, Morten Skou; Ambrasaite, Inga; Salling, Kim Bang

    2012-01-01

    Cost Benefit Analysis (CBA) is the dominating methodology for appraisal of transport infrastructure projects across the globe. In order to adequately assess the costs and benefits of such projects two types of forecasts are crucial to the validity of the appraisal. First are the forecasts of cons....... It is recommended that more attention is given to monitoring completed projects so future forecasts can benefit from better data availability through systematic ex-post evaluations, and an example of how to utilize such data in practice is presented.......Cost Benefit Analysis (CBA) is the dominating methodology for appraisal of transport infrastructure projects across the globe. In order to adequately assess the costs and benefits of such projects two types of forecasts are crucial to the validity of the appraisal. First are the forecasts...... of construction costs, which account for the majority of total project costs. Second are the forecasts of travel time savings, which account for the majority of total project benefits. The latter of these is, inter alia, determined by forecasts of travel demand, which we shall use as a proxy for the forecasting...

  17. Extraction of features from sleep EEG for Bayesian assessment of brain development.

    Directory of Open Access Journals (Sweden)

    Vitaly Schetinin

    Full Text Available Brain development can be evaluated by experts analysing age-related patterns in sleep electroencephalograms (EEG. Natural variations in the patterns, noise, and artefacts affect the evaluation accuracy as well as experts' agreement. The knowledge of predictive posterior distribution allows experts to estimate confidence intervals within which decisions are distributed. Bayesian approach to probabilistic inference has provided accurate estimates of intervals of interest. In this paper we propose a new feature extraction technique for Bayesian assessment and estimation of predictive distribution in a case of newborn brain development assessment. The new EEG features are verified within the Bayesian framework on a large EEG data set including 1,100 recordings made from newborns in 10 age groups. The proposed features are highly correlated with brain maturation and their use increases the assessment accuracy.

  18. Sparse Bayesian Inference and the Temperature Structure of the Solar Corona

    Energy Technology Data Exchange (ETDEWEB)

    Warren, Harry P. [Space Science Division, Naval Research Laboratory, Washington, DC 20375 (United States); Byers, Jeff M. [Materials Science and Technology Division, Naval Research Laboratory, Washington, DC 20375 (United States); Crump, Nicholas A. [Naval Center for Space Technology, Naval Research Laboratory, Washington, DC 20375 (United States)

    2017-02-20

    Measuring the temperature structure of the solar atmosphere is critical to understanding how it is heated to high temperatures. Unfortunately, the temperature of the upper atmosphere cannot be observed directly, but must be inferred from spectrally resolved observations of individual emission lines that span a wide range of temperatures. Such observations are “inverted” to determine the distribution of plasma temperatures along the line of sight. This inversion is ill posed and, in the absence of regularization, tends to produce wildly oscillatory solutions. We introduce the application of sparse Bayesian inference to the problem of inferring the temperature structure of the solar corona. Within a Bayesian framework a preference for solutions that utilize a minimum number of basis functions can be encoded into the prior and many ad hoc assumptions can be avoided. We demonstrate the efficacy of the Bayesian approach by considering a test library of 40 assumed temperature distributions.

  19. Basic and Advanced Bayesian Structural Equation Modeling With Applications in the Medical and Behavioral Sciences

    CERN Document Server

    Lee, Sik-Yum

    2012-01-01

    This book provides clear instructions to researchers on how to apply Structural Equation Models (SEMs) for analyzing the inter relationships between observed and latent variables. Basic and Advanced Bayesian Structural Equation Modeling introduces basic and advanced SEMs for analyzing various kinds of complex data, such as ordered and unordered categorical data, multilevel data, mixture data, longitudinal data, highly non-normal data, as well as some of their combinations. In addition, Bayesian semiparametric SEMs to capture the true distribution of explanatory latent variables are introduce

  20. Bayesian ideas and data analysis an introduction for scientists and statisticians

    CERN Document Server

    Christensen, Ronald; Branscum, Adam; Hanson, Timothy E.

    2010-01-01

    This book provides a good introduction to Bayesian approaches to applied statistical modelling. … The authors have fulfilled their main aim of introducing Bayesian ideas through examples using a large number of statistical models. An interesting feature of this book is the humour of the authors that make it more fun than typical statistics books. In summary, this is a very interesting introductory book, very well organised and has been written in a style that is extremely pleasant and enjoyable to read. Both the statistical concepts and examples are very well explained. In conclusion, I highly

  1. Bayesian quantification of thermodynamic uncertainties in dense gas flows

    International Nuclear Information System (INIS)

    Merle, X.; Cinnella, P.

    2015-01-01

    A Bayesian inference methodology is developed for calibrating complex equations of state used in numerical fluid flow solvers. Precisely, the input parameters of three equations of state commonly used for modeling the thermodynamic behavior of the so-called dense gas flows, – i.e. flows of gases characterized by high molecular weights and complex molecules, working in thermodynamic conditions close to the liquid–vapor saturation curve – are calibrated by means of Bayesian inference from reference aerodynamic data for a dense gas flow over a wing section. Flow thermodynamic conditions are such that the gas thermodynamic behavior strongly deviates from that of a perfect gas. In the aim of assessing the proposed methodology, synthetic calibration data – specifically, wall pressure data – are generated by running the numerical solver with a more complex and accurate thermodynamic model. The statistical model used to build the likelihood function includes a model-form inadequacy term, accounting for the gap between the model output associated to the best-fit parameters and the true phenomenon. Results show that, for all of the relatively simple models under investigation, calibrations lead to informative posterior probability density distributions of the input parameters and improve the predictive distribution significantly. Nevertheless, calibrated parameters strongly differ from their expected physical values. The relationship between this behavior and model-form inadequacy is discussed. - Highlights: • Development of a Bayesian inference procedure for calibrating dense-gas flow solvers. • Complex thermodynamic models calibrated by using aerodynamic data for the flow. • Preliminary Sobol analysis used to reduce parameter space. • Piecewise polynomial surrogate model constructed to reduce computational cost. • Calibration results show the crucial role played by model-form inadequacies

  2. Smartphone technologies and Bayesian networks to assess shorebird habitat selection

    Science.gov (United States)

    Zeigler, Sara; Thieler, E. Robert; Gutierrez, Ben; Plant, Nathaniel G.; Hines, Megan K.; Fraser, James D.; Catlin, Daniel H.; Karpanty, Sarah M.

    2017-01-01

    Understanding patterns of habitat selection across a species’ geographic distribution can be critical for adequately managing populations and planning for habitat loss and related threats. However, studies of habitat selection can be time consuming and expensive over broad spatial scales, and a lack of standardized monitoring targets or methods can impede the generalization of site-based studies. Our objective was to collaborate with natural resource managers to define available nesting habitat for piping plovers (Charadrius melodus) throughout their U.S. Atlantic coast distribution from Maine to North Carolina, with a goal of providing science that could inform habitat management in response to sea-level rise. We characterized a data collection and analysis approach as being effective if it provided low-cost collection of standardized habitat-selection data across the species’ breeding range within 1–2 nesting seasons and accurate nesting location predictions. In the method developed, >30 managers and conservation practitioners from government agencies and private organizations used a smartphone application, “iPlover,” to collect data on landcover characteristics at piping plover nest locations and random points on 83 beaches and barrier islands in 2014 and 2015. We analyzed these data with a Bayesian network that predicted the probability a specific combination of landcover variables would be associated with a nesting site. Although we focused on a shorebird, our approach can be modified for other taxa. Results showed that the Bayesian network performed well in predicting habitat availability and confirmed predicted habitat preferences across the Atlantic coast breeding range of the piping plover. We used the Bayesian network to map areas with a high probability of containing nesting habitat on the Rockaway Peninsula in New York, USA, as an example application. Our approach facilitated the collation of evidence-based information on habitat selection

  3. Spatio-Temporal Series Remote Sensing Image Prediction Based on Multi-Dictionary Bayesian Fusion

    Directory of Open Access Journals (Sweden)

    Chu He

    2017-11-01

    Full Text Available Contradictions in spatial resolution and temporal coverage emerge from earth observation remote sensing images due to limitations in technology and cost. Therefore, how to combine remote sensing images with low spatial yet high temporal resolution as well as those with high spatial yet low temporal resolution to construct images with both high spatial resolution and high temporal coverage has become an important problem called spatio-temporal fusion problem in both research and practice. A Multi-Dictionary Bayesian Spatio-Temporal Reflectance Fusion Model (MDBFM has been proposed in this paper. First, multiple dictionaries from regions of different classes are trained. Second, a Bayesian framework is constructed to solve the dictionary selection problem. A pixel-dictionary likehood function and a dictionary-dictionary prior function are constructed under the Bayesian framework. Third, remote sensing images before and after the middle moment are combined to predict images at the middle moment. Diverse shapes and textures information is learned from different landscapes in multi-dictionary learning to help dictionaries capture the distinctions between regions. The Bayesian framework makes full use of the priori information while the input image is classified. The experiments with one simulated dataset and two satellite datasets validate that the MDBFM is highly effective in both subjective and objective evaluation indexes. The results of MDBFM show more precise details and have a higher similarity with real images when dealing with both type changes and phenology changes.

  4. Predictive models for pressure ulcers from intensive care unit electronic health records using Bayesian networks.

    Science.gov (United States)

    Kaewprag, Pacharmon; Newton, Cheryl; Vermillion, Brenda; Hyun, Sookyung; Huang, Kun; Machiraju, Raghu

    2017-07-05

    We develop predictive models enabling clinicians to better understand and explore patient clinical data along with risk factors for pressure ulcers in intensive care unit patients from electronic health record data. Identifying accurate risk factors of pressure ulcers is essential to determining appropriate prevention strategies; in this work we examine medication, diagnosis, and traditional Braden pressure ulcer assessment scale measurements as patient features. In order to predict pressure ulcer incidence and better understand the structure of related risk factors, we construct Bayesian networks from patient features. Bayesian network nodes (features) and edges (conditional dependencies) are simplified with statistical network techniques. Upon reviewing a network visualization of our model, our clinician collaborators were able to identify strong relationships between risk factors widely recognized as associated with pressure ulcers. We present a three-stage framework for predictive analysis of patient clinical data: 1) Developing electronic health record feature extraction functions with assistance of clinicians, 2) simplifying features, and 3) building Bayesian network predictive models. We evaluate all combinations of Bayesian network models from different search algorithms, scoring functions, prior structure initializations, and sets of features. From the EHRs of 7,717 ICU patients, we construct Bayesian network predictive models from 86 medication, diagnosis, and Braden scale features. Our model not only identifies known and suspected high PU risk factors, but also substantially increases sensitivity of the prediction - nearly three times higher comparing to logistical regression models - without sacrificing the overall accuracy. We visualize a representative model with which our clinician collaborators identify strong relationships between risk factors widely recognized as associated with pressure ulcers. Given the strong adverse effect of pressure ulcers

  5. Bayesian Option Pricing Framework with Stochastic Volatility for FX Data

    Directory of Open Access Journals (Sweden)

    Ying Wang

    2016-12-01

    Full Text Available The application of stochastic volatility (SV models in the option pricing literature usually assumes that the market has sufficient option data to calibrate the model’s risk-neutral parameters. When option data are insufficient or unavailable, market practitioners must estimate the model from the historical returns of the underlying asset and then transform the resulting model into its risk-neutral equivalent. However, the likelihood function of an SV model can only be expressed in a high-dimensional integration, which makes the estimation a highly challenging task. The Bayesian approach has been the classical way to estimate SV models under the data-generating (physical probability measure, but the transformation from the estimated physical dynamic into its risk-neutral counterpart has not been addressed. Inspired by the generalized autoregressive conditional heteroskedasticity (GARCH option pricing approach by Duan in 1995, we propose an SV model that enables us to simultaneously and conveniently perform Bayesian inference and transformation into risk-neutral dynamics. Our model relaxes the normality assumption on innovations of both return and volatility processes, and our empirical study shows that the estimated option prices generate realistic implied volatility smile shapes. In addition, the volatility premium is almost flat across strike prices, so adding a few option data to the historical time series of the underlying asset can greatly improve the estimation of option prices.

  6. Can natural selection encode Bayesian priors?

    Science.gov (United States)

    Ramírez, Juan Camilo; Marshall, James A R

    2017-08-07

    The evolutionary success of many organisms depends on their ability to make decisions based on estimates of the state of their environment (e.g., predation risk) from uncertain information. These decision problems have optimal solutions and individuals in nature are expected to evolve the behavioural mechanisms to make decisions as if using the optimal solutions. Bayesian inference is the optimal method to produce estimates from uncertain data, thus natural selection is expected to favour individuals with the behavioural mechanisms to make decisions as if they were computing Bayesian estimates in typically-experienced environments, although this does not necessarily imply that favoured decision-makers do perform Bayesian computations exactly. Each individual should evolve to behave as if updating a prior estimate of the unknown environment variable to a posterior estimate as it collects evidence. The prior estimate represents the decision-maker's default belief regarding the environment variable, i.e., the individual's default 'worldview' of the environment. This default belief has been hypothesised to be shaped by natural selection and represent the environment experienced by the individual's ancestors. We present an evolutionary model to explore how accurately Bayesian prior estimates can be encoded genetically and shaped by natural selection when decision-makers learn from uncertain information. The model simulates the evolution of a population of individuals that are required to estimate the probability of an event. Every individual has a prior estimate of this probability and collects noisy cues from the environment in order to update its prior belief to a Bayesian posterior estimate with the evidence gained. The prior is inherited and passed on to offspring. Fitness increases with the accuracy of the posterior estimates produced. Simulations show that prior estimates become accurate over evolutionary time. In addition to these 'Bayesian' individuals, we also

  7. Dose-to-dose variations with single packages of counterfeit medicines and adulterated dietary supplements as a potential source of false negatives and inaccurate health risk assessments.

    Science.gov (United States)

    Venhuis, B J; Zwaagstra, M E; Keizers, P H J; de Kaste, D

    2014-02-01

    In this report, we show three examples of how the variability in dose units in single packages of counterfeit medicines and adulterated dietary supplements may contribute to a false negative screening result and inaccurate health risk assessments. We describe a counterfeit Viagra 100mg blister pack and a box of an instant coffee both containing dose units with and without an active pharmaceutical ingredient (API). We also describe a purportedly herbal slimming product with capsules that mutually differed in API and impurities. The adulterated dietary supplements contained sibutramine, benzyl-sibutramine, N-desmethyl-sibutramine (DMS), N,N-didesmethyl-sibutramine (DDMS) and several other related impurities. Counterfeit medicines and adulterated dietary supplements are a health risk because their quality is unreliable. Health risks are even greater when such unreliability extends to fundamental differences between dose units in one package. Because dose-to-dose variability for these products is unpredictable, the confidence interval of a sample size is unknown. Consequently, the analyses of a selection of dose units may not be representative for the package. In the worst case, counterfeit or unauthorised medicines are not recognised as such or a health risk is not identified. In order to reduce erroneous results particular care should be taken when analysing a composite of dose units, when finding no API in a dietary supplement and when finding conformity in a suspect counterfeit medicine. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Enhancing a Short Measure of Big Five Personality Traits with Bayesian Scaling

    Science.gov (United States)

    Jones, W. Paul

    2014-01-01

    A study in a university clinic/laboratory investigated adaptive Bayesian scaling as a supplement to interpretation of scores on the Mini-IPIP. A "probability of belonging" in categories of low, medium, or high on each of the Big Five traits was calculated after each item response and continued until all items had been used or until a…

  9. Bayesian analysis of spatial point processes in the neighbourhood of Voronoi networks

    DEFF Research Database (Denmark)

    Skare, Øivind; Møller, Jesper; Jensen, Eva Bjørn Vedel

    2007-01-01

    A model for an inhomogeneous Poisson process with high intensity near the edges of a Voronoi tessellation in 2D or 3D is proposed. The model is analysed in a Bayesian setting with priors on nuclei of the Voronoi tessellation and other model parameters. An MCMC algorithm is constructed to sample...

  10. Bayesian analysis of spatial point processes in the neighbourhood of Voronoi networks

    DEFF Research Database (Denmark)

    Skare, Øivind; Møller, Jesper; Vedel Jensen, Eva B.

    A model for an inhomogeneous Poisson process with high intensity near the edges of a Voronoi tessellation in 2D or 3D is proposed. The model is analysed in a Bayesian setting with priors on nuclei of the Voronoi tessellation and other model parameters. An MCMC algorithm is constructed to sample...

  11. A Bayesian Performance Prediction Model for Mathematics Education: A Prototypical Approach for Effective Group Composition

    Science.gov (United States)

    Bekele, Rahel; McPherson, Maggie

    2011-01-01

    This research work presents a Bayesian Performance Prediction Model that was created in order to determine the strength of personality traits in predicting the level of mathematics performance of high school students in Addis Ababa. It is an automated tool that can be used to collect information from students for the purpose of effective group…

  12. A New Bayesian Approach for Estimating the Presence of a Suspected Compound in Routine Screening Analysis

    NARCIS (Netherlands)

    Woldegebriel, M.; Vivó-Truyols, G.

    2016-01-01

    A novel method for compound identification in liquid chromatography-high resolution mass spectrometry (LC-HRMS) is proposed. The method, based on Bayesian statistics, accommodates all possible uncertainties involved, from instrumentation up to data analysis into a single model yielding the

  13. Incorporating Open Source Data for Bayesian Classification of Urban Land Use From VHR Stereo Images

    NARCIS (Netherlands)

    Li, Mengmeng; De Beurs, Kirsten M.; Stein, Alfred; Bijker, Wietske

    2017-01-01

    This study investigates the incorporation of open source data into a Bayesian classification of urban land use from very high resolution (VHR) stereo satellite images. The adopted classification framework starts from urban land cover classification, proceeds to building-type characterization, and

  14. Bayesianism and inference to the best explanation

    Directory of Open Access Journals (Sweden)

    Valeriano IRANZO

    2008-01-01

    Full Text Available Bayesianism and Inference to the best explanation (IBE are two different models of inference. Recently there has been some debate about the possibility of “bayesianizing” IBE. Firstly I explore several alternatives to include explanatory considerations in Bayes’s Theorem. Then I distinguish two different interpretations of prior probabilities: “IBE-Bayesianism” (IBE-Bay and “frequentist-Bayesianism” (Freq-Bay. After detailing the content of the latter, I propose a rule for assessing the priors. I also argue that Freq-Bay: (i endorses a role for explanatory value in the assessment of scientific hypotheses; (ii avoids a purely subjectivist reading of prior probabilities; and (iii fits better than IBE-Bayesianism with two basic facts about science, i.e., the prominent role played by empirical testing and the existence of many scientific theories in the past that failed to fulfil their promises and were subsequently abandoned.

  15. Bayesian Peak Picking for NMR Spectra

    KAUST Repository

    Cheng, Yichen

    2014-02-01

    Protein structure determination is a very important topic in structural genomics, which helps people to understand varieties of biological functions such as protein-protein interactions, protein–DNA interactions and so on. Nowadays, nuclear magnetic resonance (NMR) has often been used to determine the three-dimensional structures of protein in vivo. This study aims to automate the peak picking step, the most important and tricky step in NMR structure determination. We propose to model the NMR spectrum by a mixture of bivariate Gaussian densities and use the stochastic approximation Monte Carlo algorithm as the computational tool to solve the problem. Under the Bayesian framework, the peak picking problem is casted as a variable selection problem. The proposed method can automatically distinguish true peaks from false ones without preprocessing the data. To the best of our knowledge, this is the first effort in the literature that tackles the peak picking problem for NMR spectrum data using Bayesian method.

  16. Bayesian Modelling of Functional Whole Brain Connectivity

    DEFF Research Database (Denmark)

    Røge, Rasmus

    the prevalent strategy of standardizing of fMRI time series and model data using directional statistics or we model the variability in the signal across the brain and across multiple subjects. In either case, we use Bayesian nonparametric modeling to automatically learn from the fMRI data the number......This thesis deals with parcellation of whole-brain functional magnetic resonance imaging (fMRI) using Bayesian inference with mixture models tailored to the fMRI data. In the three included papers and manuscripts, we analyze two different approaches to modeling fMRI signal; either we accept...... of funcional units, i.e. parcels. We benchmark the proposed mixture models against state of the art methods of brain parcellation, both probabilistic and non-probabilistic. The time series of each voxel are most often standardized using z-scoring which projects the time series data onto a hypersphere...

  17. Software Health Management with Bayesian Networks

    Science.gov (United States)

    Mengshoel, Ole; Schumann, JOhann

    2011-01-01

    Most modern aircraft as well as other complex machinery is equipped with diagnostics systems for its major subsystems. During operation, sensors provide important information about the subsystem (e.g., the engine) and that information is used to detect and diagnose faults. Most of these systems focus on the monitoring of a mechanical, hydraulic, or electromechanical subsystem of the vehicle or machinery. Only recently, health management systems that monitor software have been developed. In this paper, we will discuss our approach of using Bayesian networks for Software Health Management (SWHM). We will discuss SWHM requirements, which make advanced reasoning capabilities for the detection and diagnosis important. Then we will present our approach to using Bayesian networks for the construction of health models that dynamically monitor a software system and is capable of detecting and diagnosing faults.

  18. Narrowband interference parameterization for sparse Bayesian recovery

    KAUST Repository

    Ali, Anum

    2015-09-11

    This paper addresses the problem of narrowband interference (NBI) in SC-FDMA systems by using tools from compressed sensing and stochastic geometry. The proposed NBI cancellation scheme exploits the frequency domain sparsity of the unknown signal and adopts a Bayesian sparse recovery procedure. This is done by keeping a few randomly chosen sub-carriers data free to sense the NBI signal at the receiver. As Bayesian recovery requires knowledge of some NBI parameters (i.e., mean, variance and sparsity rate), we use tools from stochastic geometry to obtain analytical expressions for the required parameters. Our simulation results validate the analysis and depict suitability of the proposed recovery method for NBI mitigation. © 2015 IEEE.

  19. Machine learning a Bayesian and optimization perspective

    CERN Document Server

    Theodoridis, Sergios

    2015-01-01

    This tutorial text gives a unifying perspective on machine learning by covering both probabilistic and deterministic approaches, which rely on optimization techniques, as well as Bayesian inference, which is based on a hierarchy of probabilistic models. The book presents the major machine learning methods as they have been developed in different disciplines, such as statistics, statistical and adaptive signal processing and computer science. Focusing on the physical reasoning behind the mathematics, all the various methods and techniques are explained in depth, supported by examples and problems, giving an invaluable resource to the student and researcher for understanding and applying machine learning concepts. The book builds carefully from the basic classical methods to the most recent trends, with chapters written to be as self-contained as possible, making the text suitable for different courses: pattern recognition, statistical/adaptive signal processing, statistical/Bayesian learning, as well as shor...

  20. Bayesian calibration : past achievements and future challenges

    International Nuclear Information System (INIS)

    Christen, J.A.

    2001-01-01

    Due to variations of the radiocarbon content in the biosphere over time, radiocarbon determinations need to be calibrated to obtain calendar years. Over the past decade a series of researchers have investigated the possibility of using Bayesian statistics to calibrate radiocarbon determinations, the main feature being the inclusion of contextual information into the calibration process. This allows for a coherent calibration of groups of determinations arising from related contexts (stratigraphical layers, peat cores, cultural events, ect.). Moreover, the 'related contexts' are also dated, and not only the material radiocarbon dated itself. We review Bayesian Calibration and state some of its current challenges like: software development, prior specification, robustness, etc. (author). 14 refs., 4 figs

  1. Disentangling Complexity in Bayesian Automatic Adaptive Quadrature

    Science.gov (United States)

    Adam, Gheorghe; Adam, Sanda

    2018-02-01

    The paper describes a Bayesian automatic adaptive quadrature (BAAQ) solution for numerical integration which is simultaneously robust, reliable, and efficient. Detailed discussion is provided of three main factors which contribute to the enhancement of these features: (1) refinement of the m-panel automatic adaptive scheme through the use of integration-domain-length-scale-adapted quadrature sums; (2) fast early problem complexity assessment - enables the non-transitive choice among three execution paths: (i) immediate termination (exceptional cases); (ii) pessimistic - involves time and resource consuming Bayesian inference resulting in radical reformulation of the problem to be solved; (iii) optimistic - asks exclusively for subrange subdivision by bisection; (3) use of the weaker accuracy target from the two possible ones (the input accuracy specifications and the intrinsic integrand properties respectively) - results in maximum possible solution accuracy under minimum possible computing time.

  2. Bayesian Prior Probability Distributions for Internal Dosimetry

    Energy Technology Data Exchange (ETDEWEB)

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

    2001-07-01

    The problem of choosing a prior distribution for the Bayesian interpretation of measurements (specifically internal dosimetry measurements) is considered using a theoretical analysis and by examining historical tritium and plutonium urine bioassay data from Los Alamos. Two models for the prior probability distribution are proposed: (1) the log-normal distribution, when there is some additional information to determine the scale of the true result, and (2) the 'alpha' distribution (a simplified variant of the gamma distribution) when there is not. These models have been incorporated into version 3 of the Bayesian internal dosimetric code in use at Los Alamos (downloadable from our web site). Plutonium internal dosimetry at Los Alamos is now being done using prior probability distribution parameters determined self-consistently from population averages of Los Alamos data. (author)

  3. Probabilistic forecasting and Bayesian data assimilation

    CERN Document Server

    Reich, Sebastian

    2015-01-01

    In this book the authors describe the principles and methods behind probabilistic forecasting and Bayesian data assimilation. Instead of focusing on particular application areas, the authors adopt a general dynamical systems approach, with a profusion of low-dimensional, discrete-time numerical examples designed to build intuition about the subject. Part I explains the mathematical framework of ensemble-based probabilistic forecasting and uncertainty quantification. Part II is devoted to Bayesian filtering algorithms, from classical data assimilation algorithms such as the Kalman filter, variational techniques, and sequential Monte Carlo methods, through to more recent developments such as the ensemble Kalman filter and ensemble transform filters. The McKean approach to sequential filtering in combination with coupling of measures serves as a unifying mathematical framework throughout Part II. Assuming only some basic familiarity with probability, this book is an ideal introduction for graduate students in ap...

  4. Identification of transmissivity fields using a Bayesian strategy and perturbative approach

    Science.gov (United States)

    Zanini, Andrea; Tanda, Maria Giovanna; Woodbury, Allan D.

    2017-10-01

    The paper deals with the crucial problem of the groundwater parameter estimation that is the basis for efficient modeling and reclamation activities. A hierarchical Bayesian approach is developed: it uses the Akaike's Bayesian Information Criteria in order to estimate the hyperparameters (related to the covariance model chosen) and to quantify the unknown noise variance. The transmissivity identification proceeds in two steps: the first, called empirical Bayesian interpolation, uses Y* (Y = lnT) observations to interpolate Y values on a specified grid; the second, called empirical Bayesian update, improve the previous Y estimate through the addition of hydraulic head observations. The relationship between the head and the lnT has been linearized through a perturbative solution of the flow equation. In order to test the proposed approach, synthetic aquifers from literature have been considered. The aquifers in question contain a variety of boundary conditions (both Dirichelet and Neuman type) and scales of heterogeneities (σY2 = 1.0 and σY2 = 5.3). The estimated transmissivity fields were compared to the true one. The joint use of Y* and head measurements improves the estimation of Y considering both degrees of heterogeneity. Even if the variance of the strong transmissivity field can be considered high for the application of the perturbative approach, the results show the same order of approximation of the non-linear methods proposed in literature. The procedure allows to compute the posterior probability distribution of the target quantities and to quantify the uncertainty in the model prediction. Bayesian updating has advantages related both to the Monte-Carlo (MC) and non-MC approaches. In fact, as the MC methods, Bayesian updating allows computing the direct posterior probability distribution of the target quantities and as non-MC methods it has computational times in the order of seconds.

  5. Sensitivity of fluvial sediment source apportionment to mixing model assumptions: A Bayesian model comparison.

    Science.gov (United States)

    Cooper, Richard J; Krueger, Tobias; Hiscock, Kevin M; Rawlins, Barry G

    2014-11-01

    Mixing models have become increasingly common tools for apportioning fluvial sediment load to various sediment sources across catchments using a wide variety of Bayesian and frequentist modeling approaches. In this study, we demonstrate how different model setups can impact upon resulting source apportionment estimates in a Bayesian framework via a one-factor-at-a-time (OFAT) sensitivity analysis. We formulate 13 versions of a mixing model, each with different error assumptions and model structural choices, and apply them to sediment geochemistry data from the River Blackwater, Norfolk, UK, to apportion suspended particulate matter (SPM) contributions from three sources (arable topsoils, road verges, and subsurface material) under base flow conditions between August 2012 and August 2013. Whilst all 13 models estimate subsurface sources to be the largest contributor of SPM (median ∼76%), comparison of apportionment estimates reveal varying degrees of sensitivity to changing priors, inclusion of covariance terms, incorporation of time-variant distributions, and methods of proportion characterization. We also demonstrate differences in apportionment results between a full and an empirical Bayesian setup, and between a Bayesian and a frequentist optimization approach. This OFAT sensitivity analysis reveals that mixing model structural choices and error assumptions can significantly impact upon sediment source apportionment results, with estimated median contributions in this study varying by up to 21% between model versions. Users of mixing models are therefore strongly advised to carefully consider and justify their choice of model structure prior to conducting sediment source apportionment investigations. An OFAT sensitivity analysis of sediment fingerprinting mixing models is conductedBayesian models display high sensitivity to error assumptions and structural choicesSource apportionment results differ between Bayesian and frequentist approaches.

  6. Bayesian networks and boundedly rational expectations

    OpenAIRE

    Ran Spiegler

    2014-01-01

    I present a framework for analyzing decision makers with an imperfect understanding of their environment's correlation structure. The framework borrows the tool of "Bayesian networks", which is ubiquitous in statistics and artificial intelligence. In the model, a decision maker faces an objective multivariate probability distribution (his own action is one of the random variables). He is characterized by a directed acyclic graph over the set of random variables. His subjective belief filters ...

  7. Approximation of Bayesian Inverse Problems for PDEs

    OpenAIRE

    Cotter, S. L.; Dashti, M.; Stuart, A. M.

    2010-01-01

    Inverse problems are often ill posed, with solutions that depend sensitively on data.n any numerical approach to the solution of such problems, regularization of some form is needed to counteract the resulting instability. This paper is based on an approach to regularization, employing a Bayesian formulation of the problem, which leads to a notion of well posedness for inverse problems, at the level of probability measures. The stability which results from this well posedness may be used as t...

  8. Multilevel Monte Carlo in Approximate Bayesian Computation

    KAUST Repository

    Jasra, Ajay

    2017-02-13

    In the following article we consider approximate Bayesian computation (ABC) inference. We introduce a method for numerically approximating ABC posteriors using the multilevel Monte Carlo (MLMC). A sequential Monte Carlo version of the approach is developed and it is shown under some assumptions that for a given level of mean square error, this method for ABC has a lower cost than i.i.d. sampling from the most accurate ABC approximation. Several numerical examples are given.

  9. Centralized Bayesian reliability modelling with sensor networks

    Czech Academy of Sciences Publication Activity Database

    Dedecius, Kamil; Sečkárová, Vladimíra

    2013-01-01

    Roč. 19, č. 5 (2013), s. 471-482 ISSN 1387-3954 R&D Projects: GA MŠk 7D12004 Grant - others:GA MŠk(CZ) SVV-265315 Keywords : Bayesian modelling * Sensor network * Reliability Subject RIV: BD - Theory of Information Impact factor: 0.984, year: 2013 http://library.utia.cas.cz/separaty/2013/AS/dedecius-0392551.pdf

  10. 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,...

  11. Bayesian estimation of Weibull distribution parameters

    International Nuclear Information System (INIS)

    Bacha, M.; Celeux, G.; Idee, E.; Lannoy, A.; Vasseur, D.

    1994-11-01

    In this paper, we expose SEM (Stochastic Expectation Maximization) and WLB-SIR (Weighted Likelihood Bootstrap - Sampling Importance Re-sampling) methods which are used to estimate Weibull distribution parameters when data are very censored. The second method is based on Bayesian inference and allow to take into account available prior informations on parameters. An application of this method, with real data provided by nuclear power plants operation feedback analysis has been realized. (authors). 8 refs., 2 figs., 2 tabs

  12. A theory of Bayesian decision making

    OpenAIRE

    Karni, Edi

    2009-01-01

    This paper presents a complete, choice-based, axiomatic Bayesian decision theory. It introduces a new choice set consisting of information-contingent plans for choosing actions and bets and subjective expected utility model with effect-dependent utility functions and action-dependent subjective probabilities which, in conjunction with the updating of the probabilities using Bayes’ rule, gives rise to a unique prior and a set of action-dependent posterior probabilities representing the decisio...

  13. Constrained bayesian inference of project performance models

    OpenAIRE

    Sunmola, Funlade

    2013-01-01

    Project performance models play an important role in the management of project success. When used for monitoring projects, they can offer predictive ability such as indications of possible delivery problems. Approaches for monitoring project performance relies on available project information including restrictions imposed on the project, particularly the constraints of cost, quality, scope and time. We study in this paper a Bayesian inference methodology for project performance modelling in ...

  14. Virtual Vector Machine for Bayesian Online Classification

    OpenAIRE

    Minka, Thomas P.; Xiang, Rongjing; Yuan; Qi

    2012-01-01

    In a typical online learning scenario, a learner is required to process a large data stream using a small memory buffer. Such a requirement is usually in conflict with a learner's primary pursuit of prediction accuracy. To address this dilemma, we introduce a novel Bayesian online classi cation algorithm, called the Virtual Vector Machine. The virtual vector machine allows you to smoothly trade-off prediction accuracy with memory size. The virtual vector machine summarizes the information con...

  15. Characteristic imsets for learning Bayesian network structure

    Czech Academy of Sciences Publication Activity Database

    Hemmecke, R.; Lindner, S.; Studený, Milan

    2012-01-01

    Roč. 53, č. 9 (2012), s. 1336-1349 ISSN 0888-613X R&D Projects: GA MŠk(CZ) 1M0572; GA ČR GA201/08/0539 Institutional support: RVO:67985556 Keywords : learning Bayesian network structure * essential graph * standard imset * characteristic imset * LP relaxation of a polytope Subject RIV: BA - General Mathematics Impact factor: 1.729, year: 2012 http://library.utia.cas.cz/separaty/2012/MTR/studeny-0382596.pdf

  16. Bayesian analysis of Markov point processes

    DEFF Research Database (Denmark)

    Berthelsen, Kasper Klitgaard; Møller, Jesper

    2006-01-01

    Recently Møller, Pettitt, Berthelsen and Reeves introduced a new MCMC methodology for drawing samples from a posterior distribution when the likelihood function is only specified up to a normalising constant. We illustrate the method in the setting of Bayesian inference for Markov point processes...... a partially ordered Markov point process as the auxiliary variable. As the method requires simulation from the "unknown" likelihood, perfect simulation algorithms for spatial point processes become useful....

  17. Decisions under uncertainty using Bayesian analysis

    Directory of Open Access Journals (Sweden)

    Stelian STANCU

    2006-01-01

    Full Text Available The present paper makes a short presentation of the Bayesian decions method, where extrainformation brings a great support to decision making process, but also attract new costs. In this situation, getting new information, generally experimentaly based, contributes to diminushing the uncertainty degree that influences decision making process. As a conclusion, in a large number of decision problems, there is the possibility that the decision makers will renew some decisions already taken because of the facilities offered by obtainig extrainformation.

  18. Bayesian nonparametric dictionary learning for compressed sensing MRI.

    Science.gov (United States)

    Huang, Yue; Paisley, John; Lin, Qin; Ding, Xinghao; Fu, Xueyang; Zhang, Xiao-Ping

    2014-12-01

    We develop a Bayesian nonparametric model for reconstructing magnetic resonance images (MRIs) from highly undersampled k -space data. We perform dictionary learning as part of the image reconstruction process. To this end, we use the beta process as a nonparametric dictionary learning prior for representing an image patch as a sparse combination of dictionary elements. The size of the dictionary and patch-specific sparsity pattern are inferred from the data, in addition to other dictionary learning variables. Dictionary learning is performed directly on the compressed image, and so is tailored to the MRI being considered. In addition, we investigate a total variation penalty term in combination with the dictionary learning model, and show how the denoising property of dictionary learning removes dependence on regularization parameters in the noisy setting. We derive a stochastic optimization algorithm based on Markov chain Monte Carlo for the Bayesian model, and use the alternating direction method of multipliers for efficiently performing total variation minimization. We present empirical results on several MRI, which show that the proposed regularization framework can improve reconstruction accuracy over other methods.

  19. Robust Bayesian Experimental Design for Conceptual Model Discrimination

    Science.gov (United States)

    Pham, H. V.; Tsai, F. T. C.

    2015-12-01

    A robust Bayesian optimal experimental design under uncertainty is presented to provide firm information for model discrimination, given the least number of pumping wells and observation wells. Firm information is the maximum information of a system can be guaranteed from an experimental design. The design is based on the Box-Hill expected entropy decrease (EED) before and after the experiment design and the Bayesian model averaging (BMA) framework. A max-min programming is introduced to choose the robust design that maximizes the minimal Box-Hill EED subject to that the highest expected posterior model probability satisfies a desired probability threshold. The EED is calculated by the Gauss-Hermite quadrature. The BMA method is used to predict future observations and to quantify future observation uncertainty arising from conceptual and parametric uncertainties in calculating EED. Monte Carlo approach is adopted to quantify the uncertainty in the posterior model probabilities. The optimal experimental design is tested by a synthetic 5-layer anisotropic confined aquifer. Nine conceptual groundwater models are constructed due to uncertain geological architecture and boundary condition. High-performance computing is used to enumerate all possible design solutions in order to identify the most plausible groundwater model. Results highlight the impacts of scedasticity in future observation data as well as uncertainty sources on potential pumping and observation locations.

  20. Bayesian signal reconstruction for 1-bit compressed sensing

    International Nuclear Information System (INIS)

    Xu, Yingying; Kabashima, Yoshiyuki; Zdeborová, Lenka

    2014-01-01

    The 1-bit compressed sensing framework enables the recovery of a sparse vector x from the sign information of each entry of its linear transformation. Discarding the amplitude information can significantly reduce the amount of data, which is highly beneficial in practical applications. In this paper, we present a Bayesian approach to signal reconstruction for 1-bit compressed sensing and analyze its typical performance using statistical mechanics. As a basic setup, we consider the case that the measuring matrix Φ has i.i.d entries and the measurements y are noiseless. Utilizing the replica method, we show that the Bayesian approach enables better reconstruction than the l 1 -norm minimization approach, asymptotically saturating the performance obtained when the non-zero entry positions of the signal are known, for signals whose non-zero entries follow zero mean Gaussian distributions. We also test a message passing algorithm for signal reconstruction on the basis of belief propagation. The results of numerical experiments are consistent with those of the theoretical analysis. (paper)

  1. Bayesian selective response-adaptive design using the historical control.

    Science.gov (United States)

    Kim, Mi-Ok; Harun, Nusrat; Liu, Chunyan; Khoury, Jane C; Broderick, Joseph P

    2018-06-13

    High quality historical control data, if incorporated, may reduce sample size, trial cost, and duration. A too optimistic use of the data, however, may result in bias under prior-data conflict. Motivated by well-publicized two-arm comparative trials in stroke, we propose a Bayesian design that both adaptively incorporates historical control data and selectively adapt the treatment allocation ratios within an ongoing trial responsively to the relative treatment effects. The proposed design differs from existing designs that borrow from historical controls. As opposed to reducing the number of subjects assigned to the control arm blindly, this design does so adaptively to the relative treatment effects only if evaluation of cumulated current trial data combined with the historical control suggests the superiority of the intervention arm. We used the effective historical sample size approach to quantify borrowed information on the control arm and modified the treatment allocation rules of the doubly adaptive biased coin design to incorporate the quantity. The modified allocation rules were then implemented under the Bayesian framework with commensurate priors addressing prior-data conflict. Trials were also more frequently concluded earlier in line with the underlying truth, reducing trial cost, and duration and yielded parameter estimates with smaller standard errors. © 2018 The Authors. Statistics in Medicine Published by John Wiley & Sons, Ltd.

  2. Bayesian inference from count data using discrete uniform priors.

    Directory of Open Access Journals (Sweden)

    Federico Comoglio

    Full Text Available We consider a set of sample counts obtained by sampling arbitrary fractions of a finite volume containing an homogeneously dispersed population of identical objects. We report a Bayesian derivation of the posterior probability distribution of the population size using a binomial likelihood and non-conjugate, discrete uniform priors under sampling with or without replacement. Our derivation yields a computationally feasible formula that can prove useful in a variety of statistical problems involving absolute quantification under uncertainty. We implemented our algorithm in the R package dupiR and compared it with a previously proposed Bayesian method based on a Gamma prior. As a showcase, we demonstrate that our inference framework can be used to estimate bacterial survival curves from measurements characterized by extremely low or zero counts and rather high sampling fractions. All in all, we provide a versatile, general purpose algorithm to infer population sizes from count data, which can find application in a broad spectrum of biological and physical problems.

  3. DPpackage: Bayesian Semi- and Nonparametric Modeling in R

    Directory of Open Access Journals (Sweden)

    Alejandro Jara

    2011-04-01

    Full Text Available Data analysis sometimes requires the relaxation of parametric assumptions in order to gain modeling flexibility and robustness against mis-specification of the probability model. In the Bayesian context, this is accomplished by placing a prior distribution on a function space, such as the space of all probability distributions or the space of all regression functions. Unfortunately, posterior distributions ranging over function spaces are highly complex and hence sampling methods play a key role. This paper provides an introduction to a simple, yet comprehensive, set of programs for the implementation of some Bayesian nonparametric and semiparametric models in R, DPpackage. Currently, DPpackage includes models for marginal and conditional density estimation, receiver operating characteristic curve analysis, interval-censored data, binary regression data, item response data, longitudinal and clustered data using generalized linear mixed models, and regression data using generalized additive models. The package also contains functions to compute pseudo-Bayes factors for model comparison and for eliciting the precision parameter of the Dirichlet process prior, and a general purpose Metropolis sampling algorithm. To maximize computational efficiency, the actual sampling for each model is carried out using compiled C, C++ or Fortran code.

  4. Decision Support System for Hepatitis Disease Diagnosis using Bayesian Network

    Directory of Open Access Journals (Sweden)

    Shamshad Lakho

    2017-12-01

    Full Text Available Medical judgments are tough and challenging as the decisions are often based on the deficient and ambiguous information. Moreover, the result of decision process has direct effects on human lives. The act of human decision declines in emergency situations due to the complication, time limit, and high risks. Therefore, provision of medical diagnosis plays a dynamic role, specifically in the preliminary stage when a physician has limited diagnosis experience and identifies the directions to be taken for the treatment process. Computerized Decision Support Systems have brought a revolution in the medical diagnosis. These automatic systems support the diagnosticians in the course of diagnosis. The major role of Decision Support Systems is to support the medical personnel in decision-making procedures regarding disease diagnosis and treatment recommendation. The proposed system provides easy support in Hepatitis disease recognition. The system is developed using the Bayesian network model. The physician provides the input to the system in the form of symptoms stated by the patient. These signs and symptoms match with the casual relationships present in the knowledge model. The Bayesian network infers conclusion from the knowledge model and calculates the probability of occurrence of Hepatitis B, C and D disorders.

  5. A Bayesian approach to particle identification in ALICE

    Energy Technology Data Exchange (ETDEWEB)

    Wilkinson, Jeremy [Physikalisches Institut, Ruprecht-Karls-Universitaet Heidelberg (Germany); Collaboration: ALICE-Collaboration

    2016-07-01

    Particle identification (PID) is one of the major strengths of the ALICE detector at the LHC, and provides essential insight into quark-gluon plasma formation in heavy-ion collisions. PID is most effective when complementary identification techniques (such as specific energy loss in the Time Projection Chamber, or flight times measured by the Time Of Flight detector) are combined, however with standard PID techniques it can be difficult to combine these signals, especially when detectors with non-Gaussian responses are used. Here, an alternative probabilistic PID approach based on Bayes' theorem will be presented. This method facilitates the combination of different detector technologies based on the combined probability of a particle type to produce the signals measured in various detectors. The Bayesian PID approach will be briefly outlined, and benchmark analyses will be presented for high-purity samples of pions, kaons, and protons, as well as for the two-pronged decay D{sup 0} → K{sup -}π{sup +}, comparing the performance of the standard PID approach with that of the Bayesian approach. Finally, prospects for measuring the Λ{sub c} baryon in the three-pronged decay channel Λ{sub c}{sup +} → pK{sup -}π{sup +} are presented.

  6. Application of Bayesian Networks to hindcast barrier island morphodynamics

    Science.gov (United States)

    Wilson, Kathleen E.; Adams, Peter N.; Hapke, Cheryl J.; Lentz, Erika E.; Brenner, Owen T.

    2015-01-01

    Prediction of coastal vulnerability is of increasing concern to policy makers, coastal managers and other stakeholders. Coastal regions and barrier islands along the Atlantic and Gulf coasts are subject to frequent, large storms, whose waves and storm surge can dramatically alter beach morphology, threaten infrastructure, and impact local economies. Given that precise forecasts of regional hazards are challenging, because of the complex interactions between processes on many scales, a range of probable geomorphic change in response to storm conditions is often more helpful than deterministic predictions. Site-specific probabilistic models of coastal change are reliable because they are formulated with observations so that local factors, of potentially high influence, are inherent in the model. The development and use of predictive tools such as Bayesian Networks in response to future storms has the potential to better inform management decisions and hazard preparation in coastal communities. We present several Bayesian Networks designed to hindcast distinct morphologic changes attributable to the Nor'Ida storm of 2009, at Fire Island, New York. Model predictions are informed with historical system behavior, initial morphologic conditions, and a parameterized treatment of wave climate.

  7. Implementation of a Bayesian Engine for Uncertainty Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Leng Vang; Curtis Smith; Steven Prescott

    2014-08-01

    In probabilistic risk assessment, it is important to have an environment where analysts have access to a shared and secured high performance computing and a statistical analysis tool package. As part of the advanced small modular reactor probabilistic risk analysis framework implementation, we have identified the need for advanced Bayesian computations. However, in order to make this technology available to non-specialists, there is also a need of a simplified tool that allows users to author models and evaluate them within this framework. As a proof-of-concept, we have implemented an advanced open source Bayesian inference tool, OpenBUGS, within the browser-based cloud risk analysis framework that is under development at the Idaho National Laboratory. This development, the “OpenBUGS Scripter” has been implemented as a client side, visual web-based and integrated development environment for creating OpenBUGS language scripts. It depends on the shared server environment to execute the generated scripts and to transmit results back to the user. The visual models are in the form of linked diagrams, from which we automatically create the applicable OpenBUGS script that matches the diagram. These diagrams can be saved locally or stored on the server environment to be shared with other users.

  8. Network structure exploration via Bayesian nonparametric models

    International Nuclear Information System (INIS)

    Chen, Y; Wang, X L; Xiang, X; Tang, B Z; Bu, J Z

    2015-01-01

    Complex networks provide a powerful mathematical representation of complex systems in nature and society. To understand complex networks, it is crucial to explore their internal structures, also called structural regularities. The task of network structure exploration is to determine how many groups there are in a complex network and how to group the nodes of the network. Most existing structure exploration methods need to specify either a group number or a certain type of structure when they are applied to a network. In the real world, however, the group number and also the certain type of structure that a network has are usually unknown in advance. To explore structural regularities in complex networks automatically, without any prior knowledge of the group number or the certain type of structure, we extend a probabilistic mixture model that can handle networks with any type of structure but needs to specify a group number using Bayesian nonparametric theory. We also propose a novel Bayesian nonparametric model, called the Bayesian nonparametric mixture (BNPM) model. Experiments conducted on a large number of networks with different structures show that the BNPM model is able to explore structural regularities in networks automatically with a stable, state-of-the-art performance. (paper)

  9. Bayesian analyses of seasonal runoff forecasts

    Science.gov (United States)

    Krzysztofowicz, R.; Reese, S.

    1991-12-01

    Forecasts of seasonal snowmelt runoff volume provide indispensable information for rational decision making by water project operators, irrigation district managers, and farmers in the western United States. Bayesian statistical models and communication frames have been researched in order to enhance the forecast information disseminated to the users, and to characterize forecast skill from the decision maker's point of view. Four products are presented: (i) a Bayesian Processor of Forecasts, which provides a statistical filter for calibrating the forecasts, and a procedure for estimating the posterior probability distribution of the seasonal runoff; (ii) the Bayesian Correlation Score, a new measure of forecast skill, which is related monotonically to the ex ante economic value of forecasts for decision making; (iii) a statistical predictor of monthly cumulative runoffs within the snowmelt season, conditional on the total seasonal runoff forecast; and (iv) a framing of the forecast message that conveys the uncertainty associated with the forecast estimates to the users. All analyses are illustrated with numerical examples of forecasts for six gauging stations from the period 1971 1988.

  10. Bayesian Analysis of Individual Level Personality Dynamics

    Directory of Open Access Journals (Sweden)

    Edward Cripps

    2016-07-01

    Full Text Available A Bayesian technique with analyses of within-person processes at the level of the individual is presented. The approach is used to examine if the patterns of within-person responses on a 12 trial simulation task are consistent with the predictions of ITA theory (Dweck, 1999. ITA theory states that the performance of an individual with an entity theory of ability is more likely to spiral down following a failure experience than the performance of an individual with an incremental theory of ability. This is because entity theorists interpret failure experiences as evidence of a lack of ability, which they believe is largely innate and therefore relatively fixed; whilst incremental theorists believe in the malleability of abilities and interpret failure experiences as evidence of more controllable factors such as poor strategy or lack of effort. The results of our analyses support ITA theory at both the within- and between-person levels of analyses and demonstrate the benefits of Bayesian techniques for the analysis of within-person processes. These include more formal specification of the theory and the ability to draw inferences about each individual, which allows for more nuanced interpretations of individuals within a personality category, such as differences in the individual probabilities of spiralling. While Bayesian techniques have many potential advantages for the analyses of within-person processes at the individual level, ease of use is not one of them for psychologists trained in traditional frequentist statistical techniques.

  11. Discriminative Bayesian Dictionary Learning for Classification.

    Science.gov (United States)

    Akhtar, Naveed; Shafait, Faisal; Mian, Ajmal

    2016-12-01

    We propose a Bayesian approach to learn discriminative dictionaries for sparse representation of data. The proposed approach infers probability distributions over the atoms of a discriminative dictionary using a finite approximation of Beta Process. It also computes sets of Bernoulli distributions that associate class labels to the learned dictionary atoms. This association signifies the selection probabilities of the dictionary atoms in the expansion of class-specific data. Furthermore, the non-parametric character of the proposed approach allows it to infer the correct size of the dictionary. We exploit the aforementioned Bernoulli distributions in separately learning a linear classifier. The classifier uses the same hierarchical Bayesian model as the dictionary, which we present along the analytical inference solution for Gibbs sampling. For classification, a test instance is first sparsely encoded over the learned dictionary and the codes are fed to the classifier. We performed experiments for face and action recognition; and object and scene-category classification using five public datasets and compared the results with state-of-the-art discriminative sparse representation approaches. Experiments show that the proposed Bayesian approach consistently outperforms the existing approaches.

  12. Bayesian posterior distributions without Markov chains.

    Science.gov (United States)

    Cole, Stephen R; Chu, Haitao; Greenland, Sander; Hamra, Ghassan; Richardson, David B

    2012-03-01

    Bayesian posterior parameter distributions are often simulated using Markov chain Monte Carlo (MCMC) methods. However, MCMC methods are not always necessary and do not help the uninitiated understand Bayesian inference. As a bridge to understanding Bayesian inference, the authors illustrate a transparent rejection sampling method. In example 1, they illustrate rejection sampling using 36 cases and 198 controls from a case-control study (1976-1983) assessing the relation between residential exposure to magnetic fields and the development of childhood cancer. Results from rejection sampling (odds ratio (OR) = 1.69, 95% posterior interval (PI): 0.57, 5.00) were similar to MCMC results (OR = 1.69, 95% PI: 0.58, 4.95) and approximations from data-augmentation priors (OR = 1.74, 95% PI: 0.60, 5.06). In example 2, the authors apply rejection sampling to a cohort study of 315 human immunodeficiency virus seroconverters (1984-1998) to assess the relation between viral load after infection and 5-year incidence of acquired immunodeficiency syndrome, adjusting for (continuous) age at seroconversion and race. In this more complex example, rejection sampling required a notably longer run time than MCMC sampling but remained feasible and again yielded similar results. The transparency of the proposed approach comes at a price of being less broadly applicable than MCMC.

  13. Bayesian methodology for reliability model acceptance

    International Nuclear Information System (INIS)

    Zhang Ruoxue; Mahadevan, Sankaran

    2003-01-01

    This paper develops a methodology to assess the reliability computation model validity using the concept of Bayesian hypothesis testing, by comparing the model prediction and experimental observation, when there is only one computational model available to evaluate system behavior. Time-independent and time-dependent problems are investigated, with consideration of both cases: with and without statistical uncertainty in the model. The case of time-independent failure probability prediction with no statistical uncertainty is a straightforward application of Bayesian hypothesis testing. However, for the life prediction (time-dependent reliability) problem, a new methodology is developed in this paper to make the same Bayesian hypothesis testing concept applicable. With the existence of statistical uncertainty in the model, in addition to the application of a predictor estimator of the Bayes factor, the uncertainty in the Bayes factor is explicitly quantified through treating it as a random variable and calculating the probability that it exceeds a specified value. The developed method provides a rational criterion to decision-makers for the acceptance or rejection of the computational model

  14. Bayesian outcome-based strategy classification.

    Science.gov (United States)

    Lee, Michael D

    2016-03-01

    Hilbig and Moshagen (Psychonomic Bulletin & Review, 21, 1431-1443, 2014) recently developed a method for making inferences about the decision processes people use in multi-attribute forced choice tasks. Their paper makes a number of worthwhile theoretical and methodological contributions. Theoretically, they provide an insightful psychological motivation for a probabilistic extension of the widely-used "weighted additive" (WADD) model, and show how this model, as well as other important models like "take-the-best" (TTB), can and should be expressed in terms of meaningful priors. Methodologically, they develop an inference approach based on the Minimum Description Length (MDL) principles that balances both the goodness-of-fit and complexity of the decision models they consider. This paper aims to preserve these useful contributions, but provide a complementary Bayesian approach with some theoretical and methodological advantages. We develop a simple graphical model, implemented in JAGS, that allows for fully Bayesian inferences about which models people use to make decisions. To demonstrate the Bayesian approach, we apply it to the models and data considered by Hilbig and Moshagen (Psychonomic Bulletin & Review, 21, 1431-1443, 2014), showing how a prior predictive analysis of the models, and posterior inferences about which models people use and the parameter settings at which they use them, can contribute to our understanding of human decision making.

  15. Being Bayesian in a quantum world

    International Nuclear Information System (INIS)

    Fuchs, C.

    2005-01-01

    Full text: To be a Bayesian about probability theory is to accept that probabilities represent subjective degrees of belief and nothing more. This is in distinction to the idea that probabilities represent long-term frequencies or objective propensities. But, how can a subjective account of probabilities coexist with the existence of quantum mechanics? To accept quantum mechanics is to accept the calculational apparatus of quantum states and the Born rule for determining probabilities in a quantum measurement. If there ever were a place for probabilities to be objective, it ought to be here. This raises the question of whether Bayesianism and quantum mechanics are compatible at all. For the Bayesian, it only suggests that we should rethink what quantum mechanics is about. Is it 'law of nature' or really more 'law of thought'? From transistors to lasers, the evidence is in that we live in a quantum world. One could infer from this that all the elements in the quantum formalism necessarily mirror nature itself: wave functions are so successful as calculational tools precisely because they represent elements of reality. A more Bayesian-like perspective is that if wave functions generate probabilities, then they too must be Bayesian degrees of belief, with all that such a radical idea entails. In particular, quantum probabilities have no firmer hold on reality than the word 'belief' in 'degrees of belief' already indicates. From this perspective, the only sense in which the quantum formalism mirrors nature is through the constraints it places on gambling agents who would like to better navigate through world. One might think that this is thin information, but it is not insubstantial. To the extent that an agent should use quantum mechanics for his uncertainty accounting rather than some other theory tells us something about the world itself - i.e., the world independent of the agent and his particular beliefs at any moment. In this talk, I will try to shore up these

  16. Learning Local Components to Understand Large Bayesian Networks

    DEFF Research Database (Denmark)

    Zeng, Yifeng; Xiang, Yanping; Cordero, Jorge

    2009-01-01

    (domain experts) to extract accurate information from a large Bayesian network due to dimensional difficulty. We define a formulation of local components and propose a clustering algorithm to learn such local components given complete data. The algorithm groups together most inter-relevant attributes......Bayesian networks are known for providing an intuitive and compact representation of probabilistic information and allowing the creation of models over a large and complex domain. Bayesian learning and reasoning are nontrivial for a large Bayesian network. In parallel, it is a tough job for users...... in a domain. We evaluate its performance on three benchmark Bayesian networks and provide results in support. We further show that the learned components may represent local knowledge more precisely in comparison to the full Bayesian networks when working with a small amount of data....

  17. 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.

  18. Towards Bayesian Inference of the Fast-Ion Distribution Function

    DEFF Research Database (Denmark)

    Stagner, L.; Heidbrink, W.W.; Salewski, Mirko

    2012-01-01

    sensitivity of the measurements are incorporated into Bayesian likelihood probabilities, while prior probabilities enforce physical constraints. As an initial step, this poster uses Bayesian statistics to infer the DIII-D electron density profile from multiple diagnostic measurements. Likelihood functions....... However, when theory and experiment disagree (for one or more diagnostics), it is unclear how to proceed. Bayesian statistics provides a framework to infer the DF, quantify errors, and reconcile discrepant diagnostic measurements. Diagnostic errors and ``weight functions" that describe the phase space...

  19. 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

  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. 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 ...

  2. 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...

  3. A surrogate-based sensitivity quantification and Bayesian inversion of a regional groundwater flow model

    Science.gov (United States)

    Chen, Mingjie; Izady, Azizallah; Abdalla, Osman A.; Amerjeed, Mansoor

    2018-02-01

    Bayesian inference using Markov Chain Monte Carlo (MCMC) provides an explicit framework for stochastic calibration of hydrogeologic models accounting for uncertainties; however, the MCMC sampling entails a large number of model calls, and could easily become computationally unwieldy if the high-fidelity hydrogeologic model simulation is time consuming. This study proposes a surrogate-based Bayesian framework to address this notorious issue, and illustrates the methodology by inverse modeling a regional MODFLOW model. The high-fidelity groundwater model is approximated by a fast statistical model using Bagging Multivariate Adaptive Regression Spline (BMARS) algorithm, and hence the MCMC sampling can be efficiently performed. In this study, the MODFLOW model is developed to simulate the groundwater flow in an arid region of Oman consisting of mountain-coast aquifers, and used to run representative simulations to generate training dataset for BMARS model construction. A BMARS-based Sobol' method is also employed to efficiently calculate input parameter sensitivities, which are used to evaluate and rank their importance for the groundwater flow model system. According to sensitivity analysis, insensitive parameters are screened out of Bayesian inversion of the MODFLOW model, further saving computing efforts. The posterior probability distribution of input parameters is efficiently inferred from the prescribed prior distribution using observed head data, demonstrating that the presented BMARS-based Bayesian framework is an efficient tool to reduce parameter uncertainties of a groundwater system.

  4. 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

  5. A Bayesian Justification for Random Sampling in Sample Survey

    Directory of Open Access Journals (Sweden)

    Glen Meeden

    2012-07-01

    Full Text Available In the usual Bayesian approach to survey sampling the sampling design, plays a minimal role, at best. Although a close relationship between exchangeable prior distributions and simple random sampling has been noted; how to formally integrate simple random sampling into the Bayesian paradigm is not clear. Recently it has been argued that the sampling design can be thought of as part of a Bayesian's prior distribution. We will show here that under this scenario simple random sample can be given a Bayesian justification in survey sampling.

  6. 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...

  7. A Bayesian Network Schema for Lessening Database Inference

    National Research Council Canada - National Science Library

    Chang, LiWu; Moskowitz, Ira S

    2001-01-01

    .... The authors introduce a formal schema for database inference analysis, based upon a Bayesian network structure, which identifies critical parameters involved in the inference problem and represents...

  8. Learning Predictive Interactions Using Information Gain and Bayesian Network Scoring.

    Directory of Open Access Journals (Sweden)

    Xia Jiang

    Full Text Available The problems of correlation and classification are long-standing in the fields of statistics and machine learning, and techniques have been developed to address these problems. We are now in the era of high-dimensional data, which is data that can concern billions of variables. These data present new challenges. In particular, it is difficult to discover predictive variables, when each variable has little marginal effect. An example concerns Genome-wide Association Studies (GWAS datasets, which involve millions of single nucleotide polymorphism (SNPs, where some of the SNPs interact epistatically to affect disease status. Towards determining these interacting SNPs, researchers developed techniques that addressed this specific problem. However, the problem is more general, and so these techniques are applicable to other problems concerning interactions. A difficulty with many of these techniques is that they do not distinguish whether a learned interaction is actually an interaction or whether it involves several variables with strong marginal effects.We address this problem using information gain and Bayesian network scoring. First, we identify candidate interactions by determining whether together variables provide more information than they do separately. Then we use Bayesian network scoring to see if a candidate interaction really is a likely model. Our strategy is called MBS-IGain. Using 100 simulated datasets and a real GWAS Alzheimer's dataset, we investigated the performance of MBS-IGain.When analyzing the simulated datasets, MBS-IGain substantially out-performed nine previous methods at locating interacting predictors, and at identifying interactions exactly. When analyzing the real Alzheimer's dataset, we obtained new results and results that substantiated previous findings. We conclude that MBS-IGain is highly effective at finding interactions in high-dimensional datasets. This result is significant because we have increasingly

  9. Uncertainty Quantification Bayesian Framework for Porous Media Flows

    Science.gov (United States)

    Demyanov, V.; Christie, M.; Erbas, D.

    2005-12-01

    Uncertainty quantification is an increasingly important aspect of many areas of applied science, where the challenge is to make reliable predictions about the performance of complex physical systems in the absence of complete or reliable data. Predicting flows of fluids through undersurface reservoirs is an example of a complex system where accuracy in prediction is needed (e.g. in oil industry it is essential for financial reasons). Simulation of fluid flow in oil reservoirs is usually carried out using large commercially written finite difference simulators solving conservation equations describing the multi-phase flow through the porous reservoir rocks, which is a highly computationally expensive task. This work examines a Bayesian Framework for uncertainty quantification in porous media flows that uses a stochastic sampling algorithm to generate models that match observed time series data. The framework is flexible for a wide range of general physical/statistical parametric models, which are used to describe the underlying hydro-geological process in its temporal dynamics. The approach is based on exploration of the parameter space and update of the prior beliefs about what the most likely model definitions are. Optimization problem for a highly parametric physical model usually have multiple solutions, which impact the uncertainty of the made predictions. Stochastic search algorithm (e.g. genetic algorithm) allows to identify multiple "good enough" models in the parameter space. Furthermore, inference of the generated model ensemble via MCMC based algorithm evaluates the posterior probability of the generated models and quantifies uncertainty of the predictions. Machine learning algorithm - Artificial Neural Networks - are used to speed up the identification of regions in parameter space where good matches to observed data can be found. Adaptive nature of ANN allows to develop different ways of integrating them into the Bayesian framework: as direct time

  10. Bayesian Uncertainty Quantification for Subsurface Inversion Using a Multiscale Hierarchical Model

    KAUST Repository

    Mondal, Anirban

    2014-07-03

    We consider a Bayesian approach to nonlinear inverse problems in which the unknown quantity is a random field (spatial or temporal). The Bayesian approach contains a natural mechanism for regularization in the form of prior information, can incorporate information from heterogeneous sources and provide a quantitative assessment of uncertainty in the inverse solution. The Bayesian setting casts the inverse solution as a posterior probability distribution over the model parameters. The Karhunen-Loeve expansion is used for dimension reduction of the random field. Furthermore, we use a hierarchical Bayes model to inject multiscale data in the modeling framework. In this Bayesian framework, we show that this inverse problem is well-posed by proving that the posterior measure is Lipschitz continuous with respect to the data in total variation norm. Computational challenges in this construction arise from the need for repeated evaluations of the forward model (e.g., in the context of MCMC) and are compounded by high dimensionality of the posterior. We develop two-stage reversible jump MCMC that has the ability to screen the bad proposals in the first inexpensive stage. Numerical results are presented by analyzing simulated as well as real data from hydrocarbon reservoir. This article has supplementary material available online. © 2014 American Statistical Association and the American Society for Quality.

  11. Development of uncertainty-based work injury model using Bayesian structural equation modelling.

    Science.gov (United States)

    Chatterjee, Snehamoy

    2014-01-01

    This paper proposed a Bayesian method-based structural equation model (SEM) of miners' work injury for an underground coal mine in India. The environmental and behavioural variables for work injury were identified and causal relationships were developed. For Bayesian modelling, prior distributions of SEM parameters are necessary to develop the model. In this paper, two approaches were adopted to obtain prior distribution for factor loading parameters and structural parameters of SEM. In the first approach, the prior distributions were considered as a fixed distribution function with specific parameter values, whereas, in the second approach, prior distributions of the parameters were generated from experts' opinions. The posterior distributions of these parameters were obtained by applying Bayesian rule. The Markov Chain Monte Carlo sampling in the form Gibbs sampling was applied for sampling from the posterior distribution. The results revealed that all coefficients of structural and measurement model parameters are statistically significant in experts' opinion-based priors, whereas, two coefficients are not statistically significant when fixed prior-based distributions are applied. The error statistics reveals that Bayesian structural model provides reasonably good fit of work injury with high coefficient of determination (0.91) and less mean squared error as compared to traditional SEM.

  12. Bayesian methodology for generic seismic fragility evaluation of components in nuclear power plants

    International Nuclear Information System (INIS)

    Yamaguchi, Akira; Campbell, R.D.; Ravindra, M.K.

    1991-01-01

    Bayesian methodology for updating the seismic fragility of components in nuclear power plants is presented. The generic fragility data which have been evaluated based on the past SPSAs are combined with the seismic experience data. Although the seismic experience is limited to the acceleration range below the median capacity of the components, it has been found that the evidence is effective to update the fragility tail. In other words, the uncertainty of the fragility is reduced although the median capacity itself is not modified to a great extent. The annual frequency of failure is also reduced as a result of the updating of the fragility tail. The PDF of the seismic capacity is handled in discrete form, which enables the use of arbitrary type of prior distribution. Accordingly, the Log-N prior can be used which is consistent with the widely used fragility model. For evaluating posterior fragility parameters (A m and B U ), two methods have been proposed. Furthermore, it has been found that the importance of evidence used in the Bayesian methodology can be quantified by the entropy of the evidence. Only the events with high entropy need to be considered in the Bayesian updating of the fragility. The currently available seismic experience database for typical components can be utilized to develop the fragility tail which is contributive to the seismically-induced failure frequency. The combined use of generic fragility and seismic experience data, with the aid of Bayesian methodology, provides refined generic fragility curves which are useful for SPSA studies. (author)

  13. 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.

  14. On local optima in learning bayesian networks

    DEFF Research Database (Denmark)

    Dalgaard, Jens; Kocka, Tomas; Pena, Jose

    2003-01-01

    This paper proposes and evaluates the k-greedy equivalence search algorithm (KES) for learning Bayesian networks (BNs) from complete data. The main characteristic of KES is that it allows a trade-off between greediness and randomness, thus exploring different good local optima. When greediness...... is set at maximum, KES corresponds to the greedy equivalence search algorithm (GES). When greediness is kept at minimum, we prove that under mild assumptions KES asymptotically returns any inclusion optimal BN with nonzero probability. Experimental results for both synthetic and real data are reported...

  15. A Bayesian concept learning approach to crowdsourcing

    DEFF Research Database (Denmark)

    Viappiani, P.; Zilles, S.; Hamilton, H.J.

    2011-01-01

    techniques, inference methods, and query selection strategies to assist a user charged with choosing a configuration that satisfies some (partially known) concept. Our model is able to simultaneously learn the concept definition and the types of the experts. We evaluate our model with simulations, showing......We develop a Bayesian approach to concept learning for crowdsourcing applications. A probabilistic belief over possible concept definitions is maintained and updated according to (noisy) observations from experts, whose behaviors are modeled using discrete types. We propose recommendation...

  16. Default Bayesian Estimation of the Fundamental Frequency

    DEFF Research Database (Denmark)

    Nielsen, Jesper Kjær; Christensen, Mads Græsbøll; Jensen, Søren Holdt

    2013-01-01

    Joint fundamental frequency and model order esti- mation is an important problem in several applications. In this paper, a default estimation algorithm based on a minimum of prior information is presented. The algorithm is developed in a Bayesian framework, and it can be applied to both real....... Moreover, several approximations of the posterior distributions on the fundamental frequency and the model order are derived, and one of the state-of-the-art joint fundamental frequency and model order estimators is demonstrated to be a special case of one of these approximations. The performance...

  17. Bayesian regression of piecewise homogeneous Poisson processes

    Directory of Open Access Journals (Sweden)

    Diego Sevilla

    2015-12-01

    Full Text Available In this paper, a Bayesian method for piecewise regression is adapted to handle counting processes data distributed as Poisson. A numerical code in Mathematica is developed and tested analyzing simulated data. The resulting method is valuable for detecting breaking points in the count rate of time series for Poisson processes. Received: 2 November 2015, Accepted: 27 November 2015; Edited by: R. Dickman; Reviewed by: M. Hutter, Australian National University, Canberra, Australia.; DOI: http://dx.doi.org/10.4279/PIP.070018 Cite as: D J R Sevilla, Papers in Physics 7, 070018 (2015

  18. Bayesian regularization of diffusion tensor images

    DEFF Research Database (Denmark)

    Frandsen, Jesper; Hobolth, Asger; Østergaard, Leif

    2007-01-01

    Diffusion tensor imaging (DTI) is a powerful tool in the study of the course of nerve fibre bundles in the human brain. Using DTI, the local fibre orientation in each image voxel can be described by a diffusion tensor which is constructed from local measurements of diffusion coefficients along...... several directions. The measured diffusion coefficients and thereby the diffusion tensors are subject to noise, leading to possibly flawed representations of the three dimensional fibre bundles. In this paper we develop a Bayesian procedure for regularizing the diffusion tensor field, fully utilizing...

  19. Bayesian estimation of core-melt probability

    International Nuclear Information System (INIS)

    Lewis, H.W.

    1984-01-01

    A very simple application of the canonical Bayesian algorithm is made to the problem of estimation of the probability of core melt in a commercial power reactor. An approximation to the results of the Rasmussen study on reactor safety is used as the prior distribution, and the observation that there has been no core melt yet is used as the single experiment. The result is a substantial decrease in the mean probability of core melt--factors of 2 to 4 for reasonable choices of parameters. The purpose is to illustrate the procedure, not to argue for the decrease

  20. Optimized Bayesian dynamic advising theory and algorithms

    CERN Document Server

    Karny, Miroslav

    2006-01-01

    Written by one of the world's leading groups in the area of Bayesian identification, control, and decision making, this book provides the theoretical and algorithmic basis of optimized probabilistic advising. Starting from abstract ideas and formulations, and culminating in detailed algorithms, the book comprises a unified treatment of an important problem of the design of advisory systems supporting supervisors of complex processes. It introduces the theoretical and algorithmic basis of developed advising, relying on novel and powerful combination black-box modelling by dynamic mixture models

  1. Bayesian Predictive Models for Rayleigh Wind Speed

    DEFF Research Database (Denmark)

    Shahirinia, Amir; Hajizadeh, Amin; Yu, David C

    2017-01-01

    predictive model of the wind speed aggregates the non-homogeneous distributions into a single continuous distribution. Therefore, the result is able to capture the variation among the probability distributions of the wind speeds at the turbines’ locations in a wind farm. More specifically, instead of using...... a wind speed distribution whose parameters are known or estimated, the parameters are considered as random whose variations are according to probability distributions. The Bayesian predictive model for a Rayleigh which only has a single model scale parameter has been proposed. Also closed-form posterior...... and predictive inferences under different reasonable choices of prior distribution in sensitivity analysis have been presented....

  2. Bayesian stratified sampling to assess corpus utility

    Energy Technology Data Exchange (ETDEWEB)

    Hochberg, J.; Scovel, C.; Thomas, T.; Hall, S.

    1998-12-01

    This paper describes a method for asking statistical questions about a large text corpus. The authors exemplify the method by addressing the question, ``What percentage of Federal Register documents are real documents, of possible interest to a text researcher or analyst?`` They estimate an answer to this question by evaluating 200 documents selected from a corpus of 45,820 Federal Register documents. Bayesian analysis and stratified sampling are used to reduce the sampling uncertainty of the estimate from over 3,100 documents to fewer than 1,000. A possible application of the method is to establish baseline statistics used to estimate recall rates for information retrieval systems.

  3. Personalized Audio Systems - a Bayesian Approach

    DEFF Research Database (Denmark)

    Nielsen, Jens Brehm; Jensen, Bjørn Sand; Hansen, Toke Jansen

    2013-01-01

    Modern audio systems are typically equipped with several user-adjustable parameters unfamiliar to most users listening to the system. To obtain the best possible setting, the user is forced into multi-parameter optimization with respect to the users's own objective and preference. To address this......, the present paper presents a general inter-active framework for personalization of such audio systems. The framework builds on Bayesian Gaussian process regression in which a model of the users's objective function is updated sequentially. The parameter setting to be evaluated in a given trial is selected...

  4. On Bayesian treatment of systematic uncertainties in confidence interval calculation

    CERN Document Server

    Tegenfeldt, Fredrik

    2005-01-01

    In high energy physics, a widely used method to treat systematic uncertainties in confidence interval calculations is based on combining a frequentist construction of confidence belts with a Bayesian treatment of systematic uncertainties. In this note we present a study of the coverage of this method for the standard Likelihood Ratio (aka Feldman & Cousins) construction for a Poisson process with known background and Gaussian or log-Normal distributed uncertainties in the background or signal efficiency. For uncertainties in the signal efficiency of upto 40 % we find over-coverage on the level of 2 to 4 % depending on the size of uncertainties and the region in signal space. Uncertainties in the background generally have smaller effect on the coverage. A considerable smoothing of the coverage curves is observed. A software package is presented which allows fast calculation of the confidence intervals for a variety of assumptions on shape and size of systematic uncertainties for different nuisance paramete...

  5. 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.

  6. Web multimedia information retrieval using improved Bayesian algorithm.

    Science.gov (United States)

    Yu, Yi-Jun; Chen, Chun; Yu, Yi-Min; Lin, Huai-Zhong

    2003-01-01

    The main thrust of this paper is application of a novel data mining approach on the log of user's feedback to improve web multimedia information retrieval performance. A user space model was constructed based on data mining, and then integrated into the original information space model to improve the accuracy of the new information space model. It can remove clutter and irrelevant text information and help to eliminate mismatch between the page author's expression and the user's understanding and expectation. User space model was also utilized to discover the relationship between high-level and low-level features for assigning weight. The authors proposed improved Bayesian algorithm for data mining. Experiment proved that the authors' proposed algorithm was efficient.

  7. 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.

  8. Experimental validation of a Bayesian model of visual acuity.

    LENUS (Irish Health Repository)

    Dalimier, Eugénie

    2009-01-01

    Based on standard procedures used in optometry clinics, we compare measurements of visual acuity for 10 subjects (11 eyes tested) in the presence of natural ocular aberrations and different degrees of induced defocus, with the predictions given by a Bayesian model customized with aberrometric data of the eye. The absolute predictions of the model, without any adjustment, show good agreement with the experimental data, in terms of correlation and absolute error. The efficiency of the model is discussed in comparison with image quality metrics and other customized visual process models. An analysis of the importance and customization of each stage of the model is also given; it stresses the potential high predictive power from precise modeling of ocular and neural transfer functions.

  9. Sampling-free Bayesian inversion with adaptive hierarchical tensor representations

    Science.gov (United States)

    Eigel, Martin; Marschall, Manuel; Schneider, Reinhold

    2018-03-01

    A sampling-free approach to Bayesian inversion with an explicit polynomial representation of the parameter densities is developed, based on an affine-parametric representation of a linear forward model. This becomes feasible due to the complete treatment in function spaces, which requires an efficient model reduction technique for numerical computations. The advocated perspective yields the crucial benefit that error bounds can be derived for all occuring approximations, leading to provable convergence subject to the discretization parameters. Moreover, it enables a fully adaptive a posteriori control with automatic problem-dependent adjustments of the employed discretizations. The method is discussed in the context of modern hierarchical tensor representations, which are used for the evaluation of a random PDE (the forward model) and the subsequent high-dimensional quadrature of the log-likelihood, alleviating the ‘curse of dimensionality’. Numerical experiments demonstrate the performance and confirm the theoretical results.

  10. Variational Bayesian Causal Connectivity Analysis for fMRI

    Directory of Open Access Journals (Sweden)

    Martin eLuessi

    2014-05-01

    Full Text Available The ability to accurately estimate effective connectivity among brain regions from neuroimaging data could help answering many open questions in neuroscience. We propose a method which uses causality to obtain a measure of effective connectivity from fMRI data. The method uses a vector autoregressive model for the latent variables describing neuronal activity in combination with a linear observation model based on a convolution with a hemodynamic response function. Due to the employed modeling, it is possible to efficiently estimate all latent variables of the model using a variational Bayesian inference algorithm. The computational efficiency of the method enables us to apply it to large scale problems with high sampling rates and several hundred regions of interest. We use a comprehensive empirical evaluation with synthetic and real fMRI data to evaluate the performance of our method under various conditions.

  11. 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...

  12. Bayesian quantitative precipitation forecasts in terms of quantiles

    Science.gov (United States)

    Bentzien, Sabrina; Friederichs, Petra

    2014-05-01

    Ensemble prediction systems (EPS) for numerical weather predictions on the mesoscale are particularly developed to obtain probabilistic guidance for high impact weather. An EPS not only issues a deterministic future state of the atmosphere but a sample of possible future states. Ensemble postprocessing then translates such a sample of forecasts into probabilistic measures. This study focus on probabilistic quantitative precipitation forecasts in terms of quantiles. Quantiles are particular suitable to describe precipitation at various locations, since no assumption is required on the distribution of precipitation. The focus is on the prediction during high-impact events and related to the Volkswagen Stiftung funded project WEX-MOP (Mesoscale Weather Extremes - Theory, Spatial Modeling and Prediction). Quantile forecasts are derived from the raw ensemble and via quantile regression. Neighborhood method and time-lagging are effective tools to inexpensively increase the ensemble spread, which results in more reliable forecasts especially for extreme precipitation events. Since an EPS provides a large amount of potentially informative predictors, a variable selection is required in order to obtain a stable statistical model. A Bayesian formulation of quantile regression allows for inference about the selection of predictive covariates by the use of appropriate prior distributions. Moreover, the implementation of an additional process layer for the regression parameters accounts for spatial variations of the parameters. Bayesian quantile regression and its spatially adaptive extension is illustrated for the German-focused mesoscale weather prediction ensemble COSMO-DE-EPS, which runs (pre)operationally since December 2010 at the German Meteorological Service (DWD). Objective out-of-sample verification uses the quantile score (QS), a weighted absolute error between quantile forecasts and observations. The QS is a proper scoring function and can be decomposed into

  13. Mechanistic curiosity will not kill the Bayesian cat

    NARCIS (Netherlands)

    Borsboom, D.; Wagenmakers, E.-J.; Romeijn, J.-W.

    2011-01-01

    Jones & Love (J&L) suggest that Bayesian approaches to the explanation of human behavior should be constrained by mechanistic theories. We argue that their proposal misconstrues the relation between process models, such as the Bayesian model, and mechanisms. While mechanistic theories can answer

  14. Mechanistic curiosity will not kill the Bayesian cat

    NARCIS (Netherlands)

    Borsboom, Denny; Wagenmakers, Eric-Jan; Romeijn, Jan-Willem

    Jones & Love (J&L) suggest that Bayesian approaches to the explanation of human behavior should be constrained by mechanistic theories. We argue that their proposal misconstrues the relation between process models, such as the Bayesian model, and mechanisms. While mechanistic theories can answer

  15. A default Bayesian hypothesis test for correlations and partial correlations

    NARCIS (Netherlands)

    Wetzels, R.; Wagenmakers, E.J.

    2012-01-01

    We propose a default Bayesian hypothesis test for the presence of a correlation or a partial correlation. The test is a direct application of Bayesian techniques for variable selection in regression models. The test is easy to apply and yields practical advantages that the standard frequentist tests

  16. Applications of Bayesian decision theory to intelligent tutoring systems

    NARCIS (Netherlands)

    Vos, Hendrik J.

    1994-01-01

    Some applications of Bayesian decision theory to intelligent tutoring systems are considered. How the problem of adapting the appropriate amount of instruction to the changing nature of a student's capabilities during the learning process can be situated in the general framework of Bayesian decision

  17. Systematic search of Bayesian statistics in the field of psychotraumatology

    NARCIS (Netherlands)

    van de Schoot, Rens; Schalken, Naomi; Olff, Miranda

    2017-01-01

    In many different disciplines there is a recent increase in interest of Bayesian analysis. Bayesian methods implement Bayes' theorem, which states that prior beliefs are updated with data, and this process produces updated beliefs about model parameters. The prior is based on how much information we

  18. Power in Bayesian Mediation Analysis for Small Sample Research

    NARCIS (Netherlands)

    Miočević, M.; MacKinnon, David; Levy, Roy

    2017-01-01

    Bayesian methods have the potential for increasing power in mediation analysis (Koopman, Howe, Hollenbeck, & Sin, 2015; Yuan & MacKinnon, 2009). This article compares the power of Bayesian credibility intervals for the mediated effect to the power of normal theory, distribution of the product,

  19. An introduction to Bayesian statistics in health psychology

    NARCIS (Netherlands)

    Depaoli, Sarah; Rus, Holly; Clifton, James; van de Schoot, A.G.J.; Tiemensma, Jitske

    2017-01-01

    The aim of the current article is to provide a brief introduction to Bayesian statistics within the field of Health Psychology. Bayesian methods are increasing in prevalence in applied fields, and they have been shown in simulation research to improve the estimation accuracy of structural equation

  20. Bayesian Estimation of Wave Spectra – Proper Formulation of ABIC

    DEFF Research Database (Denmark)

    Nielsen, Ulrik Dam

    2007-01-01

    It is possible to estimate on-site wave spectra using measured ship responses applied to Bayesian Modelling based on two prior information: the wave spectrum must be smooth both directional-wise and frequency-wise. This paper introduces two hyperparameters into Bayesian Modelling and, hence, a pr...