Hongqiang Liu
2016-06-01
Full Text Available A Bayesian random effects modeling approach was used to examine the influence of neighborhood characteristics on burglary risks in Jianghan District, Wuhan, China. This random effects model is essentially spatial; a spatially structured random effects term and an unstructured random effects term are added to the traditional non-spatial Poisson regression model. Based on social disorganization and routine activity theories, five covariates extracted from the available data at the neighborhood level were used in the modeling. Three regression models were fitted and compared by the deviance information criterion to identify which model best fit our data. A comparison of the results from the three models indicates that the Bayesian random effects model is superior to the non-spatial models in fitting the data and estimating regression coefficients. Our results also show that neighborhoods with above average bar density and department store density have higher burglary risks. Neighborhood-specific burglary risks and posterior probabilities of neighborhoods having a burglary risk greater than 1.0 were mapped, indicating the neighborhoods that should warrant more attention and be prioritized for crime intervention and reduction. Implications and limitations of the study are discussed in our concluding section.
A Bayesian Analysis of a Random Effects Small Business Loan Credit Scoring Model
Patrick J. Farrell
2011-09-01
Full Text Available One of the most important aspects of credit scoring is constructing a model that has low misclassification rates and is also flexible enough to allow for random variation. It is also well known that, when there are a large number of highly correlated variables as is typical in studies involving questionnaire data, a method must be found to reduce the number of variables to those that have high predictive power. Here we propose a Bayesian multivariate logistic regression model with both fixed and random effects for small business loan credit scoring and a variable reduction method using Bayes factors. The method is illustrated on an interesting data set based on questionnaires sent to loan officers in Canadian banks and venture capital companies
Enrique Gracia
2014-01-01
Full Text Available This paper uses spatial data of cases of intimate partner violence against women (IPVAW to examine neighborhood-level influences on small-area variations in IPVAW risk in a police district of the city of Valencia (Spain. To analyze area variations in IPVAW risk and its association with neighborhood-level explanatory variables we use a Bayesian spatial random-effects modeling approach, as well as disease mapping methods to represent risk probabilities in each area. Analyses show that IPVAW cases are more likely in areas of high immigrant concentration, high public disorder and crime, and high physical disorder. Results also show a spatial component indicating remaining variability attributable to spatially structured random effects. Bayesian spatial modeling offers a new perspective to identify IPVAW high and low risk areas, and provides a new avenue for the design of better-informed prevention and intervention strategies.
Megas Françoise
2010-03-01
Full Text Available Abstract Background Antibodies directed against haemagglutinin, measured by the haemagglutination inhibition (HI assay are essential to protective immunity against influenza infection. An HI titre of 1:40 is generally accepted to correspond to a 50% reduction in the risk of contracting influenza in a susceptible population, but limited attempts have been made to further quantify the association between HI titre and protective efficacy. Methods We present a model, using a meta-analytical approach, that estimates the level of clinical protection against influenza at any HI titre level. Source data were derived from a systematic literature review that identified 15 studies, representing a total of 5899 adult subjects and 1304 influenza cases with interval-censored information on HI titre. The parameters of the relationship between HI titre and clinical protection were estimated using Bayesian inference with a consideration of random effects and censorship in the available information. Results A significant and positive relationship between HI titre and clinical protection against influenza was observed in all tested models. This relationship was found to be similar irrespective of the type of viral strain (A or B and the vaccination status of the individuals. Conclusion Although limitations in the data used should not be overlooked, the relationship derived in this analysis provides a means to predict the efficacy of inactivated influenza vaccines when only immunogenicity data are available. This relationship can also be useful for comparing the efficacy of different influenza vaccines based on their immunological profile.
Random Effects Cox Models: A Poisson Modelling Approach
Renjun Ma; Daniel Krewski; Burnett, Richard T.
2000-01-01
We propose a Poisson modelling approach to random effects Cox proportional hazards models. Specifically we describe methods of statistical inference for a class of random effects Cox models which accommodate a wide range of nested random effects distributions. The orthodox BLUP approach to random effects Poisson modeling techniques enables us to study this new class of models as a single class, rather than as a collection of unrelated models. The explicit expressions for the random effects gi...
Ryu, Duchwan
2010-09-28
We consider nonparametric regression analysis in a generalized linear model (GLM) framework for data with covariates that are the subject-specific random effects of longitudinal measurements. The usual assumption that the effects of the longitudinal covariate processes are linear in the GLM may be unrealistic and if this happens it can cast doubt on the inference of observed covariate effects. Allowing the regression functions to be unknown, we propose to apply Bayesian nonparametric methods including cubic smoothing splines or P-splines for the possible nonlinearity and use an additive model in this complex setting. To improve computational efficiency, we propose the use of data-augmentation schemes. The approach allows flexible covariance structures for the random effects and within-subject measurement errors of the longitudinal processes. The posterior model space is explored through a Markov chain Monte Carlo (MCMC) sampler. The proposed methods are illustrated and compared to other approaches, the "naive" approach and the regression calibration, via simulations and by an application that investigates the relationship between obesity in adulthood and childhood growth curves. © 2010, The International Biometric Society.
Huang, Hung-Yu; Wang, Wen-Chung
2014-01-01
The DINA (deterministic input, noisy, and gate) model has been widely used in cognitive diagnosis tests and in the process of test development. The outcomes known as slip and guess are included in the DINA model function representing the responses to the items. This study aimed to extend the DINA model by using the random-effect approach to allow…
Random effect selection in generalised linear models
Denwood, Matt; Houe, Hans; Forkman, Björn;
We analysed abattoir recordings of meat inspection codes with possible relevance to onfarm animal welfare in cattle. Random effects logistic regression models were used to describe individual-level data obtained from 461,406 cattle slaughtered in Denmark. Our results demonstrate that the largest...
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 and...... largely due to the availability of efficient inference algorithms for answering probabilistic queries about the states of the variables in the network. Furthermore, to support the construction of Bayesian network models, learning algorithms are also available. We give an overview of the Bayesian network...
Beretvas, S. Natasha; Murphy, Daniel L.
2013-01-01
The authors assessed correct model identification rates of Akaike's information criterion (AIC), corrected criterion (AICC), consistent AIC (CAIC), Hannon and Quinn's information criterion (HQIC), and Bayesian information criterion (BIC) for selecting among cross-classified random effects models. Performance of default values for the 5…
Bayesian default probability models
Andrlíková, Petra
2014-01-01
This paper proposes a methodology for default probability estimation for low default portfolios, where the statistical inference may become troublesome. The author suggests using logistic regression models with the Bayesian estimation of parameters. The piecewise logistic regression model and Box-Cox transformation of credit risk score is used to derive the estimates of probability of default, which extends the work by Neagu et al. (2009). The paper shows that the Bayesian models are more acc...
Steyerberg Ewout W
2011-05-01
Full Text Available Abstract Background Logistic random effects models are a popular tool to analyze multilevel also called hierarchical data with a binary or ordinal outcome. Here, we aim to compare different statistical software implementations of these models. Methods We used individual patient data from 8509 patients in 231 centers with moderate and severe Traumatic Brain Injury (TBI enrolled in eight Randomized Controlled Trials (RCTs and three observational studies. We fitted logistic random effects regression models with the 5-point Glasgow Outcome Scale (GOS as outcome, both dichotomized as well as ordinal, with center and/or trial as random effects, and as covariates age, motor score, pupil reactivity or trial. We then compared the implementations of frequentist and Bayesian methods to estimate the fixed and random effects. Frequentist approaches included R (lme4, Stata (GLLAMM, SAS (GLIMMIX and NLMIXED, MLwiN ([R]IGLS and MIXOR, Bayesian approaches included WinBUGS, MLwiN (MCMC, R package MCMCglmm and SAS experimental procedure MCMC. Three data sets (the full data set and two sub-datasets were analysed using basically two logistic random effects models with either one random effect for the center or two random effects for center and trial. For the ordinal outcome in the full data set also a proportional odds model with a random center effect was fitted. Results The packages gave similar parameter estimates for both the fixed and random effects and for the binary (and ordinal models for the main study and when based on a relatively large number of level-1 (patient level data compared to the number of level-2 (hospital level data. However, when based on relatively sparse data set, i.e. when the numbers of level-1 and level-2 data units were about the same, the frequentist and Bayesian approaches showed somewhat different results. The software implementations differ considerably in flexibility, computation time, and usability. There are also differences in
A Gompertzian model with random effects to cervical cancer growth
Mazlan, Mazma Syahidatul Ayuni; Rosli, Norhayati [Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Pahang (Malaysia)
2015-05-15
In this paper, a Gompertzian model with random effects is introduced to describe the cervical cancer growth. The parameters values of the mathematical model are estimated via maximum likehood estimation. We apply 4-stage Runge-Kutta (SRK4) for solving the stochastic model numerically. The efficiency of mathematical model is measured by comparing the simulated result and the clinical data of the cervical cancer growth. Low values of root mean-square error (RMSE) of Gompertzian model with random effect indicate good fits.
David G. Gadian
2011-10-01
Full Text Available A common feature of many magnetic resonance image (MRI data processing methods is the voxel-by-voxel (a voxel is a volume element manner in which the processing is performed. In general, however, MRI data are expected to exhibit some level of spatial correlation, rendering an independent-voxels treatment inefficient in its use of the data. Bayesian random effect models are expected to be more efficient owing to their information-borrowing behaviour. To illustrate the Bayesian random effects approach, this paper outlines a Markov chain Monte Carlo (MCMC analysis of a perfusion MRI dataset, implemented in R using the BRugs package. BRugs provides an interface to WinBUGS and its GeoBUGS add-on. WinBUGS is a widely used programme for performing MCMC analyses, with a focus on Bayesian random effect models. A simultaneous modeling of both voxels (restricted to a region of interest and multiple subjects is demonstrated. Despite the low signal-to-noise ratio in the magnetic resonance signal intensity data, useful model signal intensity profiles are obtained. The merits of random effects modeling are discussed in comparison with the alternative approaches based on region-of-interest averaging and repeated independent voxels analysis. This paper focuses on perfusion MRI for the purpose of illustration, the main proposition being that random effects modeling is expected to be beneficial in many other MRI applications in which the signal-to-noise ratio is a limiting factor.
A random effects generalized linear model for reliability compositive evaluation
无
2009-01-01
This paper first proposes a random effects generalized linear model to evaluate the storage life of one kind of high reliable and small sample-sized products by combining multi-sources information of products coming from the same population but stored at different environments. The relevant algorithms are also provided. Simulation results manifest the soundness and effectiveness of the proposed model.
Short communication: Alteration of priors for random effects in Gaussian linear mixed model
Vandenplas, Jérémie; Christensen, Ole Fredslund; Gengler, Nicholas
2014-01-01
such alterations. Therefore, the aim of this study was to propose a method to alter both the mean and (co)variance of the prior multivariate normal distributions of random effects of linear mixed models while using currently available software packages. The proposed method was tested on simulated examples with 3......Linear mixed models, for which the prior multivariate normal distributions of random effects are assumed to have a mean equal to 0, are commonly used in animal breeding. However, some statistical analyses (e.g., the consideration of a population under selection into a genomic scheme breeding......, multiple-trait predictions of lactation yields, and Bayesian approaches integrating external information into genetic evaluations) need to alter both the mean and (co)variance of the prior distributions and, to our knowledge, most software packages available in the animal breeding community do not permit...
A Poisson Mixed Model with Nonnormal Random Effect Distribution
Fabio, Lizandra C.; Gilberto A. Paula; Castro, Mario
2011-01-01
We propose in this paper a random intercept Poisson model in which the random effect distribution is assumed to follow a generalized log-gamma (GLG) distribution. We derive the first two moments for the marginal distribution as well as the intraclass correlation. Even though numerical integration methods are in general required for deriving the marginal models, we obtain the multivariate negative binomial model for a particular parameter setting of the hierarchical model. An iterative process...
Interpreting parameters in the logistic regression model with random effects
Larsen, Klaus; Petersen, Jørgen Holm; Budtz-Jørgensen, Esben;
2000-01-01
interpretation, interval odds ratio, logistic regression, median odds ratio, normally distributed random effects......interpretation, interval odds ratio, logistic regression, median odds ratio, normally distributed random effects...
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
Nonparametric Estimation of Distributions in Random Effects Models
Hart, Jeffrey D.
2011-01-01
We propose using minimum distance to obtain nonparametric estimates of the distributions of components in random effects models. A main setting considered is equivalent to having a large number of small datasets whose locations, and perhaps scales, vary randomly, but which otherwise have a common distribution. Interest focuses on estimating the distribution that is common to all datasets, knowledge of which is crucial in multiple testing problems where a location/scale invariant test is applied to every small dataset. A detailed algorithm for computing minimum distance estimates is proposed, and the usefulness of our methodology is illustrated by a simulation study and an analysis of microarray data. Supplemental materials for the article, including R-code and a dataset, are available online. © 2011 American Statistical Association.
Random effects coefficient of determination for mixed and meta-analysis models
Demidenko, Eugene; Sargent, James; Onega, Tracy
2012-01-01
The key feature of a mixed model is the presence of random effects. We have developed a coefficient, called the random effects coefficient of determination, Rr2, that estimates the proportion of the conditional variance of the dependent variable explained by random effects. This coefficient takes values from 0 to 1 and indicates how strong the random effects are. The difference from the earlier suggested fixed effects coefficient of determination is emphasized. If Rr2 is close to 0, t...
Tang, An-Min; Tang, Nian-Sheng
2015-02-28
We propose a semiparametric multivariate skew-normal joint model for multivariate longitudinal and multivariate survival data. One main feature of the posited model is that we relax the commonly used normality assumption for random effects and within-subject error by using a centered Dirichlet process prior to specify the random effects distribution and using a multivariate skew-normal distribution to specify the within-subject error distribution and model trajectory functions of longitudinal responses semiparametrically. A Bayesian approach is proposed to simultaneously obtain Bayesian estimates of unknown parameters, random effects and nonparametric functions by combining the Gibbs sampler and the Metropolis-Hastings algorithm. Particularly, a Bayesian local influence approach is developed to assess the effect of minor perturbations to within-subject measurement error and random effects. Several simulation studies and an example are presented to illustrate the proposed methodologies. PMID:25404574
Bayesian model reduction and empirical Bayes for group (DCM) studies.
Friston, Karl J; Litvak, Vladimir; Oswal, Ashwini; Razi, Adeel; Stephan, Klaas E; van Wijk, Bernadette C M; Ziegler, Gabriel; Zeidman, Peter
2016-03-01
This technical note describes some Bayesian procedures for the analysis of group studies that use nonlinear models at the first (within-subject) level - e.g., dynamic causal models - and linear models at subsequent (between-subject) levels. Its focus is on using Bayesian model reduction to finesse the inversion of multiple models of a single dataset or a single (hierarchical or empirical Bayes) model of multiple datasets. These applications of Bayesian model reduction allow one to consider parametric random effects and make inferences about group effects very efficiently (in a few seconds). We provide the relatively straightforward theoretical background to these procedures and illustrate their application using a worked example. This example uses a simulated mismatch negativity study of schizophrenia. We illustrate the robustness of Bayesian model reduction to violations of the (commonly used) Laplace assumption in dynamic causal modelling and show how its recursive application can facilitate both classical and Bayesian inference about group differences. Finally, we consider the application of these empirical Bayesian procedures to classification and prediction. PMID:26569570
Bayesian parsimonious covariance estimation for hierarchical linear mixed models
Frühwirth-Schnatter, Sylvia; Tüchler, Regina
2004-01-01
We considered a non-centered parameterization of the standard random-effects model, which is based on the Cholesky decomposition of the variance-covariance matrix. The regression type structure of the non-centered parameterization allows to choose a simple, conditionally conjugate normal prior on the Cholesky factor. Based on the non-centered parameterization, we search for a parsimonious variance-covariance matrix by identifying the non-zero elements of the Cholesky factors using Bayesian va...
Bayesian Model Averaging for Propensity Score Analysis
Kaplan, David; Chen, Jianshen
2013-01-01
The purpose of this study is to explore Bayesian model averaging in the propensity score context. Previous research on Bayesian propensity score analysis does not take into account model uncertainty. In this regard, an internally consistent Bayesian framework for model building and estimation must also account for model uncertainty. The…
Bayesian modeling using WinBUGS
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 ...
Technology diffusion in hospitals: A log odds random effects regression model
J.L.T. Blank (Jos); V.G. Valdmanis (Vivian G.)
2015-01-01
textabstractThis study identifies the factors that affect the diffusion of hospital innovations. We apply a log odds random effects regression model on hospital micro data. We introduce the concept of clustering innovations and the application of a log odds random effects regression model to describ
Bayesian kinematic earthquake source models
Minson, S. E.; Simons, M.; Beck, J. L.; Genrich, J. F.; Galetzka, J. E.; Chowdhury, F.; Owen, S. E.; Webb, F.; Comte, D.; Glass, B.; Leiva, C.; Ortega, F. H.
2009-12-01
Most coseismic, postseismic, and interseismic slip models are based on highly regularized optimizations which yield one solution which satisfies the data given a particular set of regularizing constraints. This regularization hampers our ability to answer basic questions such as whether seismic and aseismic slip overlap or instead rupture separate portions of the fault zone. We present a Bayesian methodology for generating kinematic earthquake source models with a focus on large subduction zone earthquakes. Unlike classical optimization approaches, Bayesian techniques sample the ensemble of all acceptable models presented as an a posteriori probability density function (PDF), and thus we can explore the entire solution space to determine, for example, which model parameters are well determined and which are not, or what is the likelihood that two slip distributions overlap in space. Bayesian sampling also has the advantage that all a priori knowledge of the source process can be used to mold the a posteriori ensemble of models. Although very powerful, Bayesian methods have up to now been of limited use in geophysical modeling because they are only computationally feasible for problems with a small number of free parameters due to what is called the "curse of dimensionality." However, our methodology can successfully sample solution spaces of many hundreds of parameters, which is sufficient to produce finite fault kinematic earthquake models. Our algorithm is a modification of the tempered Markov chain Monte Carlo (tempered MCMC or TMCMC) method. In our algorithm, we sample a "tempered" a posteriori PDF using many MCMC simulations running in parallel and evolutionary computation in which models which fit the data poorly are preferentially eliminated in favor of models which better predict the data. We present results for both synthetic test problems as well as for the 2007 Mw 7.8 Tocopilla, Chile earthquake, the latter of which is constrained by InSAR, local high
Random effects coefficient of determination for mixed and meta-analysis models.
Demidenko, Eugene; Sargent, James; Onega, Tracy
2012-01-01
The key feature of a mixed model is the presence of random effects. We have developed a coefficient, called the random effects coefficient of determination, [Formula: see text], that estimates the proportion of the conditional variance of the dependent variable explained by random effects. This coefficient takes values from 0 to 1 and indicates how strong the random effects are. The difference from the earlier suggested fixed effects coefficient of determination is emphasized. If [Formula: see text] is close to 0, there is weak support for random effects in the model because the reduction of the variance of the dependent variable due to random effects is small; consequently, random effects may be ignored and the model simplifies to standard linear regression. The value of [Formula: see text] apart from 0 indicates the evidence of the variance reduction in support of the mixed model. If random effects coefficient of determination is close to 1 the variance of random effects is very large and random effects turn into free fixed effects-the model can be estimated using the dummy variable approach. We derive explicit formulas for [Formula: see text] in three special cases: the random intercept model, the growth curve model, and meta-analysis model. Theoretical results are illustrated with three mixed model examples: (1) travel time to the nearest cancer center for women with breast cancer in the U.S., (2) cumulative time watching alcohol related scenes in movies among young U.S. teens, as a risk factor for early drinking onset, and (3) the classic example of the meta-analysis model for combination of 13 studies on tuberculosis vaccine. PMID:23750070
A Bayesian Nonparametric IRT Model
Karabatsos, George
2015-01-01
This paper introduces a flexible Bayesian nonparametric Item Response Theory (IRT) model, which applies to dichotomous or polytomous item responses, and which can apply to either unidimensional or multidimensional scaling. This is an infinite-mixture IRT model, with person ability and item difficulty parameters, and with a random intercept parameter that is assigned a mixing distribution, with mixing weights a probit function of other person and item parameters. As a result of its flexibility...
Bayesian Stable Isotope Mixing Models
Parnell, Andrew C.; Phillips, Donald L.; Bearhop, Stuart; Semmens, Brice X.; Ward, Eric J.; Moore, Jonathan W.; Andrew L Jackson; Inger, Richard
2012-01-01
In this paper we review recent advances in Stable Isotope Mixing Models (SIMMs) and place them into an over-arching Bayesian statistical framework which allows for several useful extensions. SIMMs are used to quantify the proportional contributions of various sources to a mixture. The most widely used application is quantifying the diet of organisms based on the food sources they have been observed to consume. At the centre of the multivariate statistical model we propose is a compositional m...
A likelihood reformulation method in non-normal random effects models.
Liu, Lei; Yu, Zhangsheng
2008-07-20
In this paper, we propose a practical computational method to obtain the maximum likelihood estimates (MLE) for mixed models with non-normal random effects. By simply multiplying and dividing a standard normal density, we reformulate the likelihood conditional on the non-normal random effects to that conditional on the normal random effects. Gaussian quadrature technique, conveniently implemented in SAS Proc NLMIXED, can then be used to carry out the estimation process. Our method substantially reduces computational time, while yielding similar estimates to the probability integral transformation method (J. Comput. Graphical Stat. 2006; 15:39-57). Furthermore, our method can be applied to more general situations, e.g. finite mixture random effects or correlated random effects from Clayton copula. Simulations and applications are presented to illustrate our method. PMID:18038445
A Bayesian nonlinear mixed-effects disease progression model
Kim, Seongho; Jang, Hyejeong; Wu, Dongfeng; Abrams, Judith
2016-01-01
A nonlinear mixed-effects approach is developed for disease progression models that incorporate variation in age in a Bayesian framework. We further generalize the probability model for sensitivity to depend on age at diagnosis, time spent in the preclinical state and sojourn time. The developed models are then applied to the Johns Hopkins Lung Project data and the Health Insurance Plan for Greater New York data using Bayesian Markov chain Monte Carlo and are compared with the estimation method that does not consider random-effects from age. Using the developed models, we obtain not only age-specific individual-level distributions, but also population-level distributions of sensitivity, sojourn time and transition probability. PMID:26798562
League tables for literacy survey data based on random effect models.
Sofroniou, Nick; Hoad, Dominique; Einbeck, Jochen
2008-01-01
Data from the International Adult Literacy Survey are used to illustrate how league tables can be obtained from summary data, consisting of percentages and their standard errors, using random effects models estimated by nonparametric maximum likelihood.
Bayesian variable order Markov models: Towards Bayesian predictive state representations
C. Dimitrakakis
2009-01-01
We present a Bayesian variable order Markov model that shares many similarities with predictive state representations. The resulting models are compact and much easier to specify and learn than classical predictive state representations. Moreover, we show that they significantly outperform a more st
Standard errors for EM estimates in generalized linear models with random effects.
Friedl, H; Kauermann, G
2000-09-01
A procedure is derived for computing standard errors of EM estimates in generalized linear models with random effects. Quadrature formulas are used to approximate the integrals in the EM algorithm, where two different approaches are pursued, i.e., Gauss-Hermite quadrature in the case of Gaussian random effects and nonparametric maximum likelihood estimation for an unspecified random effect distribution. An approximation of the expected Fisher information matrix is derived from an expansion of the EM estimating equations. This allows for inferential arguments based on EM estimates, as demonstrated by an example and simulations. PMID:10985213
Nonparametric Bayesian Modeling of Complex Networks
Schmidt, Mikkel Nørgaard; Mørup, Morten
2013-01-01
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...... for complex networks can be derived and point out relevant literature....
Multilevel models for survival analysis with random effects.
Yau, K K
2001-03-01
A method for modeling survival data with multilevel clustering is described. The Cox partial likelihood is incorporated into the generalized linear mixed model (GLMM) methodology. Parameter estimation is achieved by maximizing a log likelihood analogous to the likelihood associated with the best linear unbiased prediction (BLUP) at the initial step of estimation and is extended to obtain residual maximum likelihood (REML) estimators of the variance component. Estimating equations for a three-level hierarchical survival model are developed in detail, and such a model is applied to analyze a set of chronic granulomatous disease (CGD) data on recurrent infections as an illustration with both hospital and patient effects being considered as random. Only the latter gives a significant contribution. A simulation study is carried out to evaluate the performance of the REML estimators. Further extension of the estimation procedure to models with an arbitrary number of levels is also discussed. PMID:11252624
A Fay-Herriot Model with Different Random Effect Variances
Hobza, Tomáš; Morales, D.; Herrador, M.; Esteban, M.D.
2011-01-01
Roč. 40, č. 5 (2011), s. 785-797. ISSN 0361-0926 R&D Projects: GA MŠk 1M0572 Institutional research plan: CEZ:AV0Z10750506 Keywords : small area estimation * Fay-Herriot model * Linear mixed model * Labor Force Survey Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 0.274, year: 2011 http://library.utia.cas.cz/separaty/2011/SI/hobza-a%20fay-herriot%20model%20with%20different%20random%20effect%20variances.pdf
A Bayesian approach to model uncertainty
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
Computational methods for Bayesian model choice
Robert, Christian P.; Wraith, Darren
2009-01-01
In this note, we shortly survey some recent approaches on the approximation of the Bayes factor used in Bayesian hypothesis testing and in Bayesian model choice. In particular, we reassess importance sampling, harmonic mean sampling, and nested sampling from a unified perspective.
Bayesian Variable Selection in Spatial Autoregressive Models
Jesus Crespo Cuaresma; Philipp Piribauer
2015-01-01
This paper compares the performance of Bayesian variable selection approaches for spatial autoregressive models. We present two alternative approaches which can be implemented using Gibbs sampling methods in a straightforward way and allow us to deal with the problem of model uncertainty in spatial autoregressive models in a flexible and computationally efficient way. In a simulation study we show that the variable selection approaches tend to outperform existing Bayesian model averaging tech...
Bayesian Models of Brain and Behaviour
Penny, William
2012-01-01
This paper presents a review of Bayesian models of brain and behaviour. We first review the basic principles of Bayesian inference. This is followed by descriptions of sampling and variational methods for approximate inference, and forward and backward recursions in time for inference in dynamical models. The review of behavioural models covers work in visual processing, sensory integration, sensorimotor integration, and collective decision making. The review of brain models covers a range of...
Bayesian models a statistical primer for ecologists
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
EMPIRICAL BAYES TEST PROBLEMS OF VARIANCE COMPONENTS IN RANDOM EFFECTS MODEL
Wei Laisheng; Zhang Weiping
2005-01-01
Bayes decision rule of variance components for one-way random effects model is derived and empirical Bayes (EB) decision rules are constructed by kernel estimation method. Under suitable conditions, it is shown that the proposed EB decision rules are asymptotically optimal with convergence rates near O(n-1/2). Finally, an example concerning the main result is given.
Petersen, Jørgen Holm
2016-01-01
This paper describes a new approach to the estimation in a logistic regression model with two crossed random effects where special interest is in estimating the variance of one of the effects while not making distributional assumptions about the other effect. A composite likelihood is studied. For...
A dynamic random effects multinomial logit model of household car ownership
Bue Bjørner, Thomas; Leth-Petersen, Søren
2007-01-01
Using a large household panel we estimate demand for car ownership by means of a dynamic multinomial model with correlated random effects. Results suggest that the persistence in car ownership observed in the data should be attributed to both true state dependence and to unobserved heterogeneity ...
The Impact of Five Missing Data Treatments on a Cross-Classified Random Effects Model
Hoelzle, Braden R.
2012-01-01
The present study compared the performance of five missing data treatment methods within a Cross-Classified Random Effects Model environment under various levels and patterns of missing data given a specified sample size. Prior research has shown the varying effect of missing data treatment options within the context of numerous statistical…
Xavier A. Harrison
2014-10-01
Full Text Available Overdispersion is common in models of count data in ecology and evolutionary biology, and can occur due to missing covariates, non-independent (aggregated data, or an excess frequency of zeroes (zero-inflation. Accounting for overdispersion in such models is vital, as failing to do so can lead to biased parameter estimates, and false conclusions regarding hypotheses of interest. Observation-level random effects (OLRE, where each data point receives a unique level of a random effect that models the extra-Poisson variation present in the data, are commonly employed to cope with overdispersion in count data. However studies investigating the efficacy of observation-level random effects as a means to deal with overdispersion are scarce. Here I use simulations to show that in cases where overdispersion is caused by random extra-Poisson noise, or aggregation in the count data, observation-level random effects yield more accurate parameter estimates compared to when overdispersion is simply ignored. Conversely, OLRE fail to reduce bias in zero-inflated data, and in some cases increase bias at high levels of overdispersion. There was a positive relationship between the magnitude of overdispersion and the degree of bias in parameter estimates. Critically, the simulations reveal that failing to account for overdispersion in mixed models can erroneously inflate measures of explained variance (r2, which may lead to researchers overestimating the predictive power of variables of interest. This work suggests use of observation-level random effects provides a simple and robust means to account for overdispersion in count data, but also that their ability to minimise bias is not uniform across all types of overdispersion and must be applied judiciously.
Bivariate Random Effects Meta-analysis of Diagnostic Studies Using Generalized Linear Mixed Models
Chu, Haitao; Guo, Hongfei; Zhou, Yijie
2009-01-01
Bivariate random effect models are currently one of the main methods recommended to synthesize diagnostic test accuracy studies. However, only the logit-transformation on sensitivity and specificity has been previously considered in the literature. In this paper, we consider a bivariate generalized linear mixed model to jointly model the sensitivities and specificities, and discuss the estimation of the summary receiver operating characteristic curve (ROC) and the area under the ROC curve (AU...
On the dynamics of product and process innovations: A bivariate random effects probit model
Flaig, Gebhard; Stadler, Manfred
1996-01-01
Based on a stochastic dynamic model of a firm's optimal innovative behavior we derive a simultaneous equation system for product and process innovations with intertemporal spillover effects. We estimate various versions of the model with dichotomous Innovation data at the firm level by using a bivariate dynamic random effects probit model. The data set, provided by the Ifo-Institute, covers the period between 1981 and 1989 and includes 586 firms of the West German manufacturing sector. It tur...
Generalized linear models with random effects unified analysis via H-likelihood
Lee, Youngjo; Pawitan, Yudi
2006-01-01
Since their introduction in 1972, generalized linear models (GLMs) have proven useful in the generalization of classical normal models. Presenting methods for fitting GLMs with random effects to data, Generalized Linear Models with Random Effects: Unified Analysis via H-likelihood explores a wide range of applications, including combining information over trials (meta-analysis), analysis of frailty models for survival data, genetic epidemiology, and analysis of spatial and temporal models with correlated errors.Written by pioneering authorities in the field, this reference provides an introduction to various theories and examines likelihood inference and GLMs. The authors show how to extend the class of GLMs while retaining as much simplicity as possible. By maximizing and deriving other quantities from h-likelihood, they also demonstrate how to use a single algorithm for all members of the class, resulting in a faster algorithm as compared to existing alternatives. Complementing theory with examples, many of...
Bayesian Analysis of Multivariate Probit Models
Siddhartha Chib; Edward Greenberg
1996-01-01
This paper provides a unified simulation-based Bayesian and non-Bayesian analysis of correlated binary data using the multivariate probit model. The posterior distribution is simulated by Markov chain Monte Carlo methods, and maximum likelihood estimates are obtained by a Markov chain Monte Carlo version of the E-M algorithm. Computation of Bayes factors from the simulation output is also considered. The methods are applied to a bivariate data set, to a 534-subject, four-year longitudinal dat...
Bayesian Network Models for Adaptive Testing
Plajner, Martin; Vomlel, Jiří
Achen: Sun SITE Central Europe, 2016 - (Agosta, J.; Carvalho, R.), s. 24-33. (CEUR Workshop Proceedings. Vol 1565). ISSN 1613-0073. [The Twelfth UAI Bayesian Modeling Applications Workshop (BMAW 2015). Amsterdam (NL), 16.07.2015] R&D Projects: GA ČR GA13-20012S Institutional support: RVO:67985556 Keywords : Bayesian networks * Computerized adaptive testing Subject RIV: JD - Computer Applications, Robotics http://library.utia.cas.cz/separaty/2016/MTR/plajner-0458062.pdf
Huibing Hao
2015-01-01
Full Text Available Light emitting diode (LED lamp has attracted increasing interest in the field of lighting systems due to its low energy and long lifetime. For different functions (i.e., illumination and color, it may have two or more performance characteristics. When the multiple performance characteristics are dependent, it creates a challenging problem to accurately analyze the system reliability. In this paper, we assume that the system has two performance characteristics, and each performance characteristic is governed by a random effects Gamma process where the random effects can capture the unit to unit differences. The dependency of performance characteristics is described by a Frank copula function. Via the copula function, the reliability assessment model is proposed. Considering the model is so complicated and analytically intractable, the Markov chain Monte Carlo (MCMC method is used to estimate the unknown parameters. A numerical example about actual LED lamps data is given to demonstrate the usefulness and validity of the proposed model and method.
A Bayesian Based Functional Mixed-Effects Model for Analysis of LC-MS Data
Befekadu, Getachew K.; Tadesse, Mahlet G.; Ressom, Habtom W
2009-01-01
A Bayesian multilevel functional mixed-effects model with group specific random-effects is presented for analysis of liquid chromatography-mass spectrometry (LC-MS) data. The proposed framework allows alignment of LC-MS spectra with respect to both retention time (RT) and mass-to-charge ratio (m/z). Affine transformations are incorporated within the model to account for any variability along the RT and m/z dimensions. Simultaneous posterior inference of all unknown parameters is accomplished ...
Determinants of Low Birth Weight in Malawi: Bayesian Geo-Additive Modelling
Ngwira, Alfred; Stanley, Christopher C.
2015-01-01
Studies on factors of low birth weight in Malawi have neglected the flexible approach of using smooth functions for some covariates in models. Such flexible approach reveals detailed relationship of covariates with the response. The study aimed at investigating risk factors of low birth weight in Malawi by assuming a flexible approach for continuous covariates and geographical random effect. A Bayesian geo-additive model for birth weight in kilograms and size of the child at birth (less than ...
On Bayesian Nonparametric Continuous Time Series Models
Karabatsos, George; Walker, Stephen G.
2013-01-01
This paper is a note on the use of Bayesian nonparametric mixture models for continuous time series. We identify a key requirement for such models, and then establish that there is a single type of model which meets this requirement. As it turns out, the model is well known in multiple change-point problems.
Krøigård, Thomas; Gaist, David; Otto, Marit;
2014-01-01
SUMMARY: The reproducibility of variables commonly included in studies of peripheral nerve conduction in healthy individuals has not previously been analyzed using a random effects regression model. We examined the temporal changes and variability of standard nerve conduction measures in the leg...... conduction studies have a high reproducibility, and variables are mainly unaltered during 6 months. This study provides a solid basis for the planning of future clinical trials assessing changes in nerve conduction....
Bayesian semiparametric dynamic Nelson-Siegel model
C. Cakmakli
2011-01-01
This paper proposes the Bayesian semiparametric dynamic Nelson-Siegel model where the density of the yield curve factors and thereby the density of the yields are estimated along with other model parameters. This is accomplished by modeling the error distributions of the factors according to a Diric
Bayesian calibration of car-following models
Van Hinsbergen, C.P.IJ.; Van Lint, H.W.C.; Hoogendoorn, S.P.; Van Zuylen, H.J.
2010-01-01
Recent research has revealed that there exist large inter-driver differences in car-following behavior such that different car-following models may apply to different drivers. This study applies Bayesian techniques to the calibration of car-following models, where prior distributions on each model p
Bayesian Semiparametric Modeling of Realized Covariance Matrices
Jin, Xin; John M Maheu
2014-01-01
This paper introduces several new Bayesian nonparametric models suitable for capturing the unknown conditional distribution of realized covariance (RCOV) matrices. Existing dynamic Wishart models are extended to countably infinite mixture models of Wishart and inverse-Wishart distributions. In addition to mixture models with constant weights we propose models with time-varying weights to capture time dependence in the unknown distribution. Each of our models can be combined with returns...
Complex Bayesian models: construction, and sampling strategies
Huston, Carolyn Marie
2011-01-01
Bayesian models are useful tools for realistically modeling processes occurring in the real world. In particular, we consider models for spatio-temporal data where the response vector is compositional, ie. has components that sum-to-one. A unique multivariate conditional hierarchical model (MVCAR) is proposed. Statistical methods for MVCAR models are well developed and we extend these tools for use with a discrete compositional response. We harness the advantages of an MVCAR model when the re...
Bayesian Approach to Neuro-Rough Models for Modelling HIV
Marwala, Tshilidzi
2007-01-01
This paper proposes a new neuro-rough model for modelling the risk of HIV from demographic data. The model is formulated using Bayesian framework and trained using Markov Chain Monte Carlo method and Metropolis criterion. When the model was tested to estimate the risk of HIV infection given the demographic data it was found to give the accuracy of 62% as opposed to 58% obtained from a Bayesian formulated rough set model trained using Markov chain Monte Carlo method and 62% obtained from a Bayesian formulated multi-layered perceptron (MLP) model trained using hybrid Monte. The proposed model is able to combine the accuracy of the Bayesian MLP model and the transparency of Bayesian rough set model.
Survey of Bayesian Models for Modelling of Stochastic Temporal Processes
Ng, B
2006-10-12
This survey gives an overview of popular generative models used in the modeling of stochastic temporal systems. In particular, this survey is organized into two parts. The first part discusses the discrete-time representations of dynamic Bayesian networks and dynamic relational probabilistic models, while the second part discusses the continuous-time representation of continuous-time Bayesian networks.
Boonstra, Philip S; Mukherjee, Bhramar; Taylor, Jeremy M G;
2011-01-01
Summary Genetic anticipation, described by earlier age of onset (AOO) and more aggressive symptoms in successive generations, is a phenomenon noted in certain hereditary diseases. Its extent may vary between families and/or between mutation subtypes known to be associated with the disease phenotype....... In this article, we posit a Bayesian approach to infer genetic anticipation under flexible random effects models for censored data that capture the effect of successive generations on AOO. Primary interest lies in the random effects. Misspecifying the distribution of random effects may result in......) genes known to cause hereditary nonpolyposis colorectal cancer, also called Lynch syndrome (LS). We find evidence for a decrease in AOO between generations in this article. Our model predicts family-level anticipation effects that are potentially useful in genetic counseling clinics for high...
Holst, René; Jørgensen, Bent
2015-01-01
The paper proposes a versatile class of multiplicative generalized linear longitudinal mixed models (GLLMM) with additive dispersion components, based on explicit modelling of the covariance structure. The class incorporates a longitudinal structure into the random effects models and retains a ma...... multidimensional integral of the conventional GLMM likelihood and allows an extension of the robust empirical sandwich estimator for use with both association and regression parameters. The method is applied to a set of otholit data, used for age determination of fish.......The paper proposes a versatile class of multiplicative generalized linear longitudinal mixed models (GLLMM) with additive dispersion components, based on explicit modelling of the covariance structure. The class incorporates a longitudinal structure into the random effects models and retains a...... marginal as well as a conditional interpretation. The estimation procedure is based on a computationally efficient quasi-score method for the regression parameters combined with a REML-like bias-corrected Pearson estimating function for the dispersion and correlation parameters. This avoids the...
Bayesian Spatial Modelling with R-INLA
Finn Lindgren; Håvard Rue
2015-01-01
The principles behind the interface to continuous domain spatial models in the R- INLA software package for R are described. The integrated nested Laplace approximation (INLA) approach proposed by Rue, Martino, and Chopin (2009) is a computationally effective alternative to MCMC for Bayesian inference. INLA is designed for latent Gaussian models, a very wide and flexible class of models ranging from (generalized) linear mixed to spatial and spatio-temporal models. Combined with the stochastic...
Road network safety evaluation using Bayesian hierarchical joint model.
Wang, Jie; Huang, Helai
2016-05-01
Safety and efficiency are commonly regarded as two significant performance indicators of transportation systems. In practice, road network planning has focused on road capacity and transport efficiency whereas the safety level of a road network has received little attention in the planning stage. This study develops a Bayesian hierarchical joint model for road network safety evaluation to help planners take traffic safety into account when planning a road network. The proposed model establishes relationships between road network risk and micro-level variables related to road entities and traffic volume, as well as socioeconomic, trip generation and network density variables at macro level which are generally used for long term transportation plans. In addition, network spatial correlation between intersections and their connected road segments is also considered in the model. A road network is elaborately selected in order to compare the proposed hierarchical joint model with a previous joint model and a negative binomial model. According to the results of the model comparison, the hierarchical joint model outperforms the joint model and negative binomial model in terms of the goodness-of-fit and predictive performance, which indicates the reasonableness of considering the hierarchical data structure in crash prediction and analysis. Moreover, both random effects at the TAZ level and the spatial correlation between intersections and their adjacent segments are found to be significant, supporting the employment of the hierarchical joint model as an alternative in road-network-level safety modeling as well. PMID:26945109
Bayesian modeling and classification of neural signals
Lewicki, Michael S.
1994-01-01
Signal processing and classification algorithms often have limited applicability resulting from an inaccurate model of the signal's underlying structure. We present here an efficient, Bayesian algorithm for modeling a signal composed of the superposition of brief, Poisson-distributed functions. This methodology is applied to the specific problem of modeling and classifying extracellular neural waveforms which are composed of a superposition of an unknown number of action potentials CAPs). ...
bspmma: An R Package for Bayesian Semiparametric Models for Meta-Analysis
Deborah Burr
2012-07-01
Full Text Available We introduce an R package, bspmma, which implements a Dirichlet-based random effects model specific to meta-analysis. In meta-analysis, when combining effect estimates from several heterogeneous studies, it is common to use a random-effects model. The usual frequentist or Bayesian models specify a normal distribution for the true effects. However, in many situations, the effect distribution is not normal, e.g., it can have thick tails, be skewed, or be multi-modal. A Bayesian nonparametric model based on mixtures of Dirichlet process priors has been proposed in the literature, for the purpose of accommodating the non-normality. We review this model and then describe a competitor, a semiparametric version which has the feature that it allows for a well-defined centrality parameter convenient for determining whether the overall effect is significant. This second Bayesian model is based on a different version of the Dirichlet process prior, and we call it the "conditional Dirichlet model". The package contains functions to carry out analyses based on either the ordinary or the conditional Dirichlet model, functions for calculating certain Bayes factors that provide a check on the appropriateness of the conditional Dirichlet model, and functions that enable an empirical Bayes selection of the precision parameter of the Dirichlet process. We illustrate the use of the package on two examples, and give an interpretation of the results in these two different scenarios.
Distributed Bayesian Networks for User Modeling
Tedesco, Roberto; Dolog, Peter; Nejdl, Wolfgang;
2006-01-01
The World Wide Web is a popular platform for providing eLearning applications to a wide spectrum of users. However – as users differ in their preferences, background, requirements, and goals – applications should provide personalization mechanisms. In the Web context, user models used by such...... adaptive applications are often partial fragments of an overall user model. The fragments have then to be collected and merged into a global user profile. In this paper we investigate and present algorithms able to cope with distributed, fragmented user models – based on Bayesian Networks – in the context...... mechanism efficiently combines distributed learner models without the need to exchange internal structure of local Bayesian networks, nor local evidence between the involved platforms....
Constrained bayesian inference of project performance models
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 ...
Bayesian Network Based XP Process Modelling
Mohamed Abouelela
2010-07-01
Full Text Available A Bayesian Network based mathematical model has been used for modelling Extreme Programmingsoftware development process. The model is capable of predicting the expected finish time and theexpected defect rate for each XP release. Therefore, it can be used to determine the success/failure of anyXP Project. The model takes into account the effect of three XP practices, namely: Pair Programming,Test Driven Development and Onsite Customer practices. The model’s predictions were validated againsttwo case studies. Results show the precision of our model especially in predicting the project finish time.
A Bayesian Modelling of Wildfires in Portugal
Silva, Giovani L.; Soares, Paulo; Marques, Susete; Dias, Inês M.; Oliveira, Manuela M.; Borges, Guilherme J.
2015-01-01
In the last decade wildfires became a serious problem in Portugal due to different issues such as climatic characteristics and nature of Portuguese forest. In order to analyse wildfire data, we employ beta regression for modelling the proportion of burned forest area, under a Bayesian perspective. Our main goal is to find out fire risk factors that influence the proportion of area burned and what may make a forest type susceptible or resistant to fire. Then, we analyse wildfire...
Market Segmentation Using Bayesian Model Based Clustering
Van Hattum, P.
2009-01-01
This dissertation deals with two basic problems in marketing, that are market segmentation, which is the grouping of persons who share common aspects, and market targeting, which is focusing your marketing efforts on one or more attractive market segments. For the grouping of persons who share common aspects a Bayesian model based clustering approach is proposed such that it can be applied to data sets that are specifically used for market segmentation. The cluster algorithm can handle very l...
Centralized Bayesian reliability modelling with sensor networks
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 ostatní: 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
Bayesian mixture models for Poisson astronomical images
Guglielmetti, Fabrizia; Fischer, Rainer; Dose, Volker
2012-01-01
Astronomical images in the Poisson regime are typically characterized by a spatially varying cosmic background, large variety of source morphologies and intensities, data incompleteness, steep gradients in the data, and few photon counts per pixel. The Background-Source separation technique is developed with the aim to detect faint and extended sources in astronomical images characterized by Poisson statistics. The technique employs Bayesian mixture models to reliably detect the background as...
A random-effects model for long-term degradation analysis of solid oxide fuel cells
Solid oxide fuel cells (SOFCs) are electrochemical devices converting the chemical energy into electricity with high efficiency and low pollutant emissions. Tough very promising, this technology is still in a developing phase, and degradation at the cell/stack level with operating time is still an issue of major concern. Methods to directly observe degradation modes and to measure their evolution over time are difficult to implement, and indirect performance indicators are adopted, typically related to voltage measurements in long-term tests. In order to describe long-term degradation tests, three components of the voltage measurements should be modelled: the smooth decay of voltage over time for each single unit; the variability of voltage decay among units; and the high-frequency small fluctuations of voltage due to experimental noise and lack of fit. In this paper, we propose an empirical random-effects regression model of polynomial type enabling to evaluate separately these three types of variability. Point and interval estimates are also derived for some performance measures, such as the mean voltage, the prediction of cell voltage, the reliability function and the cell-to-cell variability in SOFC stacks. Finally, the proposed methodology is applied to two real case-studies of long-term degradation tests of SOFC stacks. - Highlights: • We propose an empirical random-effects model for SOFC cells voltage in long runs. • Some SOFC performance and manufacturing quality measures are derived. • An application to two real case-studies of long-term degradation tests is provided. • The reliability function of SOFCs and its lower confidence limit are computed
Bayesian Inference of a Multivariate Regression Model
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.
Semiparametric Binary Random Effects Models: Estimating Two Types of Drinking Behavior
Dong, Yingying
2010-01-01
This paper proposes a new estimator for cross section semiparametric regressions containing an unobserved binary random effect and applies it to alcohol consumption. The unobserved random effect (health-consciousness) explains a significant proportion of the otherwise unexplained variation in alcohol consumption. Higher education positively correlates with health-consciousness.
Crossing Language Barriers: Using Crossed Random Effects Modelling in Psycholinguistics Research
Robyn J. Carson
2013-02-01
Full Text Available The purpose of this paper is to provide a brief review of multilevel modelling (MLM, also called hierarchical linear modelling (HLM, and to present a step-by-step tutorial on how to perform a crossed random effects model (CREM analysis. The first part provides an overview of how hierarchical data have been analyzed in the past and how they are being analyzed presently. It then focuses on how these types of data have been dealt with in psycholinguistic research. It concludes with an overview of the steps involved in CREM, a form of MLM used for psycholinguistics data. The second part includes a tutorial demonstrating how to conduct a CREM analysis in SPSS, using the following steps: 1 clarify your research question, 2 determine if CREM is necessary, 3 choose an estimation method, 4 build your model, and 5 estimate the models effect size. A short example on how to report CREM results in a scholarly article is also included.
Bayesian Kinematic Finite Fault Source Models (Invited)
Minson, S. E.; Simons, M.; Beck, J. L.
2010-12-01
Finite fault earthquake source models are inherently under-determined: there is no unique solution to the inverse problem of determining the rupture history at depth as a function of time and space when our data are only limited observations at the Earth's surface. Traditional inverse techniques rely on model constraints and regularization to generate one model from the possibly broad space of all possible solutions. However, Bayesian methods allow us to determine the ensemble of all possible source models which are consistent with the data and our a priori assumptions about the physics of the earthquake source. Until now, Bayesian techniques have been of limited utility because they are computationally intractable for problems with as many free parameters as kinematic finite fault models. We have developed a methodology called Cascading Adaptive Tempered Metropolis In Parallel (CATMIP) which allows us to sample very high-dimensional problems in a parallel computing framework. The CATMIP algorithm combines elements of simulated annealing and genetic algorithms with the Metropolis algorithm to dynamically optimize the algorithm's efficiency as it runs. We will present synthetic performance tests of finite fault models made with this methodology as well as a kinematic source model for the 2007 Mw 7.7 Tocopilla, Chile earthquake. This earthquake was well recorded by multiple ascending and descending interferograms and a network of high-rate GPS stations whose records can be used as near-field seismograms.
Bayesian Estimation of a Mixture Model
Ilhem Merah; Assia Chadli
2015-01-01
We present the properties of a bathtub curve reliability model having both a sufficient adaptability and a minimal number of parameters introduced by Idée and Pierrat (2010). This one is a mixture of a Gamma distribution G(2, (1/θ)) and a new distribution L(θ). We are interesting by Bayesian estimation of the parameters and survival function of this model with a squared-error loss function and non-informative prior using the approximations of Lindley (1980) and Tierney and Kadane (1986). Usin...
Bayesian mixture models for partially verified data
Kostoulas, Polychronis; Browne, William J.; Nielsen, Søren Saxmose;
2013-01-01
, where a perfect reference test does not exist. However, their discriminatory ability diminishes with increasing overlap of the distributions and with increasing number of latent infection stages to be discriminated. We provide a method that uses partially verified data, with known infection status for......Bayesian mixture models can be used to discriminate between the distributions of continuous test responses for different infection stages. These models are particularly useful in case of chronic infections with a long latent period, like Mycobacterium avium subsp. paratuberculosis (MAP) infection...
Rendao YE; Songgui WANG
2007-01-01
Various random models with balanced data that are relevant for analyzing practical test data are described, along with several hypothesis testing and interval estimation problems concerning variance components. In this paper, we mainly consider these problems in general random effect model with balanced data. Exact tests and confidence intervals for a single variance component corresponding to random effect are developed by using generalized p-values and generalized confidence intervals.The resulting procedures are easy to compute and are applicable to small samples. Exact tests and confidence intervals are also established for comparing the random-effects variance components and the sum of random-effects variance components in two independent general random effect models with balanced data. Furthermore, we investigate the statistical properties of the resulting tests. Finally,some simulation results on the type Ⅰ error probability and power of the proposed test are reported.The simulation results indicate that exact test is extremely satisfactory for controlling type Ⅰ error probability.
Ming He
2015-11-01
Full Text Available We propose a random effects panel data model with both spatially correlated error components and spatially lagged dependent variables. We focus on diagnostic testing procedures and derive Lagrange multiplier (LM test statistics for a variety of hypotheses within this model. We first construct the joint LM test for both the individual random effects and the two spatial effects (spatial error correlation and spatial lag dependence. We then provide LM tests for the individual random effects and for the two spatial effects separately. In addition, in order to guard against local model misspecification, we derive locally adjusted (robust LM tests based on the Bera and Yoon principle (Bera and Yoon, 1993. We conduct a small Monte Carlo simulation to show the good finite sample performances of these LM test statistics and revisit the cigarette demand example in Baltagi and Levin (1992 to illustrate our testing procedures.
A Nonparametric Bayesian Model for Nested Clustering.
Lee, Juhee; Müller, Peter; Zhu, Yitan; Ji, Yuan
2016-01-01
We propose a nonparametric Bayesian model for clustering where clusters of experimental units are determined by a shared pattern of clustering another set of experimental units. The proposed model is motivated by the analysis of protein activation data, where we cluster proteins such that all proteins in one cluster give rise to the same clustering of patients. That is, we define clusters of proteins by the way that patients group with respect to the corresponding protein activations. This is in contrast to (almost) all currently available models that use shared parameters in the sampling model to define clusters. This includes in particular model based clustering, Dirichlet process mixtures, product partition models, and more. We show results for two typical biostatistical inference problems that give rise to clustering. PMID:26519174
Bayesian Spatial Modelling with R-INLA
Finn Lindgren
2015-02-01
Full Text Available The principles behind the interface to continuous domain spatial models in the R- INLA software package for R are described. The integrated nested Laplace approximation (INLA approach proposed by Rue, Martino, and Chopin (2009 is a computationally effective alternative to MCMC for Bayesian inference. INLA is designed for latent Gaussian models, a very wide and flexible class of models ranging from (generalized linear mixed to spatial and spatio-temporal models. Combined with the stochastic partial differential equation approach (SPDE, Lindgren, Rue, and Lindstrm 2011, one can accommodate all kinds of geographically referenced data, including areal and geostatistical ones, as well as spatial point process data. The implementation interface covers stationary spatial mod- els, non-stationary spatial models, and also spatio-temporal models, and is applicable in epidemiology, ecology, environmental risk assessment, as well as general geostatistics.
Bayesian Discovery of Linear Acyclic Causal Models
Hoyer, Patrik O
2012-01-01
Methods for automated discovery of causal relationships from non-interventional data have received much attention recently. A widely used and well understood model family is given by linear acyclic causal models (recursive structural equation models). For Gaussian data both constraint-based methods (Spirtes et al., 1993; Pearl, 2000) (which output a single equivalence class) and Bayesian score-based methods (Geiger and Heckerman, 1994) (which assign relative scores to the equivalence classes) are available. On the contrary, all current methods able to utilize non-Gaussianity in the data (Shimizu et al., 2006; Hoyer et al., 2008) always return only a single graph or a single equivalence class, and so are fundamentally unable to express the degree of certainty attached to that output. In this paper we develop a Bayesian score-based approach able to take advantage of non-Gaussianity when estimating linear acyclic causal models, and we empirically demonstrate that, at least on very modest size networks, its accur...
Adversarial life testing: A Bayesian negotiation model
Life testing is a procedure intended for facilitating the process of making decisions in the context of industrial reliability. On the other hand, negotiation is a process of making joint decisions that has one of its main foundations in decision theory. A Bayesian sequential model of negotiation in the context of adversarial life testing is proposed. This model considers a general setting for which a manufacturer offers a product batch to a consumer. It is assumed that the reliability of the product is measured in terms of its lifetime. Furthermore, both the manufacturer and the consumer have to use their own information with respect to the quality of the product. Under these assumptions, two situations can be analyzed. For both of them, the main aim is to accept or reject the product batch based on the product reliability. This topic is related to a reliability demonstration problem. The procedure is applied to a class of distributions that belong to the exponential family. Thus, a unified framework addressing the main topics in the considered Bayesian model is presented. An illustrative example shows that the proposed technique can be easily applied in practice
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
Bayesian Estimation of a Mixture Model
Ilhem Merah
2015-05-01
Full Text Available We present the properties of a bathtub curve reliability model having both a sufficient adaptability and a minimal number of parameters introduced by Idée and Pierrat (2010. This one is a mixture of a Gamma distribution G(2, (1/θ and a new distribution L(θ. We are interesting by Bayesian estimation of the parameters and survival function of this model with a squared-error loss function and non-informative prior using the approximations of Lindley (1980 and Tierney and Kadane (1986. Using a statistical sample of 60 failure data relative to a technical device, we illustrate the results derived. Based on a simulation study, comparisons are made between these two methods and the maximum likelihood method of this two parameters model.
The Bayesian Modelling Of Inflation Rate In Romania
Mihaela Simionescu
2014-01-01
Bayesian econometrics knew a considerable increase in popularity in the last years, joining the interests of various groups of researchers in economic sciences and additional ones as specialists in econometrics, commerce, industry, marketing, finance, micro-economy, macro-economy and other domains. The purpose of this research is to achieve an introduction in Bayesian approach applied in economics, starting with Bayes theorem. For the Bayesian linear regression models the methodology of estim...
A tutorial introduction to Bayesian models of cognitive development
Perfors, Amy; Tenenbaum, Joshua B.; Griffiths, Thomas L.; Xu, Fei
2010-01-01
We present an introduction to Bayesian inference as it is used in probabilistic models of cognitive development. Our goal is to provide an intuitive and accessible guide to the what, the how, and the why of the Bayesian approach: what sorts of problems and data the framework is most relevant for, and how and why it may be useful for developmentalists. We emphasize a qualitative understanding of Bayesian inference, but also include information about additional resources for those interested in...
Merging Digital Surface Models Implementing Bayesian Approaches
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.
Bayesian Models of Graphs, Arrays and Other Exchangeable Random Structures.
Orbanz, Peter; Roy, Daniel M
2015-02-01
The natural habitat of most Bayesian methods is data represented by exchangeable sequences of observations, for which de Finetti's theorem provides the theoretical foundation. Dirichlet process clustering, Gaussian process regression, and many other parametric and nonparametric Bayesian models fall within the remit of this framework; many problems arising in modern data analysis do not. This article provides an introduction to Bayesian models of graphs, matrices, and other data that can be modeled by random structures. We describe results in probability theory that generalize de Finetti's theorem to such data and discuss their relevance to nonparametric Bayesian modeling. With the basic ideas in place, we survey example models available in the literature; applications of such models include collaborative filtering, link prediction, and graph and network analysis. We also highlight connections to recent developments in graph theory and probability, and sketch the more general mathematical foundation of Bayesian methods for other types of data beyond sequences and arrays. PMID:26353253
Modeling Social Annotation: a Bayesian Approach
Plangprasopchok, Anon
2008-01-01
Collaborative tagging systems, such as del.icio.us, CiteULike, and others, allow users to annotate objects, e.g., Web pages or scientific papers, with descriptive labels called tags. The social annotations, contributed by thousands of users, can potentially be used to infer categorical knowledge, classify documents or recommend new relevant information. Traditional text inference methods do not make best use of socially-generated data, since they do not take into account variations in individual users' perspectives and vocabulary. In a previous work, we introduced a simple probabilistic model that takes interests of individual annotators into account in order to find hidden topics of annotated objects. Unfortunately, our proposed approach had a number of shortcomings, including overfitting, local maxima and the requirement to specify values for some parameters. In this paper we address these shortcomings in two ways. First, we extend the model to a fully Bayesian framework. Second, we describe an infinite ver...
Improving randomness characterization through Bayesian model selection
R., Rafael Díaz-H; Martínez, Alí M Angulo; U'Ren, Alfred B; Hirsch, Jorge G; Marsili, Matteo; Castillo, Isaac Pérez
2016-01-01
Nowadays random number generation plays an essential role in technology with important applications in areas ranging from cryptography, which lies at the core of current communication protocols, to Monte Carlo methods, and other probabilistic algorithms. In this context, a crucial scientific endeavour is to develop effective methods that allow the characterization of random number generators. However, commonly employed methods either lack formality (e.g. the NIST test suite), or are inapplicable in principle (e.g. the characterization derived from the Algorithmic Theory of Information (ATI)). In this letter we present a novel method based on Bayesian model selection, which is both rigorous and effective, for characterizing randomness in a bit sequence. We derive analytic expressions for a model's likelihood which is then used to compute its posterior probability distribution. Our method proves to be more rigorous than NIST's suite and the Borel-Normality criterion and its implementation is straightforward. We...
Bayesian mixture models for Poisson astronomical images
Guglielmetti, Fabrizia; Dose, Volker
2012-01-01
Astronomical images in the Poisson regime are typically characterized by a spatially varying cosmic background, large variety of source morphologies and intensities, data incompleteness, steep gradients in the data, and few photon counts per pixel. The Background-Source separation technique is developed with the aim to detect faint and extended sources in astronomical images characterized by Poisson statistics. The technique employs Bayesian mixture models to reliably detect the background as well as the sources with their respective uncertainties. Background estimation and source detection is achieved in a single algorithm. A large variety of source morphologies is revealed. The technique is applied in the X-ray part of the electromagnetic spectrum on ROSAT and Chandra data sets and it is under a feasibility study for the forthcoming eROSITA mission.
Hierarchical Bayesian spatial models for alcohol availability, drug "hot spots" and violent crime
Horel Scott
2006-12-01
Full Text Available Abstract Background Ecologic studies have shown a relationship between alcohol outlet densities, illicit drug use and violence. The present study examined this relationship in the City of Houston, Texas, using a sample of 439 census tracts. Neighborhood sociostructural covariates, alcohol outlet density, drug crime density and violent crime data were collected for the year 2000, and analyzed using hierarchical Bayesian models. Model selection was accomplished by applying the Deviance Information Criterion. Results The counts of violent crime in each census tract were modelled as having a conditional Poisson distribution. Four neighbourhood explanatory variables were identified using principal component analysis. The best fitted model was selected as the one considering both unstructured and spatial dependence random effects. The results showed that drug-law violation explained a greater amount of variance in violent crime rates than alcohol outlet densities. The relative risk for drug-law violation was 2.49 and that for alcohol outlet density was 1.16. Of the neighbourhood sociostructural covariates, males of age 15 to 24 showed an effect on violence, with a 16% decrease in relative risk for each increase the size of its standard deviation. Both unstructured heterogeneity random effect and spatial dependence need to be included in the model. Conclusion The analysis presented suggests that activity around illicit drug markets is more strongly associated with violent crime than is alcohol outlet density. Unique among the ecological studies in this field, the present study not only shows the direction and magnitude of impact of neighbourhood sociostructural covariates as well as alcohol and illicit drug activities in a neighbourhood, it also reveals the importance of applying hierarchical Bayesian models in this research field as both spatial dependence and heterogeneity random effects need to be considered simultaneously.
A SEMIPARAMETRIC BAYESIAN MODEL FOR CIRCULAR-LINEAR REGRESSION
We present a Bayesian approach to regress a circular variable on a linear predictor. The regression coefficients are assumed to have a nonparametric distribution with a Dirichlet process prior. The semiparametric Bayesian approach gives added flexibility to the model and is usefu...
A new approach for Bayesian model averaging
TIAN XiangJun; XIE ZhengHui; WANG AiHui; YANG XiaoChun
2012-01-01
Bayesian model averaging (BMA) is a recently proposed statistical method for calibrating forecast ensembles from numerical weather models.However,successful implementation of BMA requires accurate estimates of the weights and variances of the individual competing models in the ensemble.Two methods,namely the Expectation-Maximization (EM) and the Markov Chain Monte Carlo (MCMC) algorithms,are widely used for BMA model training.Both methods have their own respective strengths and weaknesses.In this paper,we first modify the BMA log-likelihood function with the aim of removing the additional limitation that requires that the BMA weights add to one,and then use a limited memory quasi-Newtonian algorithm for solving the nonlinear optimization problem,thereby formulating a new approach for BMA (referred to as BMA-BFGS).Several groups of multi-model soil moisture simulation experiments from three land surface models show that the performance of BMA-BFGS is similar to the MCMC method in terms of simulation accuracy,and that both are superior to the EM algorithm.On the other hand,the computational cost of the BMA-BFGS algorithm is substantially less than for MCMC and is almost equivalent to that for EM.
Trenkel, Verena M.; Bravington, Mark V.; Lorance, Pascal; Walters , Carl
2012-01-01
Catch curves are widely used to estimate total mortality for exploited marine populations. The usual population dynamics model assumes constant recruitment across years and constant total mortality. We extend this to include annual recruitment and annual total mortality. Recruitment is treated as an uncorrelated random effect, while total mortality is modelled by a random walk. Data requirements are minimal as only proportions-at-age and total catches are needed. We obtain the effective sampl...
Bayesian Model Selection for LISA Pathfinder
Karnesis, Nikolaos; Sopuerta, Carlos F; Gibert, Ferran; Armano, Michele; Audley, Heather; Congedo, Giuseppe; Diepholz, Ingo; Ferraioli, Luigi; Hewitson, Martin; Hueller, Mauro; Korsakova, Natalia; Plagnol, Eric; Vitale, and Stefano
2013-01-01
The main goal of the LISA Pathfinder (LPF) mission is to fully characterize the acceleration noise models and to test key technologies for future space-based gravitational-wave observatories similar to the LISA/eLISA concept. The Data Analysis (DA) team has developed complex three-dimensional models of the LISA Technology Package (LTP) experiment on-board LPF. These models are used for simulations, but more importantly, they will be used for parameter estimation purposes during flight operations. One of the tasks of the DA team is to identify the physical effects that contribute significantly to the properties of the instrument noise. A way of approaching to this problem is to recover the essential parameters of the LTP which describe the data. Thus, we want to define the simplest model that efficiently explains the observations. To do so, adopting a Bayesian framework, one has to estimate the so-called Bayes Factor between two competing models. In our analysis, we use three main different methods to estimate...
Bayesian Model Averaging in the Instrumental Variable Regression Model
Gary Koop; Robert Leon Gonzalez; Rodney Strachan
2011-01-01
This paper considers the instrumental variable regression model when there is uncertainly about the set of instruments, exogeneity restrictions, the validity of identifying restrictions and the set of exogenous regressors. This uncertainly can result in a huge number of models. To avoid statistical problems associated with standard model selection procedures, we develop a reversible jump Markov chain Monte Carlo algorithm that allows us to do Bayesian model averaging. The algorithm is very fl...
EVENT MODEL: A ROBUST BAYESIAN TOOL FOR CHRONOLOGICAL MODELING
Lanos, Philippe; Philippe, Anne
2015-01-01
We propose a new modeling approach for combining dates through the Event model by using hierarchical Bayesian statistics. The Event model aims to estimate the date of a context (unit of stratification) from individual dates assumed to be contemporaneous and which are affected by errors of different types: laboratory and calibration curve errors and also irreducible errors related to contaminations, taphonomic disturbances, etc, hence the possible presence of outliers. The Event model has a hi...
Thorson, James T.; Kristensen, Kasper
2016-01-01
Statistical models play an important role in fisheries science when reconciling ecological theory with available data for wild populations or experimental studies. Ecological models increasingly include both fixed and random effects, and are often estimated using maximum likelihood techniques...... is calculated as a nonlinear function of random effects. We therefore describe and evaluate a new "epsilon" estimator as a generic bias-correction estimator for derived quantities. We use simulated data to compare the epsilon-method with an existing bias-correction algorithm for estimating...... recruitment in four configurations of an age-structured population dynamics model. This simulation experiment shows that the epsilon-method and the existing bias-correction method perform equally well in data-rich contexts, but the epsilon-method is slightly less biased in data-poor contexts. We then apply...
Stochastic model updating utilizing Bayesian approach and Gaussian process model
Wan, Hua-Ping; Ren, Wei-Xin
2016-03-01
Stochastic model updating (SMU) has been increasingly applied in quantifying structural parameter uncertainty from responses variability. SMU for parameter uncertainty quantification refers to the problem of inverse uncertainty quantification (IUQ), which is a nontrivial task. Inverse problem solved with optimization usually brings about the issues of gradient computation, ill-conditionedness, and non-uniqueness. Moreover, the uncertainty present in response makes the inverse problem more complicated. In this study, Bayesian approach is adopted in SMU for parameter uncertainty quantification. The prominent strength of Bayesian approach for IUQ problem is that it solves IUQ problem in a straightforward manner, which enables it to avoid the previous issues. However, when applied to engineering structures that are modeled with a high-resolution finite element model (FEM), Bayesian approach is still computationally expensive since the commonly used Markov chain Monte Carlo (MCMC) method for Bayesian inference requires a large number of model runs to guarantee the convergence. Herein we reduce computational cost in two aspects. On the one hand, the fast-running Gaussian process model (GPM) is utilized to approximate the time-consuming high-resolution FEM. On the other hand, the advanced MCMC method using delayed rejection adaptive Metropolis (DRAM) algorithm that incorporates local adaptive strategy with global adaptive strategy is employed for Bayesian inference. In addition, we propose the use of the powerful variance-based global sensitivity analysis (GSA) in parameter selection to exclude non-influential parameters from calibration parameters, which yields a reduced-order model and thus further alleviates the computational burden. A simulated aluminum plate and a real-world complex cable-stayed pedestrian bridge are presented to illustrate the proposed framework and verify its feasibility.
Bayesian estimation of parameters in a regional hydrological model
Engeland, K.; Gottschalk, L.
2002-01-01
This study evaluates the applicability of the distributed, process-oriented Ecomag model for prediction of daily streamflow in ungauged basins. The Ecomag model is applied as a regional model to nine catchments in the NOPEX area, using Bayesian statistics to estimate the posterior distribution of the model parameters conditioned on the observed streamflow. The distribution is calculated by Markov Chain Monte Carlo (MCMC) analysis. The Bayesian method requires formulation of a likelihood funct...
Bayesian estimation of parameters in a regional hydrological model
Engeland, K.; Gottschalk, L.
2002-01-01
This study evaluates the applicability of the distributed, process-oriented Ecomag model for prediction of daily streamflow in ungauged basins. The Ecomag model is applied as a regional model to nine catchments in the NOPEX area, using Bayesian statistics to estimate the posterior distribution of the model parameters conditioned on the observed streamflow. The distribution is calculated by Markov Chain Monte Carlo (MCMC) analysis. The Bayesian method requires formulation of ...
Bayesian Analysis of Dynamic Multivariate Models with Multiple Structural Breaks
Sugita, Katsuhiro
2006-01-01
This paper considers a vector autoregressive model or a vector error correction model with multiple structural breaks in any subset of parameters, using a Bayesian approach with Markov chain Monte Carlo simulation technique. The number of structural breaks is determined as a sort of model selection by the posterior odds. For a cointegrated model, cointegrating rank is also allowed to change with breaks. Bayesian approach by Strachan (Journal of Business and Economic Statistics 21 (2003) 185) ...
Bayesian Test of Significance for Conditional Independence: The Multinomial Model
de Morais Andrade, Pablo; Stern, Julio; de Bragança Pereira, Carlos
2014-03-01
Conditional independence tests (CI tests) have received special attention lately in Machine Learning and Computational Intelligence related literature as an important indicator of the relationship among the variables used by their models. In the field of Probabilistic Graphical Models (PGM)--which includes Bayesian Networks (BN) models--CI tests are especially important for the task of learning the PGM structure from data. In this paper, we propose the Full Bayesian Significance Test (FBST) for tests of conditional independence for discrete datasets. FBST is a powerful Bayesian test for precise hypothesis, as an alternative to frequentist's significance tests (characterized by the calculation of the \\emph{p-value}).
Hartung, Joachim; Knapp, Guido
2000-01-01
A confidence interval for the between group variance is proposed which is deduced from Wald’s exact confidence interval for the ratio of the two variance components in the one-way random effects model and the exact confidence interval for the error variance resp. an unbiased estimator of the error variance. In a simulation study the confidence coefficients for these two intervals are compared with the confidence coefficients of two other commonly used confidence intervals. There, the confiden...
Vardeman, Stephen B.; Wendelberger, Joanne R.
2004-01-01
There is a little-known but very simple generalization of the standard result that for uncorrelated variables with a common mean and variance, the expected sample variance is the marginal variance. The generalization justifies the use of the usual standard error of the sample mean in possibly heteroscedastic situations and motivates some simple estimators for unbalanced linear random effects models. The latter is illustrated for the simple one-way context.
Bayesian Nonparametrics in Topic Modeling: A Brief Tutorial
Spangher, Alexander
2015-01-01
Using nonparametric methods has been increasingly explored in Bayesian hierarchical modeling as a way to increase model flexibility. Although the field shows a lot of promise, inference in many models, including Hierachical Dirichlet Processes (HDP), remain prohibitively slow. One promising path forward is to exploit the submodularity inherent in Indian Buffet Process (IBP) to derive near-optimal solutions in polynomial time. In this work, I will present a brief tutorial on Bayesian nonparame...
Two-Stage Bayesian Model Averaging in Endogenous Variable Models.
Lenkoski, Alex; Eicher, Theo S; Raftery, Adrian E
2014-01-01
Economic modeling in the presence of endogeneity is subject to model uncertainty at both the instrument and covariate level. We propose a Two-Stage Bayesian Model Averaging (2SBMA) methodology that extends the Two-Stage Least Squares (2SLS) estimator. By constructing a Two-Stage Unit Information Prior in the endogenous variable model, we are able to efficiently combine established methods for addressing model uncertainty in regression models with the classic technique of 2SLS. To assess the validity of instruments in the 2SBMA context, we develop Bayesian tests of the identification restriction that are based on model averaged posterior predictive p-values. A simulation study showed that 2SBMA has the ability to recover structure in both the instrument and covariate set, and substantially improves the sharpness of resulting coefficient estimates in comparison to 2SLS using the full specification in an automatic fashion. Due to the increased parsimony of the 2SBMA estimate, the Bayesian Sargan test had a power of 50 percent in detecting a violation of the exogeneity assumption, while the method based on 2SLS using the full specification had negligible power. We apply our approach to the problem of development accounting, and find support not only for institutions, but also for geography and integration as development determinants, once both model uncertainty and endogeneity have been jointly addressed. PMID:24223471
Sampling Techniques in Bayesian Finite Element Model Updating
Boulkaibet, I; Mthembu, L; Friswell, M I; Adhikari, S
2011-01-01
Recent papers in the field of Finite Element Model (FEM) updating have highlighted the benefits of Bayesian techniques. The Bayesian approaches are designed to deal with the uncertainties associated with complex systems, which is the main problem in the development and updating of FEMs. This paper highlights the complexities and challenges of implementing any Bayesian method when the analysis involves a complicated structural dynamic model. In such systems an analytical Bayesian formulation might not be available in an analytic form; therefore this leads to the use of numerical methods, i.e. sampling methods. The main challenge then is to determine an efficient sampling of the model parameter space. In this paper, three sampling techniques, the Metropolis-Hastings (MH) algorithm, Slice Sampling and the Hybrid Monte Carlo (HMC) technique, are tested by updating a structural beam model. The efficiency and limitations of each technique is investigated when the FEM updating problem is implemented using the Bayesi...
Efficient Nonparametric Bayesian Modelling with Sparse Gaussian Process Approximations
Seeger, Matthias; Lawrence, Neil; Herbrich, Ralf
2006-01-01
Sparse approximations to Bayesian inference for nonparametric Gaussian Process models scale linearly in the number of training points, allowing for the application of powerful kernel-based models to large datasets. We present a general framework based on the informative vector machine (IVM) (Lawrence et.al., 2002) and show how the complete Bayesian task of inference and learning of free hyperparameters can be performed in a practically efficient manner. Our framework allows for arbitrary like...
Modelling biogeochemical cycles in forest ecosystems: a Bayesian approach
Bagnara, Maurizio
2015-01-01
Forest models are tools for explaining and predicting the dynamics of forest ecosystems. They simulate forest behavior by integrating information on the underlying processes in trees, soil and atmosphere. Bayesian calibration is the application of probability theory to parameter estimation. It is a method, applicable to all models, that quantifies output uncertainty and identifies key parameters and variables. This study aims at testing the Bayesian procedure for calibration to different t...
Bayesian Inference and Optimal Design in the Sparse Linear Model
Seeger, Matthias; Steinke, Florian; Tsuda, Koji
2007-01-01
The sparse linear model has seen many successful applications in Statistics, Machine Learning, and Computational Biology, such as identification of gene regulatory networks from micro-array expression data. Prior work has either approximated Bayesian inference by expensive Markov chain Monte Carlo, or replaced it by point estimation. We show how to obtain a good approximation to Bayesian analysis efficiently, using the Expectation Propagation method. We also address the problems of optimal de...
A Bayesian observer model constrained by efficient coding can explain 'anti-Bayesian' percepts.
Wei, Xue-Xin; Stocker, Alan A
2015-10-01
Bayesian observer models provide a principled account of the fact that our perception of the world rarely matches physical reality. The standard explanation is that our percepts are biased toward our prior beliefs. However, reported psychophysical data suggest that this view may be simplistic. We propose a new model formulation based on efficient coding that is fully specified for any given natural stimulus distribution. The model makes two new and seemingly anti-Bayesian predictions. First, it predicts that perception is often biased away from an observer's prior beliefs. Second, it predicts that stimulus uncertainty differentially affects perceptual bias depending on whether the uncertainty is induced by internal or external noise. We found that both model predictions match reported perceptual biases in perceived visual orientation and spatial frequency, and were able to explain data that have not been explained before. The model is general and should prove applicable to other perceptual variables and tasks. PMID:26343249
Modelling of JET diagnostics using Bayesian Graphical Models
Svensson, J. [IPP Greifswald, Greifswald (Germany); Ford, O. [Imperial College, London (United Kingdom); McDonald, D.; Hole, M.; Nessi, G. von; Meakins, A.; Brix, M.; Thomsen, H.; Werner, A.; Sirinelli, A.
2011-07-01
The mapping between physics parameters (such as densities, currents, flows, temperatures etc) defining the plasma 'state' under a given model and the raw observations of each plasma diagnostic will 1) depend on the particular physics model used, 2) is inherently probabilistic, from uncertainties on both observations and instrumental aspects of the mapping, such as calibrations, instrument functions etc. A flexible and principled way of modelling such interconnected probabilistic systems is through so called Bayesian graphical models. Being an amalgam between graph theory and probability theory, Bayesian graphical models can simulate the complex interconnections between physics models and diagnostic observations from multiple heterogeneous diagnostic systems, making it relatively easy to optimally combine the observations from multiple diagnostics for joint inference on parameters of the underlying physics model, which in itself can be represented as part of the graph. At JET about 10 diagnostic systems have to date been modelled in this way, and has lead to a number of new results, including: the reconstruction of the flux surface topology and q-profiles without any specific equilibrium assumption, using information from a number of different diagnostic systems; profile inversions taking into account the uncertainties in the flux surface positions and a substantial increase in accuracy of JET electron density and temperature profiles, including improved pedestal resolution, through the joint analysis of three diagnostic systems. It is believed that the Bayesian graph approach could potentially be utilised for very large sets of diagnostics, providing a generic data analysis framework for nuclear fusion experiments, that would be able to optimally utilize the information from multiple diagnostics simultaneously, and where the explicit graph representation of the connections to underlying physics models could be used for sophisticated model testing. This
Bayesian model discrimination for glucose-insulin homeostasis
Andersen, Kim Emil; Brooks, Stephen P.; Højbjerre, Malene
the reformulation of existing deterministic models as stochastic state space models which properly accounts for both measurement and process variability. The analysis is further enhanced by Bayesian model discrimination techniques and model averaged parameter estimation which fully accounts for model as well......In this paper we analyse a set of experimental data on a number of healthy and diabetic patients and discuss a variety of models for describing the physiological processes involved in glucose absorption and insulin secretion within the human body. We adopt a Bayesian approach which facilitates...
Using consensus bayesian network to model the reactive oxygen species regulatory pathway.
Liangdong Hu
Full Text Available Bayesian network is one of the most successful graph models for representing the reactive oxygen species regulatory pathway. With the increasing number of microarray measurements, it is possible to construct the bayesian network from microarray data directly. Although large numbers of bayesian network learning algorithms have been developed, when applying them to learn bayesian networks from microarray data, the accuracies are low due to that the databases they used to learn bayesian networks contain too few microarray data. In this paper, we propose a consensus bayesian network which is constructed by combining bayesian networks from relevant literatures and bayesian networks learned from microarray data. It would have a higher accuracy than the bayesian networks learned from one database. In the experiment, we validated the bayesian network combination algorithm on several classic machine learning databases and used the consensus bayesian network to model the Escherichia coli's ROS pathway.
Wu, Yuefeng; Hooker, Giles
2013-01-01
This paper introduces a hierarchical framework to incorporate Hellinger distance methods into Bayesian analysis. We propose to modify a prior over non-parametric densities with the exponential of twice the Hellinger distance between a candidate and a parametric density. By incorporating a prior over the parameters of the second density, we arrive at a hierarchical model in which a non-parametric model is placed between parameters and the data. The parameters of the family can then be estimate...
Analysis of Gumbel Model for Software Reliability Using Bayesian Paradigm
Raj Kumar
2012-12-01
Full Text Available In this paper, we have illustrated the suitability of Gumbel Model for software reliability data. The model parameters are estimated using likelihood based inferential procedure: classical as well as Bayesian. The quasi Newton-Raphson algorithm is applied to obtain the maximum likelihood estimates and associated probability intervals. The Bayesian estimates of the parameters of Gumbel model are obtained using Markov Chain Monte Carlo(MCMC simulation method in OpenBUGS(established software for Bayesian analysis using Markov Chain Monte Carlo methods. The R functions are developed to study the statistical properties, model validation and comparison tools of the model and the output analysis of MCMC samples generated from OpenBUGS. Details of applying MCMC to parameter estimation for the Gumbel model are elaborated and a real software reliability data set is considered to illustrate the methods of inference discussed in this paper.
Lack of Confidence in Approximate Bayesian Computation Model Choice
Robert, Christian P.; Cornuet, Jean-Marie; Marin, Jean-Michel; Pillai, Natesh S.
2011-01-01
Approximate Bayesian computation (ABC) have become an essential tool for the analysis of complex stochastic models. Grelaud et al. [(2009) Bayesian Anal 3:427–442] advocated the use of ABC for model choice in the specific case of Gibbs random fields, relying on an intermodel sufficiency property to show that the approximation was legitimate. We implemented ABC model choice in a wide range of phylogenetic models in the Do It Yourself-ABC (DIY-ABC) software [Cornuet et al. (2008) Bioinformatics...
A Bayesian semiparametric model for bivariate sparse longitudinal data.
Das, Kiranmoy; Li, Runze; Sengupta, Subhajit; Wu, Rongling
2013-09-30
Mixed-effects models have recently become popular for analyzing sparse longitudinal data that arise naturally in biological, agricultural and biomedical studies. Traditional approaches assume independent residuals over time and explain the longitudinal dependence by random effects. However, when bivariate or multivariate traits are measured longitudinally, this fundamental assumption is likely to be violated because of intertrait dependence over time. We provide a more general framework where the dependence of the observations from the same subject over time is not assumed to be explained completely by the random effects of the model. We propose a novel, mixed model-based approach and estimate the error-covariance structure nonparametrically under a generalized linear model framework. We use penalized splines to model the general effect of time, and we consider a Dirichlet process mixture of normal prior for the random-effects distribution. We analyze blood pressure data from the Framingham Heart Study where body mass index, gender and time are treated as covariates. We compare our method with traditional methods including parametric modeling of the random effects and independent residual errors over time. We conduct extensive simulation studies to investigate the practical usefulness of the proposed method. The current approach is very helpful in analyzing bivariate irregular longitudinal traits. PMID:23553747
On the Bayesian Nonparametric Generalization of IRT-Type Models
San Martin, Ernesto; Jara, Alejandro; Rolin, Jean-Marie; Mouchart, Michel
2011-01-01
We study the identification and consistency of Bayesian semiparametric IRT-type models, where the uncertainty on the abilities' distribution is modeled using a prior distribution on the space of probability measures. We show that for the semiparametric Rasch Poisson counts model, simple restrictions ensure the identification of a general…
Bayesian inference model for fatigue life of laminated composites
Dimitrov, Nikolay Krasimirov; Kiureghian, Armen Der; Berggreen, Christian
2016-01-01
A probabilistic model for estimating the fatigue life of laminated composite plates is developed. The model is based on lamina-level input data, making it possible to predict fatigue properties for a wide range of laminate configurations. Model parameters are estimated by Bayesian inference. The...
Modelling LGD for unsecured retail loans using Bayesian methods
Katarzyna Bijak; Thomas, Lyn C
2015-01-01
Loss Given Default (LGD) is the loss borne by the bank when a customer defaults on a loan. LGD for unsecured retail loans is often found difficult to model. In the frequentist (non-Bayesian) two-step approach, two separate regression models are estimated independently, which can be considered potentially problematic when trying to combine them to make predictions about LGD. The result is a point estimate of LGD for each loan. Alternatively, LGD can be modelled using Bayesian methods. In the B...
A Bayesian Matrix Factorization Model for Relational Data
Singh, Ajit P
2012-01-01
Relational learning can be used to augment one data source with other correlated sources of information, to improve predictive accuracy. We frame a large class of relational learning problems as matrix factorization problems, and propose a hierarchical Bayesian model. Training our Bayesian model using random-walk Metropolis-Hastings is impractically slow, and so we develop a block Metropolis- Hastings sampler which uses the gradient and Hessian of the likelihood to dynamically tune the proposal. We demonstrate that a predictive model of brain response to stimuli can be improved by augmenting it with side information about the stimuli.
Bayesian inference of chemical kinetic models from proposed reactions
Galagali, Nikhil
2015-02-01
© 2014 Elsevier Ltd. Bayesian inference provides a natural framework for combining experimental data with prior knowledge to develop chemical kinetic models and quantify the associated uncertainties, not only in parameter values but also in model structure. Most existing applications of Bayesian model selection methods to chemical kinetics have been limited to comparisons among a small set of models, however. The significant computational cost of evaluating posterior model probabilities renders traditional Bayesian methods infeasible when the model space becomes large. We present a new framework for tractable Bayesian model inference and uncertainty quantification using a large number of systematically generated model hypotheses. The approach involves imposing point-mass mixture priors over rate constants and exploring the resulting posterior distribution using an adaptive Markov chain Monte Carlo method. The posterior samples are used to identify plausible models, to quantify rate constant uncertainties, and to extract key diagnostic information about model structure-such as the reactions and operating pathways most strongly supported by the data. We provide numerical demonstrations of the proposed framework by inferring kinetic models for catalytic steam and dry reforming of methane using available experimental data.
The Bayesian Modelling Of Inflation Rate In Romania
Mihaela Simionescu (Bratu
2014-06-01
Full Text Available Bayesian econometrics knew a considerable increase in popularity in the last years, joining the interests of various groups of researchers in economic sciences and additional ones as specialists in econometrics, commerce, industry, marketing, finance, micro-economy, macro-economy and other domains. The purpose of this research is to achieve an introduction in Bayesian approach applied in economics, starting with Bayes theorem. For the Bayesian linear regression models the methodology of estimation was presented, realizing two empirical studies for data taken from the Romanian economy. Thus, an autoregressive model of order 2 and a multiple regression model were built for the index of consumer prices. The Gibbs sampling algorithm was used for estimation in R software, computing the posterior means and the standard deviations. The parameters’ stability proved to be greater than in the case of estimations based on the methods of classical Econometrics.
Bayesian Subset Modeling for High-Dimensional Generalized Linear Models
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.
Involving Stakeholders in Building Integrated Fisheries Models Using Bayesian Methods
Haapasaari, Päivi; Mäntyniemi, Samu; Kuikka, Sakari
2013-06-01
A participatory Bayesian approach was used to investigate how the views of stakeholders could be utilized to develop models to help understand the Central Baltic herring fishery. In task one, we applied the Bayesian belief network methodology to elicit the causal assumptions of six stakeholders on factors that influence natural mortality, growth, and egg survival of the herring stock in probabilistic terms. We also integrated the expressed views into a meta-model using the Bayesian model averaging (BMA) method. In task two, we used influence diagrams to study qualitatively how the stakeholders frame the management problem of the herring fishery and elucidate what kind of causalities the different views involve. The paper combines these two tasks to assess the suitability of the methodological choices to participatory modeling in terms of both a modeling tool and participation mode. The paper also assesses the potential of the study to contribute to the development of participatory modeling practices. It is concluded that the subjective perspective to knowledge, that is fundamental in Bayesian theory, suits participatory modeling better than a positivist paradigm that seeks the objective truth. The methodology provides a flexible tool that can be adapted to different kinds of needs and challenges of participatory modeling. The ability of the approach to deal with small data sets makes it cost-effective in participatory contexts. However, the BMA methodology used in modeling the biological uncertainties is so complex that it needs further development before it can be introduced to wider use in participatory contexts.
Bayesian modeling and prediction of solar particles flux
Dedecius, Kamil; Kalová, J.
Praha: FJFI ČVUT v Praze, 2009 - (Štěpán, V.), s. 77-77 ISBN 978-80-01-04430-8. [XXXI. Dny radiační ochrany. Kouty nad Desnou, Hrubý Jeseník (CZ), 02.11.2009-06.11.2009] R&D Projects: GA MŠk 1M0572 Institutional research plan: CEZ:AV0Z10750506 Keywords : Bayesian model * solar particle * solar wind Subject RIV: IN - Informatics, Computer Science http://library.utia.cas.cz/separaty/2009/AS/dedecius-bayesian modeling and prediction of solar particle s flux.pdf
Research & development and growth: A Bayesian model averaging analysis
Horváth, Roman
2011-01-01
Roč. 28, č. 6 (2011), s. 2669-2673. ISSN 0264-9993. [Society for Non-linear Dynamics and Econometrics Annual Conferencen. Washington DC, 16.03.2011-18.03.2011] R&D Projects: GA ČR GA402/09/0965 Institutional research plan: CEZ:AV0Z10750506 Keywords : Research and development * Growth * Bayesian model averaging Subject RIV: AH - Economics Impact factor: 0.701, year: 2011 http://library.utia.cas.cz/separaty/2011/E/horvath-research & development and growth a bayesian model averaging analysis.pdf
Approximate Bayesian Recursive Estimation of Linear Model with Uniform Noise
Pavelková, Lenka; Kárný, Miroslav
Brussels: IFAC, 2012, s. 1803-1807. ISBN 978-3-902823-06-9. [16th IFAC Symposium on System Identification The International Federation of Automatic Control. Brussels (BE), 11.07.2012-13.07.2012] R&D Projects: GA TA ČR TA01030123 Institutional support: RVO:67985556 Keywords : recursive parameter estimation * bounded noise * Bayesian learning * autoregressive models Subject RIV: BC - Control System s Theory http://library.utia.cas.cz/separaty/2012/AS/pavelkova-approximate bayesian recursive estimation of linear model with uniform noise.pdf
Comparing Bayesian models for multisensory cue combination without mandatory integration
Beierholm, Ulrik R.; Shams, Ladan; Kording, Konrad P; Ma, Wei Ji
2009-01-01
Bayesian models of multisensory perception traditionally address the problem of estimating an underlying variable that is assumed to be the cause of the two sensory signals. The brain, however, has to solve a more general problem: it also has to establish which signals come from the same source and should be integrated, and which ones do not and should be segregated. In the last couple of years, a few models have been proposed to solve this problem in a Bayesian fashion. One of these ha...
Bayesian model mixing for cold rolling mills: Test results
Ettler, P.; Puchr, I.; Dedecius, Kamil
Slovensko: Slovak University of Technology, 2013, s. 359-364. ISBN 978-1-4799-0926-1. [19th International Conference on Process Control . Štrbské Pleso (SK), 18.06.2013-21.06.2013] R&D Projects: GA MŠk(CZ) 7D09008; GA MŠk 7D12004 Keywords : Bayesian statistics * model mixing * process control Subject RIV: BC - Control Systems Theory http://library.utia.cas.cz/separaty/2013/AS/dedecius-bayesian model mixing for cold rolling mills test results.pdf
Bayesian Model Comparison With the g-Prior
Nielsen, Jesper Kjær; Christensen, Mads Græsbøll; Cemgil, Ali Taylan;
2014-01-01
Model comparison and selection is an important problem in many model-based signal processing applications. Often, very simple information criteria such as the Akaike information criterion or the Bayesian information criterion are used despite their shortcomings. Compared to these methods, Djuric’...
Bayesian Estimation of the DINA Model with Gibbs Sampling
Culpepper, Steven Andrew
2015-01-01
A Bayesian model formulation of the deterministic inputs, noisy "and" gate (DINA) model is presented. Gibbs sampling is employed to simulate from the joint posterior distribution of item guessing and slipping parameters, subject attribute parameters, and latent class probabilities. The procedure extends concepts in Béguin and Glas,…
Bayesian Joint Modelling for Object Localisation in Weakly Labelled Images.
Shi, Zhiyuan; Hospedales, Timothy M; Xiang, Tao
2015-10-01
We address the problem of localisation of objects as bounding boxes in images and videos with weak labels. This weakly supervised object localisation problem has been tackled in the past using discriminative models where each object class is localised independently from other classes. In this paper, a novel framework based on Bayesian joint topic modelling is proposed, which differs significantly from the existing ones in that: (1) All foreground object classes are modelled jointly in a single generative model that encodes multiple object co-existence so that "explaining away" inference can resolve ambiguity and lead to better learning and localisation. (2) Image backgrounds are shared across classes to better learn varying surroundings and "push out" objects of interest. (3) Our model can be learned with a mixture of weakly labelled and unlabelled data, allowing the large volume of unlabelled images on the Internet to be exploited for learning. Moreover, the Bayesian formulation enables the exploitation of various types of prior knowledge to compensate for the limited supervision offered by weakly labelled data, as well as Bayesian domain adaptation for transfer learning. Extensive experiments on the PASCAL VOC, ImageNet and YouTube-Object videos datasets demonstrate the effectiveness of our Bayesian joint model for weakly supervised object localisation. PMID:26340253
Menke, Jan [University Medical Center Goettingen, Institute for Diagnostic and Interventional Radiology, Goettingen (Germany); Kowalski, Joerg [Dr. Lauterbach-Klinik, Department of Cardiology, Bad Liebenstein (Germany)
2016-02-15
To meta-analyze diagnostic accuracy, test yield and utility of coronary computed tomography angiography (CCTA) in coronary artery disease (CAD) by an intention-to-diagnose approach with inclusion of unevaluable results. Four databases were searched from 1/2005 to 3/2013 for prospective studies that used 16-320-row or dual-source CTs and provided 3 x 2 patient-level data of CCTA (positive, negative, or unevaluable) versus catheter angiography (positive or negative) for diagnosing ≥50 % coronary stenoses. A Bayesian multivariate 3 x 2 random-effects meta-analysis considered unevaluable CCTAs. Thirty studies (3422 patients) were included. Compared to 16-40 row CT, test yield and accuracy of CCTA has significantly increased with ≥64-row CT (P < 0.05). In ≥64-row CT, about 2.5 % (95 %-CI, 0.9-4.8 %) of diseased patients and 7.5 % (4.5-11.2 %) of non-diseased patients had unevaluable CCTAs. A positive likelihood ratio of 8.9 (6.1-13.5) indicated moderate suitability for identifying CAD. A negative likelihood ratio of 0.022 (0.01-0.04) indicated excellent suitability for excluding CAD. Unevaluable CCTAs had an equivocal likelihood ratio of 0.42 (0.22-0.71). In the utility analysis, CCTA was useful at intermediate pre-test probabilities (16-70 %). CCTA is useful at intermediate CAD pre-test probabilities. Positive CCTAs require verification to confirm CAD, unevaluable CCTAs require alternative diagnostics, and negative CCTAs exclude obstructive CAD with high certainty. (orig.)
To meta-analyze diagnostic accuracy, test yield and utility of coronary computed tomography angiography (CCTA) in coronary artery disease (CAD) by an intention-to-diagnose approach with inclusion of unevaluable results. Four databases were searched from 1/2005 to 3/2013 for prospective studies that used 16-320-row or dual-source CTs and provided 3 x 2 patient-level data of CCTA (positive, negative, or unevaluable) versus catheter angiography (positive or negative) for diagnosing ≥50 % coronary stenoses. A Bayesian multivariate 3 x 2 random-effects meta-analysis considered unevaluable CCTAs. Thirty studies (3422 patients) were included. Compared to 16-40 row CT, test yield and accuracy of CCTA has significantly increased with ≥64-row CT (P < 0.05). In ≥64-row CT, about 2.5 % (95 %-CI, 0.9-4.8 %) of diseased patients and 7.5 % (4.5-11.2 %) of non-diseased patients had unevaluable CCTAs. A positive likelihood ratio of 8.9 (6.1-13.5) indicated moderate suitability for identifying CAD. A negative likelihood ratio of 0.022 (0.01-0.04) indicated excellent suitability for excluding CAD. Unevaluable CCTAs had an equivocal likelihood ratio of 0.42 (0.22-0.71). In the utility analysis, CCTA was useful at intermediate pre-test probabilities (16-70 %). CCTA is useful at intermediate CAD pre-test probabilities. Positive CCTAs require verification to confirm CAD, unevaluable CCTAs require alternative diagnostics, and negative CCTAs exclude obstructive CAD with high certainty. (orig.)
Spatial and spatio-temporal bayesian models with R - INLA
Blangiardo, Marta
2015-01-01
Dedication iiiPreface ix1 Introduction 11.1 Why spatial and spatio-temporal statistics? 11.2 Why do we use Bayesian methods for modelling spatial and spatio-temporal structures? 21.3 Why INLA? 31.4 Datasets 32 Introduction to 212.1 The language 212.2 objects 222.3 Data and session management 342.4 Packages 352.5 Programming in 362.6 Basic statistical analysis with 393 Introduction to Bayesian Methods 533.1 Bayesian Philosophy 533.2 Basic Probability Elements 573.3 Bayes Theorem 623.4 Prior and Posterior Distributions 643.5 Working with the Posterior Distribution 663.6 Choosing the Prior Distr
Modeling error distributions of growth curve models through Bayesian methods.
Zhang, Zhiyong
2016-06-01
Growth curve models are widely used in social and behavioral sciences. However, typical growth curve models often assume that the errors are normally distributed although non-normal data may be even more common than normal data. In order to avoid possible statistical inference problems in blindly assuming normality, a general Bayesian framework is proposed to flexibly model normal and non-normal data through the explicit specification of the error distributions. A simulation study shows when the distribution of the error is correctly specified, one can avoid the loss in the efficiency of standard error estimates. A real example on the analysis of mathematical ability growth data from the Early Childhood Longitudinal Study, Kindergarten Class of 1998-99 is used to show the application of the proposed methods. Instructions and code on how to conduct growth curve analysis with both normal and non-normal error distributions using the the MCMC procedure of SAS are provided. PMID:26019004
Asymptotically minimax Bayesian predictive densities for multinomial models
Komaki, Fumiyasu
2011-01-01
One-step ahead prediction for the multinomial model is considered. The performance of a predictive density is evaluated by the average Kullback-Leibler divergence from the true density to the predictive density. Asymptotic approximations of risk functions of Bayesian predictive densities based on Dirichlet priors are obtained. It is shown that a Bayesian predictive density based on a specific Dirichlet prior is asymptotically minimax. The asymptotically minimax prior is different from known objective priors such as the Jeffreys prior or the uniform prior.
Uncertainty Modeling Based on Bayesian Network in Ontology Mapping
LI Yuhua; LIU Tao; SUN Xiaolin
2006-01-01
How to deal with uncertainty is crucial in exact concept mapping between ontologies. This paper presents a new framework on modeling uncertainty in ontologies based on bayesian networks (BN). In our approach, ontology Web language (OWL) is extended to add probabilistic markups for attaching probability information, the source and target ontologies (expressed by patulous OWL) are translated into bayesian networks (BNs), the mapping between the two ontologies can be digged out by constructing the conditional probability tables (CPTs) of the BN using a improved algorithm named I-IPFP based on iterative proportional fitting procedure (IPFP). The basic idea of this framework and algorithm are validated by positive results from computer experiments.
Hierarchical Bayesian spatial models for multispecies conservation planning and monitoring.
Carroll, Carlos; Johnson, Devin S; Dunk, Jeffrey R; Zielinski, William J
2010-12-01
Biologists who develop and apply habitat models are often familiar with the statistical challenges posed by their data's spatial structure but are unsure of whether the use of complex spatial models will increase the utility of model results in planning. We compared the relative performance of nonspatial and hierarchical Bayesian spatial models for three vertebrate and invertebrate taxa of conservation concern (Church's sideband snails [Monadenia churchi], red tree voles [Arborimus longicaudus], and Pacific fishers [Martes pennanti pacifica]) that provide examples of a range of distributional extents and dispersal abilities. We used presence-absence data derived from regional monitoring programs to develop models with both landscape and site-level environmental covariates. We used Markov chain Monte Carlo algorithms and a conditional autoregressive or intrinsic conditional autoregressive model framework to fit spatial models. The fit of Bayesian spatial models was between 35 and 55% better than the fit of nonspatial analogue models. Bayesian spatial models outperformed analogous models developed with maximum entropy (Maxent) methods. Although the best spatial and nonspatial models included similar environmental variables, spatial models provided estimates of residual spatial effects that suggested how ecological processes might structure distribution patterns. Spatial models built from presence-absence data improved fit most for localized endemic species with ranges constrained by poorly known biogeographic factors and for widely distributed species suspected to be strongly affected by unmeasured environmental variables or population processes. By treating spatial effects as a variable of interest rather than a nuisance, hierarchical Bayesian spatial models, especially when they are based on a common broad-scale spatial lattice (here the national Forest Inventory and Analysis grid of 24 km(2) hexagons), can increase the relevance of habitat models to multispecies
Bayesian Modelling of fMRI Time Series
Højen-Sørensen, Pedro; Hansen, Lars Kai; Rasmussen, Carl Edward
2000-01-01
We present a Hidden Markov Model (HMM) for inferring the hidden psychological state (or neural activity) during single trial fMRI activation experiments with blocked task paradigms. Inference is based on Bayesian methodology, using a combination of analytical and a variety of Markov Chain Monte...
Bayesian Modelling of fMRI Time Series
Højen-Sørensen, Pedro; Hansen, Lars Kai; Rasmussen, Carl Edward
We present a Hidden Markov Model (HMM) for inferring the hidden psychological state (or neural activity) during single trial fMRI activation experiments with blocked task paradigms. Inference is based on Bayesian methodology, using a combination of analytical and a variety of Markov Chain Monte...
Bayesian nonparametric estimation of hazard rate in monotone Aalen model
Timková, Jana
2014-01-01
Roč. 50, č. 6 (2014), s. 849-868. ISSN 0023-5954 Institutional support: RVO:67985556 Keywords : Aalen model * Bayesian estimation * MCMC Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 0.541, year: 2014 http://library.utia.cas.cz/separaty/2014/SI/timkova-0438210.pdf
An Inhomogeneous Bayesian Texture Model for Spatially Varying Parameter Estimation
Dharmagunawardhana, Chathurika; Mahmoodi, Sasan; Bennett, Michael; Niranjan, Mahesan
2014-01-01
In statistical model based texture feature extraction, features based on spatially varying parameters achieve higher discriminative performances compared to spatially constant parameters. In this paper we formulate a novel Bayesian framework which achieves texture characterization by spatially varying parameters based on Gaussian Markov random fields. The parameter estimation is carried out by Metropolis-Hastings algorithm. The distributions of estimated spatially varying paramete...
Bayesian Variable Selection for Logistic Models Using Auxiliary Mixture Sampling
Tüchler, Regina
2006-01-01
The paper presents an Markov Chain Monte Carlo algorithm for both variable and covariance selection in the context of logistic mixed effects models. This algorithm allows us to sample solely from standard densities, with no additional tuning being needed. We apply a stochastic search variable approach to select explanatory variables as well as to determine the structure of the random effects covariance matrix. For logistic mixed effects models prior determination of explanatory variables and ...
Research on Bayesian Network Based User's Interest Model
ZHANG Weifeng; XU Baowen; CUI Zifeng; XU Lei
2007-01-01
It has very realistic significance for improving the quality of users' accessing information to filter and selectively retrieve the large number of information on the Internet. On the basis of analyzing the existing users' interest models and some basic questions of users' interest (representation, derivation and identification of users' interest), a Bayesian network based users' interest model is given. In this model, the users' interest reduction algorithm based on Markov Blanket model is used to reduce the interest noise, and then users' interested and not interested documents are used to train the Bayesian network. Compared to the simple model, this model has the following advantages like small space requirements, simple reasoning method and high recognition rate. The experiment result shows this model can more appropriately reflect the user's interest, and has higher performance and good usability.
Bayesian estimation of parameters in a regional hydrological model
K. Engeland
2002-01-01
Full Text Available This study evaluates the applicability of the distributed, process-oriented Ecomag model for prediction of daily streamflow in ungauged basins. The Ecomag model is applied as a regional model to nine catchments in the NOPEX area, using Bayesian statistics to estimate the posterior distribution of the model parameters conditioned on the observed streamflow. The distribution is calculated by Markov Chain Monte Carlo (MCMC analysis. The Bayesian method requires formulation of a likelihood function for the parameters and three alternative formulations are used. The first is a subjectively chosen objective function that describes the goodness of fit between the simulated and observed streamflow, as defined in the GLUE framework. The second and third formulations are more statistically correct likelihood models that describe the simulation errors. The full statistical likelihood model describes the simulation errors as an AR(1 process, whereas the simple model excludes the auto-regressive part. The statistical parameters depend on the catchments and the hydrological processes and the statistical and the hydrological parameters are estimated simultaneously. The results show that the simple likelihood model gives the most robust parameter estimates. The simulation error may be explained to a large extent by the catchment characteristics and climatic conditions, so it is possible to transfer knowledge about them to ungauged catchments. The statistical models for the simulation errors indicate that structural errors in the model are more important than parameter uncertainties. Keywords: regional hydrological model, model uncertainty, Bayesian analysis, Markov Chain Monte Carlo analysis
Extending generalized linear models with random effects and components of dispersion.
Engel, B.
1997-01-01
This dissertation was born out of a need for general and numerically feasible procedures for inference in variance components models for non-normal data. The methodology should be widely applicable within the institutes of the Agricultural Research Department (DLO) of the Dutch Ministry of Agricultu
A Bayesian Markov geostatistical model for estimation of hydrogeological properties
A geostatistical methodology based on Markov-chain analysis and Bayesian statistics was developed for probability estimations of hydrogeological and geological properties in the siting process of a nuclear waste repository. The probability estimates have practical use in decision-making on issues such as siting, investigation programs, and construction design. The methodology is nonparametric which makes it possible to handle information that does not exhibit standard statistical distributions, as is often the case for classified information. Data do not need to meet the requirements on additivity and normality as with the geostatistical methods based on regionalized variable theory, e.g., kriging. The methodology also has a formal way for incorporating professional judgments through the use of Bayesian statistics, which allows for updating of prior estimates to posterior probabilities each time new information becomes available. A Bayesian Markov Geostatistical Model (BayMar) software was developed for implementation of the methodology in two and three dimensions. This paper gives (1) a theoretical description of the Bayesian Markov Geostatistical Model; (2) a short description of the BayMar software; and (3) an example of application of the model for estimating the suitability for repository establishment with respect to the three parameters of lithology, hydraulic conductivity, and rock quality designation index (RQD) at 400--500 meters below ground surface in an area around the Aespoe Hard Rock Laboratory in southeastern Sweden
Private Wealth and Job Exit at Older Age: a Random Effects Model
Bloemen, H.G.
2008-01-01
Forthcoming in 'Empirical Economics' . Private wealth holdings are likely to become an increasingly important determinant in the job exit decision of elderly workers. Net wealth may correlate with worker's characteristics that also determine the exit out of a job. It is therefore important to include a rich set of observed characteristics in an empirical model for retirement in order to measure the (marginal) effect of wealth on the job exit rate. But even with a rich set of regressors the qu...
Extending generalized linear models with random effects and components of dispersion.
Engel, B
1997-01-01
This dissertation was born out of a need for general and numerically feasible procedures for inference in variance components models for non-normal data. The methodology should be widely applicable within the institutes of the Agricultural Research Department (DLO) of the Dutch Ministry of Agriculture, Nature Management and Fisheries. Available methodology employing maximum likelihood estimation, due to numerical limitations, was too restricted with respect to the choice of random structures....
Deletion diagnostics for the generalised linear mixed model with independent random effects.
Ganguli, B; Roy, S Sen; Naskar, M; Malloy, E J; Eisen, E A
2016-04-30
The Generalised linear mixed model (GLMM) is widely used for modelling environmental data. However, such data are prone to influential observations, which can distort the estimated exposure-response curve particularly in regions of high exposure. Deletion diagnostics for iterative estimation schemes commonly derive the deleted estimates based on a single iteration of the full system holding certain pivotal quantities such as the information matrix to be constant. In this paper, we present an approximate formula for the deleted estimates and Cook's distance for the GLMM, which does not assume that the estimates of variance parameters are unaffected by deletion. The procedure allows the user to calculate standardised DFBETAs for mean as well as variance parameters. In certain cases such as when using the GLMM as a device for smoothing, such residuals for the variance parameters are interesting in their own right. In general, the procedure leads to deleted estimates of mean parameters, which are corrected for the effect of deletion on variance components as estimation of the two sets of parameters is interdependent. The probabilistic behaviour of these residuals is investigated and a simulation based procedure suggested for their standardisation. The method is used to identify influential individuals in an occupational cohort exposed to silica. The results show that failure to conduct post model fitting diagnostics for variance components can lead to erroneous conclusions about the fitted curve and unstable confidence intervals. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26626135
The analysis of random effects regression model for predicting the shelf-life of gun propellant
Chang, Wei-Te
1995-01-01
Most gun propellant is stored at depots for a long time before it is used. While being stored, the quality of the gun propellant may deteriorate and become unstable. In an attempt to avoid disaster due to use of unstable gun propellant, accurate prediction of the safe shelf-life of gun propellant is necessary. The shelf-life estimation methods used currently for a group of similar gun propellant lots are based on a fixed effects regression model. This does not take into consideration the fact...
Bayesian and maximin optimal designs for heteroscedastic regression models
Dette, Holger; Haines, Linda M.; Imhof, Lorens A.
2003-01-01
The problem of constructing standardized maximin D-optimal designs for weighted polynomial regression models is addressed. In particular it is shown that, by following the broad approach to the construction of maximin designs introduced recently by Dette, Haines and Imhof (2003), such designs can be obtained as weak limits of the corresponding Bayesian Φq-optimal designs. The approach is illustrated for two specific weighted polynomial models and also for a particular growth model.
Bayesian modeling growth curves for quail assuming skewness in errors
Robson Marcelo Rossi
2014-06-01
Full Text Available Bayesian modeling growth curves for quail assuming skewness in errors - To assume normal distributions in the data analysis is common in different areas of the knowledge. However we can make use of the other distributions that are capable to model the skewness parameter in the situations that is needed to model data with tails heavier than the normal. This article intend to present alternatives to the assumption of the normality in the errors, adding asymmetric distributions. A Bayesian approach is proposed to fit nonlinear models when the errors are not normal, thus, the distributions t, skew-normal and skew-t are adopted. The methodology is intended to apply to different growth curves to the quail body weights. It was found that the Gompertz model assuming skew-normal errors and skew-t errors, respectively for male and female, were the best fitted to the data.
Uncertainties in ozone concentrations predicted with a Lagrangian photochemical air quality model have been estimated using Bayesian Monte Carlo (BMC) analysis. Bayesian Monte Carlo analysis provides a means of combining subjective "prior" uncertainty estimates developed ...
Bayesian inference in camera trapping studies for a class of spatial capture-recapture models
Royle, J. Andrew; Karanth, K. Ullas; Gopalaswamy, Arjun M.; Kumar, N. Samba
2009-01-01
We develop a class of models for inference about abundance or density using spatial capture-recapture data from studies based on camera trapping and related methods. The model is a hierarchical model composed of two components: a point process model describing the distribution of individuals in space (or their home range centers) and a model describing the observation of individuals in traps. We suppose that trap- and individual-specific capture probabilities are a function of distance between individual home range centers and trap locations. We show that the models can be regarded as generalized linear mixed models, where the individual home range centers are random effects. We adopt a Bayesian framework for inference under these models using a formulation based on data augmentation. We apply the models to camera trapping data on tigers from the Nagarahole Reserve, India, collected over 48 nights in 2006. For this study, 120 camera locations were used, but cameras were only operational at 30 locations during any given sample occasion. Movement of traps is common in many camera-trapping studies and represents an important feature of the observation model that we address explicitly in our application.
Non-stationarity in GARCH models: A Bayesian analysis
Kleibergen, Frank; Dijk, Herman
1993-01-01
textabstractFirst, the non-stationarity properties of the conditional variances in the GARCH(1,1) model are analysed using the concept of infinite persistence of shocks. Given a time sequence of probabilities for increasing/decreasing conditional variances, a theoretical formula for quasi-strict non-stationarity is defined. The resulting conditions for the GARCH(1,1) model are shown to differ from the weak stationarity conditions mainly used in the literature. Bayesian statistical analysis us...
A New Bayesian Unit Root Test in Stochastic Volatility Models
Yong Li; Jun Yu
2010-01-01
A new posterior odds analysis is proposed to test for a unit root in volatility dynamics in the context of stochastic volatility models. This analysis extends the Bayesian unit root test of So and Li (1999, Journal of Business Economic Statistics) in two important ways. First, a numerically more stable algorithm is introduced to compute the Bayes factor, taking into account the special structure of the competing models. Owing to its numerical stability, the algorithm overcomes the problem of ...
Bayesian Modelling in Machine Learning: A Tutorial Review
Seeger, Matthias
2006-01-01
Many facets of Bayesian Modelling are firmly established in Machine Learning and give rise to state-of-the-art solutions to application problems. The sheer number of techniques, ideas and models which have been proposed, and the terminology, can be bewildering. With this tutorial review, we aim to give a wide high-level overview over this important field, concentrating on central ideas and methods, and on their interconnections. The reader will gain a basic understanding of the topics and the...
Performance and prediction: Bayesian modelling of fallible choice in chess
Haworth, Guy McCrossan; Regan, Ken; Di Fatta, Giuseppe
2010-01-01
Evaluating agents in decision-making applications requires assessing their skill and predicting their behaviour. Both are well developed in Poker-like situations, but less so in more complex game and model domains. This paper addresses both tasks by using Bayesian inference in a benchmark space of reference agents. The concepts are explained and demonstrated using the game of chess but the model applies generically to any domain with quantifiable options and fallible choice. Demonstration ...
Bayesian modeling and prediction of solar particles flux
An autoregression model was developed based on the Bayesian approach. Considering the solar wind non-homogeneity, the idea was applied of combining the pure autoregressive properties of the model with expert knowledge based on a similar behaviour of the various phenomena related to the flux properties. Examples of such situations include the hardening of the X-ray spectrum, which is often followed by coronal mass ejection and a significant increase in the particles flux intensity
Bayesian modeling and prediction of solar particles flux
Dedecius, Kamil; Kalová, J.
18/56/, 7/8 (2010), s. 228-230. ISSN 1210-7085 R&D Projects: GA MŠk 1M0572 Institutional research plan: CEZ:AV0Z10750506 Keywords : mathematical models * solar activity * solar flares * solar flux * solar particles Subject RIV: BB - Applied Statistics, Operational Research http://library.utia.cas.cz/separaty/2010/AS/dedecius-bayesian modeling and prediction of solar particles flux.pdf
Hierarchical Bayesian Modeling of Hitting Performance in Baseball
Jensen, Shane T.; McShane, Blake; Wyner, Abraham J.
2009-01-01
We have developed a sophisticated statistical model for predicting the hitting performance of Major League baseball players. The Bayesian paradigm provides a principled method for balancing past performance with crucial covariates, such as player age and position. We share information across time and across players by using mixture distributions to control shrinkage for improved accuracy. We compare the performance of our model to current sabermetric methods on a held-out seaso...
Bayesian estimation of a DSGE model with inventories
Foerster, Marcel
2011-01-01
This paper introduces inventories in an otherwise standard Dynamic Stochastic General Equilibrium Model (DSGE) of the business cycle. Firms accumulate inventories to facilitate sales, but face a cost of doing so in terms of costly storage of intermediate goods. The paper's main contribution is to present a DSGE model with inventories that is estimated using Bayesian methods. Based on US data we show that accounting for inventory dynamics has a significant impact on parameter estimates and imp...
Application of hierarchical Bayesian unmixing models in river sediment source apportionment
Blake, Will; Smith, Hugh; Navas, Ana; Bodé, Samuel; Goddard, Rupert; Zou Kuzyk, Zou; Lennard, Amy; Lobb, David; Owens, Phil; Palazon, Leticia; Petticrew, Ellen; Gaspar, Leticia; Stock, Brian; Boeckx, Pacsal; Semmens, Brice
2016-04-01
Fingerprinting and unmixing concepts are used widely across environmental disciplines for forensic evaluation of pollutant sources. In aquatic and marine systems, this includes tracking the source of organic and inorganic pollutants in water and linking problem sediment to soil erosion and land use sources. It is, however, the particular complexity of ecological systems that has driven creation of the most sophisticated mixing models, primarily to (i) evaluate diet composition in complex ecological food webs, (ii) inform population structure and (iii) explore animal movement. In the context of the new hierarchical Bayesian unmixing model, MIXSIAR, developed to characterise intra-population niche variation in ecological systems, we evaluate the linkage between ecological 'prey' and 'consumer' concepts and river basin sediment 'source' and sediment 'mixtures' to exemplify the value of ecological modelling tools to river basin science. Recent studies have outlined advantages presented by Bayesian unmixing approaches in handling complex source and mixture datasets while dealing appropriately with uncertainty in parameter probability distributions. MixSIAR is unique in that it allows individual fixed and random effects associated with mixture hierarchy, i.e. factors that might exert an influence on model outcome for mixture groups, to be explored within the source-receptor framework. This offers new and powerful ways of interpreting river basin apportionment data. In this contribution, key components of the model are evaluated in the context of common experimental designs for sediment fingerprinting studies namely simple, nested and distributed catchment sampling programmes. Illustrative examples using geochemical and compound specific stable isotope datasets are presented and used to discuss best practice with specific attention to (1) the tracer selection process, (2) incorporation of fixed effects relating to sample timeframe and sediment type in the modelling
Markov Model of Wind Power Time Series UsingBayesian Inference of Transition Matrix
Chen, Peiyuan; Berthelsen, Kasper Klitgaard; Bak-Jensen, Birgitte; Chen, Zhe
2009-01-01
This paper proposes to use Bayesian inference of transition matrix when developing a discrete Markov model of a wind speed/power time series and 95% credible interval for the model verification. The Dirichlet distribution is used as a conjugate prior for the transition matrix. Three discrete Markov models are compared, i.e. the basic Markov model, the Bayesian Markov model and the birth-and-death Markov model. The proposed Bayesian Markov model shows the best accuracy in modeling the autocorr...
Bayesian point event modeling in spatial and environmental epidemiology.
Lawson, Andrew B
2012-10-01
This paper reviews the current state of point event modeling in spatial epidemiology from a Bayesian perspective. Point event (or case event) data arise when geo-coded addresses of disease events are available. Often, this level of spatial resolution would not be accessible due to medical confidentiality constraints. However, for the examination of small spatial scales, it is important to be capable of examining point process data directly. Models for such data are usually formulated based on point process theory. In addition, special conditioning arguments can lead to simpler Bernoulli likelihoods and logistic spatial models. Goodness-of-fit diagnostics and Bayesian residuals are also considered. Applications within putative health hazard risk assessment, cluster detection, and linkage to environmental risk fields (misalignment) are considered. PMID:23035034
The impact of spatial scales and spatial smoothing on the outcome of bayesian spatial model.
Su Yun Kang
Full Text Available Discretization of a geographical region is quite common in spatial analysis. There have been few studies into the impact of different geographical scales on the outcome of spatial models for different spatial patterns. This study aims to investigate the impact of spatial scales and spatial smoothing on the outcomes of modelling spatial point-based data. Given a spatial point-based dataset (such as occurrence of a disease, we study the geographical variation of residual disease risk using regular grid cells. The individual disease risk is modelled using a logistic model with the inclusion of spatially unstructured and/or spatially structured random effects. Three spatial smoothness priors for the spatially structured component are employed in modelling, namely an intrinsic Gaussian Markov random field, a second-order random walk on a lattice, and a Gaussian field with Matérn correlation function. We investigate how changes in grid cell size affect model outcomes under different spatial structures and different smoothness priors for the spatial component. A realistic example (the Humberside data is analyzed and a simulation study is described. Bayesian computation is carried out using an integrated nested Laplace approximation. The results suggest that the performance and predictive capacity of the spatial models improve as the grid cell size decreases for certain spatial structures. It also appears that different spatial smoothness priors should be applied for different patterns of point data.
A Bayesian growth mixture model to examine maternal hypertension and birth outcomes.
Neelon, Brian; Swamy, Geeta K; Burgette, Lane F; Miranda, Marie Lynn
2011-09-30
Maternal hypertension is a major contributor to adverse pregnancy outcomes, including preterm birth (PTB) and low birth weight (LBW). Although several studies have explored the relationship between maternal hypertension and fetal health, few have examined how the longitudinal trajectory of blood pressure, considered over the course of pregnancy, affects birth outcomes. In this paper, we propose a Bayesian growth mixture model to jointly examine the associations between longitudinal blood pressure measurements, PTB, and LBW. The model partitions women into distinct classes characterized by a mean arterial pressure (MAP) curve and joint probabilities of PTB and LBW. Each class contains a unique mixed effects model for MAP with class-specific regression coefficients and random effect covariances. To account for the strong correlation between PTB and LBW, we introduce a bivariate probit model within each class to capture residual within-class dependence between PTB and LBW. The model permits the association between PTB and LBW to vary by class, so that for some classes, PTB and LBW may be positively correlated, whereas for others, they may be uncorrelated or negatively correlated. We also allow maternal covariates to influence the class probabilities via a multinomial logit model. For posterior computation, we propose an efficient MCMC algorithm that combines full-conditional Gibbs and Metropolis steps. We apply our model to a sample of 1027 women enrolled in the Healthy Pregnancy, Healthy Baby Study, a prospective cohort study of host, social, and environmental contributors to disparities in pregnancy outcomes. PMID:21751226
Bayesian hierarchical modelling of weak lensing - the golden goal
Heavens, Alan; Jaffe, Andrew; Hoffmann, Till; Kiessling, Alina; Wandelt, Benjamin
2016-01-01
To accomplish correct Bayesian inference from weak lensing shear data requires a complete statistical description of the data. The natural framework to do this is a Bayesian Hierarchical Model, which divides the chain of reasoning into component steps. Starting with a catalogue of shear estimates in tomographic bins, we build a model that allows us to sample simultaneously from the the underlying tomographic shear fields and the relevant power spectra (E-mode, B-mode, and E-B, for auto- and cross-power spectra). The procedure deals easily with masked data and intrinsic alignments. Using Gibbs sampling and messenger fields, we show with simulated data that the large (over 67000-)dimensional parameter space can be efficiently sampled and the full joint posterior probability density function for the parameters can feasibly be obtained. The method correctly recovers the underlying shear fields and all of the power spectra, including at levels well below the shot noise.
A localization model to localize multiple sources using Bayesian inference
Dunham, Joshua Rolv
Accurate localization of a sound source in a room setting is important in both psychoacoustics and architectural acoustics. Binaural models have been proposed to explain how the brain processes and utilizes the interaural time differences (ITDs) and interaural level differences (ILDs) of sound waves arriving at the ears of a listener in determining source location. Recent work shows that applying Bayesian methods to this problem is proving fruitful. In this thesis, pink noise samples are convolved with head-related transfer functions (HRTFs) and compared to combinations of one and two anechoic speech signals convolved with different HRTFs or binaural room impulse responses (BRIRs) to simulate room positions. Through exhaustive calculation of Bayesian posterior probabilities and using a maximal likelihood approach, model selection will determine the number of sources present, and parameter estimation will result in azimuthal direction of the source(s).
Bayesian Inference and Forecasting in the Stationary Bilinear Model
Roberto Leon-Gonzalez; Fuyu Yang
2014-01-01
A stationary bilinear (SB) model can be used to describe processes with a time-varying degree of persistence that depends on past shocks. An example of such a process is inflation. This study develops methods for Bayesian inference, model comparison, and forecasting in the SB model. Using monthly U.K. inflation data, we find that the SB model outperforms the random walk and first order autoregressive AR(1) models in terms of root mean squared forecast errors for both the one-step-ahead and th...
Bayesian Age-Period-Cohort Modeling and Prediction - BAMP
Volker J. Schmid
2007-10-01
Full Text Available The software package BAMP provides a method of analyzing incidence or mortality data on the Lexis diagram, using a Bayesian version of an age-period-cohort model. A hierarchical model is assumed with a binomial model in the first-stage. As smoothing priors for the age, period and cohort parameters random walks of first and second order, with and without an additional unstructured component are available. Unstructured heterogeneity can also be included in the model. In order to evaluate the model fit, posterior deviance, DIC and predictive deviances are computed. By projecting the random walk prior into the future, future death rates can be predicted.
Introduction to Hierarchical Bayesian Modeling for Ecological Data
Parent, Eric
2012-01-01
Making statistical modeling and inference more accessible to ecologists and related scientists, Introduction to Hierarchical Bayesian Modeling for Ecological Data gives readers a flexible and effective framework to learn about complex ecological processes from various sources of data. It also helps readers get started on building their own statistical models. The text begins with simple models that progressively become more complex and realistic through explanatory covariates and intermediate hidden states variables. When fitting the models to data, the authors gradually present the concepts a
Bayesian analysis of recursive SVAR models with overidentifying restrictions
Kociecki, Andrzej; Rubaszek, Michał; Ca' Zorzi, Michele
2012-01-01
The paper provides a novel Bayesian methodological framework to estimate structural VAR (SVAR) models with recursive identification schemes that allows for the inclusion of over-identifying restrictions. The proposed framework enables the researcher to (i) elicit the prior on the non-zero contemporaneous relations between economic variables and to (ii) derive an analytical expression for the posterior distribution and marginal data density. We illustrate our methodological framework by estima...
Differential gene co-expression networks via Bayesian biclustering models
Gao, Chuan; Zhao, Shiwen; McDowell, Ian C.; Brown, Christopher D.; Barbara E Engelhardt
2014-01-01
Identifying latent structure in large data matrices is essential for exploring biological processes. Here, we consider recovering gene co-expression networks from gene expression data, where each network encodes relationships between genes that are locally co-regulated by shared biological mechanisms. To do this, we develop a Bayesian statistical model for biclustering to infer subsets of co-regulated genes whose covariation may be observed in only a subset of the samples. Our biclustering me...
Diffusion Estimation Of State-Space Models: Bayesian Formulation
Dedecius, Kamil
Reims: IEEE, 2014. ISBN 978-1-4799-3693-9. [The 24th IEEE International Workshop on Machine Learning for Signal Processing (MLSP2014). Reims (FR), 21.09.2014-24.09.2014] R&D Projects: GA ČR(CZ) GP14-06678P Keywords : distributed estimation * state-space models * Bayesian estimation Subject RIV: BB - Applied Statistics, Operational Research http://library.utia.cas.cz/separaty/2014/AS/dedecius-0431804.pdf
Bayesian Methods for Neural Networks and Related Models
Titterington, D.M.
2004-01-01
Models such as feed-forward neural networks and certain other structures investigated in the computer science literature are not amenable to closed-form Bayesian analysis. The paper reviews the various approaches taken to overcome this difficulty, involving the use of Gaussian approximations, Markov chain Monte Carlo simulation routines and a class of non-Gaussian but “deterministic” approximations called variational approximations.
Bayesian network models in brain functional connectivity analysis
Ide, Jaime S.; Zhang, Sheng; Chiang-shan R. Li
2013-01-01
Much effort has been made to better understand the complex integration of distinct parts of the human brain using functional magnetic resonance imaging (fMRI). Altered functional connectivity between brain regions is associated with many neurological and mental illnesses, such as Alzheimer and Parkinson diseases, addiction, and depression. In computational science, Bayesian networks (BN) have been used in a broad range of studies to model complex data set in the presence of uncertainty and wh...
Bayesian Models of Learning and Reasoning with Relations
Chen, Dawn
2014-01-01
How do humans acquire relational concepts such as larger, which are essential for analogical inference and other forms of high-level reasoning? Are they necessarily innate, or can they be learned from non-relational inputs? Using comparative relations as a model domain, we show that structured relations can be learned from unstructured inputs of realistic complexity, applying bottom-up Bayesian learning mechanisms that make minimal assumptions about innate representations. First, we introduce...
Bayesian regression model for seasonal forecast of precipitation over Korea
Jo, Seongil; Lim, Yaeji; Lee, Jaeyong; Kang, Hyun-Suk; Oh, Hee-Seok
2012-08-01
In this paper, we apply three different Bayesian methods to the seasonal forecasting of the precipitation in a region around Korea (32.5°N-42.5°N, 122.5°E-132.5°E). We focus on the precipitation of summer season (June-July-August; JJA) for the period of 1979-2007 using the precipitation produced by the Global Data Assimilation and Prediction System (GDAPS) as predictors. Through cross-validation, we demonstrate improvement for seasonal forecast of precipitation in terms of root mean squared error (RMSE) and linear error in probability space score (LEPS). The proposed methods yield RMSE of 1.09 and LEPS of 0.31 between the predicted and observed precipitations, while the prediction using GDAPS output only produces RMSE of 1.20 and LEPS of 0.33 for CPC Merged Analyzed Precipitation (CMAP) data. For station-measured precipitation data, the RMSE and LEPS of the proposed Bayesian methods are 0.53 and 0.29, while GDAPS output is 0.66 and 0.33, respectively. The methods seem to capture the spatial pattern of the observed precipitation. The Bayesian paradigm incorporates the model uncertainty as an integral part of modeling in a natural way. We provide a probabilistic forecast integrating model uncertainty.
Statistical modelling of railway track geometry degradation using hierarchical Bayesian models
Andrade, António Ramos; Teixeira, P. Fonseca
2015-01-01
Railway maintenance planners require a predictive model that can assess the railway track geometry degradation. The present paper uses a hierarchical Bayesian model as a tool to model the main two quality indicators related to railway track geometry degradation: the standard deviation of longitudinal level defects and the standard deviation of horizontal alignment defects. Hierarchical Bayesian Models (HBM) are flexible statistical models that allow specifying different spatially correlated c...
AIC, BIC, Bayesian evidence against the interacting dark energy model
Szydlowski, Marek [Jagiellonian University, Astronomical Observatory, Krakow (Poland); Jagiellonian University, Mark Kac Complex Systems Research Centre, Krakow (Poland); Krawiec, Adam [Jagiellonian University, Institute of Economics, Finance and Management, Krakow (Poland); Jagiellonian University, Mark Kac Complex Systems Research Centre, Krakow (Poland); Kurek, Aleksandra [Jagiellonian University, Astronomical Observatory, Krakow (Poland); Kamionka, Michal [University of Wroclaw, Astronomical Institute, Wroclaw (Poland)
2015-01-01
Recent astronomical observations have indicated that the Universe is in a phase of accelerated expansion. While there are many cosmological models which try to explain this phenomenon, we focus on the interacting ΛCDM model where an interaction between the dark energy and dark matter sectors takes place. This model is compared to its simpler alternative - the ΛCDM model. To choose between these models the likelihood ratio test was applied as well as the model comparison methods (employing Occam's principle): the Akaike information criterion (AIC), the Bayesian information criterion (BIC) and the Bayesian evidence. Using the current astronomical data: type Ia supernova (Union2.1), h(z), baryon acoustic oscillation, the Alcock- Paczynski test, and the cosmic microwave background data, we evaluated both models. The analyses based on the AIC indicated that there is less support for the interacting ΛCDM model when compared to the ΛCDM model, while those based on the BIC indicated that there is strong evidence against it in favor of the ΛCDM model. Given the weak or almost non-existing support for the interacting ΛCDM model and bearing in mind Occam's razor we are inclined to reject this model. (orig.)
AIC, BIC, Bayesian evidence against the interacting dark energy model
Szydłowski, Marek, E-mail: marek.szydlowski@uj.edu.pl [Astronomical Observatory, Jagiellonian University, Orla 171, 30-244, Kraków (Poland); Mark Kac Complex Systems Research Centre, Jagiellonian University, Reymonta 4, 30-059, Kraków (Poland); Krawiec, Adam, E-mail: adam.krawiec@uj.edu.pl [Institute of Economics, Finance and Management, Jagiellonian University, Łojasiewicza 4, 30-348, Kraków (Poland); Mark Kac Complex Systems Research Centre, Jagiellonian University, Reymonta 4, 30-059, Kraków (Poland); Kurek, Aleksandra, E-mail: alex@oa.uj.edu.pl [Astronomical Observatory, Jagiellonian University, Orla 171, 30-244, Kraków (Poland); Kamionka, Michał, E-mail: kamionka@astro.uni.wroc.pl [Astronomical Institute, University of Wrocław, ul. Kopernika 11, 51-622, Wrocław (Poland)
2015-01-14
Recent astronomical observations have indicated that the Universe is in a phase of accelerated expansion. While there are many cosmological models which try to explain this phenomenon, we focus on the interacting ΛCDM model where an interaction between the dark energy and dark matter sectors takes place. This model is compared to its simpler alternative—the ΛCDM model. To choose between these models the likelihood ratio test was applied as well as the model comparison methods (employing Occam’s principle): the Akaike information criterion (AIC), the Bayesian information criterion (BIC) and the Bayesian evidence. Using the current astronomical data: type Ia supernova (Union2.1), h(z), baryon acoustic oscillation, the Alcock–Paczynski test, and the cosmic microwave background data, we evaluated both models. The analyses based on the AIC indicated that there is less support for the interacting ΛCDM model when compared to the ΛCDM model, while those based on the BIC indicated that there is strong evidence against it in favor of the ΛCDM model. Given the weak or almost non-existing support for the interacting ΛCDM model and bearing in mind Occam’s razor we are inclined to reject this model.
AIC, BIC, Bayesian evidence against the interacting dark energy model
Recent astronomical observations have indicated that the Universe is in a phase of accelerated expansion. While there are many cosmological models which try to explain this phenomenon, we focus on the interacting ΛCDM model where an interaction between the dark energy and dark matter sectors takes place. This model is compared to its simpler alternative—the ΛCDM model. To choose between these models the likelihood ratio test was applied as well as the model comparison methods (employing Occam’s principle): the Akaike information criterion (AIC), the Bayesian information criterion (BIC) and the Bayesian evidence. Using the current astronomical data: type Ia supernova (Union2.1), h(z), baryon acoustic oscillation, the Alcock–Paczynski test, and the cosmic microwave background data, we evaluated both models. The analyses based on the AIC indicated that there is less support for the interacting ΛCDM model when compared to the ΛCDM model, while those based on the BIC indicated that there is strong evidence against it in favor of the ΛCDM model. Given the weak or almost non-existing support for the interacting ΛCDM model and bearing in mind Occam’s razor we are inclined to reject this model
Dissecting Magnetar Variability with Bayesian Hierarchical Models
Huppenkothen, Daniela; Brewer, Brendon J.; Hogg, David W.; Murray, Iain; Frean, Marcus; Elenbaas, Chris; Watts, Anna L.; Levin, Yuri; van der Horst, Alexander J.; Kouveliotou, Chryssa
2015-09-01
Neutron stars are a prime laboratory for testing physical processes under conditions of strong gravity, high density, and extreme magnetic fields. Among the zoo of neutron star phenomena, magnetars stand out for their bursting behavior, ranging from extremely bright, rare giant flares to numerous, less energetic recurrent bursts. The exact trigger and emission mechanisms for these bursts are not known; favored models involve either a crust fracture and subsequent energy release into the magnetosphere, or explosive reconnection of magnetic field lines. In the absence of a predictive model, understanding the physical processes responsible for magnetar burst variability is difficult. Here, we develop an empirical model that decomposes magnetar bursts into a superposition of small spike-like features with a simple functional form, where the number of model components is itself part of the inference problem. The cascades of spikes that we model might be formed by avalanches of reconnection, or crust rupture aftershocks. Using Markov Chain Monte Carlo sampling augmented with reversible jumps between models with different numbers of parameters, we characterize the posterior distributions of the model parameters and the number of components per burst. We relate these model parameters to physical quantities in the system, and show for the first time that the variability within a burst does not conform to predictions from ideas of self-organized criticality. We also examine how well the properties of the spikes fit the predictions of simplified cascade models for the different trigger mechanisms.
Dissecting magnetar variability with Bayesian hierarchical models
Huppenkothen, D; Hogg, D W; Murray, I; Frean, M; Elenbaas, C; Watts, A L; Levin, Y; van der Horst, A J; Kouveliotou, C
2015-01-01
Neutron stars are a prime laboratory for testing physical processes under conditions of strong gravity, high density, and extreme magnetic fields. Among the zoo of neutron star phenomena, magnetars stand out for their bursting behaviour, ranging from extremely bright, rare giant flares to numerous, less energetic recurrent bursts. The exact trigger and emission mechanisms for these bursts are not known; favoured models involve either a crust fracture and subsequent energy release into the magnetosphere, or explosive reconnection of magnetic field lines. In the absence of a predictive model, understanding the physical processes responsible for magnetar burst variability is difficult. Here, we develop an empirical model that decomposes magnetar bursts into a superposition of small spike-like features with a simple functional form, where the number of model components is itself part of the inference problem. The cascades of spikes that we model might be formed by avalanches of reconnection, or crust rupture afte...
Dynamic model based on Bayesian method for energy security assessment
Highlights: • Methodology for dynamic indicator model construction and forecasting of indicators. • Application of dynamic indicator model for energy system development scenarios. • Expert judgement involvement using Bayesian method. - Abstract: The methodology for the dynamic indicator model construction and forecasting of indicators for the assessment of energy security level is presented in this article. An indicator is a special index, which provides numerical values to important factors for the investigated area. In real life, models of different processes take into account various factors that are time-dependent and dependent on each other. Thus, it is advisable to construct a dynamic model in order to describe these dependences. The energy security indicators are used as factors in the dynamic model. Usually, the values of indicators are obtained from statistical data. The developed dynamic model enables to forecast indicators’ variation taking into account changes in system configuration. The energy system development is usually based on a new object construction. Since the parameters of changes of the new system are not exactly known, information about their influences on indicators could not be involved in the model by deterministic methods. Thus, dynamic indicators’ model based on historical data is adjusted by probabilistic model with the influence of new factors on indicators using the Bayesian method
A Bayesian Network View on Nested Effects Models
Fröhlich Holger
2009-01-01
Full Text Available Nested effects models (NEMs are a class of probabilistic models that were designed to reconstruct a hidden signalling structure from a large set of observable effects caused by active interventions into the signalling pathway. We give a more flexible formulation of NEMs in the language of Bayesian networks. Our framework constitutes a natural generalization of the original NEM model, since it explicitly states the assumptions that are tacitly underlying the original version. Our approach gives rise to new learning methods for NEMs, which have been implemented in the /Bioconductor package nem. We validate these methods in a simulation study and apply them to a synthetic lethality dataset in yeast.
Probe Error Modeling Research Based on Bayesian Network
Wu Huaiqiang; Xing Zilong; Zhang Jian; Yan Yan
2015-01-01
Probe calibration is carried out under specific conditions; most of the error caused by the change of speed parameter has not been corrected. In order to reduce the measuring error influence on measurement accuracy, this article analyzes the relationship between speed parameter and probe error, and use Bayesian network to establish the model of probe error. Model takes account of prior knowledge and sample data, with the updating of data, which can reflect the change of the errors of the probe and constantly revised modeling results.
Bayesian inference and model comparison for metallic fatigue data
Babuška, Ivo
2016-02-23
In this work, we present a statistical treatment of stress-life (S-N) data drawn from a collection of records of fatigue experiments that were performed on 75S-T6 aluminum alloys. Our main objective is to predict the fatigue life of materials by providing a systematic approach to model calibration, model selection and model ranking with reference to S-N data. To this purpose, we consider fatigue-limit models and random fatigue-limit models that are specially designed to allow the treatment of the run-outs (right-censored data). We first fit the models to the data by maximum likelihood methods and estimate the quantiles of the life distribution of the alloy specimen. To assess the robustness of the estimation of the quantile functions, we obtain bootstrap confidence bands by stratified resampling with respect to the cycle ratio. We then compare and rank the models by classical measures of fit based on information criteria. We also consider a Bayesian approach that provides, under the prior distribution of the model parameters selected by the user, their simulation-based posterior distributions. We implement and apply Bayesian model comparison methods, such as Bayes factor ranking and predictive information criteria based on cross-validation techniques under various a priori scenarios.
Bayesian inference and model comparison for metallic fatigue data
Babuška, Ivo; Sawlan, Zaid; Scavino, Marco; Szabó, Barna; Tempone, Raúl
2016-06-01
In this work, we present a statistical treatment of stress-life (S-N) data drawn from a collection of records of fatigue experiments that were performed on 75S-T6 aluminum alloys. Our main objective is to predict the fatigue life of materials by providing a systematic approach to model calibration, model selection and model ranking with reference to S-N data. To this purpose, we consider fatigue-limit models and random fatigue-limit models that are specially designed to allow the treatment of the run-outs (right-censored data). We first fit the models to the data by maximum likelihood methods and estimate the quantiles of the life distribution of the alloy specimen. To assess the robustness of the estimation of the quantile functions, we obtain bootstrap confidence bands by stratified resampling with respect to the cycle ratio. We then compare and rank the models by classical measures of fit based on information criteria. We also consider a Bayesian approach that provides, under the prior distribution of the model parameters selected by the user, their simulation-based posterior distributions. We implement and apply Bayesian model comparison methods, such as Bayes factor ranking and predictive information criteria based on cross-validation techniques under various a priori scenarios.
A Bayesian Model for Discovering Typological Implications
Daumé, Hal
2009-01-01
A standard form of analysis for linguistic typology is the universal implication. These implications state facts about the range of extant languages, such as ``if objects come after verbs, then adjectives come after nouns.'' Such implications are typically discovered by painstaking hand analysis over a small sample of languages. We propose a computational model for assisting at this process. Our model is able to discover both well-known implications as well as some novel implications that deserve further study. Moreover, through a careful application of hierarchical analysis, we are able to cope with the well-known sampling problem: languages are not independent.
DPpackage: Bayesian Semi- and Nonparametric Modeling in R
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.
KNET: Integrating Hypermedia and Bayesian Modeling
Chavez, R. Martin; Cooper, Gregory F.
2013-01-01
KNET is a general-purpose shell for constructing expert systems based on belief networks and decision networks. Such networks serve as graphical representations for decision models, in which the knowledge engineer must define clearly the alternatives, states, preferences, and relationships that constitute a decision basis. KNET contains a knowledge-engineering core written in Object Pascal and an interface that tightly integrates HyperCard, a hypertext authoring tool for the Apple Macintosh c...
Lack of confidence in approximate Bayesian computation model choice.
Robert, Christian P; Cornuet, Jean-Marie; Marin, Jean-Michel; Pillai, Natesh S
2011-09-13
Approximate Bayesian computation (ABC) have become an essential tool for the analysis of complex stochastic models. Grelaud et al. [(2009) Bayesian Anal 3:427-442] advocated the use of ABC for model choice in the specific case of Gibbs random fields, relying on an intermodel sufficiency property to show that the approximation was legitimate. We implemented ABC model choice in a wide range of phylogenetic models in the Do It Yourself-ABC (DIY-ABC) software [Cornuet et al. (2008) Bioinformatics 24:2713-2719]. We now present arguments as to why the theoretical arguments for ABC model choice are missing, because the algorithm involves an unknown loss of information induced by the use of insufficient summary statistics. The approximation error of the posterior probabilities of the models under comparison may thus be unrelated with the computational effort spent in running an ABC algorithm. We then conclude that additional empirical verifications of the performances of the ABC procedure as those available in DIY-ABC are necessary to conduct model choice. PMID:21876135
Bayesian analysis of physiologically based toxicokinetic and toxicodynamic models.
Hack, C Eric
2006-04-17
Physiologically based toxicokinetic (PBTK) and toxicodynamic (TD) models of bromate in animals and humans would improve our ability to accurately estimate the toxic doses in humans based on available animal studies. These mathematical models are often highly parameterized and must be calibrated in order for the model predictions of internal dose to adequately fit the experimentally measured doses. Highly parameterized models are difficult to calibrate and it is difficult to obtain accurate estimates of uncertainty or variability in model parameters with commonly used frequentist calibration methods, such as maximum likelihood estimation (MLE) or least squared error approaches. The Bayesian approach called Markov chain Monte Carlo (MCMC) analysis can be used to successfully calibrate these complex models. Prior knowledge about the biological system and associated model parameters is easily incorporated in this approach in the form of prior parameter distributions, and the distributions are refined or updated using experimental data to generate posterior distributions of parameter estimates. The goal of this paper is to give the non-mathematician a brief description of the Bayesian approach and Markov chain Monte Carlo analysis, how this technique is used in risk assessment, and the issues associated with this approach. PMID:16466842
Farid Zayeri; Masoud Salehi; Hasan Pirhosseini
2011-01-01
Objective:To present the geographical map of malaria and identify some of the important environmental factors of this disease in Sistan and Baluchistan province, Iran.Methods:We used the registered malaria data to compute the standard incidence rates (SIRs) of malaria in different areas of Sistan and Baluchistan province for a nine-year period (from 2001 to 2009). Statistical analyses consisted of two different parts: geographical mapping of malaria incidence rates, and modeling the environmental factors. The empirical Bayesian estimates of malaria SIRs were utilized for geographical mapping of malaria and a Poisson random effects model was used for assessing the effect of environmental factors on malaria SIRs.Results:In general, 64 926 new cases of malaria were registered in Sistan and Baluchistan Province from 2001 to 2009. Among them, 42 695 patients (65.8%) were male and 22 231 patients (34.2%) were female. Modeling the environmental factors showed that malaria incidence rates had positive relationship with humidity, elevation, average minimum temperature and average maximum temperature, while rainfall had negative effect on malaria SIRs in this province.Conclusions:The results of the present study reveals that malaria is still a serious health problem in Sistan and Baluchistan province, Iran. Geographical map and related environmental factors of malaria can help the health policy makers to intervene in high risk areas more efficiently and allocate the resources in a proper manner.
A study of finite mixture model: Bayesian approach on financial time series data
Phoong, Seuk-Yen; Ismail, Mohd Tahir
2014-07-01
Recently, statistician have emphasized on the fitting finite mixture model by using Bayesian method. Finite mixture model is a mixture of distributions in modeling a statistical distribution meanwhile Bayesian method is a statistical method that use to fit the mixture model. Bayesian method is being used widely because it has asymptotic properties which provide remarkable result. In addition, Bayesian method also shows consistency characteristic which means the parameter estimates are close to the predictive distributions. In the present paper, the number of components for mixture model is studied by using Bayesian Information Criterion. Identify the number of component is important because it may lead to an invalid result. Later, the Bayesian method is utilized to fit the k-component mixture model in order to explore the relationship between rubber price and stock market price for Malaysia, Thailand, Philippines and Indonesia. Lastly, the results showed that there is a negative effect among rubber price and stock market price for all selected countries.
Macroeconomic Forecasts in Models with Bayesian Averaging of Classical Estimates
Piotr Białowolski
2012-03-01
Full Text Available The aim of this paper is to construct a forecasting model oriented on predicting basic macroeconomic variables, namely: the GDP growth rate, the unemployment rate, and the consumer price inflation. In order to select the set of the best regressors, Bayesian Averaging of Classical Estimators (BACE is employed. The models are atheoretical (i.e. they do not reflect causal relationships postulated by the macroeconomic theory and the role of regressors is played by business and consumer tendency survey-based indicators. Additionally, survey-based indicators are included with a lag that enables to forecast the variables of interest (GDP, unemployment, and inflation for the four forthcoming quarters without the need to make any additional assumptions concerning the values of predictor variables in the forecast period. Bayesian Averaging of Classical Estimators is a method allowing for full and controlled overview of all econometric models which can be obtained out of a particular set of regressors. In this paper authors describe the method of generating a family of econometric models and the procedure for selection of a final forecasting model. Verification of the procedure is performed by means of out-of-sample forecasts of main economic variables for the quarters of 2011. The accuracy of the forecasts implies that there is still a need to search for new solutions in the atheoretical modelling.
Bayesian joint modeling of longitudinal and spatial survival AIDS data.
Martins, Rui; Silva, Giovani L; Andreozzi, Valeska
2016-08-30
Joint analysis of longitudinal and survival data has received increasing attention in the recent years, especially for analyzing cancer and AIDS data. As both repeated measurements (longitudinal) and time-to-event (survival) outcomes are observed in an individual, a joint modeling is more appropriate because it takes into account the dependence between the two types of responses, which are often analyzed separately. We propose a Bayesian hierarchical model for jointly modeling longitudinal and survival data considering functional time and spatial frailty effects, respectively. That is, the proposed model deals with non-linear longitudinal effects and spatial survival effects accounting for the unobserved heterogeneity among individuals living in the same region. This joint approach is applied to a cohort study of patients with HIV/AIDS in Brazil during the years 2002-2006. Our Bayesian joint model presents considerable improvements in the estimation of survival times of the Brazilian HIV/AIDS patients when compared with those obtained through a separate survival model and shows that the spatial risk of death is the same across the different Brazilian states. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26990773
Modeling operational risks of the nuclear industry with Bayesian networks
Basically, planning a new industrial plant requires information on the industrial management, regulations, site selection, definition of initial and planned capacity, and on the estimation of the potential demand. However, this is far from enough to assure the success of an industrial enterprise. Unexpected and extremely damaging events may occur that deviates from the original plan. The so-called operational risks are not only in the system, equipment, process or human (technical or managerial) failures. They are also in intentional events such as frauds and sabotage, or extreme events like terrorist attacks or radiological accidents and even on public reaction to perceived environmental or future generation impacts. For the nuclear industry, it is a challenge to identify and to assess the operational risks and their various sources. Early identification of operational risks can help in preparing contingency plans, to delay the decision to invest or to approve a project that can, at an extreme, affect the public perception of the nuclear energy. A major problem in modeling operational risk losses is the lack of internal data that are essential, for example, to apply the loss distribution approach. As an alternative, methods that consider qualitative and subjective information can be applied, for example, fuzzy logic, neural networks, system dynamic or Bayesian networks. An advantage of applying Bayesian networks to model operational risk is the possibility to include expert opinions and variables of interest, to structure the model via causal dependencies among these variables, and to specify subjective prior and conditional probabilities distributions at each step or network node. This paper suggests a classification of operational risks in industry and discusses the benefits and obstacles of the Bayesian networks approach to model those risks. (author)
Lawrence N Kazembe
Full Text Available Despite remarkable gains in life expectancy and declining mortality in the 21st century, in many places mostly in developing countries, adult mortality has increased in part due to HIV/AIDS or continued abject poverty levels. Moreover many factors including behavioural, socio-economic and demographic variables work simultaneously to impact on risk of mortality. Understanding risk factors of adult mortality is crucial towards designing appropriate public health interventions. In this paper we proposed a structured additive two-part random effects regression model for adult mortality data. Our proposal assumed two processes: (i whether death occurred in the household (prevalence part, and (ii number of reported deaths, if death did occur (severity part. The proposed model specification therefore consisted of two generalized linear mixed models (GLMM with correlated random effects that permitted structured and unstructured spatial components at regional level. Specifically, the first part assumed a GLMM with a logistic link and the second part explored a count model following either a Poisson or negative binomial distribution. The model was used to analyse adult mortality data of 25,793 individuals from the 2006/2007 Namibian DHS data. Inference is based on the Bayesian framework with appropriate priors discussed.
Two-stage Bayesian models-application to ZEDB project
Bunea, C. [George Washington University, School of Applied Science, 1776 G Street, NW, Suite 108, Washington, DC 20052 (United States)]. E-mail: cornel@gwu.edu; Charitos, T. [Institute of Information and Computing Sciences, Padualaan 14, de Uithof, 3508 TB, Utrecht (Netherlands)]. E-mail: theodore@cs.uu.nl; Cooke, R.M. [Delft University of Technology, EWI Faculty, Mekelweg 4, 2628 CD, Delft (Netherlands)]. E-mail: r.m.cooke@ewi.tudelft.n1; Becker, G. [RISA, Krumme Str., Berlin 10627 (Germany)]. E-mail: guenter.becker@risa.de
2005-12-01
A well-known mathematical tool to analyze plant specific reliability data for nuclear power facilities is the two-stage Bayesian model. Such two-stage Bayesian models are standard practice nowadays, for example in the German ZEDB project or in the Swedish T-Book, although they may differ in their mathematical models and software implementation. In this paper, we review the mathematical model, its underlying assumptions and supporting arguments. Reasonable conditional assumptions are made to yield tractable and mathematically valid form for the failure rate at plant of interest, given failures and operational times at other plants in the population. The posterior probability of failure rate at plant of interest is sensitive to the choice of hyperprior parameters since the effect of hyperprior distribution will never be dominated by the effect of observation. The methods of Poern and Jeffrey for choosing distributions over hyperparameters are discussed. Furthermore, we will perform verification tasks associated with the theoretical model presented in this paper. The present software implementation produces good agreement with ZEDB results for various prior distributions. The difference between our results and those of ZEDB reflect differences that may arise from numerical implementation, as that would use different step size and truncation bounds.
Two-stage Bayesian models-application to ZEDB project
A well-known mathematical tool to analyze plant specific reliability data for nuclear power facilities is the two-stage Bayesian model. Such two-stage Bayesian models are standard practice nowadays, for example in the German ZEDB project or in the Swedish T-Book, although they may differ in their mathematical models and software implementation. In this paper, we review the mathematical model, its underlying assumptions and supporting arguments. Reasonable conditional assumptions are made to yield tractable and mathematically valid form for the failure rate at plant of interest, given failures and operational times at other plants in the population. The posterior probability of failure rate at plant of interest is sensitive to the choice of hyperprior parameters since the effect of hyperprior distribution will never be dominated by the effect of observation. The methods of Poern and Jeffrey for choosing distributions over hyperparameters are discussed. Furthermore, we will perform verification tasks associated with the theoretical model presented in this paper. The present software implementation produces good agreement with ZEDB results for various prior distributions. The difference between our results and those of ZEDB reflect differences that may arise from numerical implementation, as that would use different step size and truncation bounds
Quantum-Like Bayesian Networks for Modeling Decision Making.
Moreira, Catarina; Wichert, Andreas
2016-01-01
In this work, we explore an alternative quantum structure to perform quantum probabilistic inferences to accommodate the paradoxical findings of the Sure Thing Principle. We propose a Quantum-Like Bayesian Network, which consists in replacing classical probabilities by quantum probability amplitudes. However, since this approach suffers from the problem of exponential growth of quantum parameters, we also propose a similarity heuristic that automatically fits quantum parameters through vector similarities. This makes the proposed model general and predictive in contrast to the current state of the art models, which cannot be generalized for more complex decision scenarios and that only provide an explanatory nature for the observed paradoxes. In the end, the model that we propose consists in a nonparametric method for estimating inference effects from a statistical point of view. It is a statistical model that is simpler than the previous quantum dynamic and quantum-like models proposed in the literature. We tested the proposed network with several empirical data from the literature, mainly from the Prisoner's Dilemma game and the Two Stage Gambling game. The results obtained show that the proposed quantum Bayesian Network is a general method that can accommodate violations of the laws of classical probability theory and make accurate predictions regarding human decision-making in these scenarios. PMID:26858669
Development of a cyber security risk model using Bayesian networks
Cyber security is an emerging safety issue in the nuclear industry, especially in the instrumentation and control (I and C) field. To address the cyber security issue systematically, a model that can be used for cyber security evaluation is required. In this work, a cyber security risk model based on a Bayesian network is suggested for evaluating cyber security for nuclear facilities in an integrated manner. The suggested model enables the evaluation of both the procedural and technical aspects of cyber security, which are related to compliance with regulatory guides and system architectures, respectively. The activity-quality analysis model was developed to evaluate how well people and/or organizations comply with the regulatory guidance associated with cyber security. The architecture analysis model was created to evaluate vulnerabilities and mitigation measures with respect to their effect on cyber security. The two models are integrated into a single model, which is called the cyber security risk model, so that cyber security can be evaluated from procedural and technical viewpoints at the same time. The model was applied to evaluate the cyber security risk of the reactor protection system (RPS) of a research reactor and to demonstrate its usefulness and feasibility. - Highlights: • We developed the cyber security risk model can be find the weak point of cyber security integrated two cyber analysis models by using Bayesian Network. • One is the activity-quality model signifies how people and/or organization comply with the cyber security regulatory guide. • Other is the architecture model represents the probability of cyber-attack on RPS architecture. • The cyber security risk model can provide evidence that is able to determine the key element for cyber security for RPS of a research reactor
BAYESIAN ESTIMATION IN SHARED COMPOUND POISSON FRAILTY MODELS
David D. Hanagal
2015-06-01
Full Text Available In this paper, we study the compound Poisson distribution as the shared frailty distribution and two different baseline distributions namely Pareto and linear failure rate distributions for modeling survival data. We are using the Markov Chain Monte Carlo (MCMC technique to estimate parameters of the proposed models by introducing the Bayesian estimation procedure. In the present study, a simulation is done to compare the true values of parameters with the estimated values. We try to fit the proposed models to a real life bivariate survival data set of McGrilchrist and Aisbett (1991 related to kidney infection. Also, we present a comparison study for the same data by using model selection criterion, and suggest a better frailty model out of two proposed frailty models.
Experimental validation of a Bayesian model of visual acuity.
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.
Assessing global vegetation activity using spatio-temporal Bayesian modelling
Mulder, Vera L.; van Eck, Christel M.; Friedlingstein, Pierre; Regnier, Pierre A. G.
2016-04-01
This work demonstrates the potential of modelling vegetation activity using a hierarchical Bayesian spatio-temporal model. This approach allows modelling changes in vegetation and climate simultaneous in space and time. Changes of vegetation activity such as phenology are modelled as a dynamic process depending on climate variability in both space and time. Additionally, differences in observed vegetation status can be contributed to other abiotic ecosystem properties, e.g. soil and terrain properties. Although these properties do not change in time, they do change in space and may provide valuable information in addition to the climate dynamics. The spatio-temporal Bayesian models were calibrated at a regional scale because the local trends in space and time can be better captured by the model. The regional subsets were defined according to the SREX segmentation, as defined by the IPCC. Each region is considered being relatively homogeneous in terms of large-scale climate and biomes, still capturing small-scale (grid-cell level) variability. Modelling within these regions is hence expected to be less uncertain due to the absence of these large-scale patterns, compared to a global approach. This overall modelling approach allows the comparison of model behavior for the different regions and may provide insights on the main dynamic processes driving the interaction between vegetation and climate within different regions. The data employed in this study encompasses the global datasets for soil properties (SoilGrids), terrain properties (Global Relief Model based on SRTM DEM and ETOPO), monthly time series of satellite-derived vegetation indices (GIMMS NDVI3g) and climate variables (Princeton Meteorological Forcing Dataset). The findings proved the potential of a spatio-temporal Bayesian modelling approach for assessing vegetation dynamics, at a regional scale. The observed interrelationships of the employed data and the different spatial and temporal trends support
Non-parametric Bayesian modeling of cervical mucus symptom
Bin, Riccardo De; Scarpa, Bruno
2014-01-01
The analysis of the cervical mucus symptom is useful to identify the period of maximum fertility of a woman. In this paper we analyze the daily evolution of the cervical mucus symptom during the menstrual cycle, based on the data collected in two retrospective studies, in which the mucus symptom is treated as an ordinal variable. To produce our statistical model, we follow a non-parametric Bayesian approach. In particular, we use the idea of non-parametric mixtures of rounded continuous kerne...
Bayesian statistic methods and theri application in probabilistic simulation models
Sergio Iannazzo
2007-03-01
Full Text Available Bayesian statistic methods are facing a rapidly growing level of interest and acceptance in the field of health economics. The reasons of this success are probably to be found on the theoretical fundaments of the discipline that make these techniques more appealing to decision analysis. To this point should be added the modern IT progress that has developed different flexible and powerful statistical software framework. Among them probably one of the most noticeably is the BUGS language project and its standalone application for MS Windows WinBUGS. Scope of this paper is to introduce the subject and to show some interesting applications of WinBUGS in developing complex economical models based on Markov chains. The advantages of this approach reside on the elegance of the code produced and in its capability to easily develop probabilistic simulations. Moreover an example of the integration of bayesian inference models in a Markov model is shown. This last feature let the analyst conduce statistical analyses on the available sources of evidence and exploit them directly as inputs in the economic model.
Bayesian calibration of power plant models for accurate performance prediction
Highlights: • Bayesian calibration is applied to power plant performance prediction. • Measurements from a plant in operation are used for model calibration. • A gas turbine performance model and steam cycle model are calibrated. • An integrated plant model is derived. • Part load efficiency is accurately predicted as a function of ambient conditions. - Abstract: Gas turbine combined cycles are expected to play an increasingly important role in the balancing of supply and demand in future energy markets. Thermodynamic modeling of these energy systems is frequently applied to assist in decision making processes related to the management of plant operation and maintenance. In most cases, model inputs, parameters and outputs are treated as deterministic quantities and plant operators make decisions with limited or no regard of uncertainties. As the steady integration of wind and solar energy into the energy market induces extra uncertainties, part load operation and reliability are becoming increasingly important. In the current study, methods are proposed to not only quantify various types of uncertainties in measurements and plant model parameters using measured data, but to also assess their effect on various aspects of performance prediction. The authors aim to account for model parameter and measurement uncertainty, and for systematic discrepancy of models with respect to reality. For this purpose, the Bayesian calibration framework of Kennedy and O’Hagan is used, which is especially suitable for high-dimensional industrial problems. The article derives a calibrated model of the plant efficiency as a function of ambient conditions and operational parameters, which is also accurate in part load. The article shows that complete statistical modeling of power plants not only enhances process models, but can also increases confidence in operational decisions
One-Stage and Bayesian Two-Stage Optimal Designs for Mixture Models
Lin, Hefang
1999-01-01
In this research, Bayesian two-stage D-D optimal designs for mixture experiments with or without process variables under model uncertainty are developed. A Bayesian optimality criterion is used in the first stage to minimize the determinant of the posterior variances of the parameters. The second stage design is then generated according to an optimality procedure that collaborates with the improved model from first stage data. Our results show that the Bayesian two-stage D-D optimal design...
Uncovering Transcriptional Regulatory Networks by Sparse Bayesian Factor Model
Qi Yuan(Alan
2010-01-01
Full Text Available Abstract The problem of uncovering transcriptional regulation by transcription factors (TFs based on microarray data is considered. A novel Bayesian sparse correlated rectified factor model (BSCRFM is proposed that models the unknown TF protein level activity, the correlated regulations between TFs, and the sparse nature of TF-regulated genes. The model admits prior knowledge from existing database regarding TF-regulated target genes based on a sparse prior and through a developed Gibbs sampling algorithm, a context-specific transcriptional regulatory network specific to the experimental condition of the microarray data can be obtained. The proposed model and the Gibbs sampling algorithm were evaluated on the simulated systems, and results demonstrated the validity and effectiveness of the proposed approach. The proposed model was then applied to the breast cancer microarray data of patients with Estrogen Receptor positive ( status and Estrogen Receptor negative ( status, respectively.
Efficient multilevel brain tumor segmentation with integrated bayesian model classification.
Corso, J J; Sharon, E; Dube, S; El-Saden, S; Sinha, U; Yuille, A
2008-05-01
We present a new method for automatic segmentation of heterogeneous image data that takes a step toward bridging the gap between bottom-up affinity-based segmentation methods and top-down generative model based approaches. The main contribution of the paper is a Bayesian formulation for incorporating soft model assignments into the calculation of affinities, which are conventionally model free. We integrate the resulting model-aware affinities into the multilevel segmentation by weighted aggregation algorithm, and apply the technique to the task of detecting and segmenting brain tumor and edema in multichannel magnetic resonance (MR) volumes. The computationally efficient method runs orders of magnitude faster than current state-of-the-art techniques giving comparable or improved results. Our quantitative results indicate the benefit of incorporating model-aware affinities into the segmentation process for the difficult case of glioblastoma multiforme brain tumor. PMID:18450536
Emulation: A fast stochastic Bayesian method to eliminate model space
Roberts, Alan; Hobbs, Richard; Goldstein, Michael
2010-05-01
Joint inversion of large 3D datasets has been the goal of geophysicists ever since the datasets first started to be produced. There are two broad approaches to this kind of problem, traditional deterministic inversion schemes and more recently developed Bayesian search methods, such as MCMC (Markov Chain Monte Carlo). However, using both these kinds of schemes has proved prohibitively expensive, both in computing power and time cost, due to the normally very large model space which needs to be searched using forward model simulators which take considerable time to run. At the heart of strategies aimed at accomplishing this kind of inversion is the question of how to reliably and practicably reduce the size of the model space in which the inversion is to be carried out. Here we present a practical Bayesian method, known as emulation, which can address this issue. Emulation is a Bayesian technique used with considerable success in a number of technical fields, such as in astronomy, where the evolution of the universe has been modelled using this technique, and in the petroleum industry where history matching is carried out of hydrocarbon reservoirs. The method of emulation involves building a fast-to-compute uncertainty-calibrated approximation to a forward model simulator. We do this by modelling the output data from a number of forward simulator runs by a computationally cheap function, and then fitting the coefficients defining this function to the model parameters. By calibrating the error of the emulator output with respect to the full simulator output, we can use this to screen out large areas of model space which contain only implausible models. For example, starting with what may be considered a geologically reasonable prior model space of 10000 models, using the emulator we can quickly show that only models which lie within 10% of that model space actually produce output data which is plausibly similar in character to an observed dataset. We can thus much
Bayesian Dose-Response Modeling in Sparse Data
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
Vardeman, Stephen B.; Wendelberger, Joanne R.
2003-01-01
There is a little-known but very simple generalization of the standard result that for uncorrelated variables with a common mean and variance, the expected sample variance is the marginal variance. The generalization justifies the use of the usual standard error of the sample mean in possibly heteroscedastic situations and motivates some simple estimators for unbalanced linear random effects models. The latter is illustrated for the simple one-way context.
Perceptual decision making: Drift-diffusion model is equivalent to a Bayesian model
Sebastian Bitzer
2014-02-01
Full Text Available Behavioural data obtained with perceptual decision making experiments are typically analysed with the drift-diffusion model. This parsimonious model accumulates noisy pieces of evidence towards a decision bound to explain the accuracy and reaction times of subjects. Recently, Bayesian models have been proposed to explain how the brain extracts information from noisy input as typically presented in perceptual decision making tasks. It has long been known that the drift-diffusion model is tightly linked with such functional Bayesian models but the precise relationship of the two mechanisms was never made explicit. Using a Bayesian model, we derived the equations which relate parameter values between these models. In practice we show that this equivalence is useful when fitting multi-subject data. We further show that the Bayesian model suggests different decision variables which all predict equal responses and discuss how these may be discriminated based on neural correlates of accumulated evidence. In addition, we discuss extensions to the Bayesian model which would be difficult to derive for the drift-diffusion model. We suggest that these and other extensions may be highly useful for deriving new experiments which test novel hypotheses.
MATHEMATICAL RISK ANALYSIS: VIA NICHOLAS RISK MODEL AND BAYESIAN ANALYSIS
Anass BAYAGA
2010-07-01
Full Text Available The objective of this second part of a two-phased study was to explorethe predictive power of quantitative risk analysis (QRA method andprocess within Higher Education Institution (HEI. The method and process investigated the use impact analysis via Nicholas risk model and Bayesian analysis, with a sample of hundred (100 risk analysts in a historically black South African University in the greater Eastern Cape Province.The first findings supported and confirmed previous literature (KingIII report, 2009: Nicholas and Steyn, 2008: Stoney, 2007: COSA, 2004 that there was a direct relationship between risk factor, its likelihood and impact, certiris paribus. The second finding in relation to either controlling the likelihood or the impact of occurrence of risk (Nicholas risk model was that to have a brighter risk reward, it was important to control the likelihood ofoccurrence of risks as compared with its impact so to have a direct effect on entire University. On the Bayesian analysis, thus third finding, the impact of risk should be predicted along three aspects. These aspects included the human impact (decisions made, the property impact (students and infrastructural based and the business impact. Lastly, the study revealed that although in most business cases, where as business cycles considerably vary dependingon the industry and or the institution, this study revealed that, most impacts in HEI (University was within the period of one academic.The recommendation was that application of quantitative risk analysisshould be related to current legislative framework that affects HEI.
Bayesian predictive modeling for genomic based personalized treatment selection.
Ma, Junsheng; Stingo, Francesco C; Hobbs, Brian P
2016-06-01
Efforts to personalize medicine in oncology have been limited by reductive characterizations of the intrinsically complex underlying biological phenomena. Future advances in personalized medicine will rely on molecular signatures that derive from synthesis of multifarious interdependent molecular quantities requiring robust quantitative methods. However, highly parameterized statistical models when applied in these settings often require a prohibitively large database and are sensitive to proper characterizations of the treatment-by-covariate interactions, which in practice are difficult to specify and may be limited by generalized linear models. In this article, we present a Bayesian predictive framework that enables the integration of a high-dimensional set of genomic features with clinical responses and treatment histories of historical patients, providing a probabilistic basis for using the clinical and molecular information to personalize therapy for future patients. Our work represents one of the first attempts to define personalized treatment assignment rules based on large-scale genomic data. We use actual gene expression data acquired from The Cancer Genome Atlas in the settings of leukemia and glioma to explore the statistical properties of our proposed Bayesian approach for personalizing treatment selection. The method is shown to yield considerable improvements in predictive accuracy when compared to penalized regression approaches. PMID:26575856
Development of a Bayesian Belief Network Runway Incursion Model
Green, Lawrence L.
2014-01-01
In a previous paper, a statistical analysis of runway incursion (RI) events was conducted to ascertain their relevance to the top ten Technical Challenges (TC) of the National Aeronautics and Space Administration (NASA) Aviation Safety Program (AvSP). The study revealed connections to perhaps several of the AvSP top ten TC. That data also identified several primary causes and contributing factors for RI events that served as the basis for developing a system-level Bayesian Belief Network (BBN) model for RI events. The system-level BBN model will allow NASA to generically model the causes of RI events and to assess the effectiveness of technology products being developed under NASA funding. These products are intended to reduce the frequency of RI events in particular, and to improve runway safety in general. The development, structure and assessment of that BBN for RI events by a Subject Matter Expert panel are documented in this paper.
Bayesian reduced-order models for multiscale dynamical systems
Koutsourelakis, P S
2010-01-01
While existing mathematical descriptions can accurately account for phenomena at microscopic scales (e.g. molecular dynamics), these are often high-dimensional, stochastic and their applicability over macroscopic time scales of physical interest is computationally infeasible or impractical. In complex systems, with limited physical insight on the coherent behavior of their constituents, the only available information is data obtained from simulations of the trajectories of huge numbers of degrees of freedom over microscopic time scales. This paper discusses a Bayesian approach to deriving probabilistic coarse-grained models that simultaneously address the problems of identifying appropriate reduced coordinates and the effective dynamics in this lower-dimensional representation. At the core of the models proposed lie simple, low-dimensional dynamical systems which serve as the building blocks of the global model. These approximate the latent, generating sources and parameterize the reduced-order dynamics. We d...
Extended Bayesian Information Criteria for Gaussian Graphical Models
Foygel, Rina
2010-01-01
Gaussian graphical models with sparsity in the inverse covariance matrix are of significant interest in many modern applications. For the problem of recovering the graphical structure, information criteria provide useful optimization objectives for algorithms searching through sets of graphs or for selection of tuning parameters of other methods such as the graphical lasso, which is a likelihood penalization technique. In this paper we establish the consistency of an extended Bayesian information criterion for Gaussian graphical models in a scenario where both the number of variables p and the sample size n grow. Compared to earlier work on the regression case, our treatment allows for growth in the number of non-zero parameters in the true model, which is necessary in order to cover connected graphs. We demonstrate the performance of this criterion on simulated data when used in conjunction with the graphical lasso, and verify that the criterion indeed performs better than either cross-validation or the ordi...
A Bayesian approach to the modelling of alpha Cen A
Bazot, M; Christensen-Dalsgaard, J
2012-01-01
Determining the physical characteristics of a star is an inverse problem consisting in estimating the parameters of models for the stellar structure and evolution, knowing certain observable quantities. We use a Bayesian approach to solve this problem for alpha Cen A, which allows us to incorporate prior information on the parameters to be estimated, in order to better constrain the problem. Our strategy is based on the use of a Markov Chain Monte Carlo (MCMC) algorithm to estimate the posterior probability densities of the stellar parameters: mass, age, initial chemical composition,... We use the stellar evolutionary code ASTEC to model the star. To constrain this model both seismic and non-seismic observations were considered. Several different strategies were tested to fit these values, either using two or five free parameters in ASTEC. We are thus able to show evidence that MCMC methods become efficient with respect to more classical grid-based strategies when the number of parameters increases. The resul...
Advances in Bayesian Model Based Clustering Using Particle Learning
Merl, D M
2009-11-19
Recent work by Carvalho, Johannes, Lopes and Polson and Carvalho, Lopes, Polson and Taddy introduced a sequential Monte Carlo (SMC) alternative to traditional iterative Monte Carlo strategies (e.g. MCMC and EM) for Bayesian inference for a large class of dynamic models. The basis of SMC techniques involves representing the underlying inference problem as one of state space estimation, thus giving way to inference via particle filtering. The key insight of Carvalho et al was to construct the sequence of filtering distributions so as to make use of the posterior predictive distribution of the observable, a distribution usually only accessible in certain Bayesian settings. Access to this distribution allows a reversal of the usual propagate and resample steps characteristic of many SMC methods, thereby alleviating to a large extent many problems associated with particle degeneration. Furthermore, Carvalho et al point out that for many conjugate models the posterior distribution of the static variables can be parametrized in terms of [recursively defined] sufficient statistics of the previously observed data. For models where such sufficient statistics exist, particle learning as it is being called, is especially well suited for the analysis of streaming data do to the relative invariance of its algorithmic complexity with the number of data observations. Through a particle learning approach, a statistical model can be fit to data as the data is arriving, allowing at any instant during the observation process direct quantification of uncertainty surrounding underlying model parameters. Here we describe the use of a particle learning approach for fitting a standard Bayesian semiparametric mixture model as described in Carvalho, Lopes, Polson and Taddy. In Section 2 we briefly review the previously presented particle learning algorithm for the case of a Dirichlet process mixture of multivariate normals. In Section 3 we describe several novel extensions to the original
Using Bayesian model averaging to estimate terrestrial evapotranspiration in China
Chen, Yang; Yuan, Wenping; Xia, Jiangzhou; Fisher, Joshua B.; Dong, Wenjie; Zhang, Xiaotong; Liang, Shunlin; Ye, Aizhong; Cai, Wenwen; Feng, Jinming
2015-09-01
Evapotranspiration (ET) is critical to terrestrial ecosystems as it links the water, carbon, and surface energy exchanges. Numerous ET models were developed for the ET estimations, but there are large model uncertainties. In this study, a Bayesian Model Averaging (BMA) method was used to merge eight satellite-based models, including five empirical and three process-based models, for improving the accuracy of ET estimates. At twenty-three eddy covariance flux towers, we examined the model performance on all possible combinations of eight models and found that an ensemble with four models (BMA_Best) showed the best model performance. The BMA_Best method can outperform the best of eight models, and the Kling-Gupta efficiency (KGE) value increased by 4% compared with the model with the highest KGE, and decreased RMSE by 4%. Although the correlation coefficient of BMA_Best is less than the best single model, the bias of BMA_Best is the smallest compared with the eight models. Moreover, based on the water balance principle over the river basin scale, the validation indicated the BMA_Best estimates can explain 86% variations. In general, the results showed BMA estimates will be very useful for future studies to characterize the regional water availability over long-time series.
Semi-parametric Bayesian Partially Identified Models based on Support Function
Liao, Yuan; De Simoni, Anna
2012-01-01
We provide a comprehensive semi-parametric study of Bayesian partially identified econometric models. While the existing literature on Bayesian partial identification has mostly focused on the structural parameter, our primary focus is on Bayesian credible sets (BCS's) of the unknown identified set and the posterior distribution of its support function. We construct a (two-sided) BCS based on the support function of the identified set. We prove the Bernstein-von Mises theorem for the posterio...
Williford, W. O.; Hsieh, P.; Carter, M. C.
1974-01-01
A Bayesian analysis of the two discrete probability models, the negative binomial and the modified negative binomial distributions, which have been used to describe thunderstorm activity at Cape Kennedy, Florida, is presented. The Bayesian approach with beta prior distributions is compared to the classical approach which uses a moment method of estimation or a maximum-likelihood method. The accuracy and simplicity of the Bayesian method is demonstrated.
Yu, Rongjie; Abdel-Aty, Mohamed
2014-01-01
Severe crashes are causing serious social and economic loss, and because of this, reducing crash injury severity has become one of the key objectives of the high speed facilities' (freeway and expressway) management. Traditional crash injury severity analysis utilized data mainly from crash reports concerning the crash occurrence information, drivers' characteristics and roadway geometric related variables. In this study, real-time traffic and weather data were introduced to analyze the crash injury severity. The space mean speeds captured by the Automatic Vehicle Identification (AVI) system on the two roadways were used as explanatory variables in this study; and data from a mountainous freeway (I-70 in Colorado) and an urban expressway (State Road 408 in Orlando) have been used to identify the analysis result's consistence. Binary probit (BP) models were estimated to classify the non-severe (property damage only) crashes and severe (injury and fatality) crashes. Firstly, Bayesian BP models' results were compared to the results from Maximum Likelihood Estimation BP models and it was concluded that Bayesian inference was superior with more significant variables. Then different levels of hierarchical Bayesian BP models were developed with random effects accounting for the unobserved heterogeneity at segment level and crash individual level, respectively. Modeling results from both studied locations demonstrate that large variations of speed prior to the crash occurrence would increase the likelihood of severe crash occurrence. Moreover, with considering unobserved heterogeneity in the Bayesian BP models, the model goodness-of-fit has improved substantially. Finally, possible future applications of the model results and the hierarchical Bayesian probit models were discussed. PMID:24172082
Modelling of population dynamics of red king crab using Bayesian approach
Bakanev Sergey ...
2012-10-01
Modeling population dynamics based on the Bayesian approach enables to successfully resolve the above issues. The integration of the data from various studies into a unified model based on Bayesian parameter estimation method provides a much more detailed description of the processes occurring in the population.
Dynamic Bayesian Network Modeling of Game Based Diagnostic Assessments. CRESST Report 837
Levy, Roy
2014-01-01
Digital games offer an appealing environment for assessing student proficiencies, including skills and misconceptions in a diagnostic setting. This paper proposes a dynamic Bayesian network modeling approach for observations of student performance from an educational video game. A Bayesian approach to model construction, calibration, and use in…
Determinants of Low Birth Weight in Malawi: Bayesian Geo-Additive Modelling.
Alfred Ngwira
Full Text Available Studies on factors of low birth weight in Malawi have neglected the flexible approach of using smooth functions for some covariates in models. Such flexible approach reveals detailed relationship of covariates with the response. The study aimed at investigating risk factors of low birth weight in Malawi by assuming a flexible approach for continuous covariates and geographical random effect. A Bayesian geo-additive model for birth weight in kilograms and size of the child at birth (less than average or average and higher with district as a spatial effect using the 2010 Malawi demographic and health survey data was adopted. A Gaussian model for birth weight in kilograms and a binary logistic model for the binary outcome (size of child at birth were fitted. Continuous covariates were modelled by the penalized (p splines and spatial effects were smoothed by the two dimensional p-spline. The study found that child birth order, mother weight and height are significant predictors of birth weight. Secondary education for mother, birth order categories 2-3 and 4-5, wealth index of richer family and mother height were significant predictors of child size at birth. The area associated with low birth weight was Chitipa and areas with increased risk to less than average size at birth were Chitipa and Mchinji. The study found support for the flexible modelling of some covariates that clearly have nonlinear influences. Nevertheless there is no strong support for inclusion of geographical spatial analysis. The spatial patterns though point to the influence of omitted variables with some spatial structure or possibly epidemiological processes that account for this spatial structure and the maps generated could be used for targeting development efforts at a glance.
Inversion of hierarchical Bayesian models using Gaussian processes.
Lomakina, Ekaterina I; Paliwal, Saee; Diaconescu, Andreea O; Brodersen, Kay H; Aponte, Eduardo A; Buhmann, Joachim M; Stephan, Klaas E
2015-09-01
Over the past decade, computational approaches to neuroimaging have increasingly made use of hierarchical Bayesian models (HBMs), either for inferring on physiological mechanisms underlying fMRI data (e.g., dynamic causal modelling, DCM) or for deriving computational trajectories (from behavioural data) which serve as regressors in general linear models. However, an unresolved problem is that standard methods for inverting the hierarchical Bayesian model are either very slow, e.g. Markov Chain Monte Carlo Methods (MCMC), or are vulnerable to local minima in non-convex optimisation problems, such as variational Bayes (VB). This article considers Gaussian process optimisation (GPO) as an alternative approach for global optimisation of sufficiently smooth and efficiently evaluable objective functions. GPO avoids being trapped in local extrema and can be computationally much more efficient than MCMC. Here, we examine the benefits of GPO for inverting HBMs commonly used in neuroimaging, including DCM for fMRI and the Hierarchical Gaussian Filter (HGF). Importantly, to achieve computational efficiency despite high-dimensional optimisation problems, we introduce a novel combination of GPO and local gradient-based search methods. The utility of this GPO implementation for DCM and HGF is evaluated against MCMC and VB, using both synthetic data from simulations and empirical data. Our results demonstrate that GPO provides parameter estimates with equivalent or better accuracy than the other techniques, but at a fraction of the computational cost required for MCMC. We anticipate that GPO will prove useful for robust and efficient inversion of high-dimensional and nonlinear models of neuroimaging data. PMID:26048619
Modeling Land-Use Decision Behavior with Bayesian Belief Networks
Inge Aalders
2008-06-01
Full Text Available The ability to incorporate and manage the different drivers of land-use change in a modeling process is one of the key challenges because they are complex and are both quantitative and qualitative in nature. This paper uses Bayesian belief networks (BBN to incorporate characteristics of land managers in the modeling process and to enhance our understanding of land-use change based on the limited and disparate sources of information. One of the two models based on spatial data represented land managers in the form of a quantitative variable, the area of individual holdings, whereas the other model included qualitative data from a survey of land managers. Random samples from the spatial data provided evidence of the relationship between the different variables, which I used to develop the BBN structure. The model was tested for four different posterior probability distributions, and results showed that the trained and learned models are better at predicting land use than the uniform and random models. The inference from the model demonstrated the constraints that biophysical characteristics impose on land managers; for older land managers without heirs, there is a higher probability of the land use being arable agriculture. The results show the benefits of incorporating a more complex notion of land managers in land-use models, and of using different empirical data sources in the modeling process. Future research should focus on incorporating more complex social processes into the modeling structure, as well as incorporating spatio-temporal dynamics in a BBN.
Bayesian Degree-Corrected Stochastic Block Models for Community Detection
Peng, Lijun
2013-01-01
Community detection in networks has drawn much attention in diverse fields, especially social sciences. Given its significance, there has been a large body of literature among which many are not statistically based. In this paper, we propose a novel stochastic blockmodel based on a logistic regression setup with node correction terms to better address this problem. We follow a Bayesian approach that explicitly captures the community behavior via prior specification. We then adopt a data augmentation strategy with latent Polya-Gamma variables to obtain posterior samples. We conduct inference based on a canonically mapped centroid estimator that formally addresses label non-identifiability. We demonstrate the novel proposed model and estimation on real-world as well as simulated benchmark networks and show that the proposed model and estimator are more flexible, representative, and yield smaller error rates when compared to the MAP estimator from classical degree-corrected stochastic blockmodels.