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95
Bayes Factors
, 1995
"... In a 1935 paper, and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null ..."
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Cited by 981 (70 self)
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In a 1935 paper, and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null is onehalf. Although there has been much discussion of Bayesian hypothesis testing in the context of criticism of P values, less attention has been given to the Bayes factor as a practical tool of applied statistics. In this paper we review and discuss the uses of Bayes factors in the context of five scientific applications in genetics, sports, ecology, sociology and psychology.
Bayesian Model Selection in Social Research (with Discussion by Andrew Gelman & Donald B. Rubin, and Robert M. Hauser, and a Rejoinder)
 SOCIOLOGICAL METHODOLOGY 1995, EDITED BY PETER V. MARSDEN, CAMBRIDGE,; MASS.: BLACKWELLS.
, 1995
"... It is argued that Pvalues and the tests based upon them give unsatisfactory results, especially in large samples. It is shown that, in regression, when there are many candidate independent variables, standard variable selection procedures can give very misleading results. Also, by selecting a singl ..."
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Cited by 253 (19 self)
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It is argued that Pvalues and the tests based upon them give unsatisfactory results, especially in large samples. It is shown that, in regression, when there are many candidate independent variables, standard variable selection procedures can give very misleading results. Also, by selecting a single model, they ignore model uncertainty and so underestimate the uncertainty about quantities of interest. The Bayesian approach to hypothesis testing, model selection and accounting for model uncertainty is presented. Implementing this is straightforward using the simple and accurate BIC approximation, and can be done using the output from standard software. Specific results are presented for most of the types of model commonly used in sociology. It is shown that this approach overcomes the difficulties with P values and standard model selection procedures based on them. It also allows easy comparison of nonnested models, and permits the quantification of the evidence for a null hypothesis...
Posterior Predictive Assessment of Model Fitness Via Realized Discrepancies
 Statistica Sinica
, 1996
"... Abstract: This paper considers Bayesian counterparts of the classical tests for goodness of fit and their use in judging the fit of a single Bayesian model to the observed data. We focus on posterior predictive assessment, in a framework that also includes conditioning on auxiliary statistics. The B ..."
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Cited by 166 (28 self)
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Abstract: This paper considers Bayesian counterparts of the classical tests for goodness of fit and their use in judging the fit of a single Bayesian model to the observed data. We focus on posterior predictive assessment, in a framework that also includes conditioning on auxiliary statistics. The Bayesian formulation facilitates the construction and calculation of a meaningful reference distribution not only for any (classical) statistic, but also for any parameterdependent “statistic ” or discrepancy. The latter allows us to propose the realized discrepancy assessment of model fitness, which directly measures the true discrepancy between data and the posited model, for any aspect of the model which we want to explore. The computation required for the realized discrepancy assessment is a straightforward byproduct of the posterior simulation used for the original Bayesian analysis. We illustrate with three applied examples. The first example, which serves mainly to motivate the work, illustrates the difficulty of classical tests in assessing the fitness of a Poisson model to a positron emission tomography image that is constrained to be nonnegative. The second and third examples illustrate the details of the posterior predictive approach in two problems: estimation in a model with inequality constraints on the parameters, and estimation in a mixture model. In all three examples, standard test statistics (either a χ 2 or a likelihood ratio) are not pivotal: the difficulty is not just how to compute the reference distribution for the test, but that in the classical framework no such distribution exists, independent of the unknown model parameters. Key words and phrases: Bayesian pvalue, χ 2 test, discrepancy, graphical assessment, mixture model, model criticism, posterior predictive pvalue, prior predictive
Bayes factors and model uncertainty
 DEPARTMENT OF STATISTICS, UNIVERSITY OFWASHINGTON
, 1993
"... In a 1935 paper, and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null ..."
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Cited by 89 (6 self)
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In a 1935 paper, and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null is onehalf. Although there has been much discussion of Bayesian hypothesis testing in the context of criticism of Pvalues, less attention has been given to the Bayes factor as a practical tool of applied statistics. In this paper we review and discuss the uses of Bayes factors in the context of five scientific applications. The points we emphasize are: from Jeffreys's Bayesian point of view, the purpose of hypothesis testing is to evaluate the evidence in favor of a scientific theory; Bayes factors offer a way of evaluating evidence in favor ofa null hypothesis; Bayes factors provide a way of incorporating external information into the evaluation of evidence about a hypothesis; Bayes factors are very general, and do not require alternative models to be nested; several techniques are available for computing Bayes factors, including asymptotic approximations which are easy to compute using the output from standard packages that maximize likelihoods; in "nonstandard " statistical models that do not satisfy common regularity conditions, it can be technically simpler to calculate Bayes factors than to derive nonBayesian significance
Bayesian Methods for Hidden Markov Models  Recursive Computing in the 21st Century
 JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
, 2002
"... Markov chain Monte Carlo (MCMC) sampling strategies can be used to simulate hidden Markov model (HMM) parameters from their posterior distribution given observed data. Some MCMC methods (for computing likelihood, conditional probabilities of hidden states, and the most likely sequence of states) use ..."
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Cited by 86 (8 self)
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Markov chain Monte Carlo (MCMC) sampling strategies can be used to simulate hidden Markov model (HMM) parameters from their posterior distribution given observed data. Some MCMC methods (for computing likelihood, conditional probabilities of hidden states, and the most likely sequence of states) used in practice can be improved by incorporating established recursive algorithms. The most important is a set of forwardbackward recursions calculating conditional distributions of the hidden states given observed data and model parameters. We show how to use the recursive algorithms in an MCMC context and demonstrate mathematical and empirical results showing a Gibbs sampler using the forwardbackward recursions mixes more rapidly than another sampler often used for HMM's. We introduce an augmented variables technique for obtaining unique state labels in HMM's and finite mixture models. We show how recursive computing allows statistically efficient use of MCMC output when estimating the hidden states. We directly calculate the posterior distribution of the hidden chain's state space size by MCMC, circumventing asymptotic arguments underlying the Bayesian information criterion, which is shown to be inappropriate for a frequently analyzed data set in the HMM literature. The use of loglikelihood for assessing MCMC convergence is illustrated, and posterior predictive checks are used to investigate application specific questions of model adequacy.
BUGS  Bayesian inference Using Gibbs Sampling Version 0.50
, 1995
"... e wrong, which is even worse. Please let us know of any successes or failures. Beware  Gibbs sampling can be dangerous!. BUGS c flcopyright MRC Biostatistics Unit 1995. ALL RIGHTS RESERVED. The support of the Economic and Social Research Council (UK) is gratefully acknowledged. The work was funde ..."
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Cited by 64 (0 self)
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e wrong, which is even worse. Please let us know of any successes or failures. Beware  Gibbs sampling can be dangerous!. BUGS c flcopyright MRC Biostatistics Unit 1995. ALL RIGHTS RESERVED. The support of the Economic and Social Research Council (UK) is gratefully acknowledged. The work was funded in part by ESRC (UK) Award Number H519 25 5023. 1 2 Contents 1 Introduction 5 1.1 What is BUGS? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.2 For what kind of problems is BUGS best suited? . . . . . . . . . . . . . . . . . . . . . 5 1.3 Markov Chain Monte Carlo (MCMC) techniques . . . . . . . . . . . . . . . . . . . . 5 1.4 A simple example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 1.5 Hardware platforms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1.6 Software . . .
Probabilistic topic models
 IEEE Signal Processing Magazine
, 2010
"... Probabilistic topic models are a suite of algorithms whose aim is to discover the ..."
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Cited by 51 (3 self)
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Probabilistic topic models are a suite of algorithms whose aim is to discover the
Inference in longhorizon event studies: A bayesian approach with an application to initial public offerings
 Journal of Finance
, 2000
"... Statistical inference in longhorizon event studies has been hampered by the fact that abnormal returns are neither normally distributed nor independent. This study presents a new approach to inference that overcomes these difficulties and dominates other popular testing methods. I illustrate the us ..."
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Cited by 39 (3 self)
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Statistical inference in longhorizon event studies has been hampered by the fact that abnormal returns are neither normally distributed nor independent. This study presents a new approach to inference that overcomes these difficulties and dominates other popular testing methods. I illustrate the use of the methodology by examining the longhorizon returns of initial public offerings ~IPOs!. I find that the Fama and French ~1993! threefactor model is inconsistent with the observed longhorizon price performance of these IPOs, whereas a characteristicbased model cannot be rejected. RECENT EMPIRICAL STUDIES IN FINANCE document systematic longrun abnormal price reactions subsequent to numerous corporate activities. 1 Since these results imply that stock prices react with a long delay to publicly available information, they appear to be at odds with the Efficient Markets Hypothesis ~EMH!. Longrun event studies, however, are subject to serious statistical difficulties
Probabilistic forecasts, calibration and sharpness
 Journal of the Royal Statistical Society Series B
, 2007
"... Summary. Probabilistic forecasts of continuous variables take the form of predictive densities or predictive cumulative distribution functions. We propose a diagnostic approach to the evaluation of predictive performance that is based on the paradigm of maximizing the sharpness of the predictive dis ..."
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Cited by 38 (15 self)
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Summary. Probabilistic forecasts of continuous variables take the form of predictive densities or predictive cumulative distribution functions. We propose a diagnostic approach to the evaluation of predictive performance that is based on the paradigm of maximizing the sharpness of the predictive distributions subject to calibration. Calibration refers to the statistical consistency between the distributional forecasts and the observations and is a joint property of the predictions and the events that materialize. Sharpness refers to the concentration of the predictive distributions and is a property of the forecasts only. A simple theoretical framework allows us to distinguish between probabilistic calibration, exceedance calibration and marginal calibration. We propose and study tools for checking calibration and sharpness, among them the probability integral transform histogram, marginal calibration plots, the sharpness diagram and proper scoring rules. The diagnostic approach is illustrated by an assessment and ranking of probabilistic forecasts of wind speed at the Stateline wind energy centre in the US Pacific Northwest. In combination with crossvalidation or in the time series context, our proposal provides very general, nonparametric alternatives to the use of information criteria for model diagnostics and model selection.
H: Computing Bayes factors using thermodynamic integration
 Syst Biol
"... Abstract.—In the Bayesian paradigm, a common method for comparing two models is to compute the Bayes factor, defined as the ratio of their respective marginal likelihoods. In recent phylogenetic works, the numerical evaluation of marginal likelihoods has often been performed using the harmonic mean ..."
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Cited by 33 (5 self)
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Abstract.—In the Bayesian paradigm, a common method for comparing two models is to compute the Bayes factor, defined as the ratio of their respective marginal likelihoods. In recent phylogenetic works, the numerical evaluation of marginal likelihoods has often been performed using the harmonic mean estimation procedure. In the present article, we propose to employ another method, based on an analogy with statistical physics, called thermodynamic integration. We describe the method, propose an implementation, and show on two analytical examples that this numerical method yields reliable estimates. In contrast, the harmonic mean estimator leads to a strong overestimation of the marginal likelihood, which is all the more pronounced as the model is higher dimensional. As a result, the harmonic mean estimator systematically favors more parameterrich models, an artefact that might explain some recent puzzling observations, based on harmonic mean estimates, suggesting that Bayes factors tend to overscore complex models. Finally, we apply our method to the comparison of several alternative models of aminoacid replacement. We confirm our previous observations, indicating that modeling pattern heterogeneity across sites tends to yield better models than standard empirical matrices. [Bayes factor; harmonic mean; mixture model; path sampling; phylogeny; thermodynamic integration.] Bayesian methods have become popular in molecular phylogenetics over the recent years. The simple and intuitive interpretation of the concept of probabilities