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80
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.
Model selection and accounting for model uncertainty in graphical models using Occam's window
, 1993
"... We consider the problem of model selection and accounting for model uncertainty in highdimensional contingency tables, motivated by expert system applications. The approach most used currently is a stepwise strategy guided by tests based on approximate asymptotic Pvalues leading to the selection o ..."
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Cited by 266 (46 self)
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We consider the problem of model selection and accounting for model uncertainty in highdimensional contingency tables, motivated by expert system applications. The approach most used currently is a stepwise strategy guided by tests based on approximate asymptotic Pvalues leading to the selection of a single model; inference is then conditional on the selected model. The sampling properties of such a strategy are complex, and the failure to take account of model uncertainty leads to underestimation of uncertainty about quantities of interest. In principle, a panacea is provided by the standard Bayesian formalism which averages the posterior distributions of the quantity of interest under each of the models, weighted by their posterior model probabilities. Furthermore, this approach is optimal in the sense of maximising predictive ability. However, this has not been used in practice because computing the posterior model probabilities is hard and the number of models is very large (often greater than 1011). We argue that the standard Bayesian formalism is unsatisfactory and we propose an alternative Bayesian approach that, we contend, takes full account of the true model uncertainty byaveraging overamuch smaller set of models. An efficient search algorithm is developed for nding these models. We consider two classes of graphical models that arise in expert systems: the recursive causal models and the decomposable
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...
Approximate Bayes Factors and Accounting for Model Uncertainty in Generalized Linear Models
, 1993
"... Ways of obtaining approximate Bayes factors for generalized linear models are described, based on the Laplace method for integrals. I propose a new approximation which uses only the output of standard computer programs such as GUM; this appears to be quite accurate. A reference set of proper priors ..."
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Cited by 96 (28 self)
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Ways of obtaining approximate Bayes factors for generalized linear models are described, based on the Laplace method for integrals. I propose a new approximation which uses only the output of standard computer programs such as GUM; this appears to be quite accurate. A reference set of proper priors is suggested, both to represent the situation where there is not much prior information, and to assess the sensitivity of the results to the prior distribution. The methods can be used when the dispersion parameter is unknown, when there is overdispersion, to compare link functions, and to compare error distributions and variance functions. The methods can be used to implement the Bayesian approach to accounting for model uncertainty. I describe an application to inference about relative risks in the presence of control factors where model uncertainty is large and important. Software to implement the
Statistical Themes and Lessons for Data Mining
, 1997
"... Data mining is on the interface of Computer Science and Statistics, utilizing advances in both disciplines to make progress in extracting information from large databases. It is an emerging field that has attracted much attention in a very short period of time. This article highlights some statist ..."
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Cited by 32 (3 self)
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Data mining is on the interface of Computer Science and Statistics, utilizing advances in both disciplines to make progress in extracting information from large databases. It is an emerging field that has attracted much attention in a very short period of time. This article highlights some statistical themes and lessons that are directly relevant to data mining and attempts to identify opportunities where close cooperation between the statistical and computational communities might reasonably provide synergy for further progress in data analysis.
Could Fisher, Jeffreys, and Neyman Have Agreed on Testing?
, 2002
"... Ronald Fisher advocated testing using pvalues; Harold Jeffreys proposed use of objective posterior probabilities of hypotheses; and Jerzy Neyman recommended testing with fixed error probabilities. Each was quite critical of the other approaches. ..."
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Cited by 29 (2 self)
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Ronald Fisher advocated testing using pvalues; Harold Jeffreys proposed use of objective posterior probabilities of hypotheses; and Jerzy Neyman recommended testing with fixed error probabilities. Each was quite critical of the other approaches.
Bayesian model selection in structural equation models
, 1993
"... A Bayesian approach to model selection for structural equation models is outlined. This enables us to compare individual models, nested or nonnested, and also to search through the (perhaps vast) set of possible models for the best ones. The approach selects several models rather than just one, whe ..."
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Cited by 29 (10 self)
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A Bayesian approach to model selection for structural equation models is outlined. This enables us to compare individual models, nested or nonnested, and also to search through the (perhaps vast) set of possible models for the best ones. The approach selects several models rather than just one, when appropriate, and so enables us to take account, both informally and formally, of uncertainty about model structure when making inferences about quantities of interest. The approach tends to select simpler models than strategies based on multiple Pvaluebased tests. It may thus help to overcome the criticism of structural
Toward evidencebased medical statistics. 2: The bayes factor
 Annals of Internal Medicine
, 1999
"... Bayesian inference is usually presented as a method for determining how scientific belief should be modified by data. Although Bayesian methodology has been one of the most active areas of statistical development in the past 20 years, medical researchers have been reluctant to embrace what they perc ..."
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Cited by 22 (0 self)
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Bayesian inference is usually presented as a method for determining how scientific belief should be modified by data. Although Bayesian methodology has been one of the most active areas of statistical development in the past 20 years, medical researchers have been reluctant to embrace what they perceive as a subjective approach to data analysis. It is little understood that Bayesian methods have a databased core, which can be used as a calculus of evidence. This core is the Bayes factor, which in its simplest form is also called a likelihood ratio. The minimum Bayes factor is objective and can be used in lieu of the P value as a measure of the evidential strength. Unlike P values, Bayes factors have a sound theoretical foundation and an interpretation that allows their use in both inference and decision making. Bayes factors show that P values greatly overstate the evidence against the null hypothesis. Most important, Bayes factors require the addition of background knowledge to be transformed into inferences—probabilities that a given conclusion is right or wrong. They make the distinction clear between experimental evidence and inferential conclusions while providing a framework in which to combine prior with current evidence. This paper is also available at
Bayesian inference procedures derived via the concept of relative surprise
 Communications in Statistics
, 1997
"... of least relative surprise; model checking; change of variable problem; crossvalidation. We consider the problem of deriving Bayesian inference procedures via the concept of relative surprise. The mathematical concept of surprise has been developed by I.J. Good in a long sequence of papers. We make ..."
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Cited by 17 (6 self)
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of least relative surprise; model checking; change of variable problem; crossvalidation. We consider the problem of deriving Bayesian inference procedures via the concept of relative surprise. The mathematical concept of surprise has been developed by I.J. Good in a long sequence of papers. We make a modiÞcation to this development that permits the avoidance of a serious defect; namely, the change of variable problem. We apply relative surprise to the development of estimation, hypothesis testing and model checking procedures. Important advantages of the relative surprise approach to inference include the lack of dependence on a particular loss function and complete freedom to the statistician in the choice of prior for hypothesis testing problems. Links are established with common Bayesian inference procedures such as highest posterior density regions, modal estimates and Bayes factors. From a practical perspective new inference
Bayesian hypothesis testing: A reference approach
 Internat. Statist. Rev
, 2002
"... For any probability model M ≡{p(x  θ, ω), θ ∈ Θ, ω ∈ Ω} assumed to describe the probabilistic behaviour of data x ∈ X, it is argued that testing whether or not the available data are compatible with the hypothesis H0 ≡{θ = θ0} is best considered as a formal decision problem on whether to use (a0), ..."
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Cited by 17 (5 self)
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For any probability model M ≡{p(x  θ, ω), θ ∈ Θ, ω ∈ Ω} assumed to describe the probabilistic behaviour of data x ∈ X, it is argued that testing whether or not the available data are compatible with the hypothesis H0 ≡{θ = θ0} is best considered as a formal decision problem on whether to use (a0), or not to use (a1), the simpler probability model (or null model) M0 ≡{p(x  θ0, ω), ω ∈ Ω}, where the loss difference L(a0, θ, ω) − L(a1, θ, ω) is proportional to the amount of information δ(θ0, θ, ω) which would be lost if the simplified model M0 were used as a proxy for the assumed model M. For any prior distribution π(θ, ω), the appropriate normative solution is obtained by rejecting the null model M0 whenever the corresponding posterior expectation ∫ ∫ δ(θ0, θ, ω) π(θ, ω  x) dθ dω is sufficiently large. Specification of a subjective prior is always difficult, and often polemical, in scientific communication. Information theory may be used to specify a prior, the reference prior, which only depends on the assumed model M, and mathematically describes a situation where no prior information is available about the quantity of interest. The reference posterior expectation, d(θ0, x) = ∫ δπ(δ  x) dδ, of the amount of information δ(θ0, θ, ω) which could be lost if the null model were used, provides an attractive nonnegative test function, the intrinsic statistic, which is