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50
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.
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
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 ..."
Abstract

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 model averaging
 STAT.SCI
, 1999
"... Standard statistical practice ignores model uncertainty. Data analysts typically select a model from some class of models and then proceed as if the selected model had generated the data. This approach ignores the uncertainty in model selection, leading to overcon dent inferences and decisions tha ..."
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Cited by 42 (0 self)
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Standard statistical practice ignores model uncertainty. Data analysts typically select a model from some class of models and then proceed as if the selected model had generated the data. This approach ignores the uncertainty in model selection, leading to overcon dent inferences and decisions that are more risky than one thinks they are. Bayesian model averaging (BMA) provides a coherent mechanism for accounting for this model uncertainty. Several methods for implementing BMA haverecently emerged. We discuss these methods and present anumber of examples. In these examples, BMA provides improved outofsample predictive performance. We also provide a catalogue of
Bayesian Model Averaging in proportional hazard models: Assessing the risk of a stroke
 Applied Statistics
, 1997
"... Evaluating the risk of stroke is important in reducing the incidence of this devastating disease. Here, we apply Bayesian model averaging to variable selection in Cox proportional hazard models in the context of the Cardiovascular Health Study, a comprehensive investigation into the risk factors for ..."
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Cited by 28 (5 self)
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Evaluating the risk of stroke is important in reducing the incidence of this devastating disease. Here, we apply Bayesian model averaging to variable selection in Cox proportional hazard models in the context of the Cardiovascular Health Study, a comprehensive investigation into the risk factors for stroke. We introduce a technique based on the leaps and bounds algorithm which e ciently locates and ts the best models in the very large model space and thereby extends all subsets regression to Cox models. For each independent variable considered, the method provides the posterior probability that it belongs in the model. This is more directly interpretable than the corresponding Pvalues, and also more valid in that it takes account of model uncertainty. Pvalues from models preferred by stepwise methods tend to overstate the evidence for the predictive value of a variable. In our data Bayesian model averaging predictively outperforms standard model selection methods for assessing
The Horseshoe Estimator for Sparse Signals
, 2008
"... This paper proposes a new approach to sparsity called the horseshoe estimator. The horseshoe is a close cousin of other widely used Bayes rules arising from, for example, doubleexponential and Cauchy priors, in that it is a member of the same family of multivariate scale mixtures of normals. But th ..."
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Cited by 21 (6 self)
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This paper proposes a new approach to sparsity called the horseshoe estimator. The horseshoe is a close cousin of other widely used Bayes rules arising from, for example, doubleexponential and Cauchy priors, in that it is a member of the same family of multivariate scale mixtures of normals. But the horseshoe enjoys a number of advantages over existing approaches, including its robustness, its adaptivity to different sparsity patterns, and its analytical tractability. We prove two theorems that formally characterize both the horseshoe’s adeptness at large outlying signals, and its superefficient rate of convergence to the correct estimate of the sampling density in sparse situations. Finally, using a combination of real and simulated data, we show that the horseshoe estimator corresponds quite closely to the answers one would get by pursuing a full Bayesian modelaveraging approach using a discrete mixture prior to model signals and noise.
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
Bayesian Tests And Model Diagnostics In Conditionally Independent Hierarchical Models
 Journal of the American Statistical Association
, 1994
"... Consider the conditionally independent hierarchical model (CIHM) where observations y i are independently distributed from f(y i j` i ), the parameters ` i are independently distributed from distributions g(`j), and the hyperparameters are distributed according to a distribution h(). The posterior ..."
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Cited by 16 (1 self)
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Consider the conditionally independent hierarchical model (CIHM) where observations y i are independently distributed from f(y i j` i ), the parameters ` i are independently distributed from distributions g(`j), and the hyperparameters are distributed according to a distribution h(). The posterior distribution of all parameters of the CIHM can be efficiently simulated by Monte Carlo Markov Chain (MCMC) algorithms. Although these simulation algorithms have facilitated the application of CIHM's, they generally have not addressed the problem of computing quantities useful in model selection. This paper explores how MCMC simulation algorithms and other related computational algorithms can be used to compute Bayes factors that are useful in criticizing a particular CIHM. In the case where the CIHM models a belief that the parameters are exchangeable or lie on a regression surface, the Bayes factor can measure the consistency of the data with the structural prior belief. Bayes factors can ...
Checking for priordata conflict
 Bayesian Analysis
, 2006
"... Abstract. Inference proceeds from ingredients chosen by the analyst and data. To validate any inferences drawn it is essential that the inputs chosen be deemed appropriate for the data. In the Bayesian context these inputs consist of both the sampling model and the prior. There are thus two possibil ..."
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Cited by 10 (7 self)
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Abstract. Inference proceeds from ingredients chosen by the analyst and data. To validate any inferences drawn it is essential that the inputs chosen be deemed appropriate for the data. In the Bayesian context these inputs consist of both the sampling model and the prior. There are thus two possibilities for failure: the data may not have arisen from the sampling model, or the prior may place most of its mass on parameter values that are not feasible in light of the data (referred to here as priordata conflict). Failure of the sampling model can only be fixed by modifying the model, while priordata conflict can be overcome if sufficient data is available. We examine how to assess whether or not a priordata conflict exists, and how to assess when its effects can be ignored for inferences. The concept of priordata conflict is seen to lead to a partial characterization of what is meant by a noninformative prior or a noninformative sequence of priors.
Accounting for inputmodel and inputparameter uncertainties in simulation
, 2004
"... To account for the inputmodel and inputparameter uncertainties inherent in many simulations as well as the usual stochastic uncertainty, we present a Bayesian inputmodeling technique that yields improved point and confidenceinterval estimators for a selected posterior mean response. Exploiting p ..."
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Cited by 9 (0 self)
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To account for the inputmodel and inputparameter uncertainties inherent in many simulations as well as the usual stochastic uncertainty, we present a Bayesian inputmodeling technique that yields improved point and confidenceinterval estimators for a selected posterior mean response. Exploiting prior information to specify the prior probabilities of the postulated input models and the associated prior inputparameter distributions, we use sample data to compute the posterior inputmodel and inputparameter distributions. Our Bayesian simulation replication algorithm involves: (i) estimating parameter uncertainty by randomly sampling the posterior inputparameter distributions; (ii) estimating stochastic uncertainty by running independent replications of the simulation using each set of inputmodel parameters sampled in (i); and (iii) estimating inputmodel uncertainty by weighting the responses generated in (ii) using the corresponding posterior inputmodel probabilities. Sampling effort is allocated among input models to minimize final pointestimator variance subject to a computingbudget constraint. A queueing simulation demonstrates the advantages of this approach.