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26
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 Averaging for Linear Regression Models
 Journal of the American Statistical Association
, 1997
"... We consider the problem of accounting for model uncertainty in linear regression models. Conditioning on a single selected model ignores model uncertainty, and thus leads to the underestimation of uncertainty when making inferences about quantities of interest. A Bayesian solution to this problem in ..."
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Cited by 184 (13 self)
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We consider the problem of accounting for model uncertainty in linear regression models. Conditioning on a single selected model ignores model uncertainty, and thus leads to the underestimation of uncertainty when making inferences about quantities of interest. A Bayesian solution to this problem involves averaging over all possible models (i.e., combinations of predictors) when making inferences about quantities of
Assessment and Propagation of Model Uncertainty
, 1995
"... this paper I discuss a Bayesian approach to solving this problem that has long been available in principle but is only now becoming routinely feasible, by virtue of recent computational advances, and examine its implementation in examples that involve forecasting the price of oil and estimating the ..."
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Cited by 108 (0 self)
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this paper I discuss a Bayesian approach to solving this problem that has long been available in principle but is only now becoming routinely feasible, by virtue of recent computational advances, and examine its implementation in examples that involve forecasting the price of oil and estimating the chance of catastrophic failure of the U.S. Space Shuttle.
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
Model Selection and Accounting for Model Uncertainty in Linear Regression Models
, 1993
"... We consider the problems of variable selection and accounting for model uncertainty in linear regression models. Conditioning on a single selected model ignores model uncertainty, and thus leads to the underestimation of uncertainty when making inferences about quantities of interest. The complete B ..."
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Cited by 47 (6 self)
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We consider the problems of variable selection and accounting for model uncertainty in linear regression models. Conditioning on a single selected model ignores model uncertainty, and thus leads to the underestimation of uncertainty when making inferences about quantities of interest. The complete Bayesian solution to this problem involves averaging over all possible models when making inferences about quantities of interest. This approach is often not practical. In this paper we offer two alternative approaches. First we describe a Bayesian model selection algorithm called "Occam's "Window" which involves averaging over a reduced set of models. Second, we describe a Markov chain Monte Carlo approach which directly approximates the exact solution. Both these model averaging procedures provide better predictive performance than any single model which might reasonably have been selected. In the extreme case where there are many candidate predictors but there is no relationship between any of them and the response, standard variable selection procedures often choose some subset of variables that yields a high R² and a highly significant overall F value. We refer to this unfortunate phenomenon as "Freedman's Paradox" (Freedman, 1983). In this situation, Occam's vVindow usually indicates the null model as the only one to be considered, or else a small number of models including the null model, thus largely resolving the paradox.
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
Inference from a Deterministic Population Dynamics Model for Bowhead Whales
 Journal of the American Statistical Association
, 1995
"... We consider the problem of inference about a quantity of interest given different sources of information linked by a deterministic population dynamics model. Our approach consists of translating all the available information into a joint premodel distribution on all the model inputs and outputs, an ..."
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Cited by 41 (21 self)
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We consider the problem of inference about a quantity of interest given different sources of information linked by a deterministic population dynamics model. Our approach consists of translating all the available information into a joint premodel distribution on all the model inputs and outputs, and then restricting this to the submanifold defined by the model to obtain the joint postmodel distribution. Marginalizing this yields inference, conditional on the model, about quantities of interest which can be functions of model inputs, model outputs, or both. Samples from the postmodel distribution are obtained by importance sampling and Rubin's SIR algorithm. The framework includes as a special case the situation where the premodel information about the outputs consists of measurements with error; this reduces to standard Bayesian inference. The results are in the form of a sample from the postmodel distribution and so can be examined using the full range of exploratory data analysis...
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