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20
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 ..."
Abstract

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 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
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.
Variable selection in data mining: Building a predictive model for bankruptcy
 Journal of the American Statistical Association
, 2004
"... We predict the onset of personal bankruptcy using least squares regression. Although well publicized, only 2,244 bankruptcies occur in our data set of 2.9 million months of creditcard activity. We use stepwise selection to find predictors from a mix of payment history, debt load, demographics, and ..."
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Cited by 34 (9 self)
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We predict the onset of personal bankruptcy using least squares regression. Although well publicized, only 2,244 bankruptcies occur in our data set of 2.9 million months of creditcard activity. We use stepwise selection to find predictors from a mix of payment history, debt load, demographics, and their interactions. This combination of rare responses and over 67,000 possible predictors leads to a challenging modeling question: How does one separate coincidental from useful predictors? We show that three modifications turn stepwise regression into an effective methodology for predicting bankruptcy. Our version of stepwise regression (1) organizes calculations to accommodate interactions, (2) exploits modern decision theoretic criteria to choose predictors, and (3) conservatively estimates pvalues to handle sparse data and a binary response. Omitting any one of these leads to poor performance. A final step in our procedure calibrates regression predictions. With these modifications, stepwise regression predicts bankruptcy as well, if not better, than recently developed datamining tools. When sorted, the largest 14,000 resulting predictions hold 1000 of the 1800 bankruptcies hidden in a validation sample of 2.3 million observations. If the cost of missing a bankruptcy is 200 times that of a false positive, our predictions incur less than 2/3 of the costs of classification errors produced by the treebased classifier C4.5. Key Phrases: AIC, Cp, Bonferroni, calibration, hard thresholding, risk inflation criterion (RIC),
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.
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
From association to causation: Some remarks on the history of statistics
 Statist. Sci
, 1999
"... The “numerical method ” in medicine goes back to Pierre Louis ’ study of pneumonia (1835), and John Snow’s book on the epidemiology of cholera (1855). Snow took advantage of natural experiments and used convergent lines of evidence to demonstrate that cholera is a waterborne infectious disease. More ..."
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Cited by 23 (6 self)
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The “numerical method ” in medicine goes back to Pierre Louis ’ study of pneumonia (1835), and John Snow’s book on the epidemiology of cholera (1855). Snow took advantage of natural experiments and used convergent lines of evidence to demonstrate that cholera is a waterborne infectious disease. More recently, investigators in the social and life sciences have used statistical models and significance tests to deduce causeandeffect relationships from patterns of association; an early example is Yule’s study on the causes of poverty (1899). In my view, this modeling enterprise has not been successful. Investigators tend to neglect the difficulties in establishing causal relations, and the mathematical complexities obscure rather than clarify the assumptions on which the analysis is based. Formal statistical inference is, by its nature, conditional. If maintained hypotheses A, B, C,... hold, then H can be tested against the data. However, if A, B, C,... remain in doubt, so must inferences about H. Careful scrutiny of maintained hypotheses should therefore be a critical part of empirical work—a principle honored more often in the breach than the observance. Snow’s work on cholera will be contrasted with modern studies that depend on statistical models and tests of significance. The examples may help to clarify the limits of current statistical techniques for making causal inferences from patterns of association. 1.
Variable selection and Bayesian model averaging in casecontrol studies
, 1998
"... Covariate and confounder selection in casecontrol studies is most commonly carried out using either a twostep method or a stepwise variable selection method in logistic regression. Inference is then carried out conditionally on the selected model, but this ignores the model uncertainty implicit in ..."
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Cited by 19 (7 self)
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Covariate and confounder selection in casecontrol studies is most commonly carried out using either a twostep method or a stepwise variable selection method in logistic regression. Inference is then carried out conditionally on the selected model, but this ignores the model uncertainty implicit in the variable selection process, and so underestimates uncertainty about relative risks. We report on a simulation study designed to be similar to actual casecontrol studies. This shows that pvalues computed after variable selection can greatly overstate the strength of conclusions. For example, for our simulated casecontrol studies with 1,000 subjects, of variables declared to be "significant" with pvalues between.01 and.05, only 49 % actually were risk factors when stepwise variable selection was used. We propose Bayesian model averaging as a formal way of taking account of model uncertainty in casecontrol studies. This yields an easily interpreted summary, the posterior probability that a variable is a risk factor, and our simulation study indicates this to be reasonably well calibrated in the situations simulated. The methods are applied and compared
A Hierarchical Bayes Approach to Variable Selection for Generalized Linear Models
, 2004
"... For the problem of variable selection in generalized linear models, we develop various adaptive Bayesian criteria. Using a hierarchical mixture setup for model uncertainty, combined with an integrated Laplace approximation, we derive Empirical Bayes and Fully Bayes criteria that can be computed easi ..."
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Cited by 2 (0 self)
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For the problem of variable selection in generalized linear models, we develop various adaptive Bayesian criteria. Using a hierarchical mixture setup for model uncertainty, combined with an integrated Laplace approximation, we derive Empirical Bayes and Fully Bayes criteria that can be computed easily and quickly. The performance of these criteria is assessed via simulation and compared to other criteria such as AIC and BIC on normal, logistic and Poisson regression model classes. A Fully Bayes criterion based on a restricted region hyperprior seems to be the most promising.