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Spike and slab variable selection: frequentist and bayesian strategies
 The Annals of Statistics
"... Variable selection in the linear regression model takes many apparent faces from both frequentist and Bayesian standpoints. In this paper we introduce a variable selection method referred to as a rescaled spike and slab model. We study the importance of prior hierarchical specifications and draw con ..."
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Cited by 92 (7 self)
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Variable selection in the linear regression model takes many apparent faces from both frequentist and Bayesian standpoints. In this paper we introduce a variable selection method referred to as a rescaled spike and slab model. We study the importance of prior hierarchical specifications and draw connections to frequentist generalized ridge regression estimation. Specifically, we study the usefulness of continuous bimodal priors to model hypervariance parameters, and the effect scaling has on the posterior mean through its relationship to penalization. Several model selection strategies, some frequentist and some Bayesian in nature, are developed and studied theoretically. We demonstrate the importance of selective shrinkage for effective variable selection in terms of risk misclassification, and show this is achieved using the posterior from a rescaled spike and slab model. We also show how to verify a procedure’s ability to reduce model uncertainty in finite samples using a specialized forward selection strategy. Using this tool, we illustrate the effectiveness of rescaled spike and slab models in reducing model uncertainty. 1. Introduction. We
Mixtures of gpriors for Bayesian variable selection
 Journal of the American Statistical Association
, 2008
"... Zellner’s gprior remains a popular conventional prior for use in Bayesian variable selection, despite several undesirable consistency issues. In this paper, we study mixtures of gpriors as an alternative to default gpriors that resolve many of the problems with the original formulation, while mai ..."
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Cited by 87 (7 self)
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Zellner’s gprior remains a popular conventional prior for use in Bayesian variable selection, despite several undesirable consistency issues. In this paper, we study mixtures of gpriors as an alternative to default gpriors that resolve many of the problems with the original formulation, while maintaining the computational tractability that has made the gprior so popular. We present theoretical properties of the mixture gpriors and provide real and simulated examples to compare the mixture formulation with fixed gpriors, Empirical Bayes approaches and other default procedures.
An exploration of aspects of Bayesian multiple testing
 Journal of Statistical Planning and Inference
, 2005
"... There has been increased interest of late in the Bayesian approach to multiple testing (often called the multiple comparisons problem), motivated by the need to analyze DNA microarray data in which it is desired to learn which of potentially several thousand genes are activated by a particular stimu ..."
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Cited by 76 (12 self)
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There has been increased interest of late in the Bayesian approach to multiple testing (often called the multiple comparisons problem), motivated by the need to analyze DNA microarray data in which it is desired to learn which of potentially several thousand genes are activated by a particular stimulus. We study the issue of prior specification for such multiple tests; computation of key posterior quantities; and useful ways to display these quantities. A decisiontheoretic approach is also considered.
Bayes and empiricalBayes multiplicity adjustment in the variableselection problem. The Annals of Statistics 38
, 2010
"... ar ..."
Bayes model averaging with selection of regressors
 Journal of the Royal Statistical Society. Series B, Statistical Methodology
, 2002
"... Summary. When a number of distinct models contend for use in prediction, the choice of a single model can offer rather unstable predictions. In regression, stochastic search variable selection with Bayesian model averaging offers a cure for this robustness issue but at the expense of requiring very ..."
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Cited by 58 (10 self)
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Summary. When a number of distinct models contend for use in prediction, the choice of a single model can offer rather unstable predictions. In regression, stochastic search variable selection with Bayesian model averaging offers a cure for this robustness issue but at the expense of requiring very many predictors. Here we look at Bayes model averaging incorporating variable selection for prediction. This offers similar meansquare errors of prediction but with a vastly reduced predictor space. This can greatly aid the interpretation of the model. It also reduces the cost if measured variables have costs. The development here uses decision theory in the context of the multivariate general linear model. In passing, this reduced predictor space Bayes model averaging is contrasted with singlemodel approximations. A fast algorithm for updating regressions in the Markov chain Monte Carlo searches for posterior inference is developed, allowing many more variables than observations to be contemplated. We discuss the merits of absolute rather than proportionate shrinkage in regression, especially when there are more variables than observations. The methodology is illustrated on a set of spectroscopic data used for measuring the amounts of different sugars in an aqueous solution.
Bayesian variable selection in multinomial models with application to spectral data and DNA microarrays
, 2002
"... Summary. Here we focus on discrimination problems where the number of predictors substantially exceeds the sample size and we propose a Bayesian variable selection approach to multinomial probit models. Our method makes use of mixture priors and Markov chain Monte Carlo techniques to select sets of ..."
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Cited by 51 (15 self)
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Summary. Here we focus on discrimination problems where the number of predictors substantially exceeds the sample size and we propose a Bayesian variable selection approach to multinomial probit models. Our method makes use of mixture priors and Markov chain Monte Carlo techniques to select sets of variables that differ among the classes. We apply our methodology to a problem in functional genomics using gene expression profiling data. The aim of the analysis is to identify molecular signatures that characterize two different stages of rheumatoid arthritis.
Transdimensional Markov Chains: A Decade of Progress and Future Perspectives
, 2005
"... The last 10 years have witnessed the development of sampling frameworks that permit the construction of Markov chains that simultaneously traverse both parameter and model space. Substantial methodological progress has been made during this period. In this article we present a survey of the current ..."
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Cited by 34 (3 self)
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The last 10 years have witnessed the development of sampling frameworks that permit the construction of Markov chains that simultaneously traverse both parameter and model space. Substantial methodological progress has been made during this period. In this article we present a survey of the current state of the art and evaluate some of the most recent advances in this field. We also discuss future research perspectives in the context of the drive to develop sampling mechanisms with high degrees of both efficiency and automation.
Default Priors and Predictive Performance in Bayesian Model Averaging, with Application to Growth Determinants
 Journal of Applied Econometrics
, 2011
"... Abstract Bayesian model averaging (BMA) has become widely accepted as a way of accounting for model uncertainty, notably in regression models for identifying the determinants of economic growth. To implement BMA the user must specify a prior distribution in two parts: a prior for the regression par ..."
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Cited by 30 (7 self)
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Abstract Bayesian model averaging (BMA) has become widely accepted as a way of accounting for model uncertainty, notably in regression models for identifying the determinants of economic growth. To implement BMA the user must specify a prior distribution in two parts: a prior for the regression parameters and a prior over the model space. Here we address the issue of which default prior to use for BMA in linear regression. We compare 12 candidate parameter priors: the Unit Information Prior (UIP) corresponding to the BIC or Schwarz approximation to the integrated likelihood, a proper datadependent prior, and 10 priors considered by Fernandez et al. (2001b). We also compare the uniform model prior to others that favor smaller models. We compare them on the basis of crossvalidated predictive performance on a wellknown growth dataset and on two simulated examples from the literature. We found that the UIP with uniform model prior generally outperformed the other priors considered. It also identified the largest set of growth determinants. JEL Classification: O51, O52, O53.