Bayes and empirical-Bayes multiplicity adjustment in the variable-selection problem

This paper studies the multiplicity-correction effect of standard Bayesian variable-selection priors in linear regression. Our first goal is to clarify when, and how, multiplicity correction happens automatically in Bayesian analysis, and to distinguish this correction from the Bayesian Ockham's-razor effect. Our second goal is to contrast empirical-Bayes and fully Bayesian approaches to variable selection through examples, theoretical results and simulations. Considerable differences between the two approaches are found. In particular, we prove a theorem that characterizes a surprising aymptotic discrepancy between fully Bayes and empirical Bayes. This discrepancy arises from a different source than the failure to account for hyperparameter uncertainty in the empirical-Bayes estimate. Indeed, even at the extreme, when the empirical-Bayes estimate converges asymptotically to the true variable-inclusion probability, the potential for a serious difference remains.Comment: Published in at http://dx.doi.org/10.1214/10-AOS792 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Training samples in objective Bayesian model selection

Central to several objective approaches to Bayesian model selection is the use of training samples (subsets of the data), so as to allow utilization of improper objective priors. The most common prescription for choosing training samples is to choose them to be as small as possible, subject to yielding proper posteriors; these are called minimal training samples. When data can vary widely in terms of either information content or impact on the improper priors, use of minimal training samples can be inadequate. Important examples include certain cases of discrete data, the presence of censored observations, and certain situations involving linear models and explanatory variables. Such situations require more sophisticated methods of choosing training samples. A variety of such methods are developed in this paper, and successfully applied in challenging situations

Optimal predictive model selection

Often the goal of model selection is to choose a model for future prediction, and it is natural to measure the accuracy of a future prediction by squared error loss. Under the Bayesian approach, it is commonly perceived that the optimal predictive model is the model with highest posterior probability, but this is not necessarily the case. In this paper we show that, for selection among normal linear models, the optimal predictive model is often the median probability model, which is defined as the model consisting of those variables which have overall posterior probability greater than or equal to 1/2 of being in a model. The median probability model often differs from the highest probability model

Posterior propriety and admissibility of hyperpriors in normal hierarchical models

Hierarchical modeling is wonderful and here to stay, but hyperparameter priors are often chosen in a casual fashion. Unfortunately, as the number of hyperparameters grows, the effects of casual choices can multiply, leading to considerably inferior performance. As an extreme, but not uncommon, example use of the wrong hyperparameter priors can even lead to impropriety of the posterior. For exchangeable hierarchical multivariate normal models, we first determine when a standard class of hierarchical priors results in proper or improper posteriors. We next determine which elements of this class lead to admissible estimators of the mean under quadratic loss; such considerations provide one useful guideline for choice among hierarchical priors. Finally, computational issues with the resulting posterior distributions are addressed.Comment: Published at http://dx.doi.org/10.1214/009053605000000075 in the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Objective Bayes testing of Poisson versus inflated Poisson models

The Poisson distribution is often used as a standard model for count data. Quite often, however, such data sets are not well fit by a Poisson model because they have more zeros than are compatible with this model. For these situations, a zero-inflated Poisson (ZIP) distribution is often proposed. This article addresses testing a Poisson versus a ZIP model, using Bayesian methodology based on suitable objective priors. Specific choices of objective priors are justified and their properties investigated. The methodology is extended to include covariates in regression models. Several applications are given.Comment: Published in at http://dx.doi.org/10.1214/074921708000000093 the IMS Collections (http://www.imstat.org/publications/imscollections.htm) by the Institute of Mathematical Statistics (http://www.imstat.org