Gibbs Variable Selection using BUGS

In this paper we discuss and present in detail the implementation of Gibbs variable selection as defined by Dellaportas et al. (2000, 2002) using the BUGS software (Spiegelhalter et al. ,'96a,b,c). The specification of the likelihood, prior and pseudo-prior distributions of the parameters as well as the prior term and model probabilities are described in detail. Guidance is also provided for the calculation of the posterior probabilities within BUGS environment when the number of models is limited. We illustrate the application of this methodology in a variety of problems including linear regression, log-linear and binomial response models.

Thermodynamic assessment of probability distribution divergencies and Bayesian model comparison

Within path sampling framework, we show that probability distribution divergences, such as the Chernoff information, can be estimated via thermodynamic integration. The Boltzmann-Gibbs distribution pertaining to different Hamiltonians is implemented to derive tempered transitions along the path, linking the distributions of interest at the endpoints. Under this perspective, a geometric approach is feasible, which prompts intuition and facilitates tuning the error sources. Additionally, there are direct applications in Bayesian model evaluation. Existing marginal likelihood and Bayes factor estimators are reviewed here along with their stepping-stone sampling analogues. New estimators are presented and the use of compound paths is introduced

Bivariate Poisson and Diagonal Inflated Bivariate Poisson Regression Models in R

In this paper we present an R package called bivpois for maximum likelihood estimation of the parameters of bivariate and diagonal inflated bivariate Poisson regression models. An Expectation-Maximization (EM) algorithm is implemented. Inflated models allow for modelling both over-dispersion (or under-dispersion) and negative correlation and thus they are appropriate for a wide range of applications. Extensions of the algorithms for several other models are also discussed. Detailed guidance and implementation on simulated and real data sets using bivpois package is provided.

Power-Expected-Posterior Priors for Variable Selection in Gaussian Linear Models

In the context of the expected-posterior prior (EPP) approach to Bayesian variable selection in linear models, we combine ideas from power-prior and unit-information-prior methodologies to simultaneously produce a minimally-informative prior and diminish the effect of training samples. The result is that in practice our power-expected-posterior (PEP) methodology is sufficiently insensitive to the size n* of the training sample, due to PEP's unit-information construction, that one may take n* equal to the full-data sample size n and dispense with training samples altogether. In this paper we focus on Gaussian linear models and develop our method under two different baseline prior choices: the independence Jeffreys (or reference) prior, yielding the J-PEP posterior, and the Zellner g-prior, leading to Z-PEP. We find that, under the reference baseline prior, the asymptotics of PEP Bayes factors are equivalent to those of Schwartz's BIC criterion, ensuring consistency of the PEP approach to model selection. We compare the performance of our method, in simulation studies and a real example involving prediction of air-pollutant concentrations from meteorological covariates, with that of a variety of previously-defined variants on Bayes factors for objective variable selection. Our prior, due to its unit-information structure, leads to a variable-selection procedure that (1) is systematically more parsimonious than the basic EPP with minimal training sample, while sacrificing no desirable performance characteristics to achieve this parsimony; (2) is robust to the size of the training sample, thus enjoying the advantages described above arising from the avoidance of training samples altogether; and (3) identifies maximum-a-posteriori models that achieve good out-of-sample predictive performance

Prior distributions for objective Bayesian analysis

We provide a review of prior distributions for objective Bayesian analysis. We start by examining some foundational issues and then organize our exposition into priors for: i) estimation or prediction; ii) model selection; iii) highdimensional models. With regard to i), we present some basic notions, and then move to more recent contributions on discrete parameter space, hierarchical models, nonparametric models, and penalizing complexity priors. Point ii) is the focus of this paper: it discusses principles for objective Bayesian model comparison, and singles out some major concepts for building priors, which are subsequently illustrated in some detail for the classic problem of variable selection in normal linear models. We also present some recent contributions in the area of objective priors on model space.With regard to point iii) we only provide a short summary of some default priors for high-dimensional models, a rapidly growing area of research

Bayesian Analysis of Marginal Log-Linear Graphical Models for Three Way Contingency Tables

This paper deals with the Bayesian analysis of graphical models of marginal independence for three way contingency tables. We use a marginal log-linear parametrization, under which the model is defined through suitable zero-constraints on the interaction parameters calculated within marginal distributions. We undertake a comprehensive Bayesian analysis of these models, involving suitable choices of prior distributions, estimation, model determination, as well as the allied computational issues. The methodology is illustrated with reference to two real data sets.Comment: 34 pages, 7 tables, 3 figure