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The practical implementation of Bayesian model selection
 Institute of Mathematical Statistics
, 2001
"... In principle, the Bayesian approach to model selection is straightforward. Prior probability distributions are used to describe the uncertainty surrounding all unknowns. After observing the data, the posterior distribution provides a coherent post data summary of the remaining uncertainty which is r ..."
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Cited by 85 (3 self)
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In principle, the Bayesian approach to model selection is straightforward. Prior probability distributions are used to describe the uncertainty surrounding all unknowns. After observing the data, the posterior distribution provides a coherent post data summary of the remaining uncertainty which is relevant for model selection. However, the practical implementation of this approach often requires carefully tailored priors and novel posterior calculation methods. In this article, we illustrate some of the fundamental practical issues that arise for two different model selection problems: the variable selection problem for the linear model and the CART model selection problem.
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 33 (8 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.
2003), “Policy Evaluation in Uncertain Economic Environments (with discussion
 Brookings Papers on Economic Activity
"... It will be remembered that the seventy translators of the Septuagint were shut up in seventy separate rooms with the Hebrew text and brought out with them, when they emerged, seventy identical translations. Would the same miracle be vouchsafed if seventy multiple correlators were shut up with the sa ..."
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Cited by 31 (5 self)
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It will be remembered that the seventy translators of the Septuagint were shut up in seventy separate rooms with the Hebrew text and brought out with them, when they emerged, seventy identical translations. Would the same miracle be vouchsafed if seventy multiple correlators were shut up with the same statistical material? And anyhow, I suppose, if each had a different economist perched on his a priori, that would make a difference to the outcome. 1 This paper describes some approaches to macroeconomic policy evaluation in the presence of uncertainty about the structure of the economic environment under study. The perspective we discuss is designed to facilitate policy evaluation for several forms of uncertainty. For example, our approach may be used when an analyst is unsure about the appropriate economic theory that should be assumed to apply, or about the particular functional forms that translate a general theory into a form amenable to statistical analysis. As such, the methods we describe are, we believe, particularly useful in a range of macroeconomic contexts where fundamental disagreements exist as to the determinants of the problem under study. In addition, this approach recognizes that even if economists agree on the
Bayesian wavelet regression on curves with application to a spectroscopic calibration problem
 Journal of the American Statistical Association
, 2001
"... Motivated by calibration problems in nearinfrared (N IR) spectroscopy, we consider the linear regression setting in which the many predictor variables arise from sampling an essentially continuous curve at equally spaced points and there may be multiple predictands. We tackle this regression proble ..."
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Cited by 28 (4 self)
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Motivated by calibration problems in nearinfrared (N IR) spectroscopy, we consider the linear regression setting in which the many predictor variables arise from sampling an essentially continuous curve at equally spaced points and there may be multiple predictands. We tackle this regression problem by calculating the wavelet transforms of the discretized curves, then applying a Bayesian variable selection method using mixture priors to the multivariate regression of predictands on wavelet coef � cients. For prediction purposes, we average over a set of likely models. Applied to a particular problem in N IR spectroscopy, this approach was able to � nd subsets of the wavelet coef � cients with overall better predictive performance than the more usual approaches. In the application, the available predictors are measurements of the N IR re � ectance spectrum of biscuit dough pieces at 256 equally spaced wavelengths. The aim is to predict the composition (i.e., the fat, � our, sugar, and water content) of the dough pieces using the spectral variables. Thus we have a multivariate regression of four predictands on 256 predictors with quite high intercorrelation among the predictors. A training set of 39 samples is available to � t this regression. Applying a wavelet transform replaces the 256 measurements on each spectrum with 256 wavelet coef � cients that carry the same information. The variable selection method could use subsets of these coef � cients that gave good predictions for all four compositional variables on a separate test set of samples. Selecting in the wavelet domain rather than from the original spectral variables is appealing in this application, because a single wavelet coef � cient can carry information from a band of wavelengths in the original spectrum. This band can be narrow or wide, depending on the scale of the wavelet selected.
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 26 (10 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.
Variable selection in clustering via Dirichlet process mixture models
, 2006
"... The increased collection of highdimensional data in various fields has raised a strong interest in clustering algorithms and variable selection procedures. In this paper, we propose a modelbased method that addresses the two problems simultaneously. We introduce a latent binary vector to identify ..."
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Cited by 25 (3 self)
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The increased collection of highdimensional data in various fields has raised a strong interest in clustering algorithms and variable selection procedures. In this paper, we propose a modelbased method that addresses the two problems simultaneously. We introduce a latent binary vector to identify discriminating variables and use Dirichlet process mixture models to define the cluster structure. We update the variable selection index using a Metropolis algorithm and obtain inference on the cluster structure via a splitmerge Markov chain Monte Carlo technique. We explore the performance of the methodology on simulated data and illustrate an application with a dna microarray study.
Evolutionary Monte Carlo: Applications to C_p Model Sampling and Change Point Problem
 STATISTICA SINICA
, 2000
"... Motivated by the success of genetic algorithms and simulated annealing in hard optimization problems, the authors propose a new Markov chain Monte Carlo (MCMC) algorithm so called an evolutionary Monte Carlo algorithm. This algorithm has incorporated several attractive features of genetic algorithms ..."
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Cited by 25 (5 self)
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Motivated by the success of genetic algorithms and simulated annealing in hard optimization problems, the authors propose a new Markov chain Monte Carlo (MCMC) algorithm so called an evolutionary Monte Carlo algorithm. This algorithm has incorporated several attractive features of genetic algorithms and simulated annealing into the framework of MCMC. It works by simulating a population of Markov chains in parallel, where each chain is attached to a different temperature. The population is updated by mutation (Metropolis update), crossover (partial state swapping) and exchange operators (full state swapping). The algorithm is illustrated through examples of the Cpbased model selection and changepoint identification. The numerical results and the extensive comparisons show that evolutionary Monte Carlo is a promising approach for simulation and optimization.
The choice of variables in multivariate regression: a nonconjugate Bayesian decision theory approach
, 1999
"... INTRODUCTION Choice of regressor variables in linear regression has attracted considerable attention in the literature, from forward, backward and stepwise regression, model choice criteria such as Akaike's information criterion, to Bayesian techniques. We will focus on the Bayesian University o ..."
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Cited by 17 (2 self)
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INTRODUCTION Choice of regressor variables in linear regression has attracted considerable attention in the literature, from forward, backward and stepwise regression, model choice criteria such as Akaike's information criterion, to Bayesian techniques. We will focus on the Bayesian University of Kent at Canterbury, Institute of Mathematics and Statistics, Cornwallis Building, Canterbury, CT2 7NF, UK. FAX 01227827932, email Philip.J.Brown@ukc.ac.uk y University College London, UK z Texas A & M University, USA 1 decision theory framework, first given by Lindley (1968) for univariate multiple regression, where costs attach to the inclusion of regressor variables. Here it is required to predict a future vector observation Y f comprising r components. Predictions are judged by quadratic loss to which is added a cost penalty on the regressor variables, x f
Bayesian Variable Selection Using the Gibbs Sampler
, 2000
"... Specification of the linear predictor for a generalised linear model requires determining which variables to include. We consider Bayesian strategies for performing this variable selection. In particular we focus on approaches based on the Gibbs sampler. Such approaches may be implemented using the ..."
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Cited by 11 (2 self)
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Specification of the linear predictor for a generalised linear model requires determining which variables to include. We consider Bayesian strategies for performing this variable selection. In particular we focus on approaches based on the Gibbs sampler. Such approaches may be implemented using the publically available software BUGS. We illustrate the methods using a simple example. BUGS code is provided in an appendix. 1 Introduction In a Bayesian analysis of a generalised linear model, model uncertainty may be incorporated coherently by specifying prior probabilities for plausible models and calculating posterior probabilities using f(mjy) = f(m)f(yjm) P m2M f(m)f(y jm) ; m 2 M (1.1) where m denotes the model, M is the set of all models under consideration, f (m) is the prior probability of model m and f (yjm; fi m ) the likelihood of the data y under model m. The observed data y contribute to the posterior model probabilities through f(yjm), the marginal likelihood calculated...