Bayesian Variable Selection and Post-selection Inference


Book Description

In this dissertation, we first develop a novel perspective to compare Bayesian variable selection procedures in terms of their selection criteria as well as their finite-sample properties. Secondly, we investigate Bayesian post-selection inference in two types of selection problems: linear regression and population selection. We will demonstrate that both inference problems are susceptible to selection effects since the selection procedure is data-dependent. Before comparing Bayesian variable selection procedures, we first classify the current Bayesian variable selection procedures into two classes: those with selection criteria defined on the space of candidate models, and those with selection criteria not explicitly formulated on the model space. For selection methods which do not operate on the model space, it is not obvious or well-established how to assess Bayesian selection consistency. By comparing their selection criteria, we establish connections between these classes of selection methods to facilitate discussion of Bayesian variable selection consistency for both classes. Moreover, The former group can be further divided into two sub-classes depending on their use of either the Bayes Factor (BF) or estimates of marginal inclusion probabilities. In the context of linear regression, we first consider the finite sample properties of Bayesian variable selection procedures, focusing on their associated selection uncertainties and their respective empirical frequencies of correct selection, across a broad range of data generating processes. Then we consider Bayesian inference after Bayesian variable selection. Since this type of study is completely new in the Bayesian literature, we must first address many conceptual difficulties in inference after Bayesian variable selection, and more generally Bayesian inference for different types of target parameters that are relevant to the setting of Bayesian variable selection. We give some analytic arguments and simulation-based evidence to illustrate some of the possible selection effects. For population selection problem, we propose a decision-theoretical way to investigate its post-selection inference. In particular, we focus on credible intervals. When the task is to select the best population and construct a credible interval simultaneously, a compound loss function is proposed. We then derive the corresponding Bayes rule, which has both intuitive and theoretical appeal.




Handbook of Bayesian Variable Selection


Book Description

Bayesian variable selection has experienced substantial developments over the past 30 years with the proliferation of large data sets. Identifying relevant variables to include in a model allows simpler interpretation, avoids overfitting and multicollinearity, and can provide insights into the mechanisms underlying an observed phenomenon. Variable selection is especially important when the number of potential predictors is substantially larger than the sample size and sparsity can reasonably be assumed. The Handbook of Bayesian Variable Selection provides a comprehensive review of theoretical, methodological and computational aspects of Bayesian methods for variable selection. The topics covered include spike-and-slab priors, continuous shrinkage priors, Bayes factors, Bayesian model averaging, partitioning methods, as well as variable selection in decision trees and edge selection in graphical models. The handbook targets graduate students and established researchers who seek to understand the latest developments in the field. It also provides a valuable reference for all interested in applying existing methods and/or pursuing methodological extensions. Features: Provides a comprehensive review of methods and applications of Bayesian variable selection. Divided into four parts: Spike-and-Slab Priors; Continuous Shrinkage Priors; Extensions to various Modeling; Other Approaches to Bayesian Variable Selection. Covers theoretical and methodological aspects, as well as worked out examples with R code provided in the online supplement. Includes contributions by experts in the field. Supported by a website with code, data, and other supplementary material










Bayesian Variable Selection Via a Benchmark


Book Description

With increasing appearances of high dimensional data over the past decades, variable selections through likelihood penalization remains a popular yet challenging research area in statistics. Ridge and Lasso, the two of the most popular penalized regression methods, served as the foundation of regularization technique and motivated several extensions to accommodate various circumstances, mostly through frequentist models. These two regularization problems can also be solved by their Bayesian counterparts, via putting proper priors on the regression parameters and then followed by Gibbs sampling. Compared to the frequentist version, the Bayesian framework enables easier interpretation and more straightforward inference on the parameters, based on the posterior distributional results. In general, however, the Bayesian approaches do not provide sparse estimates for the regression coefficients. In this thesis, an innovative Bayesian variable selection method via a benchmark variable in conjunction with a modified BIC is proposed under the framework of linear regression models as the first attempt, to promote both model sparsity and accuracy. The motivation of introducing such a benchmark is discussed, and the statistical properties regarding its role in the model are demonstrated. In short, it serves as a criterion to measure the importance of each variable based on the posterior inference of the corresponding coefficients, and only the most important variables providing the minimal modified BIC value are included. The Bayesian approach via a benchmark is extended to accommodate linear models with covariates exhibiting group structures. An iterative algorithm is implemented to identify both important groups and important variables within the selected groups. What's more, the method is further developed and modified to select variables for generalized linear models, by taking advantage of the normal approximation on the likelihood function. Simulation studies are carried out to assess and compare the performances among the proposed approaches and other state-of-art methods for each of the above three scenarios. The numerical results consistently illustrate our Bayesian variable selection approaches tend to select exactly the true variables or groups, while producing comparable prediction errors as other methods. Besides the numerical work, several real data sets are analyzed by these methods and the corresponding performances are further compared. The variable selection results by our approach are intuitively appealing or consistent with existing literatures in general.




Bayesian Variable Selection with Spike-and-slab Priors


Book Description

A major focus of intensive methodological research in recent times has been on knowledge extraction from high-dimensional datasets made available by advances in research technologies. Coupled with the growing popularity of Bayesian methods in statistical analysis, a range of new techniques have evolved that allow innovative model-building and inference in high-dimensional settings – an important one among these being Bayesian variable selection (BVS). The broad goal of this thesis is to explore different BVS methods and demonstrate their application in high-dimensional psychological data analysis. In particular, the focus will be on a class of sparsity-enforcing priors called 'spike-and-slab' priors which are mixture priors on regression coefficients with density functions that are peaked at zero (the 'spike') and also have large probability mass for a wide range of non-zero values (the 'slab'). It is demonstrated that BVS with spike-and-slab priors achieved a reasonable degree of dimensionality-reduction when applied to a psychiatric dataset in a logistic regression setup. BVS performance was also compared to that of LASSO (least absolute shrinkage and selection operator), a popular machine-learning technique, as reported in Ahn et al.(2016). The findings indicate that BVS with a spike-and-slab prior provides a competitive alternative to machine-learning methods, with the additional advantages of ease of interpretation and potential to handle more complex models. In conclusion, this thesis serves to add a new cutting-edge technique to the lab’s tool-shed and helps introduce Bayesian variable-selection to researchers in Cognitive Psychology where it still remains relatively unexplored as a dimensionality-reduction tool.




A Bayesian Variable Selection Method with Applications to Spatial Data


Book Description

This thesis first describes the general idea behind Bayes Inference, various sampling methods based on Bayes theorem and many examples. Then a Bayes approach to model selection, called Stochastic Search Variable Selection (SSVS) is discussed. It was originally proposed by George and McCulloch (1993). In a normal regression model where the number of covariates is large, only a small subset tend to be significant most of the times. This Bayes procedure specifies a mixture prior for each of the unknown regression coefficient, the mixture prior was originally proposed by Geweke (1996). This mixture prior will be updated as data becomes available to generate a posterior distribution that assigns higher posterior probabilities to coefficients that are significant in explaining the response. Spatial modeling method is described in this thesis. Prior distribution for all unknown parameters and latent variables are specified. Simulated studies under different models have been implemented to test the efficiency of SSVS. A real dataset taken by choosing a small region from the Cape Floristic Region in South Africa is used to analyze the plants distribution in that region. The original multi-cateogory response is transformed into a presence and absence (binary) response for simpler analysis. First, SSVS is used on this dataset to select the subset of significant covariates. Then a spatial model is fitted using the chosen covariates and, post-estimation, predictive map of posterior probabilities of presence and absence are obtained for the study region. Posterior estimates for the true regression coefficients are also provided along with map for spatial random effects.







Bayesian Variable Selection and Hypothesis Testing


Book Description

In modern statistical and machine learning applications, there is an increasing need for developing methodologies and algorithms to analyze massive data sets. Coupled with the growing popularity of Bayesian methods in statistical analysis, range of new techniques have evolved that allow innovative model-building and inference. In this dissertation, we develop Bayesian methods for variable selection and hypothesis testing. One important theme of this work is to develop computationally efficient algorithms that also enjoy strong probabilistic guarantees of convergence in a frequentist sense. Another equally important theme is to bridge the gap of classical statistical inference and Bayesian inference, in particular, through a new approach of hypothesis testing which can justify the Bayesian interpretation of classical testing framework. These methods are validated and demonstrated through simulated examples and real data applications




Bayesian Data Analysis, Third Edition


Book Description

Now in its third edition, this classic book is widely considered the leading text on Bayesian methods, lauded for its accessible, practical approach to analyzing data and solving research problems. Bayesian Data Analysis, Third Edition continues to take an applied approach to analysis using up-to-date Bayesian methods. The authors—all leaders in the statistics community—introduce basic concepts from a data-analytic perspective before presenting advanced methods. Throughout the text, numerous worked examples drawn from real applications and research emphasize the use of Bayesian inference in practice. New to the Third Edition Four new chapters on nonparametric modeling Coverage of weakly informative priors and boundary-avoiding priors Updated discussion of cross-validation and predictive information criteria Improved convergence monitoring and effective sample size calculations for iterative simulation Presentations of Hamiltonian Monte Carlo, variational Bayes, and expectation propagation New and revised software code The book can be used in three different ways. For undergraduate students, it introduces Bayesian inference starting from first principles. For graduate students, the text presents effective current approaches to Bayesian modeling and computation in statistics and related fields. For researchers, it provides an assortment of Bayesian methods in applied statistics. Additional materials, including data sets used in the examples, solutions to selected exercises, and software instructions, are available on the book’s web page.