Efficient Covariance Approximations for Large Sparse Precision Matrices

The use of sparse precision (inverse covariance) matrices has become popular because they allow for efficient algorithms for joint inference in high-dimensional models. Many applications require the computation of certain elements of the covariance matrix, such as the marginal variances, which may be nontrivial to obtain when the dimension is large. This article introduces a fast Rao–Blackwellized Monte Carlo sampling-based method for efficiently approximating selected elements of the covariance matrix. The variance and confidence bounds of the approximations can be precisely estimated without additional computational costs. Furthermore, a method that iterates over subdomains is introduced, and is shown to additionally reduce the approximation errors to practically negligible levels in an application on functional magnetic resonance imaging data. Both methods have low memory requirements, which is typically the bottleneck for competing direct methods.     

Smooth Scalar-on-Image Regression via Spatial Bayesian Variable Selection

We develop scalar-on-image regression models when images are registered multidimensional manifolds. We propose a fast and scalable Bayes’ inferential procedure to estimate the image coefficient. The central idea is the combination of an Ising prior distribution, which controls a latent binary indicator map, and an intrinsic Gaussian Markov random field, which controls the smoothness of the nonzero coefficients. The model is fit using a single-site Gibbs sampler, which allows fitting within minutes for hundreds of subjects with predictor images containing thousands of locations. The code is simple and is provided in the online Appendix (see the “Supplementary Materials” section). We apply this method to a neuroimaging study where cognitive outcomes are regressed on measures of white-matter microstructure at every voxel of the corpus callosum for hundreds of subjects.     

Nonparametric Bayesian Modeling for Multivariate Ordinal Data

This article proposes a probability model for k-dimensional ordinal outcomes, that is, it considers inference for data recorded in k-dimensional contingency tables with ordinal factors. The proposed approach is based on full posterior inference, assuming a flexible underlying prior probability model for the contingency table cell probabilities. We use a variation of the traditional multivariate probit model, with latent scores that determine the observed data. In our model, a mixture of normals prior replaces the usual single multivariate normal model for the latent variables. By augmenting the prior model to a mixture of normals we generalize inference in two important ways. First, we allow for varying local dependence structure across the contingency table. Second, inference in ordinal multivariate probit models is plagued by problems related to the choice and resampling of cutoffs defined for these latent variables. We show how the proposed mixture model approach entirely removes these problems. We illustrate the methodology with two examples, one simulated dataset and one dataset of interrater agreement.     

Zero Expectile Processes and Bayesian Spatial Regression

We introduce new classes of stationary spatial processes with asymmetric, sub-Gaussian marginal distributions using the idea of expectiles. We derive theoretical properties of the proposed processes. Moreover, we use the proposed spatial processes to formulate a spatial regression model for point-referenced data where the spatially correlated errors have skewed marginal distribution. We introduce a Bayesian computational procedure for model fitting and inference for this class of spatial regression models. We compare the performance of the proposed method with the traditional Gaussian process-based spatial regression through simulation studies and by applying it to a dataset on air pollution in California.     

Bayesian Nonparametric Modeling for Multivariate Ordinal Regression

Univariate or multivariate ordinal responses are often assumed to arise from a latent continuous parametric distribution, with covariate effects that enter linearly. We introduce a Bayesian nonparametric modeling approach for univariate and multivariate ordinal regression, which is based on mixture modeling for the joint distribution of latent responses and covariates. The modeling framework enables highly flexible inference for ordinal regression relationships, avoiding assumptions of linearity or additivity in the covariate effects. In standard parametric ordinal regression models, computational challenges arise from identifiability constraints and estimation of parameters requiring nonstandard inferential techniques. A key feature of the nonparametric model is that it achieves inferential flexibility, while avoiding these difficulties. In particular, we establish full support of the nonparametric mixture model under fixed cut-off points that relate through discretization the latent continuous responses with the ordinal responses. The practical utility of the modeling approach is illustrated through application to two datasets from econometrics, an example involving regression relationships for ozone concentration, and a multirater agreement problem. Supplementary materials with technical details on theoretical results and on computation are available online.     

Parameter Expanded Algorithms for Bayesian Latent Variable Modeling of Genetic Pleiotropy Data

Motivated by genetic association studies of pleiotropy, we propose a Bayesian latent variable approach to jointly study multiple outcomes. The models studied here can incorporate both continuous and binary responses, and can account for serial and cluster correlations. We consider Bayesian estimation for the model parameters, and we develop a novel MCMC algorithm that builds upon hierarchical centering and parameter expansion techniques to efficiently sample from the posterior distribution. We evaluate the proposed method via extensive simulations and demonstrate its utility with an application to an association study of various complication outcomes related to Type 1 diabetes. This article has supplementary material online.     

Modeling Variability Order: A Semiparametric Bayesian Approach

In comparing two populations, sometimes a model incorporating a certain probability order is desired. In this setting, Bayesian modeling is attractive since a probability order restriction imposed a priori on the population distributions is retained a posteriori. Extending the work in Gelfand and Kottas (2001) for stochastic order specifications, we formulate modeling for distributions ordered in variability. We work with Dirichlet process mixtures resulting in a fully Bayesian semiparametric approach. The details for simulation-based model fitting and prior specification are provided. An example, based on two small subsets of time intervals between eruptions of the Old Faithful geyser, illustrates the methodology.     

Hierarchical Low Rank Approximation of Likelihoods for Large Spatial Datasets

Datasets in the fields of climate and environment are often very large and irregularly spaced. To model such datasets, the widely used Gaussian process models in spatial statistics face tremendous challenges due to the prohibitive computational burden. Various approximation methods have been introduced to reduce the computational cost. However, most of them rely on unrealistic assumptions for the underlying process and retaining statistical efficiency remains an issue. We develop a new approximation scheme for maximum likelihood estimation. We show how the composite likelihood method can be adapted to provide different types of hierarchical low rank approximations that are both computationally and statistically efficient. The improvement of the proposed method is explored theoretically; the performance is investigated by numerical and simulation studies; and the practicality is illustrated through applying our methods to two million measurements of soil moisture in the area of the Mississippi River basin, which facilitates a better understanding of the climate variability. Supplementary material for this article is available online.     

Bayesian Inference on a Mixture Model With Spatial Dependence

We introduce a new technique to select the number of components of a mixture model with spatial dependence. The method consists of an estimation of the integrated completed likelihood based on a Laplace’s approximation and a new technique to deal with the normalizing constant intractability of the hidden Potts model. Our proposal is applied to a real satellite image. Supplementary materials are available online.     

Efficient Spatial Modeling Using the SPDE Approach With Bivariate Splines

Gaussian fields (GFs) are frequently used in spatial statistics for their versatility. The associated computational cost can be a bottleneck, especially in realistic applications. It has been shown that computational efficiency can be gained by doing the computations using Gaussian Markov random fields (GMRFs) as the GFs can be seen as weak solutions to corresponding stochastic partial differential equations (SPDEs) using piecewise linear finite elements. We introduce a new class of representations of GFs with bivariate splines instead of finite elements. This allows an easier implementation of piecewise polynomial representations of various degrees. It leads to GMRFs that can be inferred efficiently and can be easily extended to nonstationary fields. The solutions approximated with higher order bivariate splines converge faster, hence the computational cost can be alleviated. Numerical simulations using both real and simulated data also demonstrate that our framework increases the flexibility and efficiency. Supplementary materials are available online.     

Spatially Adaptive Bayesian Penalized Regression Splines (P-splines)

In this article we study penalized regression splines (P-splines), which are low-order basis splines with a penalty to avoid undersmoothing. Such P-splines are typically not spatially adaptive, and hence can have trouble when functions are varying rapidly. Our approach is to model the penalty parameter inherent in the P-spline method as a heteroscedastic regression function. We develop a full Bayesian hierarchical structure to do this and use Markov chain Monte Carlo techniques for drawing random samples from the posterior for inference. The advantage of using a Bayesian approach to P-splines is that it allows for simultaneous estimation of the smooth functions and the underlying penalty curve in addition to providing uncertainty intervals of the estimated curve. The Bayesian credible intervals obtained for the estimated curve are shown to have pointwise coverage probabilities close to nominal. The method is extended to additive models with simultaneous spline-based penalty functions for the unknown functions. In simulations, the approach achieves very competitive performance with the current best frequentist P-spline method in terms of frequentist mean squared error and coverage probabilities of the credible intervals, and performs better than some of the other Bayesian methods.     

Continuous Contour Monte Carlo for Marginal Density Estimation With an Application to a Spatial Statistical Model

The problem of marginal density estimation for a multivariate density function f(x) can be generally stated as a problem of density function estimation for a random vector λ(x) of dimension lower than that of x. In this article, we propose a technique, the so-called continuous Contour Monte Carlo (CCMC) algorithm, for solving this problem. CCMC can be viewed as a continuous version of the contour Monte Carlo (CMC) algorithm recently proposed in the literature. CCMC abandons the use of sample space partitioning and incorporates the techniques of kernel density estimation into its simulations. CCMC is more general than other marginal density estimation algorithms. First, it works for any density functions, even for those having a rugged or unbalanced energy landscape. Second, it works for any transformation λ(x) regardless of the availability of the analytical form of the inverse transformation. In this article, CCMC is applied to estimate the unknown normalizing constant function for a spatial autologistic model, and the estimate is then used in a Bayesian analysis for the spatial autologistic model in place of the true normalizing constant function. Numerical results on the U.S. cancer mortality data indicate that the Bayesian method can produce much more accurate estimates than the MPLE and MCMLE methods for the parameters of the spatial autologistic model.     

Bayesian Variable Selection for Logistic Models Using Auxiliary Mixture Sampling

This article presents a Markov chain Monte Carlo algorithm for both variable and covariance selection in the context of logistic mixed effects models. This algorithm allows us to sample solely from standard densities with no additional tuning. We apply a stochastic search variable approach to select explanatory variables as well as to determine the structure of the random effects covariance matrix.

Prior determination of explanatory variables and random effects is not a prerequisite because the definite structure is chosen in a data-driven manner in the course of the modeling procedure. To illustrate the method, we give two bank data examples.     

Spatial Regression Models for Extremes

Meteorological data are often recorded at a number of spatial locations. This gives rise to the possibility of pooling data through a spatial model to overcome some of the limitations imposed on an extreme value analysis by a lack of information. In this paper we develop a spatial model for extremes based on a standard representation for site-wise extremal behavior, combined with a spatial latent process for parameter variation over the region. A smooth, but possibly non-linear, spatial structure is an intrinsic feature of the model, and difficulties in computation are solved using Markov chain Monte Carlo inference. A simulation study is carried out to illustrate the potential gain in efficiency achieved by the spatial model. Finally, the model is applied to data generated from a climatological model in order to characterize the hurricane climate of the Gulf and Atlantic coasts of the United States.     

Bayesian Prediction via Partitioning

This article proposes a new Bayesian approach to prediction on continuous covariates. The Bayesian partition model constructs arbitrarily complex regression and classification surfaces by splitting the covariate space into an unknown number of disjoint regions. Within each region the data are assumed to be exchangeable and come from some simple distribution. Using conjugate priors, the marginal likelihoods of the models can be obtained analytically for any proposed partitioning of the space where the number and location of the regions is assumed unknown a priori. Markov chain Monte Carlo simulation techniques are used to obtain predictive distributions at the design points by averaging across posterior samples of partitions.     

Bayesian Case Influence Measures for Statistical Models With Missing Data

We examine three Bayesian case influence measures including the φ-divergence, Cook’s posterior mode distance, and Cook’s posterior mean distance for identifying a set of influential observations for a variety of statistical models with missing data including models for longitudinal data and latent variable models in the absence/presence of missing data. Since it can be computationally prohibitive to compute these Bayesian case influence measures in models with missing data, we derive simple first-order approximations to the three Bayesian case influence measures by using the Laplace approximation formula and examine the applications of these approximations to the identification of influential sets. All of the computations for the first-order approximations can be easily done using Markov chain Monte Carlo samples from the posterior distribution based on the full data. Simulated data and an AIDS dataset are analyzed to illustrate the methodology. Supplemental materials for the article are available online.     

Bayesian Monte Carlo estimation for profile hidden Markov models

Hidden Markov models are used as tools for pattern recognition in a number of areas, ranging from speech processing to biological sequence analysis. Profile hidden Markov models represent a class of so-called “left–right” models that have an architecture that is specifically relevant to classification of proteins into structural families based on their amino acid sequences. Standard learning methods for such models employ a variety of heuristics applied to the expectation-maximization implementation of the maximum likelihood estimation procedure in order to find the global maximum of the likelihood function. Here, we compare maximum likelihood estimation to fully Bayesian estimation of parameters for profile hidden Markov models with a small number of parameters. We find that, relative to maximum likelihood methods, Bayesian methods assign higher scores to data sequences that are distantly related to the pattern consensus, show better performance in classifying these sequences correctly, and continue to perform robustly with regard to misspecification of the number of model parameters. Though our study is limited in scope, we expect our results to remain relevant for models with a large number of parameters and other types of left–right hidden Markov models.     

Reparameterized and Marginalized Posterior and Predictive Sampling for Complex Bayesian Geostatistical Models

This article proposes a four-pronged approach to efficient Bayesian estimation and prediction for complex Bayesian hierarchical Gaussian models for spatial and spatiotemporal data. The method involves reparameterizing the covariance structure of the model, reformulating the means structure, marginalizing the joint posterior distribution, and applying a simplex-based slice sampling algorithm. The approach permits fusion of point-source data and areal data measured at different resolutions and accommodates nonspatial correlation and variance heterogeneity as well as spatial and/or temporal correlation. The method produces Markov chain Monte Carlo samplers with low autocorrelation in the output, so that fewer iterations are needed for Bayesian inference than would be the case with other sampling algorithms. Supplemental materials are available online.     

Sampling Schemes for Bayesian Variable Selection in Generalized Linear Models

Bayesian approaches to prediction and the assessment of predictive uncertainty in generalized linear models are often based on averaging predictions over different models, and this requires methods for accounting for model uncertainty. When there are linear dependencies among potential predictor variables in a generalized linear model, existing Markov chain Monte Carlo algorithms for sampling from the posterior distribution on the model and parameter space in Bayesian variable selection problems may not work well. This article describes a sampling algorithm based on the Swendsen-Wang algorithm for the Ising model, and which works well when the predictors are far from orthogonality. In problems of variable selection for generalized linear models we can index different models by a binary parameter vector, where each binary variable indicates whether or not a given predictor variable is included in the model. The posterior distribution on the model is a distribution on this collection of binary strings, and by thinking of this posterior distribution as a binary spatial field we apply a sampling scheme inspired by the Swendsen-Wang algorithm for the Ising model in order to sample from the model posterior distribution. The algorithm we describe extends a similar algorithm for variable selection problems in linear models. The benefits of the algorithm are demonstrated for both real and simulated data.     

A Pivotal Allocation-Based Algorithm for Solving the Label-Switching Problem in Bayesian Mixture Models

In Bayesian analysis of mixture models, the label-switching problem occurs as a result of the posterior distribution being invariant to any permutation of cluster indices under symmetric priors. To solve this problem, we propose a novel relabeling algorithm and its variants by investigating an approximate posterior distribution of the latent allocation variables instead of dealing with the component parameters directly. We demonstrate that our relabeling algorithm can be formulated in a rigorous framework based on information theory. Under some circumstances, it is shown to resemble the classical Kullback-Leibler relabeling algorithm and include the recently proposed equivalence classes representatives relabeling algorithm as a special case. Using simulation studies and real data examples, we illustrate the efficiency of our algorithm in dealing with various label-switching phenomena. Supplemental materials for this article are available online.