Bayesian integrative analysis for multi-fidelity computer experiments

This paper proposes a Bayesian integrative analysis method for linking multi-fidelity computer experiments. Instead of assuming covariance structures of multivariate Gaussian process models, we handle the outputs from different levels of accuracy as independent processes and link them via a penalization method that controls the distance between their overall trends. Based on the priors induced by the penalty, we build Bayesian prediction models for the output at the highest accuracy. Simulated and real examples show that the proposed method is better than existing methods in terms of prediction accuracy for many cases.     

Bayesian analysis of joint mean and covariance models for longitudinal data

Efficient estimation of the regression coefficients in longitudinal data analysis requires a correct specification of the covariance structure. If misspecification occurs, it may lead to inefficient or biased estimators of parameters in the mean. One of the most commonly used methods for handling the covariance matrix is based on simultaneous modeling of the Cholesky decomposition. Therefore, in this paper, we reparameterize covariance structures in longitudinal data analysis through the modified Cholesky decomposition of itself. Based on this modified Cholesky decomposition, the within-subject covariance matrix is decomposed into a unit lower triangular matrix involving moving average coefficients and a diagonal matrix involving innovation variances, which are modeled as linear functions of covariates. Then, we propose a fully Bayesian inference for joint mean and covariance models based on this decomposition. A computational efficient Markov chain Monte Carlo method which combines the Gibbs sampler and Metropolis–Hastings algorithm is implemented to simultaneously obtain the Bayesian estimates of unknown parameters, as well as their standard deviation estimates. Finally, several simulation studies and a real example are presented to illustrate the proposed methodology.     

Parsimonious Estimation of the Covariance Matrix in Multinomial Probit Models

This article presents a Bayesian analysis of a multinomial probit model by building on previous work that specified priors on identified parameters. The main contribution of our article is to propose a prior on the covariance matrix of the latent utilities that permits elements of the inverse of the covariance matrix to be identically zero. This allows a parsimonious representation of the covariance matrix when such parsimony exists. The methodology is applied to both simulated and real data, and its ability to obtain more efficient estimators of the covariance matrix and regression coefficients is assessed using simulated data.     

A Monte Carlo approach to quantifying discrepancies between intractable posterior distributions

The computational demand required to perform inference using Markov chain Monte Carlo methods often obstructs a Bayesian analysis. This may be a result of large datasets, complex dependence structures, or expensive computer models. In these instances, the posterior distribution is replaced by a computationally tractable approximation, and inference is based on this working model. However, the error that is introduced by this practice is not well studied. In this paper, we propose a methodology that allows one to examine the impact on statistical inference by quantifying the discrepancy between the intractable and working posterior distributions. This work provides a structure to analyse model approximations with regard to the reliability of inference and computational efficiency. We illustrate our approach through a spatial analysis of yearly total precipitation anomalies where covariance tapering approximations are used to alleviate the computational demand associated with inverting a large, dense covariance matrix.     

A permutation-based Bayesian approach for inverse covariance estimation

Abstract

Covariance estimation and selection for multivariate datasets in a high-dimensional regime is a fundamental problem in modern statistics. Gaussian graphical models are a popular class of models used for this purpose. Current Bayesian methods for inverse covariance matrix estimation under Gaussian graphical models require the underlying graph and hence the ordering of variables to be known. However, in practice, such information on the true underlying model is often unavailable. We therefore propose a novel permutation-based Bayesian approach to tackle the unknown variable ordering issue. In particular, we utilize multiple maximum a posteriori estimates under the DAG-Wishart prior for each permutation, and subsequently construct the final estimate of the inverse covariance matrix. The proposed estimator has smaller variability and yields order-invariant property. We establish posterior convergence rates under mild assumptions and illustrate that our method outperforms existing approaches in estimating the inverse covariance matrices via simulation studies.     

a bayesian analysis of the multivariate mixed-linear model

The Bayesian analysis of the multivariate mixed linear model is considered. The exact posterior distribution for the fixed effects matrix and the error covariance matrix are obtained. The exact posterior means and variances of the Bayesian estimators for the covariance matrices of random effects are also derived. These posterior moments are computed without constrained optimization and numerical integration. The calculations are feasible for arbitrary models. Reasonable approximations for the posterior distributions for the covariance matrices associated with the random effects are obtained also. Results are illustrated with a numerical example.     

Approximate reference priors for Gaussian random fields

Reference priors are theoretically attractive for the analysis of geostatistical data since they enable automatic Bayesian analysis and have desirable Bayesian and frequentist properties. But their use is hindered by computational hurdles that make their application in practice challenging. In this work, we derive a new class of default priors that approximate reference priors for the parameters of some Gaussian random fields. It is based on an approximation to the integrated likelihood of the covariance parameters derived from the spectral approximation of stationary random fields. This prior depends on the structure of the mean function and the spectral density of the model evaluated at a set of spectral points associated with an auxiliary regular grid. In addition to preserving the desirable Bayesian and frequentist properties, these approximate reference priors are more stable, and their computations are much less onerous than those of exact reference priors. Unlike exact reference priors, the marginal approximate reference prior of correlation parameter is always proper, regardless of the mean function or the smoothness of the correlation function. This property has important consequences for covariance model selection. An illustration comparing default Bayesian analyses is provided with a dataset of lead pollution in Galicia, Spain.     

Multivariate Poisson regression with covariance structure

In recent years the applications of multivariate Poisson models have increased, mainly because of the gradual increase in computer performance. The multivariate Poisson model used in practice is based on a common covariance term for all the pairs of variables. This is rather restrictive and does not allow for modelling the covariance structure of the data in a flexible way. In this paper we propose inference for a multivariate Poisson model with larger structure, i.e. different covariance for each pair of variables. Maximum likelihood estimation, as well as Bayesian estimation methods are proposed. Both are based on a data augmentation scheme that reflects the multivariate reduction derivation of the joint probability function. In order to enlarge the applicability of the model we allow for covariates in the specification of both the mean and the covariance parameters. Extension to models with complete structure with many multi-way covariance terms is discussed. The method is demonstrated by analyzing a real life data set.     

Covariance Matrix Estimation via Network Structure

In this article, we employ a regression formulation to estimate the high-dimensional covariance matrix for a given network structure. Using prior information contained in the network relationships, we model the covariance as a polynomial function of the symmetric adjacency matrix. Accordingly, the problem of estimating a high-dimensional covariance matrix is converted to one of estimating low dimensional coefficients of the polynomial regression function, which we can accomplish using ordinary least squares or maximum likelihood. The resulting covariance matrix estimator based on the maximum likelihood approach is guaranteed to be positive definite even in finite samples. Under mild conditions, we obtain the theoretical properties of the resulting estimators. A Bayesian information criterion is also developed to select the order of the polynomial function. Simulation studies and empirical examples illustrate the usefulness of the proposed methods.     

Estimation of covariance matrices based on hierarchical inverse-Wishart priors

This paper focuses on Bayesian shrinkage methods for covariance matrix estimation. We examine posterior properties and frequentist risks of Bayesian estimators based on new hierarchical inverse-Wishart priors. More precisely, we give the conditions for the existence of the posterior distributions. Advantages in terms of numerical simulations of posteriors are shown. A simulation study illustrates the performance of the estimation procedures under three loss functions for relevant sample sizes and various covariance structures.     

Robust Bayesian methods in simple ANOVA models

A robust Bayesian analysis in a conjugate normal framework for the simple ANOVA model is suggested. By fixing the prior mean and varying the prior covariance matrix over a restricted class, we obtain the so-called HiFi and core region, a union and intersection of HPD regions. Based on these robust HPD regions we develop the concept of a ‘robust Bayesian judgement’ procedure. We apply this approach to the simple analysis of variance model with orthogonal designs. The example analyses the costs of an asthma medication obtained by a two-way cross-over study.     

Bayesian covariance estimation and inference in latent Gaussian process models

This paper describes inference methods for functional data under the assumption that the functional data of interest are smooth latent functions, characterized by a Gaussian process, which have been observed with noise over a finite set of time points. The methods we propose are completely specified in a Bayesian environment that allows for all inferences to be performed through a simple Gibbs sampler. Our main focus is in estimating and describing uncertainty in the covariance function. However, these models also encompass functional data estimation, functional regression where the predictors are latent functions, and an automatic approach to smoothing parameter selection. Furthermore, these models require minimal assumptions on the data structure as the time points for observations do not need to be equally spaced, the number and placement of observations are allowed to vary among functions, and special treatment is not required when the number of functional observations is less than the dimensionality of those observations. We illustrate the effectiveness of these models in estimating latent functional data, capturing variation in the functional covariance estimate, and in selecting appropriate smoothing parameters in both a simulation study and a regression analysis of medfly fertility data.     

Bayesian multivariate normal analysis with a wishart prior

This paper considers the Bayesian analysis of the multivariate normal distribution when its covariance matrix has a Wishart prior density under the assumption of a multivariate quadratic loss function. New flexible marginal posterior distributions of the mean μ and of the covariance matrix Σ are developed and univariate cases with graphical representations are given.     

Evaluating the Use of Spatial Covariance Structures in the Analysis of Cardiovascular Imaging Data

This article investigates the choice of working covariance structures in the analysis of spatially correlated observations motivated by cardiac imaging data. Through Monte Carlo simulations, we found that the choice of covariance structure affects the efficiency of the estimator and power of the test. Choosing the popular unstructured working covariance structure results in an over-inflated Type I error possibly due to a sample size not large enough relative to the number of parameters being estimated. With regard to model fit indices, Bayesian Information Criterion outperforms Akaike Information Criterion in choosing the correct covariance structure used to generate data.     

Efficient network meta-analysis: A confidence distribution approach

Network meta-analysis synthesizes several studies of multiple treatment comparisons to simultaneously provide inference for all treatments in the network. It can often strengthen inference on pairwise comparisons by borrowing evidence from other comparisons in the network. Current network meta-analysis approaches are derived from either conventional pairwise meta-analysis or hierarchical Bayesian methods. This paper introduces a new approach for network meta-analysis by combining confidence distributions (CDs). Instead of combining point estimators from individual studies in the conventional approach, the new approach combines CDs, which contain richer information than point estimators, and thus achieves greater efficiency in its inference. The proposed CD approach can efficiently integrate all studies in the network and provide inference for all treatments, even when individual studies contain only comparisons of subsets of the treatments. Through numerical studies with real and simulated data sets, the proposed approach is shown to outperform or at least equal the traditional pairwise meta-analysis and a commonly used Bayesian hierarchical model. Although the Bayesian approach may yield comparable results with a suitably chosen prior, it is highly sensitive to the choice of priors (especially for the between-trial covariance structure), which is often subjective. The CD approach is a general frequentist approach and is prior-free. Moreover, it can always provide a proper inference for all the treatment effects regardless of the between-trial covariance structure.     

Covariance structure of wavelet coefficients: theory and models in a Bayesian perspective

We present theoretical results on the random wavelet coefficients covariance structure. We use simple properties of the coefficients to derive a recursive way to compute the within- and across-scale covariances. We point out a useful link between the algorithm proposed and the two-dimensional discrete wavelet transform. We then focus on Bayesian wavelet shrinkage for estimating a function from noisy data. A prior distribution is imposed on the coefficients of the unknown function. We show how our findings on the covariance structure make it possible to specify priors that take into account the full correlation between coefficients through a parsimonious number of hyperparameters. We use Markov chain Monte Carlo methods to estimate the parameters and illustrate our method on bench-mark simulated signals.     

Bayesian analysis of covariance under inverse Gaussian model

This paper considers the problem of analysis of covariance (ANCOVA) under the assumption of inverse Gaussian distribution for response variable from the Bayesian point of view. We develop a fully Bayesian model for ANCOVA based on the conjugate prior distributions for parameters contained in the model. The Bayes estimator of parameters, ANCOVA model and adjusted effects for both treatments and covariates along with predictive distribution of future observations are developed. We also provide the essentials for comparing adjusted treatments effects and adjusted factor effects. A simulation study and a real world application are also performed to illustrate and evaluate the proposed Bayesian model.     

BAYESIAN ANALYSIS OF THE ADDITIVE MIXED MODEL FOR RANDOMIZED BLOCK DESIGNS

This paper deals with the Bayesian analysis of the additive mixed model experiments. Consider b randomly chosen subjects who respond once to each of t treatments. The subjects are treated as random effects and the treatment effects are fixed. Suppose that some prior information is available, thus motivating a Bayesian analysis. The Bayesian computation, however, can be difficult in this situation, especially when a large number of treatments is involved. Three computational methods are suggested to perform the analysis. The exact posterior density of any parameter of interest can be simulated based on random realizations taken from a restricted multivariate t distribution. The density can also be simulated using Markov chain Monte Carlo methods. The simulated density is accurate when a large number of random realizations is taken. However, it may take substantial amount of computer time when many treatments are involved. An alternative Laplacian approximation is discussed. The Laplacian method produces smooth and very accurate approximates to posterior densities, and takes only seconds of computer time. An example of a pipeline cracks experiment is used to illustrate the Bayesian approaches and the computational methods.     

The growth curve model: a review

A survey is given of papers which have influenced or have been influenced by the Growth Curve Model due to Potthoff & Roy (1964). The review covers, among others, methods of estimating parameters, the canonical version of the model, tests, extensions, incomplete data, Bayesian approaches and covariance structures.     

Bayesian covariance matrix estimation using a mixture of decomposable graphical models

We present a Bayesian approach to estimating a covariance matrix by using a prior that is a mixture over all decomposable graphs, with the probability of each graph size specified by the user and graphs of equal size assigned equal probability. Most previous approaches assume that all graphs are equally probable. We show empirically that the prior that assigns equal probability over graph sizes outperforms the prior that assigns equal probability over all graphs in more efficiently estimating the covariance matrix. The prior requires knowing the number of decomposable graphs for each graph size and we give a simulation method for estimating these counts. We also present a Markov chain Monte Carlo method for estimating the posterior distribution of the covariance matrix that is much more efficient than current methods. Both the prior and the simulation method to evaluate the prior apply generally to any decomposable graphical model.