Univariate and multirater ordinal cumulative link regression with covariate specific cutpoints

The author considers a reparameterized version of the Bayesian ordinal cumulative link regression model as a tool for exploring relationships between covariates and “cutpoint” parameters. The use of this parameterization allows one to fit models using the leapfrog hybrid Monte Carlo method, and to bypass latent variable data augmentation and the slow convergence of the cutpoints which it usually entails. The proposed Gibbs sampler is not model specific and can be easily modified to handle different link functions. The approach is illustrated by considering data from a pediatric radiology study.     

Variable selection in quantile regression via Gibbs sampling

Due to computational challenges and non-availability of conjugate prior distributions, Bayesian variable selection in quantile regression models is often a difficult task. In this paper, we address these two issues for quantile regression models. In particular, we develop an informative stochastic search variable selection (ISSVS) for quantile regression models that introduces an informative prior distribution. We adopt prior structures which incorporate historical data into the current data by quantifying them with a suitable prior distribution on the model parameters. This allows ISSVS to search more efficiently in the model space and choose the more likely models. In addition, a Gibbs sampler is derived to facilitate the computation of the posterior probabilities. A major advantage of ISSVS is that it avoids instability in the posterior estimates for the Gibbs sampler as well as convergence problems that may arise from choosing vague priors. Finally, the proposed methods are illustrated with both simulation and real data.     

Trace Class Markov Chains for Bayesian Inference with Generalized Double Pareto Shrinkage Priors

Bayesian shrinkage methods have generated a lot of interest in recent years, especially in the context of high‐dimensional linear regression. In recent work, a Bayesian shrinkage approach using generalized double Pareto priors has been proposed. Several useful properties of this approach, including the derivation of a tractable three‐block Gibbs sampler to sample from the resulting posterior density, have been established. We show that the Markov operator corresponding to this three‐block Gibbs sampler is not Hilbert–Schmidt. We propose a simpler two‐block Gibbs sampler and show that the corresponding Markov operator is trace class (and hence Hilbert–Schmidt). Establishing the trace class property for the proposed two‐block Gibbs sampler has several useful consequences. Firstly, it implies that the corresponding Markov chain is geometrically ergodic, thereby implying the existence of a Markov chain central limit theorem, which in turn enables computation of asymptotic standard errors for Markov chain‐based estimates of posterior quantities. Secondly, because the proposed Gibbs sampler uses two blocks, standard recipes in the literature can be used to construct a sandwich Markov chain (by inserting an appropriate extra step) to gain further efficiency and to achieve faster convergence. The trace class property for the two‐block sampler implies that the corresponding sandwich Markov chain is also trace class and thereby geometrically ergodic. Finally, it also guarantees that all eigenvalues of the sandwich chain are dominated by the corresponding eigenvalues of the Gibbs sampling chain (with at least one strict domination). Our results demonstrate that a minor change in the structure of a Markov chain can lead to fundamental changes in its theoretical properties. We illustrate the improvement in efficiency resulting from our proposed Markov chains using simulated and real examples.     

A Monte Carlo Method for Estimating Prediction Limit for the Arithmetic Mean of Lognormal Sample

A Monte Carlo (MC) method is suggested for calculating an upper prediction limit for the mean of a future sample of small size N from a lognormal distribution. This is done by obtaining a Monte Carlo estimator of the limit utilizing the future sample generated from the Gibbs sampler. For the Gibbs sampler, a full conditional posterior predictive distribution of each observation in the future sample is derived. The MC method is straightforward to specify distributionally and to implement computationally, with output readily adapted for required inference summaries. In an example, practical application of the method is described.     

A Comparison of Methods for Analysing a Nested Frailty Model to Child Survival in Malawi

Demographic and Health Surveys collect child survival times that are clustered at the family and community levels. It is assumed that each cluster has a specific, unobservable, random frailty that induces an association in the survival times within the cluster. The Cox proportional hazards model, with family and community random frailties acting multiplicatively on the hazard rate, is presented. The estimation of the fixed effect and the association parameters of the modified model is then examined using the Gibbs sampler and the expectation–maximization (EM) algorithm. The methods are compared using child survival data collected in the 1992 Demographic and Health Survey of Malawi. The two methods lead to very similar estimates of fixed effect parameters. However, the estimates of random effect variances from the EM algorithm are smaller than those of the Gibbs sampler. Both estimation methods reveal considerable family variation in the survival of children, and very little variability over the communities.     

On implementation of the Gibbs sampler for estimating the accuracy of multiple diagnostic tests

Implementation of the Gibbs sampler for estimating the accuracy of multiple binary diagnostic tests in one population has been investigated. This method, proposed by Joseph, Gyorkos and Coupal, makes use of a Bayesian approach and is used in the absence of a gold standard to estimate the prevalence, the sensitivity and specificity of medical diagnostic tests. The expressions that allow this method to be implemented for an arbitrary number of tests are given. By using the convergence diagnostics procedure of Raftery and Lewis, the relation between the number of iterations of Gibbs sampling and the precision of the estimated quantiles of the posterior distributions is derived. An example concerning a data set of gastro-esophageal reflux disease patients collected to evaluate the accuracy of the water siphon test compared with 24 h pH-monitoring, endoscopy and histology tests is presented. The main message that emerges from our analysis is that implementation of the Gibbs sampler to estimate the parameters of multiple binary diagnostic tests can be critical and convergence diagnostic is advised for this method. The factors which affect the convergence of the chains to the posterior distributions and those that influence the precision of their quantiles are analyzed.     

A more efficient Gibbs sampler estimation using steady-state simulation: applications to public health studies

Markov chain Monte Carlo methods, in particular, the Gibbs sampler, are widely used algorithms both in application and theoretical works in the classical and Bayesian paradigms. However, these algorithms are often computer intensive. Samawi et al. [Steady-state ranked Gibbs sampler. J. Stat. Comput. Simul. 2012;82(8), 1223–1238. doi:10.1080/00949655.2011.575378] demonstrate through theory and simulation that the dependent steady-state Gibbs sampler is more efficient and accurate in model parameter estimation than the original Gibbs sampler. This paper proposes the independent steady-state Gibbs sampler (ISSGS) approach to improve the original Gibbs sampler in multidimensional problems. It is demonstrated that ISSGS provides accuracy with unbiased estimation and improves the performance and convergence of the Gibbs sampler in multidimensional problems.     

Random variate transformations in the Gibbs sampler: issues of efficiency and convergence

In the non-conjugate Gibbs sampler, the required sampling from the full conditional densities needs the adoption of black-box sampling methods. Recent suggestions include rejection sampling, adaptive rejection sampling, generalized ratio of uniforms, and the Griddy-Gibbs sampler. This paper describes a general idea based on variate transformations which can be tailored in all the above methods and increase the Gibbs sampler efficiency. Moreover, a simple technique to assess convergence is suggested and illustrative examples are presented.     

Monte Carlo approximation of likelihood function in spatial GLMMs through an empirical Bayes method

In spatial generalized linear mixed models (SGLMMs), statistical inference encounters problems, since random effects in the model imply high-dimensional integrals to calculate the marginal likelihood function. In this article, we temporarily treat parameters as random variables and express the marginal likelihood function as a posterior expectation. Hence, the marginal likelihood function is approximated using the obtained samples from the posterior density of the latent variables and parameters given the data. However, in this setting, misspecification of prior distribution of correlation function parameter and problems associated with convergence of Markov chain Monte Carlo (MCMC) methods could have an unpleasant influence on the likelihood approximation. To avoid these challenges, we utilize an empirical Bayes approach to estimate prior hyperparameters. We also use a computationally efficient hybrid algorithm by combining inverse Bayes formula (IBF) and Gibbs sampler procedures. A simulation study is conducted to assess the performance of our method. Finally, we illustrate the method applying a dataset of standard penetration test of soil in an area in south of Iran.     

Sequential importance sampling for nonparametric Bayes models: The next generation

There are two generations of Gibbs sampling methods for semiparametric models involving the Dirichlet process. The first generation suffered from a severe drawback: the locations of the clusters, or groups of parameters, could essentially become fixed, moving only rarely. Two strategies that have been proposed to create the second generation of Gibbs samplers are integration and appending a second stage to the Gibbs sampler wherein the cluster locations are moved. We show that these same strategies are easily implemented for the sequential importance sampler, and that the first strategy dramatically improves results. As in the case of Gibbs sampling, these strategies are applicable to a much wider class of models. They are shown to provide more uniform importance sampling weights and lead to additional Rao-Blackwellization of estimators.     

Modeling attainment of steady state of drug concentration in plasma by means of a Bayesian approach using MCMC methods

The approach of Bayesian mixed effects modeling is an appropriate method for estimating both population-specific as well as subject-specific times to steady state. In addition to pure estimation, the approach allows to determine the time until a certain fraction of individuals of a population has reached steady state with a pre-specified certainty. In this paper a mixed effects model for the parameters of a nonlinear pharmacokinetic model is used within a Bayesian framework. Model fitting by means of Markov Chain Monte Carlo methods as implemented in the Gibbs sampler as well as the extraction of estimates and probability statements of interest are described. Finally, the proposed approach is illustrated by application to trough data from a multiple dose clinical trial.     

On convergence of the EM algorithmand the Gibbs sampler

In this article we investigate the relationship between the EM algorithm and the Gibbs sampler. We show that the approximate rate of convergence of the Gibbs sampler by Gaussian approximation is equal to that of the corresponding EM-type algorithm. This helps in implementing either of the algorithms as improvement strategies for one algorithm can be directly transported to the other. In particular, by running the EM algorithm we know approximately how many iterations are needed for convergence of the Gibbs sampler. We also obtain a result that under certain conditions, the EM algorithm used for finding the maximum likelihood estimates can be slower to converge than the corresponding Gibbs sampler for Bayesian inference. We illustrate our results in a number of realistic examples all based on the generalized linear mixed models.     

Partially Collapsed Gibbs Sampling for Linear Mixed-effects Models

This article presents a novel Bayesian analysis for linear mixed-effects models. The analysis is based on the method of partial collapsing that allows some components to be partially collapsed out of a model. The resulting partially collapsed Gibbs (PCG) sampler constructed to fit linear mixed-effects models is expected to exhibit much better convergence properties than the corresponding Gibbs sampler. In order to construct the PCG sampler without complicating component updates, we consider the reparameterization of model components by expressing a between-group variance in terms of a within-group variance in a linear mixed-effects model. The proposed method of partial collapsing with reparameterization is applied to the Merton’s jump diffusion model as well as general linear mixed-effects models with proper prior distributions and illustrated using simulated data and longitudinal data on sleep deprivation.     

On adaptive Metropolis–Hastings methods

This paper presents a method for adaptation in Metropolis–Hastings algorithms. A product of a proposal density and K copies of the target density is used to define a joint density which is sampled by a Gibbs sampler including a Metropolis step. This provides a framework for adaptation since the current value of all K copies of the target distribution can be used in the proposal distribution. The methodology is justified by standard Gibbs sampling theory and generalizes several previously proposed algorithms. It is particularly suited to Metropolis-within-Gibbs updating and we discuss the application of our methods in this context. The method is illustrated with both a Metropolis–Hastings independence sampler and a Metropolis-with-Gibbs independence sampler. Comparisons are made with standard adaptive Metropolis–Hastings methods.     

Behaviour of the Gibbs sampler when conditional distributions are potentially incompatible

The Gibbs sampler has been used extensively in the statistics literature. It relies on iteratively sampling from a set of compatible conditional distributions and the sampler is known to converge to a unique invariant joint distribution. However, the Gibbs sampler behaves rather differently when the conditional distributions are not compatible. Such applications have seen increasing use in areas such as multiple imputation. In this paper, we demonstrate that what a Gibbs sampler converges to is a function of the order of the sampling scheme. Besides providing the mathematical background of this behaviour, we also explain how that happens through a thorough analysis of the examples.     

Optimal direction Gibbs sampler for truncated multivariate normal distributions

Generalized Gibbs samplers simulate from any direction, not necessarily limited to the coordinate directions of the parameters of the objective function. We study how to optimally choose such directions in a random scan Gibbs sampler setting. We consider that optimal directions will be those that minimize the Kullback–Leibler divergence of two Markov chain Monte Carlo steps. Two distributions over direction are proposed for the multivariate Normal objective function. The resulting algorithms are used to simulate from a truncated multivariate Normal distribution, and the performance of our algorithms is compared with the performance of two algorithms based on the Gibbs sampler.     

Not every Gibbs sampler is a special case of the Metropolis–Hastings algorithm

It is commonly asserted that the Gibbs sampler is a special case of the Metropolis–Hastings (MH) algorithm. While this statement is true for certain Gibbs samplers, it is not true in general for the version that is taught and used most often, namely, the deterministic scan Gibbs sampler. In this note, I prove that that there exist deterministic scan Gibbs samplers that do not exhibit detailed balance and hence cannot be considered MH samplers. The nuances of various Gibbs sampling schemes are discussed.     

An iterative Monte Carlo method for nonconjugate Bayesian analysis

The Gibbs sampler has been proposed as a general method for Bayesian calculation in Gelfand and Smith (1990). However, the predominance of experience to date resides in applications assuming conjugacy where implementation is reasonably straightforward. This paper describes a tailored approximate rejection method approach for implementation of the Gibbs sampler when nonconjugate structure is present. Several challenging applications are presented for illustration.     

Bayesian Analysis of Two-Regime Threshold Autoregressive Moving Average Model with Exogenous Inputs

We consider Bayesian analysis of threshold autoregressive moving average model with exogenous inputs (TARMAX). In order to obtain the desired marginal posterior distributions of all parameters including the threshold value of the two-regime TARMAX model, we use two different Markov chain Monte Carlo (MCMC) methods to apply Gibbs sampler with Metropolis-Hastings algorithm. The first one is used to obtain iterative least squares estimates of the parameters. The second one includes two MCMC stages for estimate the desired marginal posterior distributions and the parameters. Simulation experiments and a real data example show support to our approaches.     

Likelihood-free approximate Gibbs sampling

Likelihood-free methods such as approximate Bayesian computation (ABC) have extended the reach of statistical inference to problems with computationally intractable likelihoods. Such approaches perform well for small-to-moderate dimensional problems, but suffer a curse of dimensionality in the number of model parameters. We introduce a likelihood-free approximate Gibbs sampler that naturally circumvents the dimensionality issue by focusing on lower-dimensional conditional distributions. These distributions are estimated by flexible regression models either before the sampler is run, or adaptively during sampler implementation. As a result, and in comparison to Metropolis-Hastings-based approaches, we are able to fit substantially more challenging statistical models than would otherwise be possible. We demonstrate the sampler’s performance via two simulated examples, and a real analysis of Airbnb rental prices using a intractable high-dimensional multivariate nonlinear state-space model with a 36-dimensional latent state observed on 365 time points, which presents a real challenge to standard ABC techniques.