Computing p-values in conditional independence models for a contingency table

We present a Markov chain Monte Carlo (MCMC) method for generating Markov chains using Markov bases for conditional independence models for a four-way contingency table. We then describe a Markov basis characterized by Markov properties associated with a given conditional independence model and show how to use the Markov basis to generate random tables of a Markov chain. The estimates of exact p-values can be obtained from random tables generated by the MCMC method. Numerical experiments examine the performance of the proposed MCMC method in comparison with the χ ² approximation using large sparse contingency tables.     

Weakly Informative Reparameterizations for Location-Scale Mixtures

While mixtures of Gaussian distributions have been studied for more than a century, the construction of a reference Bayesian analysis of those models remains unsolved, with a general prohibition of improper priors due to the ill-posed nature of such statistical objects. This difficulty is usually bypassed by an empirical Bayes resolution. By creating a new parameterization centered on the mean and possibly the variance of the mixture distribution itself, we manage to develop here a weakly informative prior for a wide class of mixtures with an arbitrary number of components. We demonstrate that some posterior distributions associated with this prior and a minimal sample size are proper. We provide Markov chain Monte Carlo (MCMC) implementations that exhibit the expected exchangeability. We only study here the univariate case, the extension to multivariate location-scale mixtures being currently under study. An R package called Ultimixt is associated with this article. Supplementary material for this article is available online.     

Bayesian Inference with Wavelets: Density Estimation

Abstract

We propose a prior probability model in the wavelet coefficient space. The proposed model implements wavelet coefficient thresholding by full posterior inference in a coherent probability model. We introduce a prior probability model with mixture priors for the wavelet coefficients. The prior includes a positive prior probability mass at zero which leads to a posteriori thresholding and generally to a posteriori shrinkage on the coefficients. We discuss an efficient posterior simulation scheme to implement inference in the proposed model. The discussion is focused on the density estimation problem. However, the introduced prior probability model on the wavelet coefficient space and the Markov chain Monte Carlo scheme are general.     

Examples of Adaptive MCMC

We investigate the use of adaptive MCMC algorithms to automatically tune the Markov chain parameters during a run. Examples include the Adaptive Metropolis (AM) multivariate algorithm of Haario, Saksman, and Tamminen (2001), Metropolis-within-Gibbs algorithms for nonconjugate hierarchical models, regionally adjusted Metropolis algorithms, and logarithmic scalings. Computer simulations indicate that the algorithms perform very well compared to nonadaptive algorithms, even in high dimension.     

Markov Chain Monte Carlo Convergence Assessment via Two-Way Analysis of Variance

Abstract

In this article we discuss the problem of assessing the performance of Markov chain Monte Carlo (MCMC) algorithms on the basis of simulation output. In essence, we extend the original ideas of Gelman and Rubin and, more recently, Brooks and Gelman, to problems where we are able to split the variation inherent within the MCMC simulation output into two distinct groups. We show how such a diagnostic may be useful in assessing the performance of MCMC samplers addressing model choice problems, such as the reversible jump MCMC algorithm. In the model choice context, we show how the reversible jump MCMC simulation output for parameters that retain a coherent interpretation throughout the simulation, can be used to assess convergence. By considering various decompositions of the sampling variance of this parameter, we can assess the performance of our MCMC sampler in terms of its mixing properties both within and between models and we illustrate our approach in both the graphical Gaussian models and normal mixtures context. Finally, we provide an example of the application of our diagnostic to the assessment of the influence of different starting values on MCMC simulation output, thereby illustrating the wider utility of our method beyond the Bayesian model choice and reversible jump MCMC context.     

Honest Importance Sampling With Multiple Markov Chains

Importance sampling is a classical Monte Carlo technique in which a random sample from one probability density, π₁, is used to estimate an expectation with respect to another, π. The importance sampling estimator is strongly consistent and, as long as two simple moment conditions are satisfied, it obeys a central limit theorem (CLT). Moreover, there is a simple consistent estimator for the asymptotic variance in the CLT, which makes for routine computation of standard errors. Importance sampling can also be used in the Markov chain Monte Carlo (MCMC) context. Indeed, if the random sample from π₁ is replaced by a Harris ergodic Markov chain with invariant density π₁, then the resulting estimator remains strongly consistent. There is a price to be paid, however, as the computation of standard errors becomes more complicated. First, the two simple moment conditions that guarantee a CLT in the iid case are not enough in the MCMC context. Second, even when a CLT does hold, the asymptotic variance has a complex form and is difficult to estimate consistently. In this article, we explain how to use regenerative simulation to overcome these problems. Actually, we consider a more general setup, where we assume that Markov chain samples from several probability densities, π₁, …, π_k, are available. We construct multiple-chain importance sampling estimators for which we obtain a CLT based on regeneration. We show that if the Markov chains converge to their respective target distributions at a geometric rate, then under moment conditions similar to those required in the iid case, the MCMC-based importance sampling estimator obeys a CLT. Furthermore, because the CLT is based on a regenerative process, there is a simple consistent estimator of the asymptotic variance. We illustrate the method with two applications in Bayesian sensitivity analysis. The first concerns one-way random effect models under different priors. The second involves Bayesian variable selection in linear regression, and for this application, importance sampling based on multiple chains enables an empirical Bayes approach to variable selection.     

Bayesian reference analysis for Gaussian Markov random fields

Gaussian Markov random fields (GMRF) are important families of distributions for the modeling of spatial data and have been extensively used in different areas of spatial statistics such as disease mapping, image analysis and remote sensing. GMRFs have been used for the modeling of spatial data, both as models for the sampling distribution of the observed data and as models for the prior of latent processes/random effects; we consider mainly the former use of GMRFs. We study a large class of GMRF models that includes several models previously proposed in the literature. An objective Bayesian analysis is presented for the parameters of the above class of GMRFs, where explicit expressions for the Jeffreys (two versions) and reference priors are derived, and for each of these priors results on posterior propriety of the model parameters are established. We describe a simple MCMC algorithm for sampling from the posterior distribution of the model parameters, and study frequentist properties of the Bayesian inferences resulting from the use of these automatic priors. Finally, we illustrate the use of the proposed GMRF model and reference prior for studying the spatial variability of lip cancer cases in the districts of Scotland over the period 1975-1980.     

Adaptive Markov Chain Monte Carlo for Bayesian Variable Selection

We describe adaptive Markov chain Monte Carlo (MCMC) methods for sampling posterior distributions arising from Bayesian variable selection problems. Point-mass mixture priors are commonly used in Bayesian variable selection problems in regression. However, for generalized linear and nonlinear models where the conditional densities cannot be obtained directly, the resulting mixture posterior may be difficult to sample using standard MCMC methods due to multimodality. We introduce an adaptive MCMC scheme that automatically tunes the parameters of a family of mixture proposal distributions during simulation. The resulting chain adapts to sample efficiently from multimodal target distributions. For variable selection problems point-mass components are included in the mixture, and the associated weights adapt to approximate marginal posterior variable inclusion probabilities, while the remaining components approximate the posterior over nonzero values. The resulting sampler transitions efficiently between models, performing parameter estimation and variable selection simultaneously. Ergodicity and convergence are guaranteed by limiting the adaptation based on recent theoretical results. The algorithm is demonstrated on a logistic regression model, a sparse kernel regression, and a random field model from statistical biophysics; in each case the adaptive algorithm dramatically outperforms traditional MH algorithms. Supplementary materials for this article are available online.     

Estimation of Binary Markov Random Fields Using Markov chain Monte Carlo

This article compares three binary Markov random fields (MRFs) which are popular Bayesian priors for spatial smoothing. These are the Ising prior and two priors based on latent Gaussian MRFs. Concern is given to the selection of a suitable Markov chain Monte Carlo (MCMC) sampling scheme for each prior. The properties of the three priors and sampling schemes are investigated in the context of three empirical examples. The first is a simulated dataset, the second involves a confocal fluorescence microscopy dataset, while the third is based on the analysis of functional magnetic resonance imaging (fMRI) data. In the case of the Ising prior, single site and multi-site Swendsen-Wang sampling schemes are both considered. The single site scheme is shown to work consistently well, while it is shown that the Swendsen-Wang algorithm can have convergence problems. The sampling schemes for the priors are extended to generate the smoothing parameters, so that estimation becomes fully automatic. Although this works well, it is found that for highly contiguous images fixing smoothing parameters to very high values can improve results by injecting additional prior information concerning the level of contiguity in the image. The relative properties of the three binary MRFs are investigated, and it is shown how the Ising prior in particular defines sharp edges and encourages clustering. In addition, one of the latent Gaussian MRF priors is shown to be unable to distinguish between higher levels of smoothing. In the context of the fMRI example we also undertake a simulation study.     

Hypothesis Tests of Convergence in Markov Chain Monte Carlo

Abstract

Deciding when a Markov chain has reached its stationary distribution is a major problem in applications of Markov Chain Monte Carlo methods. Many methods have been proposed ranging from simple graphical methods to complicated numerical methods. Most such methods require a lot of user interaction with the chain which can be very tedious and time-consuming for a slowly mixing chain. This article describes a system to reduce the burden on the user in assessing convergence. The method uses simple nonparametric hypothesis testing techniques to examine the output of several independent chains and so determines whether there is any evidence against the hypothesis of convergence. We illustrate the proposed method on some examples from the literature.     

Markov chain Monte Carlo Using an Approximation

This article presents a method for generating samples from an unnormalized posterior distribution f(·) using Markov chain Monte Carlo (MCMC) in which the evaluation of f(·) is very difficult or computationally demanding. Commonly, a less computationally demanding, perhaps local, approximation to f(·) is available, say f^**_x(·). An algorithm is proposed to generate an MCMC that uses such an approximation to calculate acceptance probabilities at each step of a modified Metropolis–Hastings algorithm. Once a proposal is accepted using the approximation, f(·) is calculated with full precision ensuring convergence to the desired distribution. We give sufficient conditions for the algorithm to converge to f(·) and give both theoretical and practical justifications for its usage. Typical applications are in inverse problems using physical data models where computing time is dominated by complex model simulation. We outline Bayesian inference and computing for inverse problems. A stylized example is given of recovering resistor values in a network from electrical measurements made at the boundary. Although this inverse problem has appeared in studies of underground reservoirs, it has primarily been chosen for pedagogical value because model simulation has precisely the same computational structure as a finite element method solution of the complete electrode model used in conductivity imaging, or “electrical impedance tomography.” This example shows a dramatic decrease in CPU time, compared to a standard Metropolis–Hastings algorithm.     

Markov chain mixing time on cycles

Mixing time quantifies the convergence speed of a Markov chain to the stationary distribution. It is an important quantity related to the performance of MCMC sampling. It is known that the mixing time of a reversible chain can be significantly improved by lifting, resulting in an irreversible chain, while changing the topology of the chain. We supplement this result by showing that if the connectivity graph of a Markov chain is a cycle, then there is an Ω(n²) lower bound for the mixing time. This is the same order of magnitude that is known for reversible chains on the cycle.     

Sparse Variational Analysis of Linear Mixed Models for Large Data Sets

It is increasingly common to be faced with longitudinal or multi-level data sets that have large numbers of predictors and/or a large sample size. Current methods of fitting and inference for mixed effects models tend to perform poorly in such settings. When there are many variables, it is appealing to allow uncertainty in subset selection and to obtain a sparse characterization of the data. Bayesian methods are available to address these goals using Markov chain Monte Carlo (MCMC), but MCMC is very computationally expensive and can be infeasible in large p and/or large n problems. As a fast approximate Bayes solution, we recommend a novel approximation to the posterior relying on variational methods. Variational methods are used to approximate the posterior of the parameters in a decomposition of the variance components, with priors chosen to obtain a sparse solution that allows selection of random effects. The method is evaluated through a simulation study, and applied to an epidemiological application.     

A Markov Chain Monte Carlo Convergence Diagnostic Using Subsampling

Abstract

A new diagnostic procedure for assessing convergence of a Markov chain Monte Carlo (MCMC) simulation is proposed. The method is based on the use of subsampling for the construction of confidence regions from asymptotically stationary time series as developed in Politis, Romano, and Wolf. The MCMC subsampling diagnostic is capable of gauging at what point the chain has “forgotten” its starting points, as well as to indicate how many points are needed to estimate the parameters of interest according to the desired accuracy. Simulation examples are also presented showing that the diagnostic performs favorably in interesting cases.     

On Monte Carlo methods for Bayesian multivariate regression models with heavy-tailed errors

We consider Bayesian analysis of data from multivariate linear regression models whose errors have a distribution that is a scale mixture of normals. Such models are used to analyze data on financial returns, which are notoriously heavy-tailed. Let π denote the intractable posterior density that results when this regression model is combined with the standard non-informative prior on the unknown regression coefficients and scale matrix of the errors. Roughly speaking, the posterior is proper if and only if n≥d+k, where n is the sample size, d is the dimension of the response, and k is number of covariates. We provide a method of making exact draws from π in the special case where n=d+k, and we study Markov chain Monte Carlo (MCMC) algorithms that can be used to explore π when n>d+k. In particular, we show how the Haar PX-DA technology studied in Hobert and Marchev (2008) [11] can be used to improve upon Liu’s (1996) [7] data augmentation (DA) algorithm. Indeed, the new algorithm that we introduce is theoretically superior to the DA algorithm, yet equivalent to DA in terms of computational complexity. Moreover, we analyze the convergence rates of these MCMC algorithms in the important special case where the regression errors have a Student’s t distribution. We prove that, under conditions on n, d, k, and the degrees of freedom of the t distribution, both algorithms converge at a geometric rate. These convergence rate results are important from a practical standpoint because geometric ergodicity guarantees the existence of central limit theorems which are essential for the calculation of valid asymptotic standard errors for MCMC based estimates.     

Semiparametric Bayesian measurement error modeling

This work presents a Bayesian semiparametric approach for dealing with regression models where the covariate is measured with error. Given that (1) the error normality assumption is very restrictive, and (2) assuming a specific elliptical distribution for errors (Student-t for example), may be somewhat presumptuous; there is need for more flexible methods, in terms of assuming only symmetry of errors (admitting unknown kurtosis). In this sense, the main advantage of this extended Bayesian approach is the possibility of considering generalizations of the elliptical family of models by using Dirichlet process priors in dependent and independent situations. Conditional posterior distributions are implemented, allowing the use of Markov Chain Monte Carlo (MCMC), to generate the posterior distributions. An interesting result shown is that the Dirichlet process prior is not updated in the case of the dependent elliptical model. Furthermore, an analysis of a real data set is reported to illustrate the usefulness of our approach, in dealing with outliers. Finally, semiparametric proposed models and parametric normal model are compared, graphically with the posterior distribution density of the coefficients.     

On Burr XII Distribution Analysis Under Progressive Type-II Hybrid Censored Data

In the current paper, based on progressive type-II hybrid censored samples, the maximum likelihood and Bayes estimates for the two parameter Burr XII distribution are obtained. We propose the use of expectation-maximization (EM) algorithm to compute the maximum likelihood estimates (MLEs) of model parameters. Further, we derive the asymptotic variance-covariance matrix of the MLEs by applying the missing information principle and it can be utilized to construct asymptotic confidence intervals (CIs) for the parameters. The Bayes estimates of the unknown parameters are obtained under the assumption of gamma priors by using Lindley’s approximation and Markov chain Monte Carlo (MCMC) technique. Also, MCMC samples are used to construct the highest posterior density (HPD) credible intervals. Simulation study is conducted to investigate the accuracy of the estimates and compare the performance of CIs obtained. Finally, one real data set is analyzed for illustrative purposes.     

Automatically tuned general-purpose MCMC via new adaptive diagnostics

Adaptive Markov Chain Monte Carlo (MCMC) algorithms attempt to ‘learn’ from the results of past iterations so the Markov chain can converge quicker. Unfortunately, adaptive MCMC algorithms are no longer Markovian, so their convergence is difficult to guarantee. In this paper, we develop new diagnostics to determine whether the adaption is still improving the convergence. We present an algorithm which automatically stops adapting once it determines further adaption will not increase the convergence speed. Our algorithm allows the computer to tune a ‘good’ Markov chain through multiple phases of adaption, and then run conventional non-adaptive MCMC. In this way, the efficiency gains of adaptive MCMC can be obtained while still ensuring convergence to the target distribution.     

Langevin type limiting processes for adaptive MCMC

Adaptive Markov Chain Monte Carlo (AMCMC) is a class of MCMC algorithms where the proposal distribution changes at every iteration of the chain. In this case it is important to verify that such a Markov Chain indeed has a stationary distribution. In this paper we discuss a diffusion approximation to a discrete time AMCMC. This diffusion approximation is different when compared to the diffusion approximation as in Gelman et al. [5] where the state space increases in dimension to ∞. In our approach the time parameter is sped up in such a way that the limiting process (as the mesh size goes to 0) approaches to a non-trivial diffusion process.     

On the Convergence Rate of Random Permutation Sampler and ECR Algorithm in Missing Data Models

Label switching is a well-known phenomenon that occurs in MCMC outputs targeting the parameters’ posterior distribution of many latent variable models. Although its appearence is necessary for the convergence of the simulated Markov chain, it turns out to be a problem in the estimation procedure. In a recent paper, Papastamoulis and Iliopoulos (J Comput Graph Stat 19:313–331, 2010) introduced the Equivalence Classes Representatives (ECR) algorithm as a solution of this problem in the context of finite mixtures of distributions. In this paper, label switching is considered under a general missing data model framework that includes as special cases finite mixtures, hidden Markov models, and Markov random fields. The use of ECR algorithm is extended to this general framework and is shown that the relabelled sequence which it produces converges to its target distribution at the same rate as the Random Permutation Sampler of Frühwirth-Schnatter (2001) and that both converge at least as fast as the Markov chain generated by the original MCMC output.