Conditioning in Markov Chain Monte Carlo

Abstract

The so-called “Rao-Blackwellized” estimators proposed by Gelfand and Smith do not always reduce variance in Markov chain Monte Carlo when the dependence in the Markov chain is taken into account. An illustrative example is given, and a theorem characterizing the necessary and sufficient condition for such an estimator to always reduce variance is proved.     

A Practical Sequential Stopping Rule for High-Dimensional Markov Chain Monte Carlo

A current challenge for many Bayesian analyses is determining when to terminate high-dimensional Markov chain Monte Carlo simulations. To this end, we propose using an automated sequential stopping procedure that terminates the simulation when the computational uncertainty is small relative to the posterior uncertainty. Further, we show this stopping rule is equivalent to stopping when the effective sample size is sufficiently large. Such a stopping rule has previously been shown to work well in settings with posteriors of moderate dimension. In this article, we illustrate its utility in high-dimensional simulations while overcoming some current computational issues. As examples, we consider two complex Bayesian analyses on spatially and temporally correlated datasets. The first involves a dynamic space-time model on weather station data and the second a spatial variable selection model on fMRI brain imaging data. Our results show the sequential stopping rule is easy to implement, provides uncertainty estimates, and performs well in high-dimensional settings. Supplementary materials for this 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.     

Noisy Hamiltonian Monte Carlo for Doubly Intractable Distributions

Hamiltonian Monte Carlo (HMC) has been progressively incorporated within the statistician’s toolbox as an alternative sampling method in settings when standard Metropolis–Hastings is inefficient. HMC generates a Markov chain on an augmented state space with transitions based on a deterministic differential flow derived from Hamiltonian mechanics. In practice, the evolution of Hamiltonian systems cannot be solved analytically, requiring numerical integration schemes. Under numerical integration, the resulting approximate solution no longer preserves the measure of the target distribution, therefore an accept–reject step is used to correct the bias. For doubly intractable distributions—such as posterior distributions based on Gibbs random fields—HMC suffers from some computational difficulties: computation of gradients in the differential flow and computation of the accept–reject proposals poses difficulty. In this article, we study the behavior of HMC when these quantities are replaced by Monte Carlo estimates. Supplemental codes for implementing methods used in the article are available online.     

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.     

On Markov Chain Monte Carlo Acceleration

Abstract

Markov chain Monte Carlo (MCMC) methods are currently enjoying a surge of interest within the statistical community. The goal of this work is to formalize and support two distinct adaptive strategies that typically accelerate the convergence of an MCMC algorithm. One approach is through resampling; the other incorporates adaptive switching of the transition kernel. Support is both by analytic arguments and simulation study. Application is envisioned in low-dimensional but nontrivial problems. Two pathological illustrations are presented. Connections with reparameterization are discussed as well as possible difficulties with infinitely often adaptation.     

On solving integral equations using Markov chain Monte Carlo methods

In this paper, we propose an original approach to the solution of Fredholm equations of the second kind. We interpret the standard Von Neumann expansion of the solution as an expectation with respect to a probability distribution defined on a union of subspaces of variable dimension. Based on this representation, it is possible to use trans-dimensional Markov chain Monte Carlo (MCMC) methods such as Reversible Jump MCMC to approximate the solution numerically. This can be an attractive alternative to standard Sequential Importance Sampling (SIS) methods routinely used in this context. To motivate our approach, we sketch an application to value function estimation for a Markov decision process. Two computational examples are also provided.     

Adaptive Sequential Monte Carlo for Multiple Changepoint Analysis

Process monitoring and control requires the detection of structural changes in a data stream in real time. This article introduces an efficient sequential Monte Carlo algorithm designed for learning unknown changepoints in continuous time. The method is intuitively simple: new changepoints for the latest window of data are proposed by conditioning only on data observed since the most recent estimated changepoint, as these observations carry most of the information about the current state of the process. The proposed method shows improved performance over the current state of the art. Another advantage of the proposed algorithm is that it can be made adaptive, varying the number of particles according to the apparent local complexity of the target changepoint probability distribution. This saves valuable computing time when changes in the changepoint distribution are negligible, and enables rebalancing of the importance weights of existing particles when a significant change in the target distribution is encountered. The plain and adaptive versions of the method are illustrated using the canonical continuous time changepoint problem of inferring the intensity of an inhomogeneous Poisson process, although the method is generally applicable to any changepoint problem. Performance is demonstrated using both conjugate and nonconjugate Bayesian models for the intensity. Appendices to the article are available online, illustrating the method on other models and applications.     

Partition-Weighted Monte Carlo Estimation

Although various efficient and sophisticated Markov chain Monte Carlo sampling methods have been developed during the last decade, the sample mean is still a dominant in computing Bayesian posterior quantities. The sample mean is simple, but may not be efficient. The weighted sample mean is a natural generalization of the sample mean. In this paper, a new weighted sample mean is proposed by partitioning the support of posterior distribution, so that the same weight is assigned to observations that belong to the same subset in the partition. A novel application of this new weighted sample mean in computing ratios of normalizing constants and necessary theory are provided. Illustrative examples are given to demonstrate the methodology.     

Markov Chain Monte Carlo from Lagrangian Dynamics

Hamiltonian Monte Carlo (HMC) improves the computational efficiency of the Metropolis–Hastings algorithm by reducing its random walk behavior. Riemannian HMC (RHMC) further improves the performance of HMC by exploiting the geometric properties of the parameter space. However, the geometric integrator used for RHMC involves implicit equations that require fixed-point iterations. In some cases, the computational overhead for solving implicit equations undermines RHMC’s benefits. In an attempt to circumvent this problem, we propose an explicit integrator that replaces the momentum variable in RHMC by velocity. We show that the resulting transformation is equivalent to transforming Riemannian Hamiltonian dynamics to Lagrangian dynamics. Experimental results suggest that our method improves RHMC’s overall computational efficiency in the cases considered. All computer programs and datasets are available online (http://www.ics.uci.edu/babaks/Site/Codes.html) to allow replication of the results reported in this article.     

Bayesian and non-bayesian analysis of gamma stochastic frontier models by Markov Chain Monte Carlo methods

Summary  This paper considers simulation-based approaches for the gamma stochastic frontier model. Efficient Markov chain Monte Carlo methods are proposed for sampling the posterior distribution of the parameters. Maximum likelihood estimation is also discussed based on the stochastic approximation algorithm. The methods are applied to a data set of the U.S. electric utility industry. The authors are grateful to two anonymous referees for their useful comments, which improved an earlier version of the paper. The first author also thanks the financial support by the Japanese Ministry of Education, Culture, Sports, Science and Technology under the Grant-in-Aid for Scientific Research No.14730022.     

Robustness and applicability of Markov chain Monte Carlo algorithms for eigenvalue problems

In this paper we analyse applicability and robustness of Markov chain Monte Carlo algorithms for eigenvalue problems. We restrict our consideration to real symmetric matrices.

Almost Optimal Monte Carlo (MAO) algorithms for solving eigenvalue problems are formulated. Results for the structure of both – systematic and probability error are presented. It is shown that the values of both errors can be controlled independently by different algorithmic parameters. The results present how the systematic error depends on the matrix spectrum. The analysis of the probability error is presented. It shows that the close (in some sense) the matrix under consideration is to the stochastic matrix the smaller is this error. Sufficient conditions for constructing robust and interpolation Monte Carlo algorithms are obtained. For stochastic matrices an interpolation Monte Carlo algorithm is constructed.

A number of numerical tests for large symmetric dense matrices are performed in order to study experimentally the dependence of the systematic error from the structure of matrix spectrum. We also study how the probability error depends on the balancing of the matrix.     

Resampling Markov Chain Monte Carlo Algorithms: Basic Analysis and Empirical Comparisons

Sampling from complex distributions is an important but challenging topic in scientific and statistical computation. We synthesize three ideas, tempering, resampling, and Markov moving, and propose a general framework of resampling Markov chain Monte Carlo (MCMC). This framework not only accommodates various existing algorithms, including resample-move, importance resampling MCMC, and equi-energy sampling, but also leads to a generalized resample-move algorithm. We provide some basic analysis of these algorithms within the general framework, and present three simulation studies to compare these algorithms together with parallel tempering in the difficult situation where new modes emerge in the tails of previous tempering distributions. Our analysis and empirical results suggest that generalized resample-move tends to perform the best among all the algorithms studied when the Markov kernels lead to fast mixing or even locally so toward restricted distributions, whereas parallel tempering tends to perform the best when the Markov kernels lead to slow mixing, without even converging fast to restricted distributions. Moreover, importance resampling MCMC and equi-energy sampling perform similarly to each other, often worse than independence Metropolis resampling MCMC. Therefore, different algorithms seem to have advantages in different settings.     

Monte Carlo Maximum Likelihood in Model-Based Geostatistics

When using a model-based approach to geostatistical problems, often, due to the complexity of the models, inference relies on Markov chain Monte Carlo methods. This article focuses on the generalized linear spatial models, and demonstrates that parameter estimation and model selection using Markov chain Monte Carlo maximum likelihood is a feasible and very useful technique. A dataset of radionuclide concentrations on Rongelap Island is used to illustrate the techniques. For this dataset we demonstrate that the log-link function is not a good choice, and that there exists additional nonspatial variation which cannot be attributed to the Poisson error distribution. We also show that the interpretation of this additional variation as either micro-scale variation or measurement error has a significant impact on predictions. The techniques presented in this article would also be useful for other types of geostatistical models.     

Statistically Efficient Thinning of a Markov Chain Sampler

It is common to subsample Markov chain output to reduce the storage burden. Geyer shows that discarding k ? 1 out of every k observations will not improve statistical efficiency, as quantified through variance in a given computational budget. That observation is often taken to mean that thinning Markov chain Monte Carlo (MCMC) output cannot improve statistical efficiency. Here, we suppose that it costs one unit of time to advance a Markov chain and then θ > 0 units of time to compute a sampled quantity of interest. For a thinned process, that cost θ is incurred less often, so it can be advanced through more stages. Here, we provide examples to show that thinning will improve statistical efficiency if θ is large and the sample autocorrelations decay slowly enough. If the lag ? ? 1 autocorrelations of a scalar measurement satisfy ρ_? > ρ_{? + 1} > 0, then there is always a θ < ∞ at which thinning becomes more efficient for averages of that scalar. Many sample autocorrelation functions resemble first order AR(1) processes with ρ_? = ρ^|?| for some ? 1 < ρ < 1. For an AR(1) process, it is possible to compute the most efficient subsampling frequency k. The optimal k grows rapidly as ρ increases toward 1. The resulting efficiency gain depends primarily on θ, not ρ. Taking k = 1 (no thinning) is optimal when ρ ? 0. For ρ > 0, it is optimal if and only if θ ? (1 ? ρ)²/(2ρ). This efficiency gain never exceeds 1 + θ. This article also gives efficiency bounds for autocorrelations bounded between those of two AR(1) processes. Supplementary materials for this article are available online.     

Applications of Hybrid Monte Carlo to Bayesian Generalized Linear Models: Quasicomplete Separation and Neural Networks

Abstract

The “leapfrog” hybrid Monte Carlo algorithm is a simple and effective MCMC method for fitting Bayesian generalized linear models with canonical link. The algorithm leads to large trajectories over the posterior and a rapidly mixing Markov chain, having superior performance over conventional methods in difficult problems like logistic regression with quasicomplete separation. This method offers a very attractive solution to this common problem, providing a method for identifying datasets that are quasicomplete separated, and for identifying the covariates that are at the root of the problem. The method is also quite successful in fitting generalized linear models in which the link function is extended to include a feedforward neural network. With a large number of hidden units, however, or when the dataset becomes large, the computations required in calculating the gradient in each trajectory can become very demanding. In this case, it is best to mix the algorithm with multivariate random walk Metropolis—Hastings. However, this entails very little additional programming work.     

Explicit error bounds for lazy reversible Markov chain Monte Carlo

We prove explicit, i.e., non-asymptotic, error bounds for Markov Chain Monte Carlo methods, such as the Metropolis algorithm. The problem is to compute the expectation (or integral) of f$f$ with respect to a measure π$\pi$ which can be given by a density ?$?$ with respect to another measure. A straight simulation of the desired distribution by a random number generator is in general not possible. Thus it is reasonable to use Markov chain sampling with a burn-in. We study such an algorithm and extend the analysis of Lovasz and Simonovits [L. Lovász, M. Simonovits, Random walks in a convex body and an improved volume algorithm, Random Structures Algorithms 4 (4) (1993) 359–412] to obtain an explicit error bound.     

Monte Carlo method via a numerical algorithm to solve a parabolic problem

This paper is intended to provide a numerical algorithm consisted of the combined use of the finite difference method and Monte Carlo method to solve a one-dimensional parabolic partial differential equation. The numerical algorithm is based on the discretize governing equations by finite difference method. Due to the application of the finite difference method, a large sparse system of linear algebraic equations is obtained. An approach of Monte Carlo method is employed to solve the linear system. Numerical tests are performed in order to show the efficiency and accuracy of the present work.     

Bayesian Analysis of a Two-State Markov Modulated Poisson Process

Abstract

We postulate observations from a Poisson process whose rate parameter modulates between two values determined by an unobserved Markov chain. The theory switches from continuous to discrete time by considering the intervals between observations as a sequence of dependent random variables. A result from hidden Markov models allows us to sample from the posterior distribution of the model parameters given the observed event times using a Gibbs sampler with only two steps per iteration.     

On Determination of the Order of a Markov Chain

In this paper we propose a new and more general criterion (the efficient determination criterion, EDC) for estimating the order of a Markov chain. The consistency and the strong consistency of the estimates have been established under mild conditions. This revised version was published online in August 2006 with corrections to the Cover Date.