Perturbation bounds for Monte Carlo within Metropolis via restricted approximations

The Monte Carlo within Metropolis (MCwM) algorithm, interpreted as a perturbed Metropolis–Hastings (MH) algorithm, provides an approach for approximate sampling when the target distribution is intractable. Assuming the unperturbed Markov chain is geometrically ergodic, we show explicit estimates of the difference between the $n$th step distributions of the perturbed MCwM and the unperturbed MH chains. These bounds are based on novel perturbation results for Markov chains which are of interest beyond the MCwM setting. To apply the bounds, we need to control the difference between the transition probabilities of the two chains and to verify stability of the perturbed chain.     

Optimal Scaling for Random Walk Metropolis on Spherically Constrained Target Densities

We consider the problem of optimal scaling of the proposal variance for multidimensional random walk Metropolis algorithms. It is well known, for a wide range of continuous target densities, that the optimal scaling of the proposal variance leads to an average acceptance rate of 0.234. Therefore a natural question is, do similar results hold for target densities which have discontinuities? In the current work, we answer in the affirmative for a class of spherically constrained target densities. Even though the acceptance probability is more complicated than for continuous target densities, the optimal scaling of the proposal variance again leads to an average acceptance rate of 0.234.     

Adaptive Component-Wise Multiple-Try Metropolis Sampling

One of the most widely used samplers in practice is the component-wise Metropolis–Hastings (CMH) sampler that updates in turn the components of a vector-valued Markov chain using accept–reject moves generated from a proposal distribution. When the target distribution of a Markov chain is irregularly shaped, a “good” proposal distribution for one region of the state–space might be a “poor” one for another region. We consider a component-wise multiple-try Metropolis (CMTM) algorithm that chooses from a set of candidate moves sampled from different distributions. The computational efficiency is increased using an adaptation rule for the CMTM algorithm that dynamically builds a better set of proposal distributions as the Markov chain runs. The ergodicity of the adaptive chain is demonstrated theoretically. The performance is studied via simulations and real data examples. Supplementary material for this article is available online.     

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.     

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.     

Implementations of the Monte Carlo EM Algorithm

The Monte Carlo EM (MCEM) algorithm is a modification of the EM algorithm where the expectation in the E-step is computed numerically through Monte Carlo simulations. The most exible and generally applicable approach to obtaining a Monte Carlo sample in each iteration of an MCEM algorithm is through Markov chain Monte Carlo (MCMC) routines such as the Gibbs and Metropolis–Hastings samplers. Although MCMC estimation presents a tractable solution to problems where the E-step is not available in closed form, two issues arise when implementing this MCEM routine: (1) how do we minimize the computational cost in obtaining an MCMC sample? and (2) how do we choose the Monte Carlo sample size? We address the first question through an application of importance sampling whereby samples drawn during previous EM iterations are recycled rather than running an MCMC sampler each MCEM iteration. The second question is addressed through an application of regenerative simulation. We obtain approximate independent and identical samples by subsampling the generated MCMC sample during different renewal periods. Standard central limit theorems may thus be used to gauge Monte Carlo error. In particular, we apply an automated rule for increasing the Monte Carlo sample size when the Monte Carlo error overwhelms the EM estimate at any given iteration. We illustrate our MCEM algorithm through analyses of two datasets fit by generalized linear mixed models. As a part of these applications, we demonstrate the improvement in computational cost and efficiency of our routine over alternative MCEM strategies.     

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 optimization

Monte Carlo optimization techniques for solving mathematical programming problems have been the focus of some debate. This note reviews the debate and puts these stochastic methods in their proper perspective.     

On the swapping algorithm

The Metropolis‐coupled Markov chain method (or “Swapping Algorithm”) is an empirically successful hybrid Monte Carlo algorithm. It alternates between standard transitions on parallel versions of the system at different parameter values, and swapping two versions. We prove rapid mixing for two bimodal examples, including the mean‐field Ising model. © 2002 Wiley Periodicals, Inc. Random Struct. Alg., 22: 66–97, 2002     

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.     

Monte Carlo EM加速算法

EM算法是近年来常用的求后验众数的估计的一种数据增广算法, 但由于求出其E步中积分的显示表达式有时很困难, 甚至不可能, 限制了其应用的广泛性. 而Monte Carlo EM算法很好地解决了这个问题, 将EM算法中E步的积分用Monte Carlo模拟来有效实现, 使其适用性大大增强. 但无论是EM算法, 还是Monte Carlo EM算法, 其收敛速度都是线性的, 被缺损信息的倒数所控制, 当缺损数据的比例很高时, 收敛速度就非常缓慢. 而Newton-Raphson算法在后验众数的附近具有二次收敛速率. 本文提出Monte Carlo EM加速算法, 将Monte Carlo EM算法与Newton-Raphson算法结合, 既使得EM算法中的E步用Monte Carlo模拟得以实现, 又证明了该算法在后验众数附近具有二次收敛速度. 从而使其保留了Monte Carlo EM算法的优点, 并改进了Monte Carlo EM算法的收敛速度. 本文通过数值例子, 将Monte Carlo EM加速算法的结果与EM算法、Monte Carlo EM算法的结果进行比较, 进一步说明了Monte Carlo EM加速算法的优良性.     

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.     

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.     

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.     

Efficient implementation of the Barnes-Hut octree algorithm for Monte Carlo simulations of charged systems

Computer simulation with Monte Carlo is an important tool to investigate the function and equilibrium properties of many biological and soft matter materials solvable in solvents.The appropriate treatment of long-range electrostatic interaction is essential for these charged systems,but remains a challenging problem for large-scale simulations.We develop an efficient Barnes-Hut treecode algorithm for electrostatic evaluation in Monte Carlo simulations of Coulomb many-body systems.The algorithm is based on a divide-and-conquer strategy and fast update of the octree data structure in each trial move through a local adjustment procedure.We test the accuracy of the tree algorithm,and use it to perform computer simulations of electric double layer near a spherical interface.It is shown that the computational cost of the Monte Carlo method with treecode acceleration scales as log N in each move.For a typical system with ten thousand particles,by using the new algorithm,the speed has been improved by two orders of magnitude from the direct summation.     

An adaptive Monte Carlo algorithm for computing mixed logit estimators

Researchers and analysts are increasingly using mixed logit models for estimating responses to forecast demand and to determine the factors that affect individual choices. However the numerical cost associated to their evaluation can be prohibitive, the inherent probability choices being represented by multidimensional integrals. This cost remains high even if Monte Carlo or quasi-Monte Carlo techniques are used to estimate those integrals. This paper describes a new algorithm that uses Monte Carlo approximations in the context of modern trust-region techniques, but also exploits accuracy and bias estimators to considerably increase its computational efficiency. Numerical experiments underline the importance of the choice of an appropriate optimisation technique and indicate that the proposed algorithm allows substantial gains in time while delivering more information to the practitioner. Fabian Bastin: Research Fellow of the National Fund for Scientific Research (FNRS)     

Torpid mixing of the Wang–Swendsen–Kotecký algorithm for sampling colorings

We study the problem of sampling uniformly at random from the set of k-colorings of a graph with maximum degree Δ. We focus attention on the Markov chain Monte Carlo method, particularly on a popular Markov chain for this problem, the Wang–Swendsen–Kotecký (WSK) algorithm. The second author recently proved that the WSK algorithm quickly converges to the desired distribution when k11Δ/6. We study how far these positive results can be extended in general. In this note we prove the first non-trivial results on when the WSK algorithm takes exponentially long to reach the stationary distribution and is thus called torpidly mixing. In particular, we show that the WSK algorithm is torpidly mixing on a family of bipartite graphs when 3k<Δ/(20logΔ), and on a family of planar graphs for any number of colors. We also give a family of graphs for which, despite their small chromatic number, the WSK algorithm is not ergodic when kΔ/2, provided k is larger than some absolute constant k₀.     

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.     

Dynamically Rescaled Hamiltonian Monte Carlo for Bayesian Hierarchical Models

Dynamically rescaled Hamiltonian Monte Carlo is introduced as a computationally fast and easily implemented method for performing full Bayesian analysis in hierarchical statistical models. The method relies on introducing a modified parameterization so that the reparameterized target distribution has close to constant scaling properties, and thus is easily sampled using standard (Euclidian metric) Hamiltonian Monte Carlo. Provided that the parameterizations of the conditional distributions specifying the hierarchical model are “constant information parameterizations” (CIPs), the relation between the modified- and original parameterization is bijective, explicitly computed, and admit exploitation of sparsity in the numerical linear algebra involved. CIPs for a large catalogue of statistical models are presented, and from the catalogue, it is clear that many CIPs are currently routinely used in statistical computing. A relation between the proposed methodology and a class of explicitly integrated Riemann manifold Hamiltonian Monte Carlo methods is discussed. The methodology is illustrated on several example models, including a model for inflation rates with multiple levels of nonlinearly dependent latent variables. Supplementary materials for this article are available online.