We propose a novel Metropolis-Hastings algorithm to sample uniformly from the space of correlation matrices. Existing methods in the literature are based on elaborated representations of a correlation matrix, or on complex parametrizations of it. By contrast, our method is intuitive and simple, based the classical Cholesky factorization of a positive definite matrix and Markov chain Monte Carlo theory. We perform a detailed convergence analysis of the resulting Markov chain, and show how it benefits from fast convergence, both theoretically and empirically. Furthermore, in numerical experiments our algorithm is shown to be significantly faster than the current alternative approaches, thanks to its simple yet principled approach.
MCMC algorithms such as Metropolis-Hastings algorithms are slowed down by the computation of complex target distributions as exemplified by huge datasets. We offer in this paper a useful generalisation of the Delayed Acceptance approach, devised to reduce the computational costs of such algorithms by a simple and universal divide-and-conquer strategy. The idea behind the generic acceleration is to divide the acceptance step into several parts, aiming at a major reduction in computing time that out-ranks the corresponding reduction in acceptance probability. Each of the components can be sequen…
Pseudo-marginal Markov chain Monte Carlo methods for sampling from intractable distributions have gained recent interest and have been theoretically studied in considerable depth. Their main appeal is that they are exact, in the sense that they target marginally the correct invariant distribution. However, the pseudo-marginal Markov chain can exhibit poor mixing and slow convergence towards its target. As an alternative, a subtly different Markov chain can be simulated, where better mixing is possible but the exactness property is sacrificed. This is the noisy algorithm, initially conceptualis…
We investigate nonlinear state-space models without a closed-form transition density, and propose reformulating such models over their latent noise variables rather than their latent state variables. In doing so the tractable noise density emerges in place of the intractable transition density. For importance sampling methods such as the auxiliary particle filter, this enables importance weights to be computed where they could not be otherwise. As case studies we take two multivariate marine biogeochemical models and perform state and parameter estimation using the particle marginal Metropolis…
We analyse computational efficiency of Metropolis-Hastings algorithms with stochastic AR(1) process proposals. These proposals include, as a subclass, discretized Langevin diffusion (e.g. MALA) and discretized Hamiltonian dynamics (e.g. HMC). We derive expressions for the expected acceptance rate and expected jump size for MCMC methods with general stochastic AR(1) process proposals for the case where the target distribution is absolutely continuous with respect to a Gaussian and the covariance of the Gaussian is allowed to have off-diagonal terms. This allows us to extend what is known about …
In this article we propose multiplication based random walk Metropolis Hastings (MH) algorithm on the real line. We call it the random dive MH (RDMH) algorithm. This algorithm, even if simple to apply, was not studied earlier in Markov chain Monte Carlo literature. The associated kernel is shown to have standard properties like irreducibility, aperiodicity and Harris recurrence under some mild assumptions. These ensure basic convergence (ergodicity) of the kernel. Further the kernel is shown to be geometric ergodic for a large class of target densities on $\mathbb{R}$. This class even contains…
We show that it is feasible to carry out exact Bayesian inference for non-Gaussian state space models using an adaptive Metropolis Hastings sampling scheme with the likelihood approximated by the particle filter. Furthermore, an adapyive independent Metropolis Hastings sampler based on a mixture of normals proposal is computationally much more efficient than an adaptive random walk proposal because the cost of constructing a good adaptive proposal is negligible compared to the cost of approximating the likelihood. Independent Metropolis Hastings proposals are also attractive because they are e…
Markov Chain Monte Carlo (MCMC) methods are a powerful tool for computation with complex probability distributions. However the performance of such methods is critically dependant on properly tuned parameters, most of which are difficult if not impossible to know a priori for a given target distribution. Adaptive MCMC methods aim to address this by allowing the parameters to be updated during sampling based on previous samples from the chain at the expense of requiring a new theoretical analysis to ensure convergence. In this work we extend the convergence theory of adaptive MCMC methods to a …
Markov Chain Monte Carlo methods are widely used in signal processing and communications for statistical inference and stochastic optimization. In this work, we introduce an efficient adaptive Metropolis-Hastings algorithm to draw samples from generic multi-modal and multi-dimensional target distributions. The proposal density is a mixture of Gaussian densities with all parameters (weights, mean vectors and covariance matrices) updated using all the previously generated samples applying simple recursive rules. Numerical results for the one and two-dimensional cases are provided.
Couplings play a central role in the analysis of Markov chain Monte Carlo algorithms and appear increasingly often in the algorithms themselves, e.g. in convergence diagnostics, parallelization, and variance reduction techniques. Existing couplings of the Metropolis-Hastings algorithm handle the proposal and acceptance steps separately and fall short of the upper bound on one-step meeting probabilities given by the coupling inequality. This paper introduces maximal couplings which achieve this bound while retaining the practical advantages of current methods. We consider the properties of thes…
In this paper, we consider the implications of the fact that parallel raw-power can be exploited by a generic Metropolis--Hastings algorithm if the proposed values are independent. In particular, we present improvements to the independent Metropolis--Hastings algorithm that significantly decrease the variance of any estimator derived from the MCMC output, for a null computing cost since those improvements are based on a fixed number of target density evaluations. Furthermore, the techniques developed in this paper do not jeopardize the Markovian convergence properties of the algorithm, since t…
Bayesian modelling and computational inference by Markov chain Monte Carlo (MCMC) is a principled framework for large-scale uncertainty quantification, though is limited in practice by computational cost when implemented in the simplest form that requires simulating an accurate computer model at each iteration of the MCMC. The delayed acceptance Metropolis--Hastings MCMC leverages a reduced model for the forward map to lower the compute cost per iteration, though necessarily reduces statistical efficiency that can, without care, lead to no reduction in the computational cost of computing estim…
Reversible jump MCMC (RJ-MCMC) sampling techniques, which allow to jointly tackle model selection and parameter estimation problems in a coherent Bayesian framework, have become increasingly popular in the signal processing literature since the seminal paper of Andrieu and Doucet (IEEE Trans. Signal Process., 47(10), 1999). Crucial to the implementation of any RJ-MCMC sampler is the computation of the so-called Metropolis-Hastings-Green (MHG) ratio, which determines the acceptance probability for the proposed moves. It turns out that the expression of the MHG ratio that was given in the paper …
MCMC algorithms such as Metropolis-Hastings algorithms are slowed down by the computation of complex target distributions as exemplified by huge datasets. We offer in this paper an approach to reduce the computational costs of such algorithms by a simple and universal divide-and-conquer strategy. The idea behind the generic acceleration is to divide the acceptance step into several parts, aiming at a major reduction in computing time that outranks the corresponding reduction in acceptance probability. The division decomposes the "prior x likelihood" term into a product such that some of its co…
We consider the approximation of expectations with respect to the distribution of a latent Markov process given noisy measurements. This is known as the smoothing problem and is often approached with particle and Markov chain Monte Carlo (MCMC) methods. These methods provide consistent but biased estimators when run for a finite time. We propose a simple way of coupling two MCMC chains built using Particle Independent Metropolis-Hastings (PIMH) to produce unbiased smoothing estimators. Unbiased estimators are appealing in the context of parallel computing, and facilitate the construction of co…
Since its inception the Metropolis-Hastings kernel has been applied in sophisticated ways to address ever more challenging and diverse sampling problems. Its success stems from the flexibility brought by the fact that its verification and sampling implementation rests on a local ``detailed balance'' condition, as opposed to a global condition in the form of a typically intractable integral equation. While checking the local condition is routine in the simplest scenarios, this proves much more difficult for complicated applications involving auxiliary structures and variables. Our aim is to dev…
Couplings play a central role in the analysis of Markov chain convergence and in the construction of novel Markov chain Monte Carlo estimators, diagnostics, and variance reduction techniques. The set of possible couplings is often intractable, frustrating the search for tight bounds and efficient estimators. To address this challenge for algorithms in the Metropolis-Hastings (MH) family, we establish a simple characterization of the set of MH transition kernel couplings. We then extend this result to describe the set of maximal couplings of the MH kernel, resolving an open question of O'Leary …
We consider the problem of inference for nonlinear, multivariate diffusion processes, satisfying Itô stochastic differential equations (SDEs), using data at discrete times that may be incomplete and subject to measurement error. Our starting point is a state-of-the-art correlated pseudo-marginal Metropolis-Hastings algorithm, that uses correlated particle filters to induce strong and positive correlation between successive likelihood estimates. However, unless the measurement error or the dimension of the SDE is small, correlation can be eroded by the resampling steps in the particle filter. W…
We introduce a general framework that constructs estimators with reduced variance for random walk Metropolis and Metropolis-adjusted Langevin algorithms. The resulting estimators require negligible computational cost and are derived in a post-process manner utilising all proposal values of the Metropolis algorithms. Variance reduction is achieved by producing control variates through the approximate solution of the Poisson equation associated with the target density of the Markov chain. The proposed method is based on approximating the target density with a Gaussian and then utilising accurate…
This tutorial provides a gentle introduction to the particle Metropolis-Hastings (PMH) algorithm for parameter inference in nonlinear state-space models together with a software implementation in the statistical programming language R. We employ a step-by-step approach to develop an implementation of the PMH algorithm (and the particle filter within) together with the reader. This final implementation is also available as the package pmhtutorial in the CRAN repository. Throughout the tutorial, we provide some intuition as to how the algorithm operates and discuss some solutions to problems tha…
Statistical Data Assimilation (SDA) is the transfer of information from field or laboratory observations to a user selected model of the dynamical system producing those observations. The data is noisy and the model has errors; the information transfer addresses properties of the conditional probability distribution of the states of the model conditioned on the observations. The quantities of interest in SDA are the conditional expected values of functions of the model state, and these require the approximate evaluation of high dimensional integrals. We introduce a conditional probability dist…
We introduce the Metropolis-Hastings generative adversarial network (MH-GAN), which combines aspects of Markov chain Monte Carlo and GANs. The MH-GAN draws samples from the distribution implicitly defined by a GAN's discriminator-generator pair, as opposed to standard GANs which draw samples from the distribution defined only by the generator. It uses the discriminator from GAN training to build a wrapper around the generator for improved sampling. With a perfect discriminator, this wrapped generator samples from the true distribution on the data exactly even when the generator is imperfect. W…
Shielding studies in neutron transport, with Monte Carlo codes, yield challenging problems of small-probability estimation. The particularity of these studies is that the small probability to estimate is formulated in terms of the distribution of a Markov chain, instead of that of a random vector in more classical cases. Thus, it is not straightforward to adapt classical statistical methods, for estimating small probabilities involving random vectors, to these neutron-transport problems. A recent interacting-particle method for small-probability estimation, relying on the Hastings-Metropolis a…
We present an adaptive method for the automatic scaling of Random-Walk Metropolis-Hastings algorithms, which quickly and robustly identifies the scaling factor that yields a specified overall sampler acceptance probability. Our method relies on the use of the Robbins-Monro search process, whose performance is determined by an unknown steplength constant. We give a very simple estimator of this constant for proposal distributions that are univariate or multivariate normal, together with a sampling algorithm for automating the method. The effectiveness of the algorithm is demonstrated with both …
We consider a pseudo-marginal Metropolis--Hastings kernel $P_m$ that is constructed using an average of $m$ exchangeable random variables, as well as an analogous kernel $P_s$ that averages $s<m$ of these same random variables. Using an embedding technique to facilitate comparisons, we show that the asymptotic variances of ergodic averages associated with $P_m$ are lower bounded in terms of those associated with $P_s$. We show that the bound provided is tight and disprove a conjecture that when the random variables to be averaged are independent, the asymptotic variance under $P_m$ is never le…
University of California, Irvine（加州大学尔湾分校）；University of Cambridge（剑桥大学）；University of Amsterdam（阿姆斯特丹大学）
Can we make Bayesian posterior MCMC sampling more efficient when faced with very large datasets? We argue that computing the likelihood for N datapoints in the Metropolis-Hastings (MH) test to reach a single binary decision is computationally inefficient. We introduce an approximate MH rule based on a sequential hypothesis test that allows us to accept or reject samples with high confidence using only a fraction of the data required for the exact MH rule. While this method introduces an asymptotic bias, we show that this bias can be controlled and is more than offset by a decrease in variance …
We analyse computational efficiency of Metropolis-Hastings algorithms with AR(1) process proposals. These proposals include, as a subclass, discretized Langevin diffusion (e.g. MALA) and discretized Hamiltonian dynamics (e.g. HMC). By including the effect of Metropolis-Hastings we extend earlier work by Fox and Parker, who used matrix splitting techniques to analyse the performance and improve efficiency of AR(1) processes for targeting Gaussian distributions. Our research enables analysis of MCMC methods that draw samples from non-Gaussian target distributions by using AR(1) process proposals…
The missing data issue often complicates the task of estimating generalized linear models (GLMs). We describe why the pseudo-marginal Metropolis-Hastings algorithm, used in this setting, is an effective strategy for parameter estimation. This approach requires fewer assumptions, it provides joint inferences on the parameters in the likelihood, the covariate model, and the parameters of the missingness-mechanism, and there is no logical inconsistency of assuming that there are multiple posterior distributions. Moreover, this approach is asymptotically exact, just like most other Markov chain Mo…
A classical approach for approximating expectations of functions w.r.t. partially known distributions is to compute the average of function values along a trajectory of a Metropolis-Hastings (MH) Markov chain. A key part in the MH algorithm is a suitable acceptance/rejection of a proposed state, which ensures the correct stationary distribution of the resulting Markov chain. However, the rejection of proposals causes highly correlated samples. In particular, when a state is rejected it is not taken any further into account. In contrast to that we consider a MH importance sampling estimator whi…
Markov chain Monte Carlo (MCMC) methods to sample from a probability distribution $π$ defined on a space $(Θ,\mathcal{T})$ consist of the simulation of realisations of Markov chains $\{θ_{n},n\geq1\}$ of invariant distribution $π$ and such that the distribution of $θ_{i}$ converges to $π$ as $i\rightarrow\infty$. In practice one is typically interested in the computation of expectations of functions, say $f$, with respect to $π$ and it is also required that averages $M^{-1}\sum_{n=1}^{M}f(θ_{n})$ converge to the expectation of interest. The iterative nature of MCMC makes it difficult to develo…
Hamiltonian Monte Carlo (HMC) is a powerful Markov Chain Monte Carlo (MCMC) method for sampling from complex high-dimensional continuous distributions. However, in many situations it is necessary or desirable to combine HMC with other Metropolis-Hastings (MH) samplers. The common HMC-within-Gibbs strategy implies a trade-off between long HMC trajectories and more frequent other MH updates. Addressing this trade-off has been the focus of several recent works. In this paper we propose Metropolis Augmented Hamiltonian Monte Carlo (MAHMC), an HMC variant that allows MH updates within HMC and elimi…
High quality risk adjustment in health insurance markets weakens insurer incentives to engage in inefficient behavior to attract lower-cost enrollees. We propose a novel methodology based on Markov Chain Monte Carlo methods to improve risk adjustment by clustering diagnostic codes into risk groups optimal for health expenditure prediction. We test the performance of our methodology against common alternatives using panel data from 500 thousand enrollees of the Colombian Healthcare System. Results show that our methodology outperforms common alternatives and suggest that it has potential to imp…
In order to construct accurate proposers for Metropolis-Hastings Markov Chain Monte Carlo, we integrate ideas from probabilistic graphical models and neural networks in an open-source framework we call Lightweight Inference Compilation (LIC). LIC implements amortized inference within an open-universe declarative probabilistic programming language (PPL). Graph neural networks are used to parameterize proposal distributions as functions of Markov blankets, which during "compilation" are optimized to approximate single-site Gibbs sampling distributions. Unlike prior work in inference compilation …
Metropolis-Hastings (MH) is a commonly-used MCMC algorithm, but it can be intractable on large datasets due to requiring computations over the whole dataset. In this paper, we study minibatch MH methods, which instead use subsamples to enable scaling. We observe that most existing minibatch MH methods are inexact (i.e. they may change the target distribution), and show that this inexactness can cause arbitrarily large errors in inference. We propose a new exact minibatch MH method, TunaMH, which exposes a tunable trade-off between its batch size and its theoretically guaranteed convergence rat…
Markov Chain Monte Carlo (MCMC) algorithms are widely used for stochastic optimization, sampling, and integration of mathematical objective functions, in particular, in the context of Bayesian inverse problems and parameter estimation. For decades, the algorithm of choice in MCMC simulations has been the Metropolis-Hastings (MH) algorithm. An advancement over the traditional MH-MCMC sampler is the Delayed-Rejection Adaptive Metropolis (DRAM). In this paper, we present MatDRAM, a stochastic optimization, sampling, and Monte Carlo integration toolbox in MATLAB which implements a variant of the D…
Stanford University（斯坦福大学）；University of Sydney（悉尼大学）
Traditional MCMC algorithms are computationally intensive and do not scale well to large data. In particular, the Metropolis-Hastings (MH) algorithm requires passing over the entire dataset to evaluate the likelihood ratio in each iteration. We propose a general framework for performing MH-MCMC using mini-batches of the whole dataset and show that this gives rise to approximately a tempered stationary distribution. We prove that the algorithm preserves the modes of the original target distribution and derive an error bound on the approximation with mild assumptions on the likelihood. To furthe…
National Research University Higher School of Economics（国家研究型高等经济学院）；Skolkovo Institute of Science and Technology（斯科尔科沃科学技术研究院）；Samsung AI Center Moscow（三星莫斯科人工智能中心）；HSE（高等经济学院）；Skoltech（斯科尔科沃科学技术研究院）
A significant part of MCMC methods can be considered as the Metropolis-Hastings (MH) algorithm with different proposal distributions. From this point of view, the problem of constructing a sampler can be reduced to the question - how to choose a proposal for the MH algorithm? To address this question, we propose to learn an independent sampler that maximizes the acceptance rate of the MH algorithm, which, as we demonstrate, is highly related to the conventional variational inference. For Bayesian inference, the proposed method compares favorably against alternatives to sample from the posterio…
The Metropolis-Hastings (MH) algorithm is the prototype for a class of Markov chain Monte Carlo methods that propose transitions between states and then accept or reject the proposal. These methods generate a correlated sequence of random samples that convey information about the desired probability distribution. Deciding how this information gets recorded is an important step in the practical design of MH-class algorithm implementations. Many implementations discard most of this information in order to reduce demands on storage capacity and disk writing throughput. Here, we describe how recor…
Proposals for Metropolis-Hastings MCMC derived by discretizing Langevin diffusion or Hamiltonian dynamics are examples of stochastic autoregressive proposals that form a natural wider class of proposals with equivalent computability. We analyze Metropolis-Hastings MCMC with stochastic autoregressive proposals applied to target distributions that are absolutely continuous with respect to some Gaussian distribution to derive expressions for expected acceptance probability and expected jump size, as well as measures of computational cost, in the limit of high dimension. Thus, we are able to unify…
Component-wise MCMC algorithms, including Gibbs and conditional Metropolis-Hastings samplers, are commonly used for sampling from multivariate probability distributions. A long-standing question regarding Gibbs algorithms is whether a deterministic-scan (systematic-scan) sampler converges faster than its random-scan counterpart. We answer this question when the samplers involve two components by establishing an exact quantitative relationship between the $L^2$ convergence rates of the two samplers. The relationship shows that the deterministic-scan sampler converges faster. We also establish q…
This paper discusses a Metropolis-Hastings algorithm developed by \citeA{MarsmanIsing}. The algorithm is derived from first principles, and it is proven that the algorithm becomes more efficient with more data and meets the growing demands of large scale educational measurement.
This short note is a self-contained and basic introduction to the Metropolis-Hastings algorithm, this ubiquitous tool used for producing dependent simulations from an arbitrary distribution. The document illustrates the principles of the methodology on simple examples with R codes and provides references to the recent extensions of the method.
Many applications in signal processing require the estimation of some parameters of interest given a set of observed data. More specifically, Bayesian inference needs the computation of {\it a-posteriori} estimators which are often expressed as complicated multi-dimensional integrals. Unfortunately, analytical expressions for these estimators cannot be found in most real-world applications, and Monte Carlo methods are the only feasible approach. A very powerful class of Monte Carlo techniques is formed by the Markov Chain Monte Carlo (MCMC) algorithms. They generate a Markov chain such that it…
We propose a new kernel for Metropolis Hastings called Directional Metropolis Hastings (DMH) with multivariate update where the proposal kernel has state dependent covariance matrix. We use the derivative of the target distribution at the current state to change the orientation of the proposal distribution, therefore producing a more plausible proposal. We study the conditions for geometric ergodicity of our algorithm and provide necessary and sufficient conditions for convergence. We also suggest a scheme for adaptively update the variance parameter and study the conditions of ergodicity of t…
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 …
When an unbiased estimator of the likelihood is used within a Metropolis--Hastings chain, it is necessary to trade off the number of Monte Carlo samples used to construct this estimator against the asymptotic variances of averages computed under this chain. Many Monte Carlo samples will typically result in Metropolis--Hastings averages with lower asymptotic variances than the corresponding Metropolis--Hastings averages using fewer samples. However, the computing time required to construct the likelihood estimator increases with the number of Monte Carlo samples. Under the assumption that the d…
We present a new multiple-try Metropolis-Hastings algorithm designed to be especially beneficial when a tailored proposal distribution is available. The algorithm is based on a given acyclic graph $G$, where one of the nodes in $G$, $k$ say, contains the current state of the Markov chain and the remaining nodes contain proposed states generated by applying the tailored proposal distribution. The Metropolis-Hastings algorithm alternates between two types of updates. The first update type is using the tailored proposal distribution to generate new states in all nodes in $G$ except in node $k$. T…
