We consider importance sampling (IS) type weighted estimators based on Markov chain Monte Carlo (MCMC) targeting an approximate marginal of the target distribution. In the context of Bayesian latent variable models, the MCMC typically operates on the hyperparameters, and the subsequent weighting may be based on IS or sequential Monte Carlo (SMC), but allows for multilevel techniques as well. The IS approach provides a natural alternative to delayed acceptance (DA) pseudo-marginal/particle MCMC, and has many advantages over DA, including a straightforward parallelisation and additional flexibility in MCMC implementation. We detail minimal conditions which ensure strong consistency of the suggested estimators, and provide central limit theorems with expressions for asymptotic variances. We demonstrate how our method can make use of SMC in the state space models context, using Laplace approximations and time-discretised diffusions. Our experimental results are promising and show that the IS type approach can provide substantial gains relative to an analogous DA scheme, and is often competitive even without parallelisation.
We establish an ordering criterion for the asymptotic variances of two consistent Markov chain Monte Carlo (MCMC) estimators: an importance sampling (IS) estimator, based on an approximate reversible chain and subsequent IS weighting, and a standard MCMC estimator, based on an exact reversible chain. Essentially, we relax the criterion of the Peskun type covariance ordering by considering two different invariant probabilities, and obtain, in place of a strict ordering of asymptotic variances, a bound of the asymptotic variance of IS by that of the direct MCMC. Simple examples show that IS can …
Speeding up Markov Chain Monte Carlo (MCMC) for datasets with many observations by data subsampling has recently received considerable attention. A pseudo-marginal MCMC method is proposed that estimates the likelihood by data subsampling using a block-Poisson estimator. The estimator is a product of Poisson estimators, allowing us to update a single block of subsample indicators in each MCMC iteration so that a desired correlation is achieved between the logs of successive likelihood estimates. This is important since pseudo-marginal MCMC with positively correlated likelihood estimates can use…
Particle Markov chain Monte Carlo (pMCMC) is now a popular method for performing Bayesian statistical inference on challenging state space models (SSMs) with unknown static parameters. It uses a particle filter (PF) at each iteration of an MCMC algorithm to unbiasedly estimate the likelihood for a given static parameter value. However, pMCMC can be computationally intensive when a large number of particles in the PF is required, such as when the data is highly informative, the model is misspecified and/or the time series is long. In this paper we exploit the ensemble Kalman filter (EnKF) devel…
A general methodology is presented for the construction and effective use of control variates for reversible MCMC samplers. The values of the coefficients of the optimal linear combination of the control variates are computed, and adaptive, consistent MCMC estimators are derived for these optimal coefficients. All methodological and asymptotic arguments are rigorously justified. Numerous MCMC simulation examples from Bayesian inference applications demonstrate that the resulting variance reduction can be quite dramatic.
Gaussian processes (GPs) are frequently used in machine learning and statistics to construct powerful models. However, when employing GPs in practice, important considerations must be made, regarding the high computational burden, approximation of the posterior, choice of the covariance function and inference of its hyperparmeters. To address these issues, Hensman et al. (2015) combine variationally sparse GPs with Markov chain Monte Carlo (MCMC) to derive a scalable, flexible and general framework for GP models. Nevertheless, the resulting approach requires intractable likelihood evaluations …
Selecting between competing statistical models is a challenging problem especially when the competing models are non-nested. In this paper we offer a simple solution by devising an algorithm which combines MCMC and importance sampling to obtain computationally efficient estimates of the marginal likelihood which can then be used to compare the models. The algorithm is successfully applied to longitudinal epidemic and time series data sets and shown to outperform existing methods for computing the marginal likelihood.
We investigate the efficiency of a marginal likelihood estimator where the product of the marginal posterior distributions is used as an importance-sampling function. The approach is generally applicable to multi-block parameter vector settings, does not require additional Markov Chain Monte Carlo (MCMC) sampling and is not dependent on the type of MCMC scheme used to sample from the posterior. The proposed approach is applied to normal regression models, finite normal mixtures and longitudinal Poisson models, and leads to accurate marginal likelihood estimates.
Markov chain Monte Carlo (MCMC) methods asymptotically sample from complex probability distributions. The pseudo-marginal MCMC framework only requires an unbiased estimator of the unnormalized probability distribution function to construct a Markov chain. However, the resulting chains are harder to tune to a target distribution than conventional MCMC, and the types of updates available are limited. We describe a general way to clamp and update the random numbers used in a pseudo-marginal method's unbiased estimator. In this framework we can use slice sampling and other adaptive methods. We obt…
We consider batch size selection for a general class of multivariate batch means variance estimators, which are computationally viable for high-dimensional Markov chain Monte Carlo simulations. We derive the asymptotic mean squared error for this class of estimators. Further, we propose a parametric technique for estimating optimal batch sizes and discuss practical issues regarding the estimating process. Vector auto-regressive, Bayesian logistic regression, and Bayesian dynamic space-time examples illustrate the quality of the estimation procedure where the proposed optimal batch sizes outper…
Autocovariances are a fundamental quantity of interest in Markov chain Monte Carlo (MCMC) simulations with autocorrelation function (ACF) plots being an integral visualization tool for performance assessment. Unfortunately, for slow-mixing Markov chains, the empirical autocovariance can highly underestimate the truth. For multiple-chain MCMC sampling, we propose a globally-centered estimator of the autocovariance function (G-ACvF) that exhibits significant theoretical and empirical improvements. We show that the bias of the G-ACvF estimator is smaller than the bias of the current state-of-the-…
Constructing unbiased estimators from Markov chain Monte Carlo (MCMC) outputs is a difficult problem that has recently received a lot of attention in the statistics and machine learning communities. However, the current unbiased MCMC framework only works when the quantity of interest is an expectation, which excludes many practical applications. In this paper, we propose a general method for constructing unbiased estimators for functions of expectations and extend it to construct unbiased estimators for nested expectations. Our approach combines and generalizes the unbiased MCMC and Multilevel…
We propose a generic Markov Chain Monte Carlo (MCMC) algorithm to speed up computations for datasets with many observations. A key feature of our approach is the use of the highly efficient difference estimator from the survey sampling literature to estimate the log-likelihood accurately using only a small fraction of the data. Our algorithm improves on the $O(n)$ complexity of regular MCMC by operating over local data clusters instead of the full sample when computing the likelihood. The likelihood estimate is used in a Pseudo-marginal framework to sample from a perturbed posterior which is w…
Markov chain Monte Carlo (MCMC) is an established approach for uncertainty quantification and propagation in scientific applications. A key challenge in applying MCMC to scientific domains is computation: the target density of interest is often a function of expensive computations, such as a high-fidelity physical simulation, an intractable integral, or a slowly-converging iterative algorithm. Thus, using an MCMC algorithms with an expensive target density becomes impractical, as these expensive computations need to be evaluated at each iteration of the algorithm. In practice, these computatio…
Recently-proposed particle MCMC methods provide a flexible way of performing Bayesian inference for parameters governing stochastic kinetic models defined as Markov (jump) processes (MJPs). Each iteration of the scheme requires an estimate of the marginal likelihood calculated from the output of a sequential Monte Carlo scheme (also known as a particle filter). Consequently, the method can be extremely computationally intensive. We therefore aim to avoid most instances of the expensive likelihood calculation through use of a fast approximation. We consider two approximations: the chemical Lang…
Markov chain Monte Carlo (MCMC) algorithms are widely used to sample from complicated distributions, especially to sample from the posterior distribution in Bayesian inference. However, MCMC is not directly applicable when facing the doubly intractable problem. In this paper, we discussed and compared two existing solutions -- Pseudo-marginal Monte Carlo and Exchange Algorithm. This paper also proposes a novel algorithm: Multi-armed Bandit MCMC (MABMC), which chooses between two (or more) randomized acceptance ratios in each step. MABMC could be applied directly to incorporate Pseudo-marginal …
The generalized partial credit model (GPCM) is a popular polytomous IRT model that has been widely used in large-scale educational surveys and health care services. Same as other IRT models, GPCM can be estimated via marginal maximum likelihood estimation (MMLE) and Markov chain Monte Carlo (MCMC) methods. While studies comparing MMLE and MCMC as estimation methods for other polytomous IRT models such as the nominal response model and the graded response model exist in literature, no studies have compared how well MMLE and MCMC recover the model parameters of GPCM. In the current study, a comp…
I show how any reversible Markov chain on a finite state space that is irreducible, and hence suitable for estimating expectations with respect to its invariant distribution, can be used to construct a non-reversible Markov chain on a related state space that can also be used to estimate these expectations, with asymptotic variance at least as small as that using the reversible chain (typically smaller). The non-reversible chain achieves this improvement by avoiding (to the extent possible) transitions that backtrack to the state from which the chain just came. The proof that this modification…
Performing numerical integration when the integrand itself cannot be evaluated point-wise is a challenging task that arises in statistical analysis, notably in Bayesian inference for models with intractable likelihood functions. Markov chain Monte Carlo (MCMC) algorithms have been proposed for this setting, such as the pseudo-marginal method for latent variable models and the exchange algorithm for a class of undirected graphical models. As with any MCMC algorithm, the resulting estimators are justified asymptotically in the limit of the number of iterations, but exhibit a bias for any fixed n…
Exact approximations of Markov chain Monte Carlo (MCMC) algorithms are a general emerging class of sampling algorithms. One of the main ideas behind exact approximations consists of replacing intractable quantities required to run standard MCMC algorithms, such as the target probability density in a Metropolis-Hastings algorithm, with estimators. Perhaps surprisingly, such approximations lead to powerful algorithms which are exact in the sense that they are guaranteed to have correct limiting distributions. In this paper we discover a general framework which allows one to compare, or order, pe…
In applications of Gaussian processes where quantification of uncertainty is a strict requirement, it is necessary to accurately characterize the posterior distribution over Gaussian process covariance parameters. Normally, this is done by means of standard Markov chain Monte Carlo (MCMC) algorithms. Motivated by the issues related to the complexity of calculating the marginal likelihood that can make MCMC algorithms inefficient, this paper develops an alternative inference framework based on Adaptive Multiple Importance Sampling (AMIS). This paper studies the application of AMIS in the case o…
Zalando Research, Zalando SE（Zalando研究部，Zalando公司）；Zuse Institute Berlin（柏林Zuse研究所）
Markov chain (MC) algorithms are ubiquitous in machine learning and statistics and many other disciplines. Typically, these algorithms can be formulated as acceptance rejection methods. In this work we present a novel estimator applicable to these methods, dubbed Markov chain importance sampling (MCIS), which efficiently makes use of rejected proposals. For the unadjusted Langevin algorithm, it provides a novel way of correcting the discretization error. Our estimator satisfies a central limit theorem and improves on error per CPU cycle, often to a large extent. As a by-product it enables esti…
We consider Metropolis Hastings MCMC in cases where the log of the ratio of target distributions is replaced by an estimator. The estimator is based on m samples from an independent online Monte Carlo simulation. Under some conditions on the distribution of the estimator the process resembles Metropolis Hastings MCMC with a randomized transition kernel. When this is the case there is a correction to the estimated acceptance probability which ensures that the target distribution remains the equilibrium distribution. The simplest versions of the Penalty Method of Ceperley and Dewing (1999), the …
We consider the efficient use of an approximation within Markov chain Monte Carlo (MCMC), with subsequent importance sampling (IS) correction of the Markov chain inexact output, leading to asymptotically exact inference. We detail convergence and central limit theorems for the resulting MCMC-IS estimators. We also consider the case where the approximate Markov chain is pseudo-marginal, requiring unbiased estimators for its approximate marginal target. Convergence results with asymptotic variance formulae are shown for this case, and for the case where the IS weights based on unbiased estimator…
University of Liège（列日大学）；University of Vienna（维也纳大学）
Posterior inference with an intractable likelihood is becoming an increasingly common task in scientific domains which rely on sophisticated computer simulations. Typically, these forward models do not admit tractable densities forcing practitioners to make use of approximations. This work introduces a novel approach to address the intractability of the likelihood and the marginal model. We achieve this by learning a flexible amortized estimator which approximates the likelihood-to-evidence ratio. We demonstrate that the learned ratio estimator can be embedded in MCMC samplers to approximate l…
We propose Subsampling MCMC, a Markov Chain Monte Carlo (MCMC) framework where the likelihood function for $n$ observations is estimated from a random subset of $m$ observations. We introduce a highly efficient unbiased estimator of the log-likelihood based on control variates, such that the computing cost is much smaller than that of the full log-likelihood in standard MCMC. The likelihood estimate is bias-corrected and used in two dependent pseudo-marginal algorithms to sample from a perturbed posterior, for which we derive the asymptotic error with respect to $n$ and $m$, respectively. We p…
Markov chain Monte Carlo (MCMC) is a sampling-based method for estimating features of probability distributions. MCMC methods produce a serially correlated, yet representative, sample from the desired distribution. As such it can be difficult to know when the MCMC method is producing reliable results. We introduce some fundamental methods for ensuring a trustworthy simulation experiment. In particular, we present a workflow for output analysis in MCMC providing estimators, approximate sampling distributions, stopping rules, and visualization tools.
A general methodology is introduced for the construction and effective application of control variates to estimation problems involving data from reversible MCMC samplers. We propose the use of a specific class of functions as control variates, and we introduce a new, consistent estimator for the values of the coefficients of the optimal linear combination of these functions. The form and proposed construction of the control variates is derived from our solution of the Poisson equation associated with a specific MCMC scenario. The new estimator, which can be applied to the same MCMC sample, is…
Interest is in evaluating, by Markov chain Monte Carlo (MCMC) simulation, the expected value of a function with respect to a, possibly unnormalized, probability distribution. A general purpose variance reduction technique for the MCMC estimator, based on the zero-variance principle introduced in the physics literature, is proposed. Conditions for asymptotic unbiasedness of the zero-variance estimator are derived. A central limit theorem is also proved under regularity conditions. The potential of the idea is illustrated with real applications to probit, logit and GARCH Bayesian models. For all…
We assume a drift condition towards a small set and bound the mean square error of estimators obtained by taking averages along a single trajectory of a Markov chain Monte Carlo algorithm. We use these bounds to construct fixed-width nonasymptotic confidence intervals. For a possibly unbounded function $f:\stany \to R,$ let $I=\int_{\stany} f(x) π(x) dx$ be the value of interest and $\hat{I}_{t,n}=(1/n)\sum_{i=t}^{t+n-1}f(X_i)$ its MCMC estimate. Precisely, we derive lower bounds for the length of the trajectory $n$ and burn-in time $t$ which ensure that $$P(|\hat{I}_{t,n}-I|\leq \varepsilon)\…
Determining risk contributions of unit exposures to portfolio-wide economic capital is an important task in financial risk management. Computing risk contributions involves difficulties caused by rare-event simulations. In this study, we address the problem of estimating risk contributions when the total risk is measured by value-at-risk (VaR). Our proposed estimator of VaR contributions is based on the Metropolis-Hasting (MH) algorithm, which is one of the most prevalent Markov chain Monte Carlo (MCMC) methods. Unlike existing estimators, our MH-based estimator consists of samples from condit…
A generalized method of moments (GMM) estimator is unreliable for a large number of moment conditions, that is, it is comparable, or larger than the sample size. While classical GMM literature proposes several provisions to this problem, its Bayesian counterpart (i.e., Bayesian inference using a GMM criterion as a quasi-likelihood) almost totally ignores it. This study bridges this gap by proposing an adaptive Markov Chain Monte Carlo (MCMC) approach to a GMM inference with many moment conditions. Particularly, this study focuses on the adaptive tuning of a weighting matrix on the fly. Our pro…
Markov chain Monte Carlo (MCMC) methods provide consistent of integrals as the number of iterations goes to infinity. MCMC estimators are generally biased after any fixed number of iterations. We propose to remove this bias by using couplings of Markov chains together with a telescopic sum argument of Glynn and Rhee (2014). The resulting unbiased estimators can be computed independently in parallel. We discuss practical couplings for popular MCMC algorithms. We establish the theoretical validity of the proposed estimators and study their efficiency relative to the underlying MCMC algorithms. F…
Convergence Speed and Approximation Accuracy of Numerical MCMC
Monash University（莫纳什大学）；Columbia University（哥伦比亚大学）；King Abdullah University of Science and Technology（阿卜杜拉国王科技大学）；National University of Singapore（新加坡国立大学）
In the thesis we take the split chain approach to analyzing Markov chains and use it to establish fixed-width results for estimators obtained via Markov chain Monte Carlo procedures (MCMC). Theoretical results include necessary and sufficient conditions in terms of regeneration for central limit theorems for ergodic Markov chains and a regenerative proof of a CLT version for uniformly ergodic Markov chains with $E_πf^2< \infty.$ To obtain asymptotic confidence intervals for MCMC estimators, strongly consistent estimators of the asymptotic variance are essential. We relax assumptions required t…
Estimating Transition Rates in Two-State Non-Homogeneous Markov Jump Processes with Intermittent Observations: A Pseudo-Marginal McMC Approach via Honest Times
Bayesian inference in the presence of an intractable likelihood function is computationally challenging. When following a Markov chain Monte Carlo (MCMC) approach to approximate the posterior distribution in this context, one typically either uses MCMC schemes which target the joint posterior of the parameters and some auxiliary latent variables, or pseudo-marginal Metropolis--Hastings (MH) schemes. The latter mimic a MH algorithm targeting the marginal posterior of the parameters by approximating unbiasedly the intractable likelihood. However, in scenarios where the parameters and auxiliary v…
We present an R package bssm for Bayesian non-linear/non-Gaussian state space modelling. Unlike the existing packages, bssm allows for easy-to-use approximate inference based on Gaussian approximations such as the Laplace approximation and the extended Kalman filter. The package accommodates also discretely observed latent diffusion processes. The inference is based on fully automatic, adaptive Markov chain Monte Carlo (MCMC) on the hyperparameters, with optional importance sampling post-correction to eliminate any approximation bias. The package implements also a direct pseudo-marginal MCMC a…
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…
In this paper we examine the implications of the statistical large sample theory for the computational complexity of Bayesian and quasi-Bayesian estimation carried out using Metropolis random walks. Our analysis is motivated by the Laplace-Bernstein-Von Mises central limit theorem, which states that in large samples the posterior or quasi-posterior approaches a normal density. Using the conditions required for the central limit theorem to hold, we establish polynomial bounds on the computational complexity of general Metropolis random walks methods in large samples. Our analysis covers cases w…
When targeting a distribution that is artificially invariant under some permutations, Markov chain Monte Carlo (MCMC) algorithms face the label-switching problem, rendering marginal inference particularly cumbersome. Such a situation arises, for example, in the Bayesian analysis of finite mixture models. Adaptive MCMC algorithms such as adaptive Metropolis (AM), which self-calibrates its proposal distribution using an online estimate of the covariance matrix of the target, are no exception. To address the label-switching issue, relabeling algorithms associate a permutation to each MCMC sample,…
University of Washington（华盛顿大学）；UC Berkeley（加州大学伯克利分校）
State space models (SSMs) are a flexible approach to modeling complex time series. However, inference in SSMs is often computationally prohibitive for long time series. Stochastic gradient MCMC (SGMCMC) is a popular method for scalable Bayesian inference for large independent data. Unfortunately when applied to dependent data, such as in SSMs, SGMCMC's stochastic gradient estimates are biased as they break crucial temporal dependencies. To alleviate this, we propose stochastic gradient estimators that control this bias by performing additional computation in a `buffer' to reduce breaking depen…
Markov chain Monte Carlo (MCMC) is widely regarded as one of the most important algorithms of the 20th century. Its guarantees of asymptotic convergence, stability, and estimator-variance bounds using only unnormalized probability functions make it indispensable to probabilistic programming. In this paper, we introduce the TensorFlow Probability MCMC toolkit, and discuss some of the considerations that motivated its design.
Markov chain Monte Carlo (MCMC) algorithms are used to estimate features of interest of a distribution. The Monte Carlo error in estimation has an asymptotic normal distribution whose multivariate nature has so far been ignored in the MCMC community. We present a class of multivariate spectral variance estimators for the asymptotic covariance matrix in the Markov chain central limit theorem and provide conditions for strong consistency. We examine the finite sample properties of the multivariate spectral variance estimators and its eigenvalues in the context of a vector autoregressive process …
Handling multimodality that commonly arises from complicated statistical models remains a challenge. Current Markov chain Monte Carlo (MCMC) methodology tackling this subject is based on an ensemble of chains targeting a product of power-tempered distributions. Despite the theoretical validity of such methods, practical implementations typically suffer from bad mixing and slow convergence due to the high-computation cost involved. In this work we study novel extensions of the t-walk algorithm, an existing MCMC method that is inexpensive and invariant to affine transformations of the state spac…
In many hierarchical inverse problems, not only do we want to estimate high- or infinite-dimensional model parameters in the parameter-to-observable maps, but we also have to estimate hyperparameters that represent critical assumptions in the statistical and mathematical modeling processes. As a joint effect of high-dimensionality, nonlinear dependence, and non-concave structures in the joint posterior posterior distribution over model parameters and hyperparameters, solving inverse problems in the hierarchical Bayesian setting poses a significant computational challenge. In this work, we aim …
Purdue University（普渡大学）；University of Southern California（南加州大学）；Durham University（杜伦大学）
Replica exchange stochastic gradient Langevin dynamics (reSGLD) has shown promise in accelerating the convergence in non-convex learning; however, an excessively large correction for avoiding biases from noisy energy estimators has limited the potential of the acceleration. To address this issue, we study the variance reduction for noisy energy estimators, which promotes much more effective swaps. Theoretically, we provide a non-asymptotic analysis on the exponential acceleration for the underlying continuous-time Markov jump process; moreover, we consider a generalized Girsanov theorem which …
The rapid development of computing power and efficient Markov Chain Monte Carlo (MCMC) simulation algorithms have revolutionized Bayesian statistics, making it a highly practical inference method in applied work. However, MCMC algorithms tend to be computationally demanding, and are particularly slow for large datasets. Data subsampling has recently been suggested as a way to make MCMC methods scalable on massively large data, utilizing efficient sampling schemes and estimators from the survey sampling literature. These developments tend to be unknown by many survey statisticians who tradition…
Stochastic gradient MCMC (SG-MCMC) algorithms have proven useful in scaling Bayesian inference to large datasets under an assumption of i.i.d data. We instead develop an SG-MCMC algorithm to learn the parameters of hidden Markov models (HMMs) for time-dependent data. There are two challenges to applying SG-MCMC in this setting: The latent discrete states, and needing to break dependencies when considering minibatches. We consider a marginal likelihood representation of the HMM and propose an algorithm that harnesses the inherent memory decay of the process. We demonstrate the effectiveness of …
An MCMC simulation method based on a two stage delayed rejection Metropolis-Hastings algorithm is proposed to estimate a factor multivariate stochastic volatility model. The first stage uses kstep iteration towards the mode, with k small, and the second stage uses an adaptive random walk proposal density. The marginal likelihood approach of Chib (1995) is used to choose the number of factors, with the posterior density ordinates approximated by Gaussian copula. Simulation and real data applications suggest that the proposed simulation method is computationally much more efficient than the appr…
