High-dimensional limit theorems have been shown useful to derive tuning rules for finding the optimal scaling in random-walk Metropolis algorithms. The assumptions under which weak convergence results are proved are however restrictive: the target density is typically assumed to be of a product form. Users may thus doubt the validity of such tuning rules in practical applications. In this paper, we shed some light on optimal-scaling problems from a different perspective, namely a large-sample one. This allows to prove weak convergence results under realistic assumptions and to propose novel parameter-dimension-dependent tuning guidelines. The proposed guidelines are consistent with previous ones when the target density is close to having a product form, and the results highlight that the correlation structure has to be accounted for to avoid performance deterioration if that is not the case, while justifying the use of a natural (asymptotically exact) approximation to the correlation matrix that can be employed for the very first algorithm run.
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.
In this paper we study the asymptotic behavior of the Random-Walk Metropolis algorithm on probability densities with two different `scales', where most of the probability mass is distributed along certain key directions with the `orthogonal' directions containing relatively less mass. Such class of probability measures arise in various applied contexts including Bayesian inverse problems where the posterior measure concentrates on a sub-manifold when the noise variance goes to zero. When the target measure concentrates on a linear sub-manifold, we derive analytically a diffusion limit for the …
We study the computational complexity of a Metropolis-Hastings algorithm for Bayesian community detection. We first establish a posterior strong consistency result for a natural prior distribution on stochastic block models under the optimal signal-to-noise ratio condition in the literature. We then give a set of conditions that guarantee rapid mixing of a simple Metropolis-Hastings algorithm. The mixing time analysis is based on a careful study of posterior ratios and a canonical path argument to control the spectral gap of the Markov chain.
Motivated by Bayesian inference with highly informative data we analyze the performance of random walk-like Metropolis-Hastings algorithms for approximate sampling of increasingly concentrating target distributions. We focus on Gaussian proposals which use a Hessian-based approximation of the target covariance. By means of pushforward transition kernels we show that for Gaussian target measures the spectral gap of the corresponding Metropolis-Hastings algorithm is independent of the concentration of the posterior, i.e., the noise level in the observational data that is used for Bayesian infere…
This paper considers the optimal scaling problem for high-dimensional random walk Metropolis algorithms for densities which are differentiable in Lp mean but which may be irregular at some points (like the Laplace density for example) and/or are supported on an interval. Our main result is the weak convergence of the Markov chain (appropriately rescaled in time and space) to a Langevin diffusion process as the dimension d goes to infinity. Because the log-density might be non-differentiable, the limiting diffusion could be singular. The scaling limit is established under assumptions which are …
We present a Metropolis-Hastings Markov chain Monte Carlo (MCMC) algorithm for detecting hidden variables in a continuous time Bayesian network (CTBN), which uses reversible jumps in the sense defined by (Green 1995). In common with several Monte Carlo algorithms, one of the most recent and important by (Rao and Teh 2013), our algorithm exploits uniformization techniques under which a continuous time Markov process can be represented as a marked Poisson process. We exploit this in a novel way. We show that our MCMC algorithm can be more efficient than those of likelihood weighting type, as in …
University of South Carolina（南卡罗来纳大学）；University of North Carolina Charlotte（北卡罗来纳大学夏洛特分校）
Markov Chain Monte Carlo (MCMC) methods have a drawback when working with a target distribution or likelihood function that is computationally expensive to evaluate, specially when working with big data. This paper focuses on Metropolis-Hastings (MH) algorithm for unimodal distributions. Here, an enhanced MH algorithm is proposed that requires less number of expensive function evaluations, has shorter burn-in period, and uses a better proposal distribution. The main innovations include the use of Bayesian optimization to reach the high probability region quickly, emulating the target distribut…
A random-walk Metropolis sampler is geometrically ergodic if its equilibrium density is super-exponentially light and satisfies a curvature condition [Stochastic Process. Appl. 85 (2000) 341-361]. Many applications, including Bayesian analysis with conjugate priors of logistic and Poisson regression and of log-linear models for categorical data result in posterior distributions that are not super-exponentially light. We show how to apply the change-of-variable formula for diffeomorphisms to obtain new densities that do satisfy the conditions for geometric ergodicity. Sampling the new variable …
University of Oxford（牛津大学）；University of British Columbia（不列颠哥伦比亚大学）；The Alan Turing Institute（艾伦·图灵研究所）
Bayesian inference via standard Markov Chain Monte Carlo (MCMC) methods is too computationally intensive to handle large datasets, since the cost per step usually scales like $Θ(n)$ in the number of data points $n$. We propose the Scalable Metropolis-Hastings (SMH) kernel that exploits Gaussian concentration of the posterior to require processing on average only $O(1)$ or even $O(1/\sqrt{n})$ data points per step. This scheme is based on a combination of factorized acceptance probabilities, procedures for fast simulation of Bernoulli processes, and control variate ideas. Contrary to many MCMC …
Markov chain Monte Carlo (MCMC) methods are powerful computational tools for analysis of complex statistical problems. However, their computational efficiency is highly dependent on the chosen proposal distribution, which is generally difficult to find. One way to solve this problem is to use adaptive MCMC algorithms which automatically tune the statistics of a proposal distribution during the MCMC run. A new adaptive MCMC algorithm, called the variational Bayesian adaptive Metropolis (VBAM) algorithm, is developed. The VBAM algorithm updates the proposal covariance matrix using the variationa…
This paper discusses the challenges presented by tall data problems associated with Bayesian classification (specifically binary classification) and the existing methods to handle them. Current methods include parallelizing the likelihood, subsampling, and consensus Monte Carlo. A new method based on the two-stage Metropolis-Hastings algorithm is also proposed. The purpose of this algorithm is to reduce the exact likelihood computational cost in the tall data situation. In the first stage, a new proposal is tested by the approximate likelihood based model. The full likelihood based posterior c…
Biips is a software platform for automatic Bayesian inference with interacting particle systems. Biips allows users to define their statistical model in the probabilistic programming BUGS language, as well as to add custom functions or samplers within this language. Then it runs sequential Monte Carlo based algorithms (particle filters, particle independent Metropolis-Hastings, particle marginal Metropolis-Hastings) in a black-box manner so that to approximate the posterior distribution of interest as well as the marginal likelihood. The software is developed in C++ with interfaces with the so…
In this expository paper we abstract and describe a simple MCMC scheme for sampling from intractable target densities. The approach has been introduced in Gonçalves et al. (2017a) in the specific context of jump-diffusions, and is based on the Barker's algorithm paired with a simple Bernoulli factory type scheme, the so called 2-coin algorithm. In many settings it is an alternative to standard Metropolis-Hastings pseudo-marginal method for simulating from intractable target densities. Although Barker's is well-known to be slightly less efficient than Metropolis-Hastings, the key advantage of o…
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…
Poisson log-linear models are ubiquitous in many applications, and one of the most popular approaches for parametric count regression. In the Bayesian context, however, there are no sufficient specific computational tools for efficient sampling from the posterior distribution of parameters, and standard algorithms, such as random walk Metropolis-Hastings or Hamiltonian Monte Carlo algorithms, are typically used. Herein, we developed an efficient Metropolis-Hastings algorithm and importance sampler to simulate from the posterior distribution of the parameters of Poisson log-linear models under …
Particle Metropolis-Hastings enables Bayesian parameter inference in general nonlinear state space models (SSMs). However, in many implementations a random walk proposal is used and this can result in poor mixing if not tuned correctly using tedious pilot runs. Therefore, we consider a new proposal inspired by quasi-Newton algorithms that may achieve similar (or better) mixing with less tuning. An advantage compared to other Hessian based proposals, is that it only requires estimates of the gradient of the log-posterior. A possible application is parameter inference in the challenging class of…
This paper develops a Bayesian computational platform at the interface between posterior sampling and optimization in models whose marginal likelihoods are difficult to evaluate. Inspired by adversarial optimization, namely Generative Adversarial Networks (GAN), we reframe the likelihood function estimation problem as a classification problem. Pitting a Generator, who simulates fake data, against a Classifier, who tries to distinguish them from the real data, one obtains likelihood (ratio) estimators which can be plugged into the Metropolis-Hastings algorithm. The resulting Markov chains gener…
Bayesian regression trees are flexible non-parametric models that are well suited to many modern statistical regression problems. Many such tree models have been proposed, from the simple single- tree model to more complex tree ensembles. Their non-parametric formulation allows for effective and efficient modeling of datasets exhibiting complex non-linear relationships between the model pre- dictors and observations. However, the mixing behavior of the Markov Chain Monte Carlo (MCMC) sampler is sometimes poor. This is because the proposals in the sampler are typically local alterations of the …
University of Washington（华盛顿大学）；Carnegie Mellon University（卡内基梅隆大学）
Relational learning can be used to augment one data source with other correlated sources of information, to improve predictive accuracy. We frame a large class of relational learning problems as matrix factorization problems, and propose a hierarchical Bayesian model. Training our Bayesian model using random-walk Metropolis-Hastings is impractically slow, and so we develop a block Metropolis-Hastings sampler which uses the gradient and Hessian of the likelihood to dynamically tune the proposal. We demonstrate that a predictive model of brain response to stimuli can be improved by augmenting it…
The multiple-try Metropolis (MTM) algorithm is an extension of the Metropolis-Hastings (MH) algorithm by selecting the proposed state among multiple trials according to some weight function. Although MTM has gained great popularity owing to its faster empirical convergence and mixing than the standard MH algorithm, its theoretical mixing property is rarely studied in the literature due to its complex proposal scheme. We prove that MTM can achieve a mixing time bound smaller than that of MH by a factor of the number of trials under a general setting applicable to high-dimensional model selectio…
We consider the application of active subspaces to inform a Metropolis-Hastings algorithm, thereby aggressively reducing the computational dimension of the sampling problem. We show that the original formulation, as proposed by Constantine, Kent, and Bui-Thanh (SIAM J. Sci. Comput., 38(5):A2779-A2805, 2016), possesses asymptotic bias. Using pseudo-marginal arguments, we develop an asymptotically unbiased variant. Our algorithm is applied to a synthetic multimodal target distribution as well as a Bayesian formulation of a parameter inference problem for a Lorenz-96 system.
Dirichlet process mixture model (DPMM) is a popular Bayesian nonparametric model. In this paper, we apply this model to weighted data and then estimate the un-weighted distribution from the corresponding weighted distribution using the metropolis-Hastings algorithm. We then apply the DPMM with different kernels to simulated and real data sets. In particular, we work with lifetime data in the presence of censored data and then calculate estimated density and survival values.
Pseudo-marginal Metropolis-Hastings (pmMH) is a powerful method for Bayesian inference in models where the posterior distribution is analytical intractable or computationally costly to evaluate directly. It operates by introducing additional auxiliary variables into the model and form an extended target distribution, which then can be evaluated point-wise. In many cases, the standard Metropolis-Hastings is then applied to sample from the extended target and the sought posterior can be obtained by marginalisation. However, in some implementations this approach suffers from poor mixing as the au…
Deterministic compartmental models are predominantly used in the modeling of infectious diseases, though stochastic models are considered more realistic, yet are complicated to estimate due to missing data. In this paper we present a novel algorithm for estimating the stochastic SIR/SEIR epidemic model within a Bayesian framework, which can be readily extended to more complex stochastic compartmental models. Specifically, based on the infinitesimal conditional independence properties of the model, we are able to find a proposal distribution for a Metropolis algorithm which is very close to the…
This work considers black-box Bayesian inference over high-dimensional parameter spaces. The well-known adaptive Metropolis (AM) algorithm of (Haario etal. 2001) is extended herein to scale asymptotically uniformly with respect to the underlying parameter dimension for Gaussian targets, by respecting the variance of the target. The resulting algorithm, referred to as the dimension-independent adaptive Metropolis (DIAM) algorithm, also shows improved performance with respect to adaptive Metropolis on non-Gaussian targets. This algorithm is further improved, and the possibility of probing high-d…
This paper introduces the parallel hierarchical sampler (PHS), a Markov chain Monte Carlo algorithm using several chains simultaneously. The connections between PHS and the parallel tempering (PT) algorithm are illustrated, convergence of PHS joint transition kernel is proved and and its practical advantages are emphasized. We illustrate the inferences obtained using PHS, parallel tempering and the Metropolis-Hastings algorithm for three Bayesian model selection problems, namely Gaussian clustering, the selection of covariates for a linear regression model and the selection of the structure of…
Particle Metropolis-Hastings (PMH) allows for Bayesian parameter inference in nonlinear state space models by combining Markov chain Monte Carlo (MCMC) and particle filtering. The latter is used to estimate the intractable likelihood. In its original formulation, PMH makes use of a marginal MCMC proposal for the parameters, typically a Gaussian random walk. However, this can lead to a poor exploration of the parameter space and an inefficient use of the generated particles. We propose a number of alternative versions of PMH that incorporate gradient and Hessian information about the posterior …
The use of Cauchy Markov random field priors in statistical inverse problems can potentially lead to posterior distributions which are non-Gaussian, high-dimensional, multimodal and heavy-tailed. In order to use such priors successfully, sophisticated optimization and Markov chain Monte Carlo (MCMC) methods are usually required. In this paper, our focus is largely on reviewing recently developed Cauchy difference priors, while introducing interesting new variants, whilst providing a comparison. We firstly propose a one-dimensional second order Cauchy difference prior, and construct new first a…
By mixing the target posterior distribution with a surrogate distribution, of which the normalizing constant is tractable, we propose a method for estimating the marginal likelihood using the Wang-Landau algorithm. We show that a faster convergence of the proposed method can be achieved via the momentum acceleration. Two implementation strategies are detailed: (i) facilitating global jumps between the posterior and surrogate distributions via the Multiple-try Metropolis; (ii) constructing the surrogate via the variational approximation. When a surrogate is difficult to come by, we describe a n…
Bayesian models that can handle both over and under dispersed counts are rare in the literature, perhaps because full probability distributions for dispersed counts are rather difficult to construct. This note takes a first look at Bayesian Conway-Maxwell-Poisson generalized linear models that can handle both over and under dispersion yet retain the parsimony and interpretability of classical count regression models. The focus is on providing an explicit demonstration of Bayesian regression inferences for dispersed counts via a Metropolis-Hastings algorithm. We illustrate the approach on two d…
The computation of Bayesian estimates of system parameters and functions of them on the basis of observed system performance data is a common problem within system identification. This is a previously studied issue where stochastic simulation approaches have been examined using the popular Metropolis--Hastings (MH) algorithm. This prior study has identified a recognised difficulty of tuning the {proposal distribution so that the MH method provides realisations with sufficient mixing to deliver efficient convergence. This paper proposes and empirically examines a method of tuning the proposal u…
We describe a computational framework for hierarchical Bayesian inference with simple (typically single-plate) parametric graphical models that uses graphics processing units (GPUs) to accelerate computations, enabling deployment on very large datasets. Its C++ implementation, CUDAHM (CUDA for Hierarchical Models) exploits conditional independence between instances of a plate, facilitating massively parallel exploration of the replication parameter space using the single instruction, multiple data architecture of GPUs. It provides support for constructing Metropolis-within-Gibbs samplers that …
An algorithm for sampling from non-log-concave multivariate distributions is proposed, which improves the adaptive rejection Metropolis sampling (ARMS) algorithm by incorporating the hit and run sampling. It is not rare that the ARMS is trapped away from some subspace with significant probability in the support of the multivariate distribution. While the ARMS updates samples only in the directions that are parallel to dimensions, our proposed method, the hit and run ARMS (HARARMS), updates samples in arbitrary directions determined by the hit and run algorithm, which makes it almost not possib…
We propose a new sampling algorithm combining two quite powerful ideas in the Markov chain Monte Carlo literature -- adaptive Metropolis sampler and two-stage Metropolis-Hastings sampler. The proposed sampling method will be particularly very useful for high-dimensional posterior sampling in Bayesian models with expensive likelihoods. In the first stage of the proposed algorithm, an adaptive proposal is used based on the previously sampled states and the corresponding acceptance probability is computed based on an approximated inexpensive target density. The true expensive target density is ev…
We present MH-MGT, a multivariate technique for sampling from twice-differentiable, log-concave probability density functions. MH-MGT is Metropolis-Hastings sampling using asymmetric, multivariate Gaussian proposal functions constructed from Taylor-series expansion of the log-density function. The mean of the Gaussian proposal function represents the full Newton step, and thus MH-MGT is the stochastic counterpart to Newton optimization. Convergence analysis shows that MH-MGT is well suited for sampling from computationally-expensive log-densities with contributions from many independent observ…
This paper is about variable selection, clustering and estimation in an unsupervised high-dimensional setting. Our approach is based on fitting constrained Gaussian mixture models, where we learn the number of clusters $K$ and the set of relevant variables $S$ using a generalized Bayesian posterior with a sparsity inducing prior. We prove a sparsity oracle inequality which shows that this procedure selects the optimal parameters $K$ and $S$. This procedure is implemented using a Metropolis-Hastings algorithm, based on a clustering-oriented greedy proposal, which makes the convergence to the po…
The Reversible Jump algorithm is one of the most widely used Markov chain Monte Carlo algorithms for Bayesian estimation and model selection. A generalized multiple-try version of this algorithm is proposed. The algorithm is based on drawing several proposals at each step and randomly choosing one of them on the basis of weights (selection probabilities) that may be arbitrary chosen. Among the possible choices, a method is employed which is based on selection probabilities depending on a quadratic approximation of the posterior distribution. Moreover, the implementation of the proposed algorit…
We deal with Bayesian inference for Beta autoregressive processes. We restrict our attention to the class of conditionally linear processes. These processes are particularly suitable for forecasting purposes, but are difficult to estimate due to the constraints on the parameter space. We provide a full Bayesian approach to the estimation and include the parameter restrictions in the inference problem by a suitable specification of the prior distributions. Moreover in a Bayesian framework parameter estimation and model choice can be solved simultaneously. In particular we suggest a Markov-Chain…
Couplings play a central role in contemporary Markov chain Monte Carlo methods and in the analysis of their convergence to stationarity. In most cases, a coupling must induce relatively fast meeting between chains to ensure good performance. In this paper we fix attention on the random walk Metropolis algorithm and examine a range of coupling design choices. We introduce proposal and acceptance step couplings based on geometric, optimal transport, and maximality considerations. We consider the theoretical properties of these choices and examine their implication for the meeting time of the cha…
This paper proposes a generalization of Gaussian mixture models, where the mixture weight is allowed to behave as an unknown function of time. This model is capable of successfully capturing the features of the data, as demonstrated by simulated and real datasets. It can be useful in studies such as clustering, change-point and process control. In order to estimate the mixture weight function, we propose two new Bayesian nonlinear dynamic approaches for polynomial models, that can be extended to other problems involving polynomial nonlinear dynamic models. One of the methods, called here compo…
Community detection has been an active research area for decades. Among all probabilistic models, Stochastic Block Model has been the most popular one. This paper introduces a novel probabilistic model: RW-HDP, based on random walks and Hierarchical Dirichlet Process, for community extraction. In RW-HDP, random walks conducted in a social network are treated as documents; nodes are treated as words. By using Hierarchical Dirichlet Process, a nonparametric Bayesian model, we are not only able to cluster nodes into different communities, but also determine the number of communities automatically…
We incorporate heteroskedasticity into Bayesian Additive Regression Trees (BART) by modeling the log of the error variance parameter as a linear function of prespecified covariates. Under this scheme, the Gibbs sampling procedure for the original sum-of- trees model is easily modified, and the parameters for the variance model are updated via a Metropolis-Hastings step. We demonstrate the promise of our approach by providing more appropriate posterior predictive intervals than homoskedastic BART in heteroskedastic settings and demonstrating the model's resistance to overfitting. Our implementa…
We consider a Metropolis--Hastings method with proposal $\mathcal{N}(x, hG(x)^{-1})$, where $x$ is the current state, and study its ergodicity properties. We show that suitable choices of $G(x)$ can change these compared to the Random Walk Metropolis case $\mathcal{N}(x, hΣ)$, either for better or worse. We find that if the proposal variance is allowed to grow unboundedly in the tails of the distribution then geometric ergodicity can be established when the target distribution for the algorithm has tails that are heavier than exponential, but that the growth rate must be carefully controlled t…
Consider the problem of modeling hysteresis for finite-state random walks using higher-order Markov chains. This Letter introduces a Bayesian framework to determine, from data, the number of prior states of recent history upon which a trajectory is statistically dependent. The general recommendation is to use leave-one-out cross validation, using an easily-computable formula that is provided in closed form. Importantly, Bayes factors using flat model priors are biased in favor of too-complex a model (more hysteresis) when a large amount of data is present and the Akaike information criterion (…
Composite likelihoods are increasingly used in applications where the full likelihood is analytically unknown or computationally prohibitive. Although the maximum composite likelihood estimator has frequentist properties akin to those of the usual maximum likelihood estimator, Bayesian inference based on composite likelihoods has yet to be explored. In this paper we investigate the use of the Metropolis--Hastings algorithm to compute a pseudo-posterior distribution based on the composite likelihood. Two methodologies for adjusting the algorithm are presented and their performance on approximat…
The choice of the increment distribution is crucial for the random-walk Metropolis-Hastings (RWM) algorithm. In this paper we study the optimal choice in high-dimension setting among all possible increment distributions. The conclusion is rather counter intuitive, but the optimal rate of convergence is attained by the usual choice, the normal distribution as the increment distribution. In particular, no heavy-tailed increment distribution can improve the rate.
