Monte Carlo (MC) methods are widely used for Bayesian inference and optimization in statistics, signal processing and machine learning. A well-known class of MC methods are Markov Chain Monte Carlo (MCMC) algorithms. In order to foster better exploration of the state space, specially in high-dimensional applications, several schemes employing multiple parallel MCMC chains have been recently introduced. In this work, we describe a novel parallel interacting MCMC scheme, called {\it orthogonal MCMC} (O-MCMC), where a set of "vertical" parallel MCMC chains share information using some "horizontal" MCMC techniques working on the entire population of current states. More specifically, the vertical chains are led by random-walk proposals, whereas the horizontal MCMC techniques employ independent proposals, thus allowing an efficient combination of global exploration and local approximation. The interaction is contained in these horizontal iterations. Within the analysis of different implementations of O-MCMC, novel schemes in order to reduce the overall computational cost of parallel multiple try Metropolis (MTM) chains are also presented. Furthermore, a modified version of O-MCMC for optimization is provided by considering parallel simulated annealing (SA) algorithms. Numerical results show the advantages of the proposed sampling scheme in terms of efficiency in the estimation, as well as robustness in terms of independence with respect to initial values and the choice of the parameters.
For Bayesian computation in big data contexts, the divide-and-conquer MCMC concept splits the whole data set into batches, runs MCMC algorithms separately over each batch to produce samples of parameters, and combines them to produce an approximation of the target distribution. In this article, we embed random forests into this framework and use each subposterior/partial-posterior as a proposal distribution to implement importance sampling. Unlike the existing divide-and-conquer MCMC, our methods are based on scaled subposteriors, whose scale factors are not necessarily restricted to being equ…
In big data context, traditional MCMC methods, such as Metropolis-Hastings algorithms and hybrid Monte Carlo, scale poorly because of their need to evaluate the likelihood over the whole data set at each iteration. In order to resurrect MCMC methods, numerous approaches belonging to two categories: divide-and-conquer and subsampling, are proposed. In this article, we study the parallel MCMC and propose a new combination method in the divide-and-conquer framework. Compared with some parallel MCMC methods, such as consensus Monte Carlo, Weierstrass Sampler, instead of sampling from subposteriors…
We introduce a novel approach for parallelizing MCMC inference in models with spatially determined conditional independence relationships, for which existing techniques exploiting graphical model structure are not applicable. Our approach is motivated by a model of seismic events and signals, where events detected in distant regions are approximately independent given those in intermediate regions. We perform parallel inference by coloring a factor graph defined over regions of latent space, rather than individual model variables. Evaluating on a model of seismic event detection, we achieve si…
Comparison of parallel SMC and MCMC for Bayesian deep learning
Mathematics Department, University of Manchester（曼彻斯特大学数学系）；Department of Electrical and Computer Engineering, Southern Methodist University（南方 Methodist 大学电气与计算机工程系）；DEVCOM US Army Research Laboratory（美国陆军研发实验室）；Department of Electrical and Computer Engineering, University of Illinois Chicago（伊利诺伊大学芝加哥分校电气与计算机工程系）；Cognizant AI Labs（Cognizant AI 实验室）；Quantum Information Science Section, Oak Ridge National Laboratory（橡树岭国家实验室量子信息科学部）；Tulane University（Tulane 大学）
Efficient sampling of many-dimensional and multimodal density functions is a task of great interest in many research fields. We describe an algorithm that allows parallelizing inherently serial Markov chain Monte Carlo (MCMC) sampling by partitioning the space of the function parameters into multiple subspaces and sampling each of them independently. The samples of the different subspaces are then reweighted by their integral values and stitched back together. This approach allows reducing sampling wall-clock time by parallel operation. It also improves sampling of multimodal target densities …
We introduce a new version of particle filter in which the number of "children" of a particle at a given time has a Poisson distribution. As a result, the number of particles is random and varies with time. An advantage of this scheme is that descendants of different particles can evolve independently. It makes easy to parallelize computations. Moreover, particle filter with Poisson resampling is readily adapted to the case when a hidden process is a continuous time, piecewise deterministic semi-Markov process. We show that the basic techniques of particle MCMC, namely particle independent Met…
Helsinki Institute for Information Technology HIIT（赫尔辛基信息技术研究所HIIT）；Aalto University（阿尔托大学）
While MCMC methods have become a main work-horse for Bayesian inference, scaling them to large distributed datasets is still a challenge. Embarrassingly parallel MCMC strategies take a divide-and-conquer stance to achieve this by writing the target posterior as a product of subposteriors, running MCMC for each of them in parallel and subsequently combining the results. The challenge then lies in devising efficient aggregation strategies. Current strategies trade-off between approximation quality, and costs of communication and computation. In this work, we introduce a novel method that address…
Markov chain Monte Carlo (MCMC) methods are often used in clustering since they guarantee asymptotically exact expectations in the infinite-time limit. In finite time, though, slow mixing often leads to poor performance. Modern computing environments offer massive parallelism, but naive implementations of parallel MCMC can exhibit substantial bias. In MCMC samplers of continuous random variables, Markov chain couplings can overcome bias. But these approaches depend crucially on paired chains meetings after a small number of transitions. We show that straightforward applications of existing cou…
We consider parallel asynchronous Markov Chain Monte Carlo (MCMC) sampling for problems where we can leverage (stochastic) gradients to define continuous dynamics which explore the target distribution. We outline a solution strategy for this setting based on stochastic gradient Hamiltonian Monte Carlo sampling (SGHMC) which we alter to include an elastic coupling term that ties together multiple MCMC instances. The proposed strategy turns inherently sequential HMC algorithms into asynchronous parallel versions. First experiments empirically show that the resulting parallel sampler significantl…
ParaMonte::Python (standing for Parallel Monte Carlo in Python) is a serial and MPI-parallelized library of (Markov Chain) Monte Carlo (MCMC) routines for sampling mathematical objective functions, in particular, the posterior distributions of parameters in Bayesian modeling and analysis in data science, Machine Learning, and scientific inference in general. In addition to providing access to fast high-performance serial/parallel Monte Carlo and MCMC sampling routines, the ParaMonte::Python library provides extensive post-processing and visualization tools that aim to automate and streamline t…
We propose a novel hybrid quantum computing strategy for parallel MCMC algorithms that generate multiple proposals at each step. This strategy makes the rate-limiting step within parallel MCMC amenable to quantum parallelization by using the Gumbel-max trick to turn the generalized accept-reject step into a discrete optimization problem. When combined with new insights from the parallel MCMC literature, such an approach allows us to embed target density evaluations within a well-known extension of Grover's quantum search algorithm. Letting $P$ denote the number of proposals in a single MCMC it…
Markov Chain Monte Carlo (MCMC) is a well-established family of algorithms which are primarily used in Bayesian statistics to sample from a target distribution when direct sampling is challenging. Single instances of MCMC methods are widely considered hard to parallelise in a problem-agnostic fashion and hence, unsuitable to meet both constraints of high accuracy and high throughput. Sequential Monte Carlo (SMC) Samplers can address the same problem, but are parallelisable: they share with Particle Filters the same key tasks and bottleneck. Although a rich literature already exists on MCMC met…
Performing Bayesian inference via Markov chain Monte Carlo (MCMC) can be exceedingly expensive when posterior evaluations invoke the evaluation of a computationally expensive model, such as a system of partial differential equations. In recent work [Conrad et al. JASA 2016, arXiv:1402.1694], we described a framework for constructing and refining local approximations of such models during an MCMC simulation. These posterior--adapted approximations harness regularity of the model to reduce the computational cost of inference while preserving asymptotic exactness of the Markov chain. Here we desc…
Topic models, and more specifically the class of Latent Dirichlet Allocation (LDA), are widely used for probabilistic modeling of text. MCMC sampling from the posterior distribution is typically performed using a collapsed Gibbs sampler. We propose a parallel sparse partially collapsed Gibbs sampler and compare its speed and efficiency to state-of-the-art samplers for topic models on five well-known text corpora of differing sizes and properties. In particular, we propose and compare two different strategies for sampling the parameter block with latent topic indicators. The experiments show th…
University College London（伦敦大学学院）；Aalto University（阿尔托大学）；Getulio Vargas Foundation（热图利奥·瓦加斯基金会）；University of Manchester（曼彻斯特大学）；University of Helsinki（赫尔辛基大学）
Embarrassingly parallel Markov Chain Monte Carlo (MCMC) exploits parallel computing to scale Bayesian inference to large datasets by using a two-step approach. First, MCMC is run in parallel on (sub)posteriors defined on data partitions. Then, a server combines local results. While efficient, this framework is very sensitive to the quality of subposterior sampling. Common sampling problems such as missing modes or misrepresentation of low-density regions are amplified -- instead of being corrected -- in the combination phase, leading to catastrophic failures. In this work, we propose a novel c…
Mad Props: Parallelism in Markov Chain Monte Carlo Through the Lens of the Infinite Proposal Limit
Indiana University（印第安纳大学）；University of California, Los Angeles（加州大学洛杉矶分校）；Virginia Polytechnic Institute and State University（弗吉尼亚理工大学）；Drexel University（德雷塞尔大学）
As it has become common to use many computer cores in routine applications, finding good ways to parallelize popular algorithms has become increasingly important. In this paper, we present a parallelization scheme for Markov chain Monte Carlo (MCMC) methods based on spectral clustering of the underlying state space, generalizing earlier work on parallelization of MCMC methods by state space partitioning. We show empirically that this approach speeds up MCMC sampling for multimodal distributions and that it can be usefully applied in greater generality than several related algorithms. Our algor…
Parallel tempering (PT) methods are a popular class of Markov chain Monte Carlo schemes used to sample complex high-dimensional probability distributions. They rely on a collection of $N$ interacting auxiliary chains targeting tempered versions of the target distribution to improve the exploration of the state-space. We provide here a new perspective on these highly parallel algorithms and their tuning by identifying and formalizing a sharp divide in the behaviour and performance of reversible versus non-reversible PT schemes. We show theoretically and empirically that a class of non-reversibl…
Markov Chain Monte Carlo (MCMC) is a well-established family of algorithms primarily used in Bayesian statistics to sample from a target distribution when direct sampling is challenging. Existing work on Bayesian decision trees uses MCMC. Unfortunately, this can be slow, especially when considering large volumes of data. It is hard to parallelise the accept-reject component of the MCMC. None-the-less, we propose two methods for exploiting parallelism in the MCMC: in the first, we replace the MCMC with another numerical Bayesian approach, the Sequential Monte Carlo (SMC) sampler, which has the …
Petuum, Inc.（Petuum公司）；Imperial College London（帝国理工学院）；Carnegie Mellon University（卡内基梅隆大学）
Markov Chain Monte Carlo (MCMC) methods such as Gibbs sampling are finding widespread use in applied statistics and machine learning. These often lead to difficult computational problems, which are increasingly being solved on parallel and distributed systems such as compute clusters. Recent work has proposed running iterative algorithms such as gradient descent and MCMC in parallel asynchronously for increased performance, with good empirical results in certain problems. Unfortunately, for MCMC this parallelization technique requires new convergence theory, as it has been explicitly demonstra…
In this paper we propose a general framework of performing MCMC with only a mini-batch of data. We show by estimating the Metropolis-Hasting ratio with only a mini-batch of data, one is essentially sampling from the true posterior raised to a known temperature. We show by experiments that our method, Mini-batch Tempered MCMC (MINT-MCMC), can efficiently explore multiple modes of a posterior distribution. Based on the Equi-Energy sampler (Kou et al. 2006), we developed a new parallel MCMC algorithm based on the Equi-Energy sampler, which enables efficient sampling from high-dimensional multi-mo…
Motivated by applications to Bayesian inference for statistical models with orthogonal matrix parameters, we present $\textit{polar expansion},$ a general approach to Monte Carlo simulation from probability distributions on the Stiefel manifold. To bypass many of the well-established challenges of simulating from the distribution of a random orthogonal matrix $\boldsymbol{Q},$ we construct a distribution for an unconstrained random matrix $\boldsymbol{X}$ such that $\boldsymbol{Q}_X,$ the orthogonal component of the polar decomposition of $\boldsymbol{X},$ is equal in distribution to $\boldsym…
AQR Capital Management LLC（AQR资本管理有限责任公司）；University of Texas at Austin（德克萨斯大学奥斯汀分校）
Embarrassingly (communication-free) parallel Markov chain Monte Carlo (MCMC) methods are commonly used in learning graphical models. However, MCMC cannot be directly applied in learning topic models because of the quasi-ergodicity problem caused by multimodal distribution of topics. In this paper, we develop an embarrassingly parallel MCMC algorithm for sLDA. Our algorithm works by switching the order of sampled topics combination and labeling variable prediction in sLDA, in which it overcomes the quasi-ergodicity problem because high-dimension topics that follow a multimodal distribution are …
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 flexibil…
We present the simplicial sampler, a class of parallel MCMC methods that generate and choose from multiple proposals at each iteration. The algorithm's multiproposal randomly rotates a simplex connected to the current Markov chain state in a way that inherently preserves symmetry between proposals. As a result, the simplicial sampler leads to a simplified acceptance step: it simply chooses from among the simplex nodes with probability proportional to their target density values. We also investigate a multivariate Gaussian-based symmetric multiproposal mechanism and prove that it also enjoys th…
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…
Bayesian inference for factorial hidden Markov models is challenging due to the exponentially sized latent variable space. Standard Monte Carlo samplers can have difficulties effectively exploring the posterior landscape and are often restricted to exploration around localised regions that depend on initialisation. We introduce a general purpose ensemble Markov Chain Monte Carlo (MCMC) technique to improve on existing poorly mixing samplers. This is achieved by combining parallel tempering and an auxiliary variable scheme to exchange information between the chains in an efficient way. The latt…
Developing efficient MCMC algorithms is indispensable in Bayesian inference. In parallel tempering, multiple interacting MCMC chains run to more efficiently explore the state space and improve performance. The multiple chains advance independently through local moves, and the performance enhancement steps are exchange moves, where the chains pause to exchange their current sample amongst each other. To accelerate the independent local moves, they may be performed simultaneously on multiple processors. Another problem is then encountered: depending on the MCMC implementation and inference probl…
Institute of Mathematical Sciences (ICMAT)（数学科学研究所（ICMAT））；SAMSI, Duke University（杜克大学统计与应用数学研究所（SAMSI））；Duke University（杜克大学）
We propose a unifying view of two different Bayesian inference algorithms, Stochastic Gradient Markov Chain Monte Carlo (SG-MCMC) and Stein Variational Gradient Descent (SVGD), leading to improved and efficient novel sampling schemes. We show that SVGD combined with a noise term can be framed as a multiple chain SG-MCMC method. Instead of treating each parallel chain independently from others, our proposed algorithm implements a repulsive force between particles, avoiding collapse and facilitating a better exploration of the parameter space. We also show how the addition of this noise term is …
Spectral divide-and-conquer MCMC for long stationary time series
University of Technology Sydney（悉尼科技大学）；Human Technology Institute, University of Technology Sydney（悉尼科技大学人类技术研究所）；Guanghua School of Management, Peking University（北京大学光华管理学院）；Stockholm University（斯德哥尔摩大学）；University of New South Wales（新南威尔士大学）
Autoencoders gained popularity in the deep learning revolution given their ability to compress data and provide dimensionality reduction. Although prominent deep learning methods have been used to enhance autoencoders, the need to provide robust uncertainty quantification remains a challenge. This has been addressed with variational autoencoders so far. Bayesian inference via Markov Chain Monte Carlo (MCMC) sampling has faced several limitations for large models; however, recent advances in parallel computing and advanced proposal schemes have opened routes less traveled. This paper presents B…
Gibbs sampling is a Markov Chain Monte Carlo (MCMC) method often used in Bayesian learning. MCMC methods can be difficult to deploy on parallel and distributed systems due to their inherently sequential nature. We study asynchronous Gibbs sampling, which achieves parallelism by simply ignoring sequential requirements. This method has been shown to produce good empirical results for some hierarchical models, and is popular in the topic modeling community, but was also shown to diverge for other targets. We introduce a theoretical framework for analyzing asynchronous Gibbs sampling and other ext…
