Bayesian feature allocation models are a popular tool for modelling data with a combinatorial latent structure. Exact inference in these models is generally intractable and so practitioners typically apply Markov Chain Monte Carlo (MCMC) methods for posterior inference. The most widely used MCMC strategies rely on an element wise Gibbs update of the feature allocation matrix. These element wise updates can be inefficient as features are typically strongly correlated. To overcome this problem we have developed a Gibbs sampler that can update an entire row of the feature allocation matrix in a single move. However, this sampler is impractical for models with a large number of features as the computational complexity scales exponentially in the number of features. We develop a Particle Gibbs sampler that targets the same distribution as the row wise Gibbs updates, but has computational complexity that only grows linearly in the number of features. We compare the performance of our proposed methods to the standard Gibbs sampler using synthetic data from a range of feature allocation models. Our results suggest that row wise updates using the PG methodology can significantly improve the performance of samplers for feature allocation models.
Departement of Computer Science, KU Leuven（计算机科学系，鲁汶大学）；Department of Electrical Engineering, ESAT - STADIUS, KU Leuven（电气工程系，ESAT - STADIUS，鲁汶大学）
Bayesian regression remains a simple but effective tool based on Bayesian inference techniques. For large-scale applications, with complicated posterior distributions, Markov Chain Monte Carlo methods are applied. To improve the well-known computational burden of Markov Chain Monte Carlo approach for Bayesian regression, we developed a multilevel Gibbs sampler for Bayesian regression of linear mixed models. The level hierarchy of data matrices is created by clustering the features and/or samples of data matrices. Additionally, the use of correlated samples is investigated for variance reductio…
This article is a discussion of Zanella and Roberts' paper: Multilevel linear models, gibbs samplers and multigrid decompositions. We consider several extensions in which the multigrid decomposition would bring us interesting insights, including vector hierarchical models, linear mixed effects models and partial centering parametrizations.
University of California Irvine（加利福尼亚大学欧文分校）；University College London（伦敦大学学院）；Radboud University Nijmegen（拉德堡德大学）
Variational Bayesian inference and (collapsed) Gibbs sampling are the two important classes of inference algorithms for Bayesian networks. Both have their advantages and disadvantages: collapsed Gibbs sampling is unbiased but is also inefficient for large count values and requires averaging over many samples to reduce variance. On the other hand, variational Bayesian inference is efficient and accurate for large count values but suffers from bias for small counts. We propose a hybrid algorithm that combines the best of both worlds: it samples very small counts and applies variational updates t…
Regularization by denoising: Bayesian model and Langevin-within-split Gibbs sampling
Institut Denis Poisson, University of Orléans（德尼·泊松研究所，奥尔良大学）；University of Toulouse, IRIT/INP-ENSEEIHT, CNRS（图卢兹大学，法国国家信息与自动化研究所/国立高等电子、电子技术、计算机与机械学院，法国国家科学研究中心）
本文提出一种基于去噪正则化（RED）的图像反演贝叶斯框架，并设计了内含Langevin Monte Carlo步骤的分裂Gibbs采样算法，通过去模糊等任务验证了其有效性。
The combinatorial sequential Monte Carlo (CSMC) has been demonstrated to be an efficient complementary method to the standard Markov chain Monte Carlo (MCMC) for Bayesian phylogenetic tree inference using biological sequences. It is appealing to combine the CSMC and MCMC in the framework of the particle Gibbs (PG) sampler to jointly estimate the phylogenetic trees and evolutionary parameters. However, the Markov chain of the particle Gibbs may mix poorly if the underlying SMC suffers from the path degeneracy issue. Some remedies, including the particle Gibbs with ancestor sampling and the inte…
Hyper-parameters play a major role in the learning and inference process of latent Dirichlet allocation (LDA). In order to begin the LDA latent variables learning process, these hyper-parameters values need to be pre-determined. We propose an extension for LDA that we call 'Latent Dirichlet allocation Gibbs Newton' (LDA-GN), which places non-informative priors over these hyper-parameters and uses Gibbs sampling to learn appropriate values for them. At the heart of LDA-GN is our proposed 'Gibbs-Newton' algorithm, which is a new technique for learning the parameters of multivariate Polya distrib…
Nanyang Technological University（南洋理工大学）；National University of Singapore（新加坡国立大学）；Institute for Infocomm Research（信息通信研究院）
Bayesian graphical models have been shown to be a powerful tool for discovering uncertainty and causal structure from real-world data in many application fields. Current inference methods primarily follow different kinds of trade-offs between computational complexity and predictive accuracy. At one end of the spectrum, variational inference approaches perform well in computational efficiency, while at the other end, Gibbs sampling approaches are known to be relatively accurate for prediction in practice. In this paper, we extend an existing Gibbs sampling method, and propose a new deterministi…
P-splines provide a flexible setting for modeling nonlinear model components based on a discretized penalty structure with a relatively simple computational backbone. Under a Bayesian inferential framework based on Markov chain Monte Carlo, estimates of model coefficients in P-splines models are typically obtained by means of Metropolis-type algorithms. These algorithms rely on a proposal distribution that has to be carefully chosen to generate Markov chains that efficiently explore the parameter space. To avoid such a sensitive tuning choice, we extend the Gibbs sampler to Bayesian P-splines …
We study parameter inference in large-scale latent variable models. We first propose an unified treatment of online inference for latent variable models from a non-canonical exponential family, and draw explicit links between several previously proposed frequentist or Bayesian methods. We then propose a novel inference method for the frequentist estimation of parameters, that adapts MCMC methods to online inference of latent variable models with the proper use of local Gibbs sampling. Then, for latent Dirich-let allocation,we provide an extensive set of experiments and comparisons with existin…
We present a hybrid algorithm for Bayesian topic models that combines the efficiency of sparse Gibbs sampling with the scalability of online stochastic inference. We used our algorithm to analyze a corpus of 1.2 million books (33 billion words) with thousands of topics. Our approach reduces the bias of variational inference and generalizes to many Bayesian hidden-variable models.
We introduce a dynamic generative model, Bayesian allocation model (BAM), which establishes explicit connections between nonnegative tensor factorization (NTF), graphical models of discrete probability distributions and their Bayesian extensions, and the topic models such as the latent Dirichlet allocation. BAM is based on a Poisson process, whose events are marked by using a Bayesian network, where the conditional probability tables of this network are then integrated out analytically. We show that the resulting marginal process turns out to be a Polya urn, an integer valued self-reinforcing …
Gibbs sampling, as a model learning method, is known to produce the most accurate results available in a variety of domains, and is a de facto standard in these domains. Yet, it is also well known that Gibbs random walks usually have bottlenecks, sometimes termed "local maxima", and thus samplers often return suboptimal solutions. In this paper we introduce a variation of the Gibbs sampler which yields high likelihood solutions significantly more often than the regular Gibbs sampler. Specifically, we show that combining multiple samplers, with certain dependence (coupling) between them, result…
Gibbs sampling methods are standard tools to perform posterior inference for mixture models. These have been broadly classified into two categories: marginal and conditional methods. While conditional samplers are more widely applicable than marginal ones, they may suffer from slow mixing in infinite mixtures, where some form of truncation, either deterministic or random, is required. In mixtures with random number of components, the exploration of parameter spaces of different dimensions can also be challenging. We tackle these issues by expressing the mixture components in the random order o…
University of California, Irvine（加州大学尔湾分校）；Google（谷歌）；Yahoo Labs（雅虎实验室）；University of Amsterdam（阿姆斯特丹大学）
Despite having various attractive qualities such as high prediction accuracy and the ability to quantify uncertainty and avoid over-fitting, Bayesian Matrix Factorization has not been widely adopted because of the prohibitive cost of inference. In this paper, we propose a scalable distributed Bayesian matrix factorization algorithm using stochastic gradient MCMC. Our algorithm, based on Distributed Stochastic Gradient Langevin Dynamics, can not only match the prediction accuracy of standard MCMC methods like Gibbs sampling, but at the same time is as fast and simple as stochastic gradient desc…
One of the fundamental problems in Bayesian statistics is the approximation of the posterior distribution. Gibbs sampler and coordinate ascent variational inference are renownedly utilized approximation techniques that rely on stochastic and deterministic approximations. In this paper, we define fundamental sets of densities frequently used in Bayesian inference. We shall be concerned with the clarification of the two schemes from the set-theoretical point of view. This new way provides an alternative mechanism for analyzing the two schemes endowed with pedagogical insights.
Bregman geometry-aware split Gibbs sampling for Bayesian Poisson inverse problems
Institut Denis Poisson（德尼·泊松研究所）；CNRS（法国国家科学研究中心）；University of Tours（图尔大学）；Univ Rouen Normandie（鲁昂诺曼底大学）；INSA Rouen Normandie（鲁昂诺曼底国立应用科学学院）；Normandie Univ（诺曼底大学）；LITIS（信息、信号与图像处理实验室）；University of Toulouse（图卢兹大学）；IRIT（图卢兹计算机研究所）；INP-ENSEEIHT（图卢兹国立综合理工学院-高等电力、电子、计算机、水力与电信学院）；CEA（法国原子能和替代能源委员会）；University of Paris-Saclay（巴黎萨克雷大学）
TNO（荷兰应用科学研究组织）；Utrecht University（乌得勒支大学）；University of Amsterdam（阿姆斯特丹大学）
We introduce and characterise the performance of the Markov chain Monte Carlo (MCMC) inference method Prune Sampling for discrete and deterministic Bayesian networks (BNs). We developed a procedure to obtain the performance of a MCMC sampling method in the limit of infinite simulation time, extrapolated from relatively short simulations. This approach was used to conduct a study to compare the accuracy, rate of convergence and the time consumption of Prune Sampling with two conventional MCMC sampling methods: Gibbs- and Metropolis sampling. We show that Markov chains created by Prune Sampling …
In geostatistics, Gaussian random fields are often used to model heterogeneities of soil or subsurface parameters. To give spatial approximations of these random fields, they are discretized. Then, different techniques of geostatistical inversion are used to condition them on measurement data. Among these techniques, Markov chain Monte Carlo (MCMC) techniques stand out, because they yield asymptotically unbiased conditional realizations. However, standard Markov Chain Monte Carlo (MCMC) methods suffer the curse of dimensionality when refining the discretization. This means that their efficienc…
Gibbs random fields (GRF) are polymorphous statistical models that can be used to analyse different types of dependence, in particular for spatially correlated data. However, when those models are faced with the challenge of selecting a dependence structure from many, the use of standard model choice methods is hampered by the unavailability of the normalising constant in the Gibbs likelihood. In particular, from a Bayesian perspective, the computation of the posterior probabilities of the models under competition requires special likelihood-free simulation techniques like the Approximate Baye…
The application of the lasso is espoused in high-dimensional settings where only a small number of the regression coefficients are believed to be nonzero. Moreover, statistical properties of high-dimensional lasso estimators are often proved under the assumption that the correlation between the predictors is bounded. In this vein, coordinatewise methods, the most common means of computing the lasso solution, work well in the presence of low to moderate multicollinearity. The computational speed of coordinatewise algorithms degrades however as sparsity decreases and multicollinearity increases.…
Selecting between different dependency structures of hidden Markov random field can be very challenging, due to the intractable normalizing constant in the likelihood. We answer this question with approximate Bayesian computation (ABC) which provides a model choice method in the Bayesian paradigm. This comes after the work of Grelaud et al. (2009) who exhibited sufficient statistics on directly observed Gibbs random fields. But when the random field is latent, the sufficiency falls and we complement the set with geometric summary statistics. The general approach to construct these intuitive st…
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…
The latent Dirichlet allocation (LDA) model is a widely-used latent variable model in machine learning for text analysis. Inference for this model typically involves a single-site collapsed Gibbs sampling step for latent variables associated with observations. The efficiency of the sampling is critical to the success of the model in practical large scale applications. In this article, we introduce a blocking scheme to the collapsed Gibbs sampler for the LDA model which can, with a theoretical guarantee, improve chain mixing efficiency. We develop two procedures, an O(K)-step backward simulatio…
When performing Bayesian data analysis using a general linear mixed model, the resulting posterior density is almost always analytically intractable. However, if proper conditionally conjugate priors are used, there is a simple two-block Gibbs sampler that is geometrically ergodic in nearly all practical settings, including situations where $p > n$ (Abrahamsen and Hobert, 2017). Unfortunately, the (conditionally conjugate) multivariate normal prior on $β$ does not perform well in the high-dimensional setting where $p \gg n$. In this paper, we consider an alternative model in which the multivar…
Markov Chain Monte Carlo (MCMC) methods are a popular technique in Bayesian statistical modeling. They have long been used to obtain samples from posterior distributions, but recent research has focused on the scalability of these techniques for large problems. We do not develop new sampling methods but instead describe a blocked Gibbs sampler which is sufficiently scalable to accomodate many interesting problems. The sampler we describe applies to a restricted subset of the Generalized Linear Mixed-effects Models (GLMM's); this subset includes Poisson and Gaussian regression models. The block…
University College London（伦敦大学学院）；University of Toronto（多伦多大学）；University of Oxford（牛津大学）
Additive regression trees are flexible non-parametric models and popular off-the-shelf tools for real-world non-linear regression. In application domains, such as bioinformatics, where there is also demand for probabilistic predictions with measures of uncertainty, the Bayesian additive regression trees (BART) model, introduced by Chipman et al. (2010), is increasingly popular. As data sets have grown in size, however, the standard Metropolis-Hastings algorithms used to perform inference in BART are proving inadequate. In particular, these Markov chains make local changes to the trees and suff…
We consider three Bayesian penalized regression models and show that the respective deterministic scan Gibbs samplers are geometrically ergodic regardless of the dimension of the regression problem. We prove geometric ergodicity of the Gibbs samplers for the Bayesian fused lasso, the Bayesian group lasso, and the Bayesian sparse group lasso. Geometric ergodicity along with a moment condition results in the existence of a Markov chain central limit theorem for Monte Carlo averages and ensures reliable output analysis. Our results of geometric ergodicity allow us to also provide default starting…
Gibbs random fields play an important role in statistics, for example the autologistic model is commonly used to model the spatial distribution of binary variables defined on a lattice. However they are complicated to work with due to an intractability of the likelihood function. It is therefore natural to consider tractable approximations to the likelihood function. Composite likelihoods offer a principled approach to constructing such approximation. The contribution of this paper is to examine the performance of a collection of composite likelihood approximations in the context of Bayesian i…
We characterise the convergence of the Gibbs sampler which samples from the joint posterior distribution of parameters and missing data in hierarchical linear models with arbitrary symmetric error distributions. We show that the convergence can be uniform, geometric or sub-geometric depending on the relative tail behaviour of the error distributions, and on the parametrisation chosen. Our theory is applied to characterise the convergence of the Gibbs sampler on latent Gaussian process models. We indicate how the theoretical framework we introduce will be useful in analyzing more complex models…
This paper presents a new Markov chain Monte Carlo method to sample from the posterior distribution of conjugate mixture models. This algorithm relies on a flexible split-merge procedure built using the particle Gibbs sampler. Contrary to available split-merge procedures, the resulting so-called Particle Gibbs Split-Merge sampler does not require the computation of a complex acceptance ratio, is simple to implement using existing sequential Monte Carlo libraries and can be parallelized. We investigate its performance experimentally on synthetic problems as well as on geolocation and cancer gen…
The MC$^3$ (Madigan and York, 1995) and Gibbs (George and McCulloch, 1997) samplers are the most widely implemented algorithms for Bayesian Model Averaging (BMA) in linear regression models. These samplers draw a variable at random in each iteration using uniform selection probabilities and then propose to update that variable. This may be computationally inefficient if the number of variables is large and many variables are redundant. In this work, we introduce adaptive versions of these samplers that retain their simplicity in implementation and reduce the selection probabilities of the many…
The emergence of big data has led to a growing interest in so-called convergence complexity analysis, which is the study of how the convergence rate of a Monte Carlo Markov chain (for an intractable Bayesian posterior distribution) scales as the underlying data set grows in size. Convergence complexity analysis of practical Monte Carlo Markov chains on continuous state spaces is quite challenging, and there have been very few successful analyses of such chains. One fruitful analysis was recently presented by Qin and Hobert (2021b), who studied a Gibbs sampler for a simple Bayesian random effec…
Although the block Gibbs sampler for the Bayesian graphical LASSO proposed by Wang (2012) has been widely applied and extended to various shrinkage priors in recent years, it has a less noticeable but possibly severe disadvantage that the positive definiteness of a precision matrix in the Gaussian graphical model is not guaranteed in each cycle of the Gibbs sampler. Specifically, if the dimension of the precision matrix exceeds the sample size, the positive definiteness of the precision matrix will be barely satisfied and the Gibbs sampler will almost surely fail. In this paper, we propose mod…
Dalian University of Technology（大连理工大学）；University College London（伦敦大学学院）
We present a Bayesian scheme for the approximate diagonalisation of several square matrices which are not necessarily symmetric. A Gibbs sampler is derived to simulate samples of the common eigenvectors and the eigenvalues for these matrices. Several synthetic examples are used to illustrate the performance of the proposed Gibbs sampler and we then provide comparisons to several other joint diagonalization algorithms, which shows that the Gibbs sampler achieves the state-of-the-art performance on the examples considered. As a byproduct, the output of the Gibbs sampler could be used to estimate…
We consider a Bayesian hierarchical version of the normal theory general linear model which is practically relevant in the sense that it is general enough to have many applications and it is not straightforward to sample directly from the corresponding posterior distribution. Thus we study a block Gibbs sampler that has the posterior as its invariant distribution. In particular, we establish that the Gibbs sampler converges at a geometric rate. This allows us to establish conditions for a central limit theorem for the ergodic averages used to estimate features of the posterior. Geometric ergod…
Duke University（杜克大学）；George Mason University（乔治梅森大学）
In this work, we adopt a general framework based on the Gibbs posterior to update belief distributions for inverse problems governed by partial differential equations (PDEs). The Gibbs posterior formulation is a generalization of standard Bayesian inference that only relies on a loss function connecting the unknown parameters to the data. It is particularly useful when the true data generating mechanism (or noise distribution) is unknown or difficult to specify. The Gibbs posterior coincides with Bayesian updating when a true likelihood function is known and the loss function corresponds to th…
Bayesian model selection, with precedents in George and McCulloch (1993) and Abramovich et al. (1998), support credibility measures that relate model uncertainty, but computation can be costly when sparse priors are approximate. We design an exact selection engine suitable for Gauss noise, t-distributed noise, and logistic learning, benefiting from data-structures derived from coordinate descent lasso. Gibbs sampler chains are stored in a compressed binary format compatible with Equi-Energy (Kou et al., 2006) tempering. We achieve a grouped-effects selection model, similar to the setting for g…
Latent class analysis is used to perform model based clustering for multivariate categorical responses. Selection of the variables most relevant for clustering is an important task which can affect the quality of clustering considerably. This work considers a Bayesian approach for selecting the number of clusters and the best clustering variables. The main idea is to reformulate the problem of group and variable selection as a probabilistically driven search over a large discrete space using Markov chain Monte Carlo (MCMC) methods. This approach results in estimates of degree of relevance of e…
We present a modified Gibbs sampler for general state spaces. We establish that this modification can lead to substantial gains in statistical efficiency while maintaining the overall quality of convergence. We illustrate our results in two examples including a toy Normal-Normal model and a Bayesian version of the random effects model.
We describe an adaptation of the simulated annealing algorithm to nonparametric clustering and related probabilistic models. This new algorithm learns nonparametric latent structure over a growing and constantly churning subsample of training data, where the portion of data subsampled can be interpreted as the inverse temperature beta(t) in an annealing schedule. Gibbs sampling at high temperature (i.e., with a very small subsample) can more quickly explore sketches of the final latent state by (a) making longer jumps around latent space (as in block Gibbs) and (b) lowering energy barriers (as…
We study Bayesian estimation of mixture models and argue in favor of fitting the marginal posterior distribution over component assignments directly, rather than Gibbs sampling from the joint posterior on components and parameters as is commonly done. Some previous authors have found the former approach to have slow mixing, but we show that, implemented correctly, it can achieve excellent performance. In particular, we describe a new Monte Carlo algorithm for sampling from the marginal posterior of a general integrable mixture that makes use of rejection-free sampling from the prior over compo…
Feature allocation models postulate a sampling distribution whose parameters are derived from shared features. Bayesian models place a prior distribution on the feature allocation, and Markov chain Monte Carlo is typically used for model fitting, which results in thousands of feature allocations sampled from the posterior distribution. Based on these samples, we propose a method to provide a point estimate of a latent feature allocation. First, we introduce FARO loss, a function between feature allocations which satisfies quasi-metric properties and allows for comparing feature allocations wit…
In a modern observational study based on healthcare databases, the number of observations and of predictors typically range in the order of $10^5$ ~ $10^6$ and of $10^4$ ~ $10^5$. Despite the large sample size, data rarely provide sufficient information to reliably estimate such a large number of parameters. Sparse regression techniques provide potential solutions, one notable approach being the Bayesian methods based on shrinkage priors. In the "large n & large p" setting, however, posterior computation encounters a major bottleneck at repeated sampling from a high-dimensional Gaussian distri…
We consider Markov chain Monte Carlo (MCMC) algorithms for Bayesian high-dimensional regression with continuous shrinkage priors. A common challenge with these algorithms is the choice of the number of iterations to perform. This is critical when each iteration is expensive, as is the case when dealing with modern data sets, such as genome-wide association studies with thousands of rows and up to hundred of thousands of columns. We develop coupling techniques tailored to the setting of high-dimensional regression with shrinkage priors, which enable practical, non-asymptotic diagnostics of conv…
Likelihood-free Bayesian inference algorithms are popular methods for calibrating the parameters of complex, stochastic models, required when the likelihood of the observed data is intractable. These algorithms characteristically rely heavily on repeated model simulations. However, whenever the computational cost of simulation is even moderately expensive, the significant burden incurred by likelihood-free algorithms leaves them unviable in many practical applications. The multifidelity approach has been introduced (originally in the context of approximate Bayesian computation) to reduce the s…
