Synthetic likelihood is an attractive approach to likelihood-free inference when an approximately Gaussian summary statistic for the data, informative for inference about the parameters, is available. The synthetic likelihood method derives an approximate likelihood function from a plug-in normal density estimate for the summary statistic, with plug-in mean and covariance matrix obtained by Monte Carlo simulation from the model. In this article, we develop alternatives to Markov chain Monte Carlo implementations of Bayesian synthetic likelihoods with reduced computational overheads. Our approach uses stochastic gradient variational inference methods for posterior approximation in the synthetic likelihood context, employing unbiased estimates of the log likelihood. We compare the new method with a related likelihood free variational inference technique in the literature, while at the same time improving the implementation of that approach in a number of ways. These new algorithms are feasible to implement in situations which are challenging for conventional approximate Bayesian computation (ABC) methods, in terms of the dimensionality of the parameter and summary statistic.
Variational Bayes (VB) is a popular estimation method for Bayesian inference. However, most existing VB algorithms are restricted to cases where the likelihood is tractable, which precludes their use in many important situations. Tran et al. (2017) extend the scope of application of VB to cases where the likelihood is intractable but can be estimated unbiasedly, and name the method Variational Bayes with Intractable Likelihood (VBIL). This paper presents a version of VBIL, named Variational Bayes with Intractable Log-Likelihood (VBILL), that is useful for cases as Big Data and Big Panel Data m…
Variable selection is a classic problem in statistics. In this paper, we consider a Bayes variable selection problem based on spike-and-slab prior with mixed normal distribution proposed by Ročková and George (2014). Motivated by Ormerod and You (2017, 2023), we use the variational inference and collapsed variational inference method to solve the Bayesian problem instead of MCMC. Like Ormerod and You (2017, 2023), we also explain how the sparsity estimator is induced, and under certain mild assumptions, we also prove the consistent and asymptotic results.
This technical report presents a variational Bayes algorithm for semisupervised hyperspectral image unmixing. The presented Bayesian model employs a heavy tailed, nonnegatively truncated Laplace prior over the abundance coefficients. This prior imposes both the sparsity assumption and the nonnegativity constraint on the abundance coefficients. Experimental results conducted on the Aviris Cuprite data set are presented that demonstrate the effectiveness of the proposed method.
Variational Bayes (VB) is rapidly becoming a popular tool for Bayesian inference in statistical modeling. However, the existing VB algorithms are restricted to cases where the likelihood is tractable, which precludes the use of VB in many interesting situations such as in state space models and in approximate Bayesian computation (ABC), where application of VB methods was previously impossible. This paper extends the scope of application of VB to cases where the likelihood is intractable, but can be estimated unbiasedly. The proposed VB method therefore makes it possible to carry out Bayesian …
We propose using model reparametrization to improve variational Bayes inference for hierarchical models whose variables can be classified as global (shared across observations) or local (observation specific). Posterior dependence between local and global variables is minimized by applying an invertible affine transformation on the local variables. The functional form of this transformation is deduced by approximating the posterior distribution of each local variable conditional on the global variables by a Gaussian density via a second order Taylor expansion. Variational Bayes inference for t…
W-graph refers to a general class of random graph models that can be seen as a random graph limit. It is characterized by both its graphon function and its motif frequencies. In this paper, relying on an existing variational Bayes algorithm for the stochastic block models along with the corresponding weights for model averaging, we derive an estimate of the graphon function as an average of stochastic block models with increasing number of blocks. In the same framework, we derive the variational posterior frequency of any motif. A simulation study and an illustration on a social network comple…
This chapter will appear in the forthcoming Handbook of Approximate Bayesian Computation (2018). The conceptual and methodological framework that underpins approximate Bayesian computation (ABC) is targetted primarily towards problems in which the likelihood is either challenging or missing. ABC uses a simulation-based non-parametric estimate of the likelihood of a summary statistic and assumes that the generation of data from the model is computationally cheap. This chapter reviews two alternative approaches for estimating the intractable likelihood, with the goal of reducing the necessary mo…
University of Nottingham（诺丁汉大学）；University of Oxford（牛津大学）
Bayesian methods have proved powerful in many applications for the inference of model parameters from data. These methods are based on Bayes' theorem, which itself is deceptively simple. However, in practice the computations required are intractable even for simple cases. Hence methods for Bayesian inference have historically either been significantly approximate, e.g., the Laplace approximation, or achieve samples from the exact solution at significant computational expense, e.g., Markov Chain Monte Carlo methods. Since around the year 2000 so-called Variational approaches to Bayesian inferen…
Bayesian entity resolution merges together multiple, noisy databases and returns the minimal collection of unique individuals represented, together with their true, latent record values. Bayesian methods allow flexible generative models that share power across databases as well as principled quantification of uncertainty for queries of the final, resolved database. However, existing Bayesian methods for entity resolution use Markov monte Carlo method (MCMC) approximations and are too slow to run on modern databases containing millions or billions of records. Instead, we propose applying variat…
Parameter estimation for model-based clustering using a finite mixture of normal inverse Gaussian (NIG) distributions is achieved through variational Bayes approximations. Univariate NIG mixtures and multivariate NIG mixtures are considered. The use of variational Bayes approximations here is a substantial departure from the traditional EM approach and alleviates some of the associated computational complexities and uncertainties. Our variational algorithm is applied to simulated and real data. The paper concludes with discussion and suggestions for future work.
This tutorial gives a quick introduction to Variational Bayes (VB), also called Variational Inference or Variational Approximation, from a practical point of view. The paper covers a range of commonly used VB methods and an attempt is made to keep the materials accessible to the wide community of data analysis practitioners. The aim is that the reader can quickly derive and implement their first VB algorithm for Bayesian inference with their data analysis problem. An end-user software package in Matlab together with the documentation can be found at https://vbayeslab.github.io/VBLabDocs/
Ising models originated in statistical physics and are widely used in modeling spatial data and computer vision problems. However, statistical inference of this model remains challenging due to intractable nature of the normalizing constant in the likelihood. Here, we use a pseudo-likelihood instead to study the Bayesian estimation of two-parameter, inverse temperature, and magnetization, Ising model with a fully specified coupling matrix. We develop a computationally efficient variational Bayes procedure for model estimation. Under the Gaussian mean-field variational family, we derive posteri…
Bayesian hierarchical models are increasing popular in economics. When using hierarchical models, it is useful not only to calculate posterior expectations, but also to measure the robustness of these expectations to reasonable alternative prior choices. We use variational Bayes and linear response methods to provide fast, accurate posterior means and robustness measures with an application to measuring the effectiveness of microcredit in the developing world.
Deep neural networks have achieved impressive results on a wide variety of tasks. However, quantifying uncertainty in the network's output is a challenging task. Bayesian models offer a mathematical framework to reason about model uncertainty. Variational methods have been used for approximating intractable integrals that arise in Bayesian inference for neural networks. In this report, we review the major variational inference concepts pertinent to Bayesian neural networks and compare various approximation methods used in literature. We also talk about the applications of variational bayes in …
Columbia University（哥伦比亚大学）；Princeton University（普林斯顿大学）
Implicit probabilistic models are a flexible class of models defined by a simulation process for data. They form the basis for theories which encompass our understanding of the physical world. Despite this fundamental nature, the use of implicit models remains limited due to challenges in specifying complex latent structure in them, and in performing inferences in such models with large data sets. In this paper, we first introduce hierarchical implicit models (HIMs). HIMs combine the idea of implicit densities with hierarchical Bayesian modeling, thereby defining models via simulators of data …
In this article, we describe a {\tt R} package for sampling from an empirical likelihood-based posterior using a Hamiltonian Monte Carlo method. Empirical likelihood-based methodologies have been used in Bayesian modeling of many problems of interest in recent times. This semiparametric procedure can easily combine the flexibility of a non-parametric distribution estimator together with the interpretability of a parametric model. The model is specified by estimating equations-based constraints. Drawing an inference from a Bayesian empirical likelihood (BayesEL) posterior is challenging. The li…
We study a mean-field spike and slab variational Bayes (VB) approximation to Bayesian model selection priors in sparse high-dimensional linear regression. Under compatibility conditions on the design matrix, oracle inequalities are derived for the mean-field VB approximation, implying that it converges to the sparse truth at the optimal rate and gives optimal prediction of the response vector. The empirical performance of our algorithm is studied, showing that it works comparably well as other state-of-the-art Bayesian variable selection methods. We also numerically demonstrate that the widely…
This paper presents studies on a deterministic annealing algorithm based on quantum annealing for variational Bayes (QAVB) inference, which can be seen as an extension of the simulated annealing for variational Bayes (SAVB) inference. QAVB is as easy as SAVB to implement. Experiments revealed QAVB finds a better local optimum than SAVB in terms of the variational free energy in latent Dirichlet allocation (LDA).
This paper establishes the asymptotic consistency of the {\it loss-calibrated variational Bayes} (LCVB) method. LCVB was proposed in~\cite{LaSiGh2011} as a method for approximately computing Bayesian posteriors in a `loss aware' manner. This methodology is also highly relevant in general data-driven decision-making contexts. Here, we not only establish the asymptotic consistency of the calibrated approximate posterior, but also the asymptotic consistency of decision rules. We also establish the asymptotic consistency of decision rules obtained from a `naive' variational Bayesian procedure.
Imperial College London（帝国理工学院）；Vrije Universiteit Amsterdam（阿姆斯特丹自由大学）
Variational Bayes (VB) is a popular scalable alternative to Markov chain Monte Carlo for Bayesian inference. We study a mean-field spike and slab VB approximation of widely used Bayesian model selection priors in sparse high-dimensional logistic regression. We provide non-asymptotic theoretical guarantees for the VB posterior in both $\ell_2$ and prediction loss for a sparse truth, giving optimal (minimax) convergence rates. Since the VB algorithm does not depend on the unknown truth to achieve optimality, our results shed light on effective prior choices. We confirm the improved performance o…
In this note, we study the relationship between the variational gap and the variance of the (log) likelihood ratio. We show that the gap can be upper bounded by some form of dispersion measure of the likelihood ratio, which suggests the bias of variational inference can be reduced by making the distribution of the likelihood ratio more concentrated, such as via averaging and variance reduction.
The article addresses a long-standing open problem on the justification of using variational Bayes methods for parameter estimation. We provide general conditions for obtaining optimal risk bounds for point estimates acquired from mean-field variational Bayesian inference. The conditions pertain to the existence of certain test functions for the distance metric on the parameter space and minimal assumptions on the prior. A general recipe for verification of the conditions is outlined which is broadly applicable to existing Bayesian models with or without latent variables. As illustrations, spe…
This paper shows how the variational Bayes method provides a computational efficient technique in the context of hierarchical modelling using Dirichlet process priors, in particular without requiring conjugate prior assumption. It shows, using the so called parameter separation parameterization, a simple criterion under which the variational method works well. Based on this framework, its provides a full variational solution for the Dirichlet process. The numerical results show that the method is very computationally efficient when compared to MCMC. Finally, we propose an empirical method to e…
A key challenge for modern Bayesian statistics is how to perform scalable inference of posterior distributions. To address this challenge, variational Bayes (VB) methods have emerged as a popular alternative to the classical Markov chain Monte Carlo (MCMC) methods. VB methods tend to be faster while achieving comparable predictive performance. However, there are few theoretical results around VB. In this paper, we establish frequentist consistency and asymptotic normality of VB methods. Specifically, we connect VB methods to point estimates based on variational approximations, called frequenti…
Stochastic variational inference is an established way to carry out approximate Bayesian inference for deep models. While there have been effective proposals for good initializations for loss minimization in deep learning, far less attention has been devoted to the issue of initialization of stochastic variational inference. We address this by proposing a novel layer-wise initialization strategy based on Bayesian linear models. The proposed method is extensively validated on regression and classification tasks, including Bayesian DeepNets and ConvNets, showing faster and better convergence com…
We present SDA-Bayes, a framework for (S)treaming, (D)istributed, (A)synchronous computation of a Bayesian posterior. The framework makes streaming updates to the estimated posterior according to a user-specified approximation batch primitive. We demonstrate the usefulness of our framework, with variational Bayes (VB) as the primitive, by fitting the latent Dirichlet allocation model to two large-scale document collections. We demonstrate the advantages of our algorithm over stochastic variational inference (SVI) by comparing the two after a single pass through a known amount of data---a case …
Variational Bayes (VB) inference is one of the most important algorithms in machine learning and widely used in engineering and industry. However, VB is known to suffer from the problem of local optima. In this Letter, we generalize VB by using quantum mechanics, and propose a new algorithm, which we call quantum annealing variational Bayes (QAVB) inference. We then show that QAVB drastically improve the performance of VB by applying them to a clustering problem described by a Gaussian mixture model. Finally, we discuss an intuitive understanding on how QAVB works well.
London School of Economics（伦敦政治经济学院）；JP Morgan Chase & Co.（摩根大通公司）
Current variational inference methods for hierarchical Bayesian nonparametric models can neither characterize the correlation structure among latent variables due to the mean-field setting, nor infer the true posterior dimension because of the universal truncation. To overcome these limitations, we propose the conditional and adaptively truncated variational inference method (CATVI) by maximizing the nonparametric evidence lower bound and integrating Monte Carlo into the variational inference framework. CATVI enjoys several advantages over traditional methods, including a smaller divergence be…
Localisation of a source of a toxic release of biochemical aerosols in the atmosphere is a problem of great importance for public safety. Two main practical difficulties are encountered in this problem: the lack of knowledge of the likelihood function of measurements collected by biochemical sensors, and the plethora of candidate dispersion models, developed under various assumptions (e.g. meteorological conditions, terrain). Aiming to overcome these two difficulties, the paper proposes a likelihood-free approximate Bayesian computation method, which simultaneously uses a set of candidate disp…
Variational Bayes (VB) is a critical method in machine learning and statistics, underpinning the recent success of Bayesian deep learning. The natural gradient is an essential component of efficient VB estimation, but it is prohibitively computationally expensive in high dimensions. We propose a computationally efficient regression-based method for natural gradient estimation, with convergence guarantees under standard assumptions. The method enables the use of quantum matrix inversion to further speed up VB. We demonstrate that the problem setup fulfills the conditions required for quantum ma…
Variational Bayes (VB) has shown itself to be a powerful approximation method in many application areas. This paper describes some diagnostics methods which can assess how well the VB approximates the true posterior, particularly with regards to its covariance structure. The methods proposed also allow us to generate simple corrections when the approximation error is large. It looks at joint, marginal and conditional aspects of the approximate posterior and shows how to apply these techniques in both simulated and real data examples.
Fast and Robust Likelihood-Guided Diffusion Posterior Sampling with Amortized Variational Inference
Institute of Foundation Models, MBZUAI（基础模型研究所，MBZUAI）；Huawei Lagrange Mathematics and Computing Research Center, Paris, France（华为拉格朗日数学与计算研究中心，法国巴黎）；Mohamed Bin Zayed University of AI, Chair of the ML Department, EPITA, Laboratoire Recherche de l'EPITA（穆罕默德·本·扎耶德人工智能大学，机器学习系主任，EPITA，EPITA研究实验室）
We propose a novel interpretation of the collapsed variational Bayes inference with a zero-order Taylor expansion approximation, called CVB0 inference, for latent Dirichlet allocation (LDA). We clarify the properties of the CVB0 inference by using the alpha-divergence. We show that the CVB0 inference is composed of two different divergence projections: alpha=1 and -1. This interpretation will help shed light on CVB0 works.
Variational Bayes (VB) is a recent approximate method for Bayesian inference. It has the merit of being a fast and scalable alternative to Markov Chain Monte Carlo (MCMC) but its approximation error is often unknown. In this paper, we derive the approximation error of VB in terms of mean, mode, variance, predictive density and KL divergence for the linear Gaussian multi-equation regression. Our results indicate that VB approximates the posterior mean perfectly. Factors affecting the magnitude of underestimation in posterior variance and mode are revealed. Importantly, We demonstrate that VB es…
Stochastic approximation methods play a central role in maximum likelihood estimation problems involving intractable likelihood functions, such as marginal likelihoods arising in problems with missing or incomplete data, and in parametric empirical Bayesian estimation. Combined with Markov chain Monte Carlo algorithms, these stochastic optimisation methods have been successfully applied to a wide range of problems in science and industry. However, this strategy scales poorly to large problems because of methodological and theoretical difficulties related to using high-dimensional Markov chain …
We highlight a pitfall when applying stochastic variational inference to general Bayesian networks. For global random variables approximated by an exponential family distribution, natural gradient steps, commonly starting from a unit length step size, are averaged to convergence. This useful insight into the scaling of initial step sizes is lost when the approximation factorizes across a general Bayesian network, and care must be taken to ensure practical convergence. We experimentally investigate how much of the baby (well-scaled steps) is thrown out with the bath water (exact gradients).
Konstanz University of Applied Sciences（康斯坦茨应用科学大学）；Zurich University of Applied Sciences（苏黎世应用科学大学）；University of Zurich（苏黎世大学）
The main challenge in Bayesian models is to determine the posterior for the model parameters. Already, in models with only one or few parameters, the analytical posterior can only be determined in special settings. In Bayesian neural networks, variational inference is widely used to approximate difficult-to-compute posteriors by variational distributions. Usually, Gaussians are used as variational distributions (Gaussian-VI) which limits the quality of the approximation due to their limited flexibility. Transformation models on the other hand are flexible enough to fit any distribution. Here w…
Variational inference is a powerful paradigm for approximate Bayesian inference with a number of appealing properties, including support for model learning and data subsampling. By contrast MCMC methods like Hamiltonian Monte Carlo do not share these properties but remain attractive since, contrary to parametric methods, MCMC is asymptotically unbiased. For these reasons researchers have sought to combine the strengths of both classes of algorithms, with recent approaches coming closer to realizing this vision in practice. However, supporting data subsampling in these hybrid methods can be a c…
University College of London（伦敦大学学院）；Athens University of Economics and Business（雅典经济与商业大学）；The Alan Turing Institute（艾伦·图灵研究所）
We present a scalable approach to performing approximate fully Bayesian inference in generic state space models. The proposed method is an alternative to particle MCMC that provides fully Bayesian inference of both the dynamic latent states and the static parameters of the model. We build up on recent advances in computational statistics that combine variational methods with sequential Monte Carlo sampling and we demonstrate the advantages of performing full Bayesian inference over the static parameters rather than just performing variational EM approximations. We illustrate how our approach e…
While stochastic variational inference is relatively well known for scaling inference in Bayesian probabilistic models, related methods also offer ways to circumnavigate the approximation of analytically intractable expectations. The key challenge in either setting is controlling the variance of gradient estimates: recent work has shown that for continuous latent variables, particularly multivariate Gaussians, this can be achieved by using the gradient of the log posterior. In this paper we apply the same idea to gamma distributed latent variables given gamma variational distributions, enablin…
A composite likelihood is a non-genuine likelihood function that allows to make inference on limited aspects of a model, such as marginal or conditional distributions. Composite likelihoods are not proper likelihoods and need therefore calibration for their use in inference, from both a frequentist and a Bayesian perspective. The maximizer to the composite likelihood can serve as an estimator and its variance is assessed by means of a suitably defined sandwich matrix. In the Bayesian setting, the composite likelihood can be adjusted by means of magnitude and curvature methods. Magnitude method…
In statistical practice, a realistic Bayesian model for a given data set can be defined by a likelihood function that is analytically or computationally intractable, due to large data sample size, high parameter dimensionality, or complex likelihood functional form. This in turn poses challenges to the computation and inference of the posterior distribution of the model parameters. For such a model, a tractable likelihood function is introduced which approximates the exact likelihood through its quantile function. It is defined by an asymptotic chi-square confidence distribution for a pivotal …
The celebrated Bernstein von-Mises theorem ensures that credible regions from Bayesian posterior are well-calibrated when the model is correctly-specified, in the frequentist sense that their coverage probabilities tend to the nominal values as data accrue. However, this conventional Bayesian framework is known to lack robustness when the model is misspecified or only partly specified, such as in quantile regression, risk minimization based supervised/unsupervised learning and robust estimation. To overcome this difficulty, we propose a new Bayesian inferential approach that substitutes the (m…
A Bayesian design is given by maximising an expected utility over a design space. The utility is chosen to represent the aim of the experiment and its expectation is taken with respect to all unknowns: responses, parameters and/or models. Although straightforward in principle, there are several challenges to finding Bayesian designs in practice. Firstly, the utility and expected utility are rarely available in closed form and require approximation. Secondly, the design space can be of high-dimensionality. In the case of intractable likelihood models, these problems are compounded by the fact t…
This article describes a full Bayesian treatment for simultaneous fixed-effect selection and parameter estimation in high-dimensional generalized linear mixed models. The approach consists of using a Bayesian adaptive Lasso penalty for signal-level adaptive shrinkage and a fast Variational Bayes scheme for estimating the posterior mode of the coefficients. The proposed approach offers several advantages over the existing methods, for example, the adaptive shrinkage parameters are automatically incorporated, no Laplace approximation step is required to integrate out the random effects. The perf…
We compared Bayes factors to normalized maximum likelihood for the simple case of selecting between an order-constrained versus a full binomial model. This comparison revealed two qualitative differences in testing order constraints regarding data dependence and model preference.
