We propose a novel algorithm to solve the expectation propagation relaxation of Bayesian inference for continuous-variable graphical models. In contrast to most previous algorithms, our method is provably convergent. By marrying convergent EP ideas from (Opper&Winther 05) with covariance decoupling techniques (Wipf&Nagarajan 08, Nickisch&Seeger 09), it runs at least an order of magnitude faster than the most commonly used EP solver.
Bayesian graphical models are a useful tool for understanding dependence relationships among many variables, particularly in situations with external prior information. In high-dimensional settings, the space of possible graphs becomes enormous, rendering even state-of-the-art Bayesian stochastic search computationally infeasible. We propose a deterministic alternative to estimate Gaussian and Gaussian copula graphical models using an Expectation Conditional Maximization (ECM) algorithm, extending the EM approach from Bayesian variable selection to graphical model estimation. We show that the …
We consider two areas of research that have been developing in parallel over the last decade: blind source separation (BSS) and electromagnetic source estimation (ESE). BSS deals with the recovery of source signals when only mixtures of signals can be obtained from an array of detectors and the only prior knowledge consists of some information about the nature of the source signals. On the other hand, ESE utilizes knowledge of the electromagnetic forward problem to assign source signals to their respective generators, while information about the signals themselves is typically ignored. We demo…
University of Massachusetts Amherst（马萨诸塞大学阿默斯特分校）；US Army Research Laboratory（美国陆军研究实验室）
In this paper, we present a general framework for distilling expectations with respect to the Bayesian posterior distribution of a deep neural network classifier, extending prior work on the Bayesian Dark Knowledge framework. The proposed framework takes as input "teacher" and student model architectures and a general posterior expectation of interest. The distillation method performs an online compression of the selected posterior expectation using iteratively generated Monte Carlo samples. We focus on the posterior predictive distribution and expected entropy as distillation targets. We inve…
Approximate Bayesian inference methods provide a powerful suite of tools for finding approximations to intractable posterior distributions. However, machine learning applications typically involve selecting actions, which -- in a Bayesian setting -- depend on the posterior distribution only via its contribution to expected utility. A growing body of work on loss-calibrated approximate inference methods has therefore sought to develop posterior approximations sensitive to the influence of the utility function. Here we introduce loss-calibrated expectation propagation (Loss-EP), a loss-calibrate…
Deep Gaussian processes (DGPs) are multi-layer hierarchical generalisations of Gaussian processes (GPs) and are formally equivalent to neural networks with multiple, infinitely wide hidden layers. DGPs are probabilistic and non-parametric and as such are arguably more flexible, have a greater capacity to generalise, and provide better calibrated uncertainty estimates than alternative deep models. The focus of this paper is scalable approximate Bayesian learning of these networks. The paper develops a novel and efficient extension of probabilistic backpropagation, a state-of-the-art method for …
We propose a new Bayesian nonparametric prior for latent feature models, which we call the convergent Indian buffet process (CIBP). We show that under the CIBP, the number of latent features is distributed as a Poisson distribution with the mean monotonically increasing but converging to a certain value as the number of objects goes to infinity. That is, the expected number of features is bounded above even when the number of objects goes to infinity, unlike the standard Indian buffet process under which the expected number of features increases with the number of objects. We provide two alter…
This paper makes two contributions to Bayesian machine learning algorithms. Firstly, we propose stochastic natural gradient expectation propagation (SNEP), a novel alternative to expectation propagation (EP), a popular variational inference algorithm. SNEP is a black box variational algorithm, in that it does not require any simplifying assumptions on the distribution of interest, beyond the existence of some Monte Carlo sampler for estimating the moments of the EP tilted distributions. Further, as opposed to EP which has no guarantee of convergence, SNEP can be shown to be convergent, even wh…
Max Planck Institute for Molecular Genetics（马克斯·普朗克分子遗传学研究所）
We present a Bayesian method for feature selection in the presence of grouping information with sparsity on the between- and within group level. Instead of using a stochastic algorithm for parameter inference, we employ expectation propagation, which is a deterministic and fast algorithm. Available methods for feature selection in the presence of grouping information have a number of short-comings: on one hand, lasso methods, while being fast, underestimate the regression coefficients and do not make good use of the grouping information, and on the other hand, Bayesian approaches, while accura…
We propose a novel, theoretically-grounded, acquisition function for Batch Bayesian optimization informed by insights from distributionally ambiguous optimization. Our acquisition function is a lower bound on the well-known Expected Improvement function, which requires evaluation of a Gaussian Expectation over a multivariate piecewise affine function. Our bound is computed instead by evaluating the best-case expectation over all probability distributions consistent with the same mean and variance as the original Gaussian distribution. Unlike alternative approaches, including Expected Improveme…
Fluorescence microscopy is widely used for the study of biological specimens. Deconvolution can significantly improve the resolution and contrast of images produced using fluorescence microscopy; in particular, Bayesian-based methods have become very popular in deconvolution fluorescence microscopy. An ongoing challenge with Bayesian-based methods is in dealing with the presence of noise in low SNR imaging conditions. In this study, we present a Bayesian-based method for performing deconvolution using dynamically updated nonparametric nonstationary expectation estimates that can improve the fl…
Exact inference in the linear regression model with spike and slab priors is often intractable. Expectation propagation (EP) can be used for approximate inference. However, the regular sequential form of EP (R-EP) may fail to converge in this model when the size of the training set is very small. As an alternative, we propose a provably convergent EP algorithm (PC-EP). PC-EP is proved to minimize an energy function which, under some constraints, is bounded from below and whose stationary points coincide with the solution of R-EP. Experiments with synthetic data indicate that when R-EP does not…
The authors of the discussed paper simplified the information-based acquisition on estimating statistical expectation and developed analytical computation for each involved quantity under uniform input distribution. In this discussion, we show that (1) the last three terms of the acquisition always add up to zero, leaving a concise form with a much more intuitive interpretation of the acquisition; (2) the analytical computation of the acquisition can be generalized to arbitrary input distribution, greatly broadening the application of the developed framework.
A common divide-and-conquer approach for Bayesian computation with big data is to partition the data, perform local inference for each piece separately, and combine the results to obtain a global posterior approximation. While being conceptually and computationally appealing, this method involves the problematic need to also split the prior for the local inferences; these weakened priors may not provide enough regularization for each separate computation, thus eliminating one of the key advantages of Bayesian methods. To resolve this dilemma while still retaining the generalizability of the un…
Bayesian optimal design of experiments (BODE) has been successful in acquiring information about a quantity of interest (QoI) which depends on a black-box function. BODE is characterized by sequentially querying the function at specific designs selected by an infill-sampling criterion. However, most current BODE methods operate in specific contexts like optimization, or learning a universal representation of the black-box function. The objective of this paper is to design a BODE for estimating the statistical expectation of a physical response surface. This QoI is omnipresent in uncertainty pr…
Ordinary stochastic neural networks mostly rely on the expected values of their weights to make predictions, whereas the induced noise is mostly used to capture the uncertainty, prevent overfitting and slightly boost the performance through test-time averaging. In this paper, we introduce variance layers, a different kind of stochastic layers. Each weight of a variance layer follows a zero-mean distribution and is only parameterized by its variance. We show that such layers can learn surprisingly well, can serve as an efficient exploration tool in reinforcement learning tasks and provide a dec…
We consider the inverse problem of reconstructing the posterior measure over the trajec- tories of a diffusion process from discrete time observations and continuous time constraints. We cast the problem in a Bayesian framework and derive approximations to the posterior distributions of single time marginals using variational approximate inference. We then show how the approximation can be extended to a wide class of discrete-state Markov jump pro- cesses by making use of the chemical Langevin equation. Our empirical results show that the proposed method is computationally efficient and provid…
University of Cambridge（剑桥大学）；Universidad Autónoma de Madrid（马德里自治大学）；Harvard University（哈佛大学）
Deep Gaussian processes (DGPs) are multi-layer hierarchical generalisations of Gaussian processes (GPs) and are formally equivalent to neural networks with multiple, infinitely wide hidden layers. DGPs are nonparametric probabilistic models and as such are arguably more flexible, have a greater capacity to generalise, and provide better calibrated uncertainty estimates than alternative deep models. This paper develops a new approximate Bayesian learning scheme that enables DGPs to be applied to a range of medium to large scale regression problems for the first time. The new method uses an appr…
University of Cambridge（剑桥大学）；Harvard University（哈佛大学）
Expectation propagation (EP) is a deterministic approximation algorithm that is often used to perform approximate Bayesian parameter learning. EP approximates the full intractable posterior distribution through a set of local approximations that are iteratively refined for each datapoint. EP can offer analytic and computational advantages over other approximations, such as Variational Inference (VI), and is the method of choice for a number of models. The local nature of EP appears to make it an ideal candidate for performing Bayesian learning on large models in large-scale dataset settings. H…
This paper considers the problem of learning the parameters in Bayesian networks of discrete variables with known structure and hidden variables. Previous approaches in these settings typically use expectation maximization; when the network has high treewidth, the required expectations might be approximated using Monte Carlo or variational methods. We show how to avoid inference altogether during learning by giving a polynomial-time algorithm based on the method-of-moments, building upon recent work on learning discrete-valued mixture models. In particular, we show how to learn the parameters …
Expectation-Propagation for Bayesian Empirical Likelihood Inference
College of Computing and Data Science, Nanyang Technological University（南洋理工大学计算与数据科学学院）；School of Mathematics and Statistics, The University of Melbourne（墨尔本大学数学与统计学院）
The Australian National University（澳大利亚国立大学）；Data61；Inria（法国国家信息与自动化研究所）；University College London（伦敦大学学院）
Conditional Value at Risk (CVaR) is a family of "coherent risk measures" which generalize the traditional mathematical expectation. Widely used in mathematical finance, it is garnering increasing interest in machine learning, e.g., as an alternate approach to regularization, and as a means for ensuring fairness. This paper presents a generalization bound for learning algorithms that minimize the CVaR of the empirical loss. The bound is of PAC-Bayesian type and is guaranteed to be small when the empirical CVaR is small. We achieve this by reducing the problem of estimating CVaR to that of merel…
Max Planck Institute（马克斯·普朗克研究所）；Université Laval（拉瓦尔大学）；University College London（伦敦大学学院）；University of Leoben（莱奥本大学）
We present two alternative ways to apply PAC-Bayesian analysis to sequences of dependent random variables. The first is based on a new lemma that enables to bound expectations of convex functions of certain dependent random variables by expectations of the same functions of independent Bernoulli random variables. This lemma provides an alternative tool to Hoeffding-Azuma inequality to bound concentration of martingale values. Our second approach is based on integration of Hoeffding-Azuma inequality with PAC-Bayesian analysis. We also introduce a way to apply PAC-Bayesian analysis in situation …
Scientific theories can often be formulated using equality and order constraints on the relative effects in a linear regression model. For example, it may be expected that the effect of the first predictor is larger than the effect of the second predictor, and the second predictor is expected to be larger than the third predictor. The goal is then to test such expectations against competing scientific expectations or theories. In this paper a simple default Bayes factor test is proposed for testing multiple hypotheses with equality and order constraints on the effects of interest. The proposed…
Verifiable Regularity Criterion for Conditional Expectation Operators and Conditional Mean Embeddings with Applications to Nonparametric Regression, Bayesian Inverse Problems, and Koopman Operators
Technische Universität Ilmenau（伊尔梅瑙工业大学）；Freie Universität Berlin（柏林自由大学）；Chemnitz University of Technology（开姆尼茨工业大学）
Structural identification and damage detection can be generalized as the simultaneous estimation of input forces, physical parameters, and dynamical states. Although Kalman-type filters are efficient tools to address this problem, the calibration of noise covariance matrices is cumbersome. For instance, calibration of input noise covariance matrix in augmented or dual Kalman filters is a critical task since a slight variation in its value can adversely affect estimations. The present study develops a Bayesian Expectation-Maximization (BEM) methodology for the uncertainty quantification and pro…
Politecnico di Torino（都灵理工大学）；Italian Institute for Genomic Medicine（意大利基因组医学研究所）；INFN Sezione di Torino（意大利国家核物理研究所都灵分部）；Amazon Alexa（亚马逊Alexa）
Efficient feature selection from high-dimensional datasets is a very important challenge in many data-driven fields of science and engineering. We introduce a statistical mechanics inspired strategy that addresses the problem of sparse feature selection in the context of binary classification by leveraging a computational scheme known as expectation propagation (EP). The algorithm is used in order to train a continuous-weights perceptron learning a classification rule from a set of (possibly partly mislabeled) examples provided by a teacher perceptron with diluted continuous weights. We test t…
We present a Bayesian data fusion method to approximate a posterior distribution from an ensemble of particle estimates that only have access to subsets of the data. Our approach relies on approximate probabilistic inference of model parameters through Monte Carlo methods, followed by an update and resample scheme related to multiple importance sampling to combine information from the initial estimates. We show the method is convergent in the particle limit and directly suited to application on multi-sensor data fusion problems by demonstrating efficacy on a multi-sensor Keplerian orbit determ…
This dissertation shows that careful injection of noise into sample data can substantially speed up Expectation-Maximization algorithms. Expectation-Maximization algorithms are a class of iterative algorithms for extracting maximum likelihood estimates from corrupted or incomplete data. The convergence speed-up is an example of a noise benefit or "stochastic resonance" in statistical signal processing. The dissertation presents derivations of sufficient conditions for such noise-benefits and demonstrates the speed-up in some ubiquitous signal-processing algorithms. These algorithms include par…
We explain how effective automatic probability density function estimates can be constructed using contemporary Bayesian inference engines such as those based on no-U-turn sampling and expectation propagation. Extensive simulation studies demonstrate that the proposed density estimates have excellent comparative performance and scale well to very large sample sizes due to a binning strategy. Moreover, the approach is fully Bayesian and all estimates are accompanied by pointwise credible intervals. An accompanying package in the R language facilitates easy use of the new density estimates.
Articles in Marketing and choice literatures have demonstrated the need for incorporating person-level heterogeneity into behavioral models (e.g., logit models for multiple binary outcomes as studied here). However, the logit likelihood extended with a population distribution of heterogeneity doesn't yield closed-form inferences, and therefore numerical integration techniques are relied upon (e.g., MCMC methods). We present here an alternative, closed-form Bayesian inferences for the logit model, which we obtain by approximating the logit likelihood via a polynomial expansion, and then positin…
I propose a novel approach for nonlinear Logistic regression using a two-layer neural network (NN) model structure with hierarchical priors on the network weights. I present a hybrid of expectation propagation called Variational Expectation Propagation approach (VEP) for approximate integration over the posterior distribution of the weights, the hierarchical scale parameters of the priors and zeta. Using a factorized posterior approximation I derive a computationally efficient algorithm, whose complexity scales similarly to an ensemble of independent sparse logistic models. The approach can be…
University of Oxford（牛津大学）；Carnegie Mellon University（卡内基梅隆大学）
The problem of sequentially maximizing the expectation of a function seeks to maximize the expected value of a function of interest without having direct control on its features. Instead, the distribution of such features depends on a given context and an action taken by an agent. In contrast to Bayesian optimization, the arguments of the function are not under agent's control, but are indirectly determined by the agent's action based on a given context. If the information of the features is to be included in the maximization problem, the full conditional distribution of such features, rather …
The choice of the summary statistics used in Bayesian inference and in particular in ABC algorithms has bearings on the validation of the resulting inference. Those statistics are nonetheless customarily used in ABC algorithms without consistency checks. We derive necessary and sufficient conditions on summary statistics for the corresponding Bayes factor to be convergent, namely to asymptotically select the true model. Those conditions, which amount to the expectations of the summary statistics to asymptotically differ under both models, are quite natural and can be exploited in ABC settings …
Max Planck Institute for Intelligent Systems（马克斯·普朗克智能系统研究所）；University College London（伦敦大学学院）；Université Laval（拉瓦尔大学）；Università degli Studi di Milano（米兰大学）；Montanuniversität Leoben（莱奥本矿业大学）
We present a set of high-probability inequalities that control the concentration of weighted averages of multiple (possibly uncountably many) simultaneously evolving and interdependent martingales. Our results extend the PAC-Bayesian analysis in learning theory from the i.i.d. setting to martingales opening the way for its application to importance weighted sampling, reinforcement learning, and other interactive learning domains, as well as many other domains in probability theory and statistics, where martingales are encountered. We also present a comparison inequality that bounds the expecta…
This paper uses Gaussian mixture model instead of linear Gaussian model to fit the distribution of every node in Bayesian network. We will explain why and how we use Gaussian mixture models in Bayesian network. Meanwhile we propose a new method, called double iteration algorithm, to optimize the mixture model, the double iteration algorithm combines the expectation maximization algorithm and gradient descent algorithm, and it performs perfectly on the Bayesian network with mixture models. In experiments we test the Gaussian mixture model and the optimization algorithm on different graphs which…
When a posterior distribution has multiple modes, unconditional expectations, such as the posterior mean, may not offer informative summaries of the distribution. Motivated by this problem, we propose to decompose the sample space of a multimodal distribution into domains of attraction of local modes. Domain-based representations are defined to summarize the probability masses of and conditional expectations on domains of attraction, which are much more informative than the mean and other unconditional expectations. A computational method, the multi-domain sampler, is developed to construct do…
Bayesian optimization is popular for optimizing time-consuming black-box objectives. Nonetheless, for hyperparameter tuning in deep neural networks, the time required to evaluate the validation error for even a few hyperparameter settings remains a bottleneck. Multi-fidelity optimization promises relief using cheaper proxies to such objectives --- for example, validation error for a network trained using a subset of the training points or fewer iterations than required for convergence. We propose a highly flexible and practical approach to multi-fidelity Bayesian optimization, focused on effic…
As an automatic method of determining model complexity using the training data alone, Bayesian linear regression provides us a principled way to select hyperparameters. But one often needs approximation inference if distribution assumption is beyond Gaussian distribution. In this paper, we propose a Bayesian linear regression model with Student-t assumptions (BLRS), which can be inferred exactly. In this framework, both conjugate prior and expectation maximization (EM) algorithm are generalized. Meanwhile, we prove that the maximum likelihood solution is equivalent to the standard Bayesian lin…
This paper studies the E-Bayesian (expectation of the Bayesian estimation) estimation of the parameter of Lomax distribution based on different loss functions. Under different loss functions, we calculate the Bayesian estimation of the parameter and then calculate the expectation of the estimated value to get the E-Bayesian estimation. To measure the estimated error, the E-MSE (expected mean squared error) is introduced. And the formulas of E-Bayesian estimation and E-MSE are given. By applying Markov Chain Monte Carlo technology, we analyze the performances of the proposed methods. Results ar…
Equation Discovery with Bayesian Spike-and-Slab Priors and Efficient Kernels
The University of Utah（犹他大学）；The University of Sheffield（谢菲尔德大学）；University of California, Berkeley（加利福尼亚大学伯克利分校）；Lawrence Berkeley National Laboratory（劳伦斯伯克利国家实验室）；International Computer Science Institute（国际计算机科学研究所）
Traditionally Bayesian decision-theoretic design of experiments proceeds by choosing a design to minimise expectation of a given loss function over the space of all designs. The loss function encapsulates the aim of the experiment, and the expectation is taken with respect to the joint distribution of all unknown quantities implied by the statistical model that will be fitted to observed responses. In this paper, an extended framework is proposed whereby the expectation of the loss is taken with respect to a joint distribution implied by an alternative statistical model. Motivation for this in…
Bayesian adaptive inference is widely used in psychophysics to estimate psychometric parameters. Most applications used myopic one-step ahead strategy which only optimizes the immediate utility. The widely held expectation is that global optimization strategies that explicitly optimize over some horizon can largely improve the performance of the myopic strategy. With limited studies that compared myopic and global strategies, the expectation was not challenged and researchers are still investing heavily to achieve global optimization. Is that really worthwhile? This paper provides a discouragi…
Relevance Vector Machine (RVM) is a supervised learning algorithm extended from Support Vector Machine (SVM) based on the Bayesian sparsity model. Compared with the regression problem, RVM classification is difficult to be conducted because there is no closed-form solution for the weight parameter posterior. Original RVM classification algorithm used Newton's method in optimization to obtain the mode of weight parameter posterior then approximated it by a Gaussian distribution in Laplace's method. It would work but just applied the frequency methods in a Bayesian framework. This paper proposes…
Approximate Bayesian computation (ABC) has become an essential tool for the analysis of complex stochastic models when the likelihood function is numerically unavailable. However, the well-established statistical method of empirical likelihood provides another route to such settings that bypasses simulations from the model and the choices of the ABC parameters (summary statistics, distance, tolerance), while being convergent in the number of observations. Furthermore, bypassing model simulations may lead to significant time savings in complex models, for instance those found in population gene…
We develop a scoring and classification procedure based on the PAC-Bayesian approach and the AUC (Area Under Curve) criterion. We focus initially on the class of linear score functions. We derive PAC-Bayesian non-asymptotic bounds for two types of prior for the score parameters: a Gaussian prior, and a spike-and-slab prior; the latter makes it possible to perform feature selection. One important advantage of our approach is that it is amenable to powerful Bayesian computational tools. We derive in particular a Sequential Monte Carlo algorithm, as an efficient method which may be used as a gold…
Robust Survival Estimation under Interval Censoring: Expectation-Maximization and Bayesian Accelerated Failure Time Assessment via Simulation and Application
In many applications of Bayesian clustering, posterior sampling on the discrete state space of cluster allocations is achieved via Markov chain Monte Carlo (MCMC) techniques. As it is typically challenging to design transition kernels to explore this state space efficiently, MCMC convergence diagnostics for clustering applications is especially important. For general MCMC problems, state-of-the-art convergence diagnostics involve comparisons across multiple chains. However, single-chain alternatives can be appealing for computationally intensive and slowly-mixing MCMC, as is typically the case…
A computational framework for infinite-dimensional Bayesian inverse problems. Part I: The linearized case, with application to global seismic inversion
Institute for Computational Engineering & Sciences, The University of Texas at Austin（计算工程与科学研究所，德克萨斯大学奥斯汀分校）；Department of Mechanical Engineering, The University of Texas at Austin（机械工程系，德克萨斯大学奥斯汀分校）；Department of Geological Sciences, The University of Texas at Austin（地质科学系，德克萨斯大学奥斯汀分校）
