While Gaussian probability densities are omnipresent in applied mathematics, Gaussian cumulative probabilities are hard to calculate in any but the univariate case. We study the utility of Expectation Propagation (EP) as an approximate integration method for this problem. For rectangular integration regions, the approximation is highly accurate. We also extend the derivations to the more general case of polyhedral integration regions. However, we find that in this polyhedral case, EP's answer, though often accurate, can be almost arbitrarily wrong. We consider these unexpected results empirically and theoretically, both for the problem of Gaussian probabilities and for EP more generally. These results elucidate an interesting and non-obvious feature of EP not yet studied in detail.
Variational inference is a powerful concept that underlies many iterative approximation algorithms; expectation propagation, mean-field methods and belief propagations were all central themes at the school that can be perceived from this unifying framework. The lectures of Manfred Opper introduce the archetypal example of Expectation Propagation, before establishing the connection with the other approximation methods. Corrections by expansion about the expectation propagation are then explained. Finally some advanced inference topics and applications are explored in the final sections.
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.
We consider the problem of joint modelling of metabolic signals and gene expression in systems biology applications. We propose an approach based on input-output factorial hidden Markov models and propose a structured variational inference approach to infer the structure and states of the model. We start from the classical free form structured variational mean field approach and use a expectation propagation to approximate the expectations needed in the variational loop. We show that this corresponds to a factored expectation constrained approximate inference. We validate our model through ext…
Many inference problems involving questions of optimality ask for the maximum or the minimum of a finite set of unknown quantities. This technical report derives the first two posterior moments of the maximum of two correlated Gaussian variables and the first two posterior moments of the two generating variables (corresponding to Gaussian approximations minimizing relative entropy). It is shown how this can be used to build a heuristic approximation to the maximum relationship over a finite set of Gaussian variables, allowing approximate inference by Expectation Propagation on such quantities.
Variational methods have been recently considered for scaling the training process of Gaussian process classifiers to large datasets. As an alternative, we describe here how to train these classifiers efficiently using expectation propagation. The proposed method allows for handling datasets with millions of data instances. More precisely, it can be used for (i) training in a distributed fashion where the data instances are sent to different nodes in which the required computations are carried out, and for (ii) maximizing an estimate of the marginal likelihood using a stochastic approximation …
A method for large scale Gaussian process classification has been recently proposed based on expectation propagation (EP). Such a method allows Gaussian process classifiers to be trained on very large datasets that were out of the reach of previous deployments of EP and has been shown to be competitive with related techniques based on stochastic variational inference. Nevertheless, the memory resources required scale linearly with the dataset size, unlike in variational methods. This is a severe limitation when the number of instances is very large. Here we show that this problem is avoided wh…
Exponential family distributions are highly useful in machine learning since their calculation can be performed efficiently through natural parameters. The exponential family has recently been extended to the t-exponential family, which contains Student-t distributions as family members and thus allows us to handle noisy data well. However, since the t-exponential family is denied by the deformed exponential, we cannot derive an efficient learning algorithm for the t-exponential family such as expectation propagation (EP). In this paper, we borrow the mathematical tools of q-algebra from stati…
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…
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 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…
This paper describes an expectation propagation (EP) method for multi-class classification with Gaussian processes that scales well to very large datasets. In such a method the estimate of the log-marginal-likelihood involves a sum across the data instances. This enables efficient training using stochastic gradients and mini-batches. When this type of training is used, the computational cost does not depend on the number of data instances $N$. Furthermore, extra assumptions in the approximate inference process make the memory cost independent of $N$. The consequence is that the proposed EP met…
We consider probabilistic multinomial probit classification using Gaussian process (GP) priors. The challenges with the multiclass GP classification are the integration over the non-Gaussian posterior distribution, and the increase of the number of unknown latent variables as the number of target classes grows. Expectation propagation (EP) has proven to be a very accurate method for approximate inference but the existing EP approaches for the multinomial probit GP classification rely on numerical quadratures or independence assumptions between the latent values from different classes to facili…
Several numerical approximation strategies for the expectation-propagation algorithm are studied in the context of large-scale learning: the Laplace method, a faster variant of it, Gaussian quadrature, and a deterministic version of variational sampling (i.e., combining quadrature with variational approximation). Experiments in training linear binary classifiers show that the expectation-propagation algorithm converges best using variational sampling, while it also converges well using Laplace-style methods with smooth factors but tends to be unstable with non-differentiable ones. Gaussian qua…
Expectation propagation (EP) is a powerful approximate inference algorithm. However, a critical barrier in applying EP is that the moment matching in message updates can be intractable. Handcrafting approximations is usually tricky, and lacks generalizability. Importance sampling is very expensive. While Laplace propagation provides a good solution, it has to run numerical optimizations to find Laplace approximations in every update, which is still quite inefficient. To overcome these practical barriers, we propose conditional expectation propagation (CEP) that performs conditional moment matc…
We propose a novel approach for nonlinear regression using a two-layer neural network (NN) model structure with sparsity-favoring hierarchical priors on the network weights. We present an expectation propagation (EP) approach for approximate integration over the posterior distribution of the weights, the hierarchical scale parameters of the priors, and the residual scale. Using a factorized posterior approximation we derive a computationally efficient algorithm, whose complexity scales similarly to an ensemble of independent sparse linear models. The approach enables flexible definition of wei…
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…
University College London（伦敦大学学院）；Google Deepmind（谷歌DeepMind）
We propose to learn a kernel-based message operator which takes as input all expectation propagation (EP) incoming messages to a factor node and produces an outgoing message. In ordinary EP, computing an outgoing message involves estimating a multivariate integral which may not have an analytic expression. Learning such an operator allows one to bypass the expensive computation of the integral during inference by directly mapping all incoming messages into an outgoing message. The operator can be learned from training data (examples of input and output messages) which allows automated inferenc…
University of Tübingen（蒂宾根大学）；International Max Planck Research School for Intelligent Systems（国际马克斯·普朗克智能系统研究所）；University of British Columbia（不列颠哥伦比亚大学）
We are interested in privatizing an approximate posterior inference algorithm called Expectation Propagation (EP). EP approximates the posterior by iteratively refining approximations to the local likelihoods, and is known to provide better posterior uncertainties than those by variational inference (VI). However, EP needs a large memory to maintain all local approximates associated with each datapoint in the training data. To overcome this challenge, stochastic expectation propagation (SEP) considers a single unique local factor that captures the average effect of each likelihood term to the …
Aalto University（阿尔托大学）；Technical University of Denmark（丹麦技术大学）
We formulate approximate Bayesian inference in non-conjugate temporal and spatio-temporal Gaussian process models as a simple parameter update rule applied during Kalman smoothing. This viewpoint encompasses most inference schemes, including expectation propagation (EP), the classical (Extended, Unscented, etc.) Kalman smoothers, and variational inference. We provide a unifying perspective on these algorithms, showing how replacing the power EP moment matching step with linearisation recovers the classical smoothers. EP provides some benefits over the traditional methods via introduction of th…
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…
We develop a framework for approximating collapsed Gibbs sampling in generative latent variable cluster models. Collapsed Gibbs is a popular MCMC method, which integrates out variables in the posterior to improve mixing. Unfortunately for many complex models, integrating out these variables is either analytically or computationally intractable. We efficiently approximate the necessary collapsed Gibbs integrals by borrowing ideas from expectation propagation. We present two case studies where exact collapsed Gibbs sampling is intractable: mixtures of Student-t's and time series clustering. Our …
We propose an original particle-based implementation of the Loopy Belief Propagation (LPB) algorithm for pairwise Markov Random Fields (MRF) on a continuous state space. The algorithm constructs adaptively efficient proposal distributions approximating the local beliefs at each note of the MRF. This is achieved by considering proposal distributions in the exponential family whose parameters are updated iterately in an Expectation Propagation (EP) framework. The proposed particle scheme provides consistent estimation of the LBP marginals as the number of particles increases. We demonstrate that…
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…
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 Michigan（密歇根大学）；DEVCOM Army Research Laboratory（DEVCOM陆军研究实验室）；BI Norwegian Business School（BI挪威商学院）；University of Brescia（布雷西亚大学）
In second-order uncertain Bayesian networks, the conditional probabilities are only known within distributions, i.e., probabilities over probabilities. The delta-method has been applied to extend exact first-order inference methods to propagate both means and variances through sum-product networks derived from Bayesian networks, thereby characterizing epistemic uncertainty, or the uncertainty in the model itself. Alternatively, second-order belief propagation has been demonstrated for polytrees but not for general directed acyclic graph structures. In this work, we extend Loopy Belief Propagat…
Approximations of loopy belief propagation, including expectation propagation and approximate message passing, have attracted considerable attention for probabilistic inference problems. This paper proposes and analyzes a generalization of Opper and Winther's expectation consistent (EC) approximate inference method. The proposed method, called Generalized Expectation Consistency (GEC), can be applied to both maximum a posteriori (MAP) and minimum mean squared error (MMSE) estimation. Here we characterize its fixed points, convergence, and performance relative to the replica prediction of optim…
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…
Gaussian processes (GPs) are flexible distributions over functions that enable high-level assumptions about unknown functions to be encoded in a parsimonious, flexible and general way. Although elegant, the application of GPs is limited by computational and analytical intractabilities that arise when data are sufficiently numerous or when employing non-Gaussian models. Consequently, a wealth of GP approximation schemes have been developed over the last 15 years to address these key limitations. Many of these schemes employ a small set of pseudo data points to summarise the actual data. In this…
We propose an efficient nonparametric strategy for learning a message operator in expectation propagation (EP), which takes as input the set of incoming messages to a factor node, and produces an outgoing message as output. This learned operator replaces the multivariate integral required in classical EP, which may not have an analytic expression. We use kernel-based regression, which is trained on a set of probability distributions representing the incoming messages, and the associated outgoing messages. The kernel approach has two main advantages: first, it is fast, as it is implemented usin…
Bayesian inference is a popular method to build learning algorithms but it is hampered by the fact that its key object, the posterior probability distribution, is often uncomputable. Expectation Propagation (EP) (Minka (2001)) is a popular algorithm that solves this issue by computing a parametric approximation (e.g: Gaussian) to the density of the posterior. However, while it is known empirically to quickly compute fine approximations, EP is extremely poorly understood which prevents it from being adopted by a larger fraction of the community. The object of the present article is to shed intu…
Many models of interest in the natural and social sciences have no closed-form likelihood function, which means that they cannot be treated using the usual techniques of statistical inference. In the case where such models can be efficiently simulated, Bayesian inference is still possible thanks to the Approximate Bayesian Computation (ABC) algorithm. Although many refinements have been suggested, ABC inference is still far from routine. ABC is often excruciatingly slow due to very low acceptance rates. In addition, ABC requires introducing a vector of "summary statistics", the choice of which…
Sorbonne Université（索邦大学）；CNRS（法国国家科学研究中心）；Institut de Biologie Paris-Seine（巴黎塞纳河生物学研究所）
Many interesting problems in fields ranging from telecommunications to computational biology can be formalized in terms of large underdetermined systems of linear equations with additional constraints or regularizers. One of the most studied ones, the Compressed Sensing problem (CS), consists in finding the solution with the smallest number of non-zero components of a given system of linear equations $\boldsymbol y = \mathbf{F} \boldsymbol{w}$ for known measurement vector $\boldsymbol{y}$ and sensing matrix $\mathbf{F}$. Here, we will address the compressed sensing problem within a Bayesian in…
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…
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…
