We describe a class of algorithms for amortized inference in Bayesian networks. In this setting, we invest computation upfront to support rapid online inference for a wide range of queries. Our approach is based on learning an inverse factorization of a model's joint distribution: a factorization that turns observations into root nodes. Our algorithms accumulate information to estimate the local conditional distributions that constitute such a factorization. These stochastic inverses can be used to invert each of the computation steps leading to an observation, sampling backwards in order to quickly find a likely explanation. We show that estimated inverses converge asymptotically in number of (prior or posterior) training samples. To make use of inverses before convergence, we describe the Inverse MCMC algorithm, which uses stochastic inverses to make block proposals for a Metropolis-Hastings sampler. We explore the efficiency of this sampler for a variety of parameter regimes and Bayes nets.

This paper extends factorized asymptotic Bayesian (FAB) inference for latent feature models~(LFMs). FAB inference has not been applicable to models, including LFMs, without a specific condition on the Hesqsian matrix of a complete log-likelihood, which is required to derive a factorized information criterion''~(FIC). Our asymptotic analysis of the Hessian matrix of LFMs shows that FIC of LFMs has the same form as those of mixture models. FAB/LFMs have several desirable properties (e.g., automatic hidden states selection and parameter identifiability) and empirically perform better than state-of-the-art Indian Buffet processes in terms of model selection, prediction, and computational efficiency."

Max-product ‘belief propagation’ (BP) is a popular distributed heuristic for finding the Maximum A Posteriori (MAP) assignment in a joint probability distribution represented by a Graphical Model (GM). It was recently shown that BP converges to the correct MAP assignment for a class of loopy GMs with the following common feature: the Linear Programming (LP) relaxation to the MAP problem is tight (has no integrality gap). Unfortunately, tightness of the LP relaxation does not, in general, guarantee convergence and correctness of the BP algorithm. The failure of BP in such cases motivates reverse engineering a solution – namely, given a tight LP, can we design a ‘good’ BP algorithm. In this paper, we design a BP algorithm for the Maximum Weight Matching (MWM) problem over general graphs. We prove that the algorithm converges to the correct optimum if the respective LP relaxation, which may include inequalities associated with non-intersecting odd-sized cycles, is tight. The most significant part of our approach is the introduction of a novel graph transformation designed to force convergence of BP. Our theoretical result suggests an efficient BP-based heuristic for the MWM problem, which consists of making sequential, “cutting plane”, modifications to the underlying GM. Our experiments show that this heuristic performs as well as traditional cutting-plane algorithms using LP solvers on MWM problems.

Shannon's entropy is a basic quantity in information theory, and a fundamental building block for the analysis of neural codes. Estimating the entropy of a discrete distribution from samples is an important and difficult problem that has received considerable attention in statistics and theoretical neuroscience. However, neural responses have characteristic statistical structure that generic entropy estimators fail to exploit. For example, existing Bayesian entropy estimators make the naive assumption that all spike words are equally likely a priori, which makes for an inefficient allocation of prior probability mass in cases where spikes are sparse. Here we develop Bayesian estimators for the entropy of binary spike trains using priors designed to flexibly exploit the statistical structure of simultaneously-recorded spike responses. We define two prior distributions over spike words using mixtures of Dirichlet distributions centered on simple parametric models. The parametric model captures high-level statistical features of the data, such as the average spike count in a spike word, which allows the posterior over entropy to concentrate more rapidly than with standard estimators (e.g., in cases where the probability of spiking differs strongly from 0.5). Conversely, the Dirichlet distributions assign prior mass to distributions far from the parametric model, ensuring consistent estimates for arbitrary distributions. We devise a compact representation of the data and prior that allow for computationally efficient implementations of Bayesian least squares and empirical Bayes entropy estimators with large numbers of neurons. We apply these estimators to simulated and real neural data and show that they substantially outperform traditional methods.

EDML is a recently proposed algorithm for learning parameters in Bayesian networks. It was originally derived in terms of approximate inference on a meta-network, which underlies the Bayesian approach to parameter estimation. While this initial derivation helped discover EDML in the first place and provided a concrete context for identifying some of its properties (e.g., in contrast to EM), the formal setting was somewhat tedious in the number of concepts it drew on. In this paper, we propose a greatly simplified perspective on EDML, which casts it as a general approach to continuous optimization. The new perspective has several advantages. First, it makes immediate some results that were non-trivial to prove initially. Second, it facilitates the design of EDML algorithms for new graphical models, leading to a new algorithm for learning parameters in Markov networks. We derive this algorithm in this paper, and show, empirically, that it can sometimes learn better estimates from complete data, several times faster than commonly used optimization methods, such as conjugate gradient and L-BFGS.

Reliance on computationally expensive algorithms for inference has been limiting the use of Bayesian nonparametric models in large scale applications. To tackle this problem, we propose a Bayesian learning algorithm for DP mixture models. Instead of following the conventional paradigm -- random initialization plus iterative update, we take an progressive approach. Starting with a given prior, our method recursively transforms it into an approximate posterior through sequential variational approximation. In this process, new components will be incorporated on the fly when needed. The algorithm can reliably estimate a DP mixture model in one pass, making it particularly suited for applications with massive data. Experiments on both synthetic data and real datasets demonstrate remarkable improvement on efficiency -- orders of magnitude speed-up compared to the state-of-the-art.

We address the problem of learning a sparse Bayesian network structure for continuous variables in a high-dimensional space. The constraint that the estimated Bayesian network structure must be a directed acyclic graph (DAG) makes the problem challenging because of the huge search space of network structures. Most previous methods were based on a two-stage approach that prunes the search space in the first stage and then searches for a network structure that satisfies the DAG constraint in the second stage. Although this approach is effective in a low-dimensional setting, it is difficult to ensure that the correct network structure is not pruned in the first stage in a high-dimensional setting. In this paper, we propose a single-stage method, called A* lasso, that recovers the optimal sparse Bayesian network structure by solving a single optimization problem with A* search algorithm that uses lasso in its scoring system. Our approach substantially improves the computational efficiency of the well-known exact methods based on dynamic programming. We also present a heuristic scheme that further improves the efficiency of A* lasso without significantly compromising the quality of solutions and demonstrate this on benchmark Bayesian networks and real data.

We present a non-factorized variational method for full posterior inference in Bayesian hierarchical models, with the goal of capturing the posterior variable dependencies via efficient and possibly parallel computation. Our approach unifies the integrated nested Laplace approximation (INLA) under the variational framework. The proposed method is applicable in more challenging scenarios than typically assumed by INLA, such as Bayesian Lasso, which is characterized by the non-differentiability of the $\ell_{1}$ norm arising from independent Laplace priors. We derive an upper bound for the Kullback-Leibler divergence, which yields a fast closed-form solution via decoupled optimization. Our method is a reliable analytic alternative to Markov chain Monte Carlo (MCMC), and it results in a tighter evidence lower bound than that of mean-field variational Bayes (VB) method.

Kernel embedding of distributions has led to many recent advances in machine learning. However, latent and low rank structures prevalent in real world distributions have rarely been taken into account in this setting. Furthermore, no prior work in kernel embedding literature has addressed the issue of robust embedding when the latent and low rank information are misspecified. In this paper, we propose a hierarchical low rank decomposition of kernels embeddings which can exploit such low rank structures in data while being robust to model misspecification. We also illustrate with empirical evidence that the estimated low rank embeddings lead to improved performance in density estimation.

In this paper we investigate the use of Langevin Monte Carlo methods on the probability simplex and propose a new method, Stochastic gradient Riemannian Langevin dynamics, which is simple to implement and can be applied to large scale data. We apply this method to latent Dirichlet allocation in an online minibatch setting,and demonstrate that it achieves substantial performance improvements overthe state of the art online variational Bayesian methods.