Efficient computational strategies to learn the structure of probabilistic graphical models of cumulative phenomena

Structural learning of Bayesian Networks (BNs) is a NP-hard problem, which is further complicated by many theoretical issues, such as the I-equivalence among different structures. In this work, we focus on a specific subclass of BNs, named Suppes-Bayes Causal Networks (SBCNs), which include specific structural constraints based on Suppes' probabilistic causation to efficiently model cumulative phenomena. Here we compare the performance, via extensive simulations, of various state-of-the-art search strategies, such as local search techniques and Genetic Algorithms, as well as of distinct regularization methods. The assessment is performed on a large number of simulated datasets from topologies with distinct levels of complexity, various sample size and different rates of errors in the data. Among the main results, we show that the introduction of Suppes' constraints dramatically improve the inference accuracy, by reducing the solution space and providing a temporal ordering on the variables. We also report on trade-offs among different search techniques that can be efficiently employed in distinct experimental settings. This manuscript is an extended version of the paper "Structural Learning of Probabilistic Graphical Models of Cumulative Phenomena" presented at the 2018 International Conference on Computational Science

Network inference and community detection, based on covariance matrices, correlations and test statistics from arbitrary distributions

In this paper we propose methodology for inference of binary-valued adjacency matrices from various measures of the strength of association between pairs of network nodes, or more generally pairs of variables. This strength of association can be quantified by sample covariance and correlation matrices, and more generally by test-statistics and hypothesis test p-values from arbitrary distributions. Community detection methods such as block modelling typically require binary-valued adjacency matrices as a starting point. Hence, a main motivation for the methodology we propose is to obtain binary-valued adjacency matrices from such pairwise measures of strength of association between variables. The proposed methodology is applicable to large high-dimensional data-sets and is based on computationally efficient algorithms. We illustrate its utility in a range of contexts and data-sets

The Infinite Hierarchical Factor Regression Model

We propose a nonparametric Bayesian factor regression model that accounts for uncertainty in the number of factors, and the relationship between factors. To accomplish this, we propose a sparse variant of the Indian Buffet Process and couple this with a hierarchical model over factors, based on Kingman's coalescent. We apply this model to two problems (factor analysis and factor regression) in gene-expression data analysis

Bayesian stochastic blockmodeling

This chapter provides a self-contained introduction to the use of Bayesian inference to extract large-scale modular structures from network data, based on the stochastic blockmodel (SBM), as well as its degree-corrected and overlapping generalizations. We focus on nonparametric formulations that allow their inference in a manner that prevents overfitting, and enables model selection. We discuss aspects of the choice of priors, in particular how to avoid underfitting via increased Bayesian hierarchies, and we contrast the task of sampling network partitions from the posterior distribution with finding the single point estimate that maximizes it, while describing efficient algorithms to perform either one. We also show how inferring the SBM can be used to predict missing and spurious links, and shed light on the fundamental limitations of the detectability of modular structures in networks.Comment: 44 pages, 16 figures. Code is freely available as part of graph-tool at https://graph-tool.skewed.de . See also the HOWTO at https://graph-tool.skewed.de/static/doc/demos/inference/inference.htm

Variational Walkback: Learning a Transition Operator as a Stochastic Recurrent Net

We propose a novel method to directly learn a stochastic transition operator whose repeated application provides generated samples. Traditional undirected graphical models approach this problem indirectly by learning a Markov chain model whose stationary distribution obeys detailed balance with respect to a parameterized energy function. The energy function is then modified so the model and data distributions match, with no guarantee on the number of steps required for the Markov chain to converge. Moreover, the detailed balance condition is highly restrictive: energy based models corresponding to neural networks must have symmetric weights, unlike biological neural circuits. In contrast, we develop a method for directly learning arbitrarily parameterized transition operators capable of expressing non-equilibrium stationary distributions that violate detailed balance, thereby enabling us to learn more biologically plausible asymmetric neural networks and more general non-energy based dynamical systems. The proposed training objective, which we derive via principled variational methods, encourages the transition operator to "walk back" in multi-step trajectories that start at data-points, as quickly as possible back to the original data points. We present a series of experimental results illustrating the soundness of the proposed approach, Variational Walkback (VW), on the MNIST, CIFAR-10, SVHN and CelebA datasets, demonstrating superior samples compared to earlier attempts to learn a transition operator. We also show that although each rapid training trajectory is limited to a finite but variable number of steps, our transition operator continues to generate good samples well past the length of such trajectories, thereby demonstrating the match of its non-equilibrium stationary distribution to the data distribution. Source Code: http://github.com/anirudh9119/walkback_nips17Comment: To appear at NIPS 201