In the Bayesian approach to structure learning of graphical models, the equivalent sample size (ESS) in the Dirichlet prior over the model parameters was recently shown to have an important effect on the maximum-a-posteriori estimate of the Bayesian network structure. In our first contribution, we theoretically analyze the case of large ESS-values, which complements previous work: among other results, we find that the presence of an edge in a Bayesian network is favoured over its absence even if both the Dirichlet prior and the data imply independence, as long as the conditional empirical distribution is notably different from uniform. In our second contribution, we focus on realistic ESS-values, and provide an analytical approximation to the "optimal" ESS-value in a predictive sense (its accuracy is also validated experimentally): this approximation provides an understanding as to which properties of the data have the main effect determining the "optimal" ESS-value.

Gaussian Markov random fields (GMRFs) are useful in a broad range of applications. In this paper we tackle the problem of learning a sparse GMRF in a high-dimensional space. Our approach uses the l1-norm as a regularization on the inverse covariance matrix. We utilize a novel projected gradient method, which is faster than previous methods in practice and equal to the best performing of these in asymptotic complexity. We also extend the l1-regularized objective to the problem of sparsifying entire blocks within the inverse covariance matrix. Our methods generalize fairly easily to this case, while other methods do not. We demonstrate that our extensions give better generalization performance on two real domains--biological network analysis and a 2D-shape modeling image task.

We introduce Clique Matrices as an alternative representation of undirected graphs, being a generalisation of the incidence matrix representation. Here we use clique matrices to decompose a graph into a set of possibly overlapping clusters, de ned as well-connected subsets of vertices. The decomposition is based on a statistical description which encourages clusters to be well connected and few in number. Inference is carried out using a variational approximation. Clique matrices also play a natural role in parameterising positive de nite matrices under zero constraints on elements of the matrix. We show that clique matrices can parameterise all positive de nite matrices restricted according to a decomposable graph and form a structured Factor Analysis approximation in the non-decomposable case.

Variational Bayesian inference and (collapsed) Gibbs sampling are the two important classes of inference algorithms for Bayesian networks. Both have their advantages and disadvantages: collapsed Gibbs sampling is unbiased but is also inefficient for large count values and requires averaging over many samples to reduce variance. On the other hand, variational Bayesian inference is efficient and accurate for large count values but suffers from bias for small counts. We propose a hybrid algorithm that combines the best of both worlds: it samples very small counts and applies variational updates to large counts. This hybridization is shown to significantly improve testset perplexity relative to variational inference at no computational cost.

A Bayesian treatment of latent directed graph structure for non-iid data is provided where each child datum is sampled with a directed conditional dependence on a single unknown parent datum. The latent graph structure is assumed to lie in the family of directed out-tree graphs which leads to efficient Bayesian inference. The latent likelihood of the data and its gradients are computable in closed form via Tutte's directed matrix tree theorem using determinants and inverses of the out-Laplacian. This novel likelihood subsumes iid likelihood, is exchangeable and yields efficient unsupervised and semi-supervised learning algorithms. In addition to handling taxonomy and phylogenetic datasets the out-tree assumption performs surprisingly well as a semi-parametric density estimator on standard iid datasets. Experiments with unsupervised and semisupervised learning are shown on various UCI and taxonomy datasets.

Parameter estimation in Markov random fields (MRFs) is a difficult task, in which inference over the network is run in the inner loop of a gradient descent procedure. Replacing exact inference with approximate methods such as loopy belief propagation (LBP) can suffer from poor convergence. In this paper, we provide a different approach for combining MRF learning and Bethe approximation. We consider the dual of maximum likelihood Markov network learning - maximizing entropy with moment matching constraints - and then approximate both the objective and the constraints in the resulting optimization problem. Unlike previous work along these lines (Teh & Welling, 2003), our formulation allows parameter sharing between features in a general log-linear model, parameter regularization and conditional training. We show that piecewise training (Sutton & McCallum, 2005) is a very restricted special case of this formulation. We study two optimization strategies: one based on a single convex approximation and one that uses repeated convex approximations. We show results on several real-world networks that demonstrate that these algorithms can significantly outperform learning with loopy and piecewise. Our results also provide a framework for analyzing the trade-offs of different relaxations of the entropy objective and of the constraints.

Graphical models trained using maximum likelihood are a common tool for probabilistic inference of marginal distributions. However, this approach suffers difficulties when either the inference process or the model is approximate. In this paper, the inference process is first defined to be the minimization of a convex function, inspired by free energy approximations. Learning is then done directly in terms of the performance of the inference process at univariate marginal prediction. The main novelty is that this is a direct minimization of emperical risk, where the risk measures the accuracy of predicted marginals.

Chordal graphs can be used to encode dependency models that are representable by both directed acyclic and undirected graphs. This paper discusses a very simple and efficient algorithm to learn the chordal structure of a probabilistic model from data. The algorithm is a greedy hill-climbing search algorithm that uses the inclusion boundary neighborhood over chordal graphs. In the limit of a large sample size and under appropriate hypotheses on the scoring criterion, we prove that the algorithm will find a structure that is inclusion-optimal when the dependency model of the data-generating distribution can be represented exactly by an undirected graph. The algorithm is evaluated on simulated datasets.

We present an algorithm that identifies the reasoning patterns of agents in a game, by iteratively examining the graph structure of its Multi-Agent Influence Diagram (MAID) representation. If the decision of an agent participates in no reasoning patterns, then we can effectively ignore that decision for the purpose of calculating a Nash equilibrium for the game. In some cases, this can lead to exponential time savings in the process of equilibrium calculation. Moreover, our algorithm can be used to enumerate the reasoning patterns in a game, which can be useful for constructing more effective computerized agents interacting with humans.

In this paper, we consider planning in stochastic shortest path (SSP) problems, a subclass of Markov Decision Problems (MDP). We focus on medium-size problems whose state space can be fully enumerated. This problem has numerous important applications, such as navigation and planning under uncertainty. We propose a new approach for constructing a multi-level hierarchy of progressively simpler abstractions of the original problem. Once computed, the hierarchy can be used to speed up planning by first finding a policy for the most abstract level and then recursively refining it into a solution to the original problem. This approach is fully automated and delivers a speed-up of two orders of magnitude over a state-of-the-art MDP solver on sample problems while returning near-optimal solutions. We also prove theoretical bounds on the loss of solution optimality resulting from the use of abstractions.