Methods for learning Bayesian network structure can discover dependency structure between observed variables, and have been shown to be useful in many applications. However, in domains that involve a large number of variables, the space of possible network structures is enormous, making it difficult, for both computational and statistical reasons, to identify a good model. In this paper, we consider a solution to this problem, suitable for domains where many variables have similar behavior. Our method is based on a new class of models, which we call module networks. A module network explicitly represents the notion of a module - a set of variables that have the same parents in the network and share the same conditional probability distribution. We define the semantics of module networks, and describe an algorithm that learns a module network from data. The algorithm learns both the partitioning of the variables into modules and the dependency structure between the variables. We evaluate our algorithm on synthetic data, and on real data in the domains of gene expression and the stock market. Our results show that module networks generalize better than Bayesian networks, and that the learned module network structure reveals regularities that are obscured in learned Bayesian networks.

We present and implement two algorithms for analytic asymptotic evaluation of the marginal likelihood of data given a Bayesian network with hidden nodes. As shown by previous work, this evaluation is particularly hard for latent Bayesian network models, namely networks that include hidden variables, where asymptotic approximation deviates from the standard BIC score. Our algorithms solve two central difficulties in asymptotic evaluation of marginal likelihood integrals, namely, evaluation of regular dimensionality drop for latent Bayesian network models and computation of non-standard approximation formulas for singular statistics for these models. The presented algorithms are implemented in Matlab and Maple and their usage is demonstrated for marginal likelihood approximations for Bayesian networks with hidden variables.

We propose a solution to the problem of estimating a Riemannian metric associated with a given differentiable manifold. The metric learning problem is based on minimizing the relative volume of a given set of points. We derive the details for a family of metrics on the multinomial simplex. The resulting metric has applications in text classification and bears some similarity to TFIDF representation of text documents.

Bayesian networks are now being used in enormous fields, for example, diagnosis of a system, data mining, clustering and so on. In spite of their wide range of applications, the statistical properties have not yet been clarified, because the models are nonidentifiable and non-regular. In a Bayesian network, the set of its parameter for a smaller model is an analytic set with singularities in the space of large ones. Because of these singularities, the Fisher information matrices are not positive definite. In other words, the mathematical foundation for learning was not constructed. In recent years, however, we have developed a method to analyze non-regular models using algebraic geometry. This method revealed the relation between the models singularities and its statistical properties. In this paper, applying this method to Bayesian networks with latent variables, we clarify the order of the stochastic complexities.Our result claims that the upper bound of those is smaller than the dimension of the parameter space. This means that the Bayesian generalization error is also far smaller than that of regular model, and that Schwarzs model selection criterion BIC needs to be improved for Bayesian networks.

We present CLP(BN), a novel approach that aims at expressing Bayesian networks through the constraint logic programming framework. Arguably, an important limitation of traditional Bayesian networks is that they are propositional, and thus cannot represent relations between multiple similar objects in multiple contexts. Several researchers have thus proposed first-order languages to describe such networks. Namely, one very successful example of this approach are the Probabilistic Relational Models (PRMs), that combine Bayesian networks with relational database technology. The key difficulty that we had to address when designing CLP(cal{BN}) is that logic based representations use ground terms to denote objects. With probabilitic data, we need to be able to uniquely represent an object whose value we are not sure about. We use {sl Skolem functions} as unique new symbols that uniquely represent objects with unknown value. The semantics of CLP(cal{BN}) programs then naturally follow from the general framework of constraint logic programming, as applied to a specific domain where we have probabilistic data. This paper introduces and defines CLP(cal{BN}), and it describes an implementation and initial experiments. The paper also shows how CLP(cal{BN}) relates to Probabilistic Relational Models (PRMs), Ngo and Haddawys Probabilistic Logic Programs, AND Kersting AND De Raedts Bayesian Logic Programs.

The motivation for this paper is to apply Bayesian structure learning using Model Averaging in large-scale networks. Currently, Bayesian model averaging algorithm is applicable to networks with only tens of variables, restrained by its super-exponential complexity. We present a novel framework, called LSBN(Large-Scale Bayesian Network), making it possible to handle networks with infinite size by following the principle of divide-and-conquer. The method of LSBN comprises three steps. In general, LSBN first performs the partition by using a second-order partition strategy, which achieves more robust results. LSBN conducts sampling and structure learning within each overlapping community after the community is isolated from other variables by Markov Blanket. Finally LSBN employs an efficient algorithm, to merge structures of overlapping communities into a whole. In comparison with other four state-of-art large-scale network structure learning algorithms such as ARACNE, PC, Greedy Search and MMHC, LSBN shows comparable results in five common benchmark datasets, evaluated by precision, recall and f-score. What's more, LSBN makes it possible to learn large-scale Bayesian structure by Model Averaging which used to be intractable. In summary, LSBN provides an scalable and parallel framework for the reconstruction of network structures. Besides, the complete information of overlapping communities serves as the byproduct, which could be used to mine meaningful clusters in biological networks, such as protein-protein-interaction network or gene regulatory network, as well as in social network.

Hierarchical beta process has found interesting applications in recent years. In this paper we present a modified hierarchical beta process prior with applications to hierarchical modeling of multiple data sources. The novel use of the prior over a hierarchical factor model allows factors to be shared across different sources. We derive a slice sampler for this model, enabling tractable inference even when the likelihood and the prior over parameters are non-conjugate. This allows the application of the model in much wider contexts without restrictions. We present two different data generative models a linear GaussianGaussian model for real valued data and a linear Poisson-gamma model for count data. Encouraging transfer learning results are shown for two real world applications text modeling and content based image retrieval.

We consider the problem of Probably Approximate Correct (PAC) learning of a binary classifier from noisy labeled examples acquired from multiple annotators (each characterized by a respective classification noise rate). First, we consider the complete information scenario, where the learner knows the noise rates of all the annotators. For this scenario, we derive sample complexity bound for the Minimum Disagreement Algorithm (MDA) on the number of labeled examples to be obtained from each annotator. Next, we consider the incomplete information scenario, where each annotator is strategic and holds the respective noise rate as a private information. For this scenario, we design a cost optimal procurement auction mechanism along the lines of Myerson's optimal auction design framework in a non-trivial manner. This mechanism satisfies incentive compatibility property, thereby facilitating the learner to elicit true noise rates of all the annotators.

Previous work on recommender systems mainly focus on fitting the ratings provided by users. However, the response patterns, i.e., some items are rated while others not, are generally ignored. We argue that failing to observe such response patterns can lead to biased parameter estimation and sub-optimal model performance. Although several pieces of work have tried to model users' response patterns, they miss the effectiveness and interpretability of the successful matrix factorization collaborative filtering approaches. To bridge the gap, in this paper, we unify explicit response models and PMF to establish the Response Aware Probabilistic Matrix Factorization (RAPMF) framework. We show that RAPMF subsumes PMF as a special case. Empirically we demonstrate the merits of RAPMF from various aspects.

Multi-modal data collections, such as corpora of paired images and text snippets, require analysis methods beyond single-view component and topic models. For continuous observations the current dominant approach is based on extensions of canonical correlation analysis, factorizing the variation into components shared by the different modalities and those private to each of them. For count data, multiple variants of topic models attempting to tie the modalities together have been presented. All of these, however, lack the ability to learn components private to one modality, and consequently will try to force dependencies even between minimally correlating modalities. In this work we combine the two approaches by presenting a novel HDP-based topic model that automatically learns both shared and private topics. The model is shown to be especially useful for querying the contents of one domain given samples of the other.