We develop a Bayesian Poisson matrix factorization model for forming recommendations from sparse user behavior data. These data are large user/item matrices where each user has provided feedback on only a small subset of items, either explicitly (e.g., through star ratings) or implicitly (e.g., through views or purchases). In contrast to traditional matrix factorization approaches, Poisson factorization implicitly models each user's limited attention to consume items. Moreover, because of the mathematical form of the Poisson likelihood, the model needs only to explicitly consider the observed entries in the matrix, leading to both scalable computation and good predictive performance. We develop a variational inference algorithm for approximate posterior inference that scales up to massive data sets. This is an efficient algorithm that iterates over the observed entries and adjusts an approximate posterior over the user/item representations. We apply our method to large real-world user data containing users rating movies, users listening to songs, and users reading scientific papers. In all these settings, Bayesian Poisson factorization outperforms state-of-the-art matrix factorization methods.

In recent years, there has been considerable theoretical development regarding variable selection consistency of penalized regression techniques, such as the lasso. However, there has been relatively little work on quantifying the uncertainty in these selection procedures. In this paper, we propose a new method for inference in high dimensions using a score test based on penalized regression. In this test, we perform penalized regression of an outcome on all but a single feature, and test for correlation of the residuals with the held-out feature. This procedure is applied to each feature in turn. Interestingly, when an $\ell_1$ penalty is used, the sparsity pattern of the lasso corresponds exactly to a decision based on the proposed test. Further, when an $\ell_2$ penalty is used, the test corresponds precisely to a score test in a mixed effects model, in which the effects of all but one feature are assumed to be random. We formulate the hypothesis being tested as a compromise between the null hypotheses tested in simple linear regression on each feature and in multiple linear regression on all features, and develop reference distributions for some well-known penalties. We also examine the behavior of the test on real and simulated data.

We consider learning the possible causal direction of two observed variables in the presence of latent confounding variables. Several existing methods have been shown to consistently estimate causal direction assuming linear or some type of nonlinear relationship and no latent confounders. However, the estimation results could be distorted if either assumption is actually violated. In this paper, we first propose a new linear non-Gaussian acyclic structural equation model with individual-specific effects that allows latent confounders to be considered. We then propose an empirical Bayesian approach for estimating possible causal direction using the new model. We demonstrate the effectiveness of our method using artificial and real-world data.

We study the problem of learning a distribution from samples, when the underlying distribution is a mixture of product distributions over discrete domains. This problem is motivated by several practical applications such as crowd-sourcing, recommendation systems, and learning Boolean functions. The existing solutions either heavily rely on the fact that the number of components in the mixtures is finite or have sample/time complexity that is exponential in the number of components. In this paper, we introduce a polynomial time/sample complexity method for learning a mixture of $r$ discrete product distributions over $\{1, 2, \dots, \ell\}^n$, for general $\ell$ and $r$. We show that our approach is statistically consistent and further provide finite sample guarantees. We use techniques from the recent work on tensor decompositions for higher-order moment matching. A crucial step in these moment matching methods is to construct a certain matrix and a certain tensor with low-rank spectral decompositions. These tensors are typically estimated directly from the samples. The main challenge in learning mixtures of discrete product distributions is that these low-rank tensors cannot be obtained directly from the sample moments. Instead, we reduce the tensor estimation problem to: $a$) estimating a low-rank matrix using only off-diagonal block elements; and $b$) estimating a tensor using a small number of linear measurements. Leveraging on recent developments in matrix completion, we give an alternating minimization based method to estimate the low-rank matrix, and formulate the tensor completion problem as a least-squares problem.

Enzyme sequences and structures are routinely used in the biological sciences as queries to search for functionally related enzymes in online databases. To this end, one usually departs from some notion of similarity, comparing two enzymes by looking for correspondences in their sequences, structures or surfaces. For a given query, the search operation results in a ranking of the enzymes in the database, from very similar to dissimilar enzymes, while information about the biological function of annotated database enzymes is ignored. In this work we show that rankings of that kind can be substantially improved by applying kernel-based learning algorithms. This approach enables the detection of statistical dependencies between similarities of the active cleft and the biological function of annotated enzymes. This is in contrast to search-based approaches, which do not take annotated training data into account. Similarity measures based on the active cleft are known to outperform sequence-based or structure-based measures under certain conditions. We consider the Enzyme Commission (EC) classification hierarchy for obtaining annotated enzymes during the training phase. The results of a set of sizeable experiments indicate a consistent and significant improvement for a set of similarity measures that exploit information about small cavities in the surface of enzymes.

Time series of counts arise in a variety of forecasting applications, for which traditional models are generally inappropriate. This paper introduces a hierarchical Bayesian formulation applicable to count time series that can easily account for explanatory variables and share statistical strength across groups of related time series. We derive an efficient approximate inference technique, and illustrate its performance on a number of datasets from supply chain planning.

Given a real matrix A with n columns, the problem is to approximate the Gram product AA^T by c << n weighted outer products of columns of A. Necessary and sufficient conditions for the exact computation of AA^T (in exact arithmetic) from c >= rank(A) columns depend on the right singular vector matrix of A. For a Monte-Carlo matrix multiplication algorithm by Drineas et al. that samples outer products, we present probabilistic bounds for the 2-norm relative error due to randomization. The bounds depend on the stable rank or the rank of A, but not on the matrix dimensions. Numerical experiments illustrate that the bounds are informative, even for stringent success probabilities and matrices of small dimension. We also derive bounds for the smallest singular value and the condition number of matrices obtained by sampling rows from orthonormal matrices.

Extensional higher-order logic programming has been introduced as a generalization of classical logic programming. An important characteristic of this paradigm is that it preserves all the well-known properties of traditional logic programming. In this paper we consider the semantics of negation in the context of the new paradigm. Using some recent results from non-monotonic fixed-point theory, we demonstrate that every higher-order logic program with negation has a unique minimum infinite-valued model. In this way we obtain the first purely model-theoretic semantics for negation in extensional higher-order logic programming. Using our approach, we resolve an old paradox that was introduced by W. W. Wadge in order to demonstrate the semantic difficulties of higher-order logic programming.

Social network analysis (SNA), which is a research field describing and modeling the social connection of a certain group of people, is popular among network services. Our topic words analysis project is a SNA method to visualize the topic words among emails from Obama.com to accounts registered in Columbus, Ohio. Based on Latent Dirichlet Allocation (LDA) model, a popular topic model of SNA, our project characterizes the preference of senders for target group of receptors. Gibbs sampling is used to estimate topic and word distribution. Our training and testing data are emails from the carbon-free server Datagreening.com. We use parallel computing tool BashReduce for word processing and generate related words under each latent topic to discovers typical information of political news sending specially to local Columbus receptors. Running on two instances using paralleling tool BashReduce, our project contributes almost 30% speedup processing the raw contents, comparing with processing contents on one instance locally. Also, the experimental result shows that the LDA model applied in our project provides precision rate 53.96% higher than TF-IDF model finding target words, on the condition that appropriate size of topic words list is selected.

Alternating Minimization is a widely used and empirically successful heuristic for matrix completion and related low-rank optimization problems. Theoretical guarantees for Alternating Minimization have been hard to come by and are still poorly understood. This is in part because the heuristic is iterative and non-convex in nature. We give a new algorithm based on Alternating Minimization that provably recovers an unknown low-rank matrix from a random subsample of its entries under a standard incoherence assumption. Our results reduce the sample size requirements of the Alternating Minimization approach by at least a quartic factor in the rank and the condition number of the unknown matrix. These improvements apply even if the matrix is only close to low-rank in the Frobenius norm. Our algorithm runs in nearly linear time in the dimension of the matrix and, in a broad range of parameters, gives the strongest sample bounds among all subquadratic time algorithms that we are aware of. Underlying our work is a new robust convergence analysis of the well-known Power Method for computing the dominant singular vectors of a matrix. This viewpoint leads to a conceptually simple understanding of Alternating Minimization. In addition, we contribute a new technique for controlling the coherence of intermediate solutions arising in iterative algorithms based on a smoothed analysis of the QR factorization. These techniques may be of interest beyond their application here.