The number of possible methods of generalizing binary classification to multi-class classification increases exponentially with the number of class labels. Often, the best method of doing so will be highly problem dependent. Here we present classification software in which the partitioning of multi-class classification problems into binary classification problems is specified using a recursive control language.

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.

We consider the problem of offline, pool-based active semi-supervised learning on graphs. This problem is important when the labeled data is scarce and expensive whereas unlabeled data is easily available. The data points are represented by the vertices of an undirected graph with the similarity between them captured by the edge weights. Given a target number of nodes to label, the goal is to choose those nodes that are most informative and then predict the unknown labels. We propose a novel framework for this problem based on our recent results on sampling theory for graph signals. A graph signal is a real-valued function defined on each node of the graph. A notion of frequency for such signals can be defined using the spectrum of the graph Laplacian matrix. The sampling theory for graph signals aims to extend the traditional Nyquist-Shannon sampling theory by allowing us to identify the class of graph signals that can be reconstructed from their values on a subset of vertices. This approach allows us to define a criterion for active learning based on sampling set selection which aims at maximizing the frequency of the signals that can be reconstructed from their samples on the set. Experiments show the effectiveness of our method.

This paper establishes non-asymptotic oracle inequalities for the prediction error and estimation accuracy of the LASSO in stationary vector autoregressive models. These inequalities are used to establish consistency of the LASSO even when the number of parameters is of a much larger order of magnitude than the sample size. We also give conditions under which no relevant variables are excluded. Next, non-asymptotic probabilities are given for the Adaptive LASSO to select the correct sparsity pattern. We then give conditions under which the Adaptive LASSO reveals the correct sparsity pattern asymptotically. We establish that the estimates of the non-zero coefficients are asymptotically equivalent to the oracle assisted least squares estimator. This is used to show that the rate of convergence of the estimates of the non-zero coefficients is identical to the one of least squares only including the relevant covariates.

We propose a new two stage algorithm LING for large scale regression problems. LING has the same risk as the well known Ridge Regression under the fixed design setting and can be computed much faster. Our experiments have shown that LING performs well in terms of both prediction accuracy and computational efficiency compared with other large scale regression algorithms like Gradient Descent, Stochastic Gradient Descent and Principal Component Regression on both simulated and real datasets.

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.

Several methods have been recently proposed for estimating sparse Gaussian graphical models using $\ell_{1}$ regularization on the inverse covariance matrix. Despite recent advances, contemporary applications require methods that are even faster in order to handle ill-conditioned high dimensional modern day datasets. In this paper, we propose a new method, G-AMA, to solve the sparse inverse covariance estimation problem using Alternating Minimization Algorithm (AMA), that effectively works as a proximal gradient algorithm on the dual problem. Our approach has several novel advantages over existing methods. First, we demonstrate that G-AMA is faster than the previous best algorithms by many orders of magnitude and is thus an ideal approach for modern high throughput applications. Second, global linear convergence of G-AMA is demonstrated rigorously, underscoring its good theoretical properties. Third, the dual algorithm operates on the covariance matrix, and thus easily facilitates incorporating additional constraints on pairwise/marginal relationships between feature pairs based on domain specific knowledge. Over and above estimating a sparse inverse covariance matrix, we also illustrate how to (1) incorporate constraints on the (bivariate) correlations and, (2) incorporate equality (equisparsity) or linear constraints between individual inverse covariance elements. Fourth, we also show that G-AMA is better adept at handling extremely ill-conditioned problems, as is often the case with real data. The methodology is demonstrated on both simulated and real datasets to illustrate its superior performance over recently proposed methods.

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.

Additive models play an important role in semiparametric statistics. This paper gives learning rates for regularized kernel based methods for additive models. These learning rates compare favourably in particular in high dimensions to recent results on optimal learning rates for purely nonparametric regularized kernel based quantile regression using the Gaussian radial basis function kernel, provided the assumption of an additive model is valid. Additionally, a concrete example is presented to show that a Gaussian function depending only on one variable lies in a reproducing kernel Hilbert space generated by an additive Gaussian kernel, but does not belong to the reproducing kernel Hilbert space generated by the multivariate Gaussian kernel of the same variance.