There is a broad range of BioNLP tasks for which active learning (AL) can significantly reduce annotation costs and a specific AL algorithm we have developed is particularly effective in reducing annotation costs for these tasks. We have previously developed an AL algorithm called ClosestInitPA that works best with tasks that have the following characteristics: redundancy in training material, burdensome annotation costs, Support Vector Machines (SVMs) work well for the task, and imbalanced datasets (i.e. when set up as a binary classification problem, one class is substantially rarer than the other). Many BioNLP tasks have these characteristics and thus our AL algorithm is a natural approach to apply to BioNLP tasks.

Sparse high dimensional graphical model selection is a popular topic in contemporary machine learning. To this end, various useful approaches have been proposed in the context of $\ell_1$-penalized estimation in the Gaussian framework. Though many of these inverse covariance estimation approaches are demonstrably scalable and have leveraged recent advances in convex optimization, they still depend on the Gaussian functional form. To address this gap, a convex pseudo-likelihood based partial correlation graph estimation method (CONCORD) has been recently proposed. This method uses coordinate-wise minimization of a regression based pseudo-likelihood, and has been shown to have robust model selection properties in comparison with the Gaussian approach. In direct contrast to the parallel work in the Gaussian setting however, this new convex pseudo-likelihood framework has not leveraged the extensive array of methods that have been proposed in the machine learning literature for convex optimization. In this paper, we address this crucial gap by proposing two proximal gradient methods (CONCORD-ISTA and CONCORD-FISTA) for performing $\ell_1$-regularized inverse covariance matrix estimation in the pseudo-likelihood framework. We present timing comparisons with coordinate-wise minimization and demonstrate that our approach yields tremendous payoffs for $\ell_1$-penalized partial correlation graph estimation outside the Gaussian setting, thus yielding the fastest and most scalable approach for such problems. We undertake a theoretical analysis of our approach and rigorously demonstrate convergence, and also derive rates thereof.

e-Valuate is a game on arithmetic expressions. The players have contrasting roles of maximizing and minimizing the given expression. The maximizer proposes values and the minimizer substitutes them for variables of his choice. When the expression is fully instantiated, its value is compared with a certain minimax value that would result if the players played to their optimal strategies. The winner is declared based on this comparison. We use a game tree to represent the state of the game and show how the minimax value can be computed efficiently using backward induction and alpha-beta pruning. The efficacy of alpha-beta pruning depends on the order in which the nodes are evaluated. Further improvements can be obtained by using transposition tables to prevent reevaluation of the same nodes. We propose a heuristic for node ordering. We show how the use of the heuristic and transposition tables lead to improved performance by comparing the number of nodes pruned by each method. We describe some domain-specific variants of this game. The first is a graph theoretic formulation wherein two players share a set of elements of a graph by coloring a related set with each player looking to maximize his share. The set being shared could be either the set of vertices, edges or faces (for a planar graph). An application of this is the sharing of regions enclosed by a planar graph where each player's aim is to maximize the area of his share. Another variant is a tiling game where the players alternately place dominoes on a $8 \times 8$ checkerboard to construct a maximal partial tiling. We show that the size of the tiling $x$ satisfies $22 \le x \le 32$ by proving that any maximal partial tiling requires at least $22$ dominoes.

This paper studies the off-policy evaluation problem, where one aims to estimate the value of a target policy based on a sample of observations collected by another policy. We first consider the multi-armed bandit case, establish a minimax risk lower bound, and analyze the risk of two standard estimators. It is shown, and verified in simulation, that one is minimax optimal up to a constant, while another can be arbitrarily worse, despite its empirical success and popularity. The results are applied to related problems in contextual bandits and fixed-horizon Markov decision processes, and are also related to semi-supervised learning.

We address structured covariance estimation in elliptical distributions by assuming that the covariance is a priori known to belong to a given convex set, e.g., the set of Toeplitz or banded matrices. We consider the General Method of Moments (GMM) optimization applied to robust Tyler's scatter M-estimator subject to these convex constraints. Unfortunately, GMM turns out to be non-convex due to the objective. Instead, we propose a new COCA estimator - a convex relaxation which can be efficiently solved. We prove that the relaxation is tight in the unconstrained case for a finite number of samples, and in the constrained case asymptotically. We then illustrate the advantages of COCA in synthetic simulations with structured compound Gaussian distributions. In these examples, COCA outperforms competing methods such as Tyler's estimator and its projection onto the structure set.

We propose a parsimonious topic model for text corpora. In related models such as Latent Dirichlet Allocation (LDA), all words are modeled topic-specifically, even though many words occur with similar frequencies across different topics. Our modeling determines salient words for each topic, which have topic-specific probabilities, with the rest explained by a universal shared model. Further, in LDA all topics are in principle present in every document. By contrast our model gives sparse topic representation, determining the (small) subset of relevant topics for each document. We derive a Bayesian Information Criterion (BIC), balancing model complexity and goodness of fit. Here, interestingly, we identify an effective sample size and corresponding penalty specific to each parameter type in our model. We minimize BIC to jointly determine our entire model -- the topic-specific words, document-specific topics, all model parameter values, {\it and} the total number of topics -- in a wholly unsupervised fashion. Results on three text corpora and an image dataset show that our model achieves higher test set likelihood and better agreement with ground-truth class labels, compared to LDA and to a model designed to incorporate sparsity.

We present a novel, scalable and Bayesian approach to modelling the occurrence of pairs of symbols (i,j) drawn from a large vocabulary. Observed pairs are assumed to be generated by a simple popularity based selection process followed by censoring using a preference function. By basing inference on the well-founded principle of variational bounding, and using new site-independent bounds, we show how a scalable inference procedure can be obtained for large data sets. State of the art results are presented on real-world movie viewing data.

This paper highlights new opportunities for designing large-scale machine learning systems as a consequence of blurring traditional boundaries that have allowed algorithm designers and application-level practitioners to stay -- for the most part -- oblivious to the details of the underlying hardware-level implementations. The hardware/software co-design methodology advocated here hinges on the deployment of compute-intensive machine learning kernels onto compute platforms that trade-off determinism in the computation for improvement in speed and/or energy efficiency. To achieve this, we revisit digital stochastic circuits for approximating matrix computations that are ubiquitous in machine learning algorithms. Theoretical and empirical evaluation is undertaken to assess the impact of the hardware-induced computational noise on algorithm performance. As a proof-of-concept, a stochastic hardware simulator is employed for training deep neural networks for image recognition problems.

We consider a problem of grouping multiple graphs into several clusters using singular value thesholding and non-negative factorization. We derive a model selection information criterion to estimate the number of clusters. We demonstrate our approach using "Swimmer data set" as well as simulated data set, and compare its performance with two standard clustering algorithms.

Log-linear models are the popular workhorses of analyzing contingency tables. A log-linear parameterization of an interaction model can be more expressive than a direct parameterization based on probabilities, leading to a powerful way of defining restrictions derived from marginal, conditional and context-specific independence. However, parameter estimation is often simpler under a direct parameterization, provided that the model enjoys certain decomposability properties. Here we introduce a cyclical projection algorithm for obtaining maximum likelihood estimates of log-linear parameters under an arbitrary context-specific graphical log-linear model, which needs not satisfy criteria of decomposability. We illustrate that lifting the restriction of decomposability makes the models more expressive, such that additional context-specific independencies embedded in real data can be identified. It is also shown how a context-specific graphical model can correspond to a non-hierarchical log-linear parameterization with a concise interpretation. This observation can pave way to further development of non-hierarchical log-linear models, which have been largely neglected due to their believed lack of interpretability.