Computational approaches to transcription factor binding site identification have been actively researched for the past decade. Negative examples have long been utilized in de novo motif discovery and have been shown useful in transcription factor binding site search as well. However, understanding of the roles of negative examples in binding site search is still very limited. We propose the 2-centroid and optimal discriminating vector methods, taking into account negative examples. Cross-validation results on E. coli transcription factors show that the proposed methods benefit from negative examples, outperforming the centroid and position-specific scoring matrix methods. We further show that our proposed methods perform better than a state-of-the-art method. We characterize the proposed methods in the context of the other compared methods and show that, coupled with motif subtype identification, the proposed methods can be effectively applied to a wide range of transcription factors. Finally, we argue that the proposed methods are well-suited for eukaryotic transcription factors as well. Software tools are available at: http://biogrid.engr.uconn.edu/tfbs_search/.

Nonparametric methods are widely applicable to statistical inference problems, since they rely on a few modeling assumptions. In this context, the fresh look advocated here permeates benefits from variable selection and compressive sampling, to robustify nonparametric regression against outliers - that is, data markedly deviating from the postulated models. A variational counterpart to least-trimmed squares regression is shown closely related to an L0-(pseudo)norm-regularized estimator, that encourages sparsity in a vector explicitly modeling the outliers. This connection suggests efficient solvers based on convex relaxation, which lead naturally to a variational M-type estimator equivalent to the least-absolute shrinkage and selection operator (Lasso). Outliers are identified by judiciously tuning regularization parameters, which amounts to controlling the sparsity of the outlier vector along the whole robustification path of Lasso solutions. Reduced bias and enhanced generalization capability are attractive features of an improved estimator obtained after replacing the L0-(pseudo)norm with a nonconvex surrogate. The novel robust spline-based smoother is adopted to cleanse load curve data, a key task aiding operational decisions in the envisioned smart grid system. Computer simulations and tests on real load curve data corroborate the effectiveness of the novel sparsity-controlling robust estimators.

Users who need several queries before finding what they need can benefit from an automatic search assistant that provides feedback on their query modification strategies. We present a method to learn from a search log which types of query modifications have and have not been effective in the past. The method analyses query modifications along two dimensions: a traditional term-based dimension and a semantic dimension, for which queries are enriches with linked data entities. Applying the method to the search logs of two search engines, we identify six opportunities for a query modification assistant to improve search: modification strategies that are commonly used, but that often do not lead to satisfactory results.

With the growing popularity of Social Web applications, more and more user data is published on the Web everyday. Our research focuses on investigating ways of mining data from such platforms that can be used for modeling users and for semantically augmenting user profiles. This process can enhance adaptation and personalization in various adaptive Web-based systems. In this paper, we present the U-Sem people modeling service, a framework for the semantic enrichment and mining of people's profiles from usage data on the Social Web. We explain the architecture of our people modeling service and describe its application in an adult e-learning context as an example.

Many web-search queries serve as the beginning of an exploration of an unknown space of information, rather than looking for a specific web page. To answer such queries effec- tively, the search engine should attempt to organize the space of relevant information in a way that facilitates exploration. We describe the Aspector system that computes aspects for a given query. Each aspect is a set of search queries that together represent a distinct information need relevant to the original search query. To serve as an effective means to explore the space, Aspector computes aspects that are orthogonal to each other and to have high combined coverage. Aspector combines two sources of information to compute aspects. We discover candidate aspects by analyzing query logs, and cluster them to eliminate redundancies. We then use a mass-collaboration knowledge base (e.g., Wikipedia) to compute candidate aspects for queries that occur less frequently and to group together aspects that are likely to be semantically related. We present a user study that indicates that the aspects we compute are rated favorably against three competing alternatives related searches proposed by Google, cluster labels assigned by the Clusty search engine, and navigational searches proposed by Bing.

We study the problem of learning a sparse linear regression vector under additional conditions on the structure of its sparsity pattern. This problem is relevant in machine learning, statistics and signal processing. It is well known that a linear regression can benefit from knowledge that the underlying regression vector is sparse. The combinatorial problem of selecting the nonzero components of this vector can be "relaxed" by regularizing the squared error with a convex penalty function like the $\ell_1$ norm. However, in many applications, additional conditions on the structure of the regression vector and its sparsity pattern are available. Incorporating this information into the learning method may lead to a significant decrease of the estimation error. In this paper, we present a family of convex penalty functions, which encode prior knowledge on the structure of the vector formed by the absolute values of the regression coefficients. This family subsumes the $\ell_1$ norm and is flexible enough to include different models of sparsity patterns, which are of practical and theoretical importance. We establish the basic properties of these penalty functions and discuss some examples where they can be computed explicitly. Moreover, we present a convergent optimization algorithm for solving regularized least squares with these penalty functions. Numerical simulations highlight the benefit of structured sparsity and the advantage offered by our approach over the Lasso method and other related methods.

The Elo system for rating chess players, also used in other games and sports, was adopted by the World Chess Federation over four decades ago. Although not without controversy, it is accepted as generally reliable and provides a method for assessing players' strengths and ranking them in official tournaments. It is generally accepted that the distribution of players' rating data is approximately normal but, to date, no stochastic model of how the distribution might have arisen has been proposed. We propose such an evolutionary stochastic model, which models the arrival of players into the rating pool, the games they play against each other, and how the results of these games affect their ratings. Using a continuous approximation to the discrete model, we derive the distribution for players' ratings at time $t$ as a normal distribution, where the variance increases in time as a logarithmic function of $t$. We validate the model using published rating data from 2007 to 2010, showing that the parameters obtained from the data can be recovered through simulations of the stochastic model. The distribution of players' ratings is only approximately normal and has been shown to have a small negative skew. We show how to modify our evolutionary stochastic model to take this skewness into account, and we validate the modified model using the published official rating data.

We study online learnability of a wide class of problems, extending the results of (Rakhlin, Sridharan, Tewari, 2010) to general notions of performance measure well beyond external regret. Our framework simultaneously captures such well-known notions as internal and general Phi-regret, learning with non-additive global cost functions, Blackwell's approachability, calibration of forecasters, adaptive regret, and more. We show that learnability in all these situations is due to control of the same three quantities: a martingale convergence term, a term describing the ability to perform well if future is known, and a generalization of sequential Rademacher complexity, studied in (Rakhlin, Sridharan, Tewari, 2010). Since we directly study complexity of the problem instead of focusing on efficient algorithms, we are able to improve and extend many known results which have been previously derived via an algorithmic construction.

Nonmonotonic causal logic, introduced by Norman McCain and Hudson Turner, became a basis for the semantics of several expressive action languages. McCain's embedding of definite propositional causal theories into logic programming paved the way to the use of answer set solvers for answering queries about actions described in such languages. In this paper we extend this embedding to nondefinite theories and to first-order causal logic.

In large systems, it is important for agents to learn to act effectively, but sophisticated multi-agent learning algorithms generally do not scale. An alternative approach is to find restricted classes of games where simple, efficient algorithms converge. It is shown that stage learning efficiently converges to Nash equilibria in large anonymous games if best-reply dynamics converge. Two features are identified that improve convergence. First, rather than making learning more difficult, more agents are actually beneficial in many settings. Second, providing agents with statistical information about the behavior of others can significantly reduce the number of observations needed.