A wide class of regularization problems in machine learning and statistics employ a regularization term which is obtained by composing a simple convex function \omega with a linear transformation. This setting includes Group Lasso methods, the Fused Lasso and other total variation methods, multi-task learning methods and many more. In this paper, we present a general approach for computing the proximity operator of this class of regularizers, under the assumption that the proximity operator of the function \omega is known in advance. Our approach builds on a recent line of research on optimal first order optimization methods and uses fixed point iterations for numerically computing the proximity operator. It is more general than current approaches and, as we show with numerical simulations, computationally more efficient than available first order methods which do not achieve the optimal rate. In particular, our method outperforms state of the art O(1/T) methods for overlapping Group Lasso and matches optimal O(1/T^2) methods for the Fused Lasso and tree structured Group Lasso.

Structural equation models and Bayesian networks have been widely used to analyze causal relations between continuous variables. In such frameworks, linear acyclic models are typically used to model the data-generating process of variables. Recently, it was shown that use of non-Gaussianity identifies the full structure of a linear acyclic model, i.e., a causal ordering of variables and their connection strengths, without using any prior knowledge on the network structure, which is not the case with conventional methods. However, existing estimation methods are based on iterative search algorithms and may not converge to a correct solution in a finite number of steps. In this paper, we propose a new direct method to estimate a causal ordering and connection strengths based on non-Gaussianity. In contrast to the previous methods, our algorithm requires no algorithmic parameters and is guaranteed to converge to the right solution within a small fixed number of steps if the data strictly follows the model.

Many statistical methods have been proposed to estimate causal models in classical situations with fewer variables than observations (p>n). In this paper, we propose a method to find exogenous variables in a linear non-Gaussian causal model, which requires much smaller sample sizes than conventional methods and works even when p>>n. The key idea is to identify which variables are exogenous based on non-Gaussianity instead of estimating the entire structure of the model. Exogenous variables work as triggers that activate a causal chain in the model, and their identification leads to more efficient experimental designs and better understanding of the causal mechanism. We present experiments with artificial data and real-world gene expression data to evaluate the method.

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/.

We describe a new variational lower-bound on the minimum energy configuration of a planar binary Markov Random Field (MRF). Our method is based on adding auxiliary nodes to every face of a planar embedding of the graph in order to capture the effect of unary potentials. A ground state of the resulting approximation can be computed efficiently by reduction to minimum-weight perfect matching. We show that optimization of variational parameters achieves the same lower-bound as dual-decomposition into the set of all cycles of the original graph. We demonstrate that our variational optimization converges quickly and provides high-quality solutions to hard combinatorial problems 10-100x faster than competing algorithms that optimize the same bound.

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.

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. Versions: Mar 21, 10:10, Mar 25, 09:37

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.

In this paper, auto-associative models are proposed as candidates to the generalization of Principal Component Analysis. We show that these models are dedicated to the approximation of the dataset by a manifold. Here, the word "manifold" refers to the topology properties of the structure. The approximating manifold is built by a projection pursuit algorithm. At each step of the algorithm, the dimension of the manifold is incremented. Some theoretical properties are provided. In particular, we can show that, at each step of the algorithm, the mean residuals norm is not increased. Moreover, it is also established that the algorithm converges in a finite number of steps. Some particular auto-associative models are exhibited and compared to the classical PCA and some neural networks models. Implementation aspects are discussed. We show that, in numerous cases, no optimization procedure is required. Some illustrations on simulated and real data are presented.

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.