Non-negative blind source separation (non-negative BSS), which is also referred to as non-negative matrix factorization (NMF), is a very active field in domains as different as astrophysics, audio processing or biomedical signal processing. In this context, the efficient retrieval of the sources requires the use of signal priors such as sparsity. If NMF has now been well studied with sparse constraints in the direct domain, only very few algorithms can encompass non-negativity together with sparsity in a transformed domain since simultaneously dealing with two priors in two different domains is challenging. In this article, we show how a sparse NMF algorithm coined non-negative generalized morphological component analysis (nGMCA) can be extended to impose non-negativity in the direct domain along with sparsity in a transformed domain, with both analysis and synthesis formulations. To our knowledge, this work presents the first comparison of analysis and synthesis priors ---as well as their reweighted versions--- in the context of blind source separation. Comparisons with state-of-the-art NMF algorithms on realistic data show the efficiency as well as the robustness of the proposed algorithms.

In this paper we study lifted inference for the Weighted First-Order Model Counting problem (WFOMC), which counts the assignments that satisfy a given sentence in first-order logic (FOL); it has applications in Statistical Relational Learning (SRL) and Probabilistic Databases (PDB). We present several results. First, we describe a lifted inference algorithm that generalizes prior approaches in SRL and PDB. Second, we provide a novel dichotomy result for a non-trivial fragment of FO CNF sentences, showing that for each sentence the WFOMC problem is either in PTIME or #P-hard in the size of the input domain; we prove that, in the first case our algorithm solves the WFOMC problem in PTIME, and in the second case it fails. Third, we present several properties of the algorithm. Finally, we discuss limitations of lifted inference for symmetric probabilistic databases (where the weights of ground literals depend only on the relation name, and not on the constants of the domain), and prove the impossibility of a dichotomy result for the complexity of probabilistic inference for the entire language FOL.

We study propagation for the Sequence constraint in the context of constraint programming based on limited-width MDDs. Our first contribution is proving that establishing MDD-consistency for Sequence is NP-hard. Yet, we also show that this task is fixed parameter tractable with respect to the length of the sub-sequences. In addition, we propose a partial filtering algorithm that relies on a specific decomposition of the constraint and a novel extension of MDD filtering to node domains. We experimentally evaluate the performance of our proposed filtering algorithm, and demonstrate that the strength of the MDD propagation increases as the maximum width is increased. In particular, MDD propagation can outperform conventional domain propagation for Sequence by reducing the search tree size and solving time by several orders of magnitude. Similar improvements are observed with respect to the current best MDD approach that applies the decomposition of Sequence into Among constraints.

In the field of domain-independent planning, several powerful planners implementing different techniques have been developed. However, no one of these systems outperforms all others in every known benchmark domain. In this work, we propose a multi-planner approach that automatically configures a portfolio of planning techniques for each given domain. The configuration process for a given domain uses a set of training instances to: (i) compute and analyze some alternative sets of macro-actions for each planner in the portfolio identifying a (possibly empty) useful set, (ii) select a cluster of planners, each one with the identified useful set of macro-actions, that is expected to perform best, and (iii) derive some additional information for configuring the execution scheduling of the selected planners at planning time. The resulting planning system, called PbP (Portfolio- based Planner), has two variants focusing on speed and plan quality. Different versions of PbP entered and won the learning track of the sixth and seventh International Planning Competitions. In this paper, we experimentally analyze PbP considering planning speed and plan quality in depth. We provide a collection of results that help to understand PbPs behavior, and demonstrate the effectiveness of our approach to configuring a portfolio of planners with macro-actions.

Credal networks are graph-based statistical models whose parameters take values in a set, instead of being sharply specified as in traditional statistical models (e.g., Bayesian networks). The computational complexity of inferences on such models depends on the irrelevance/independence concept adopted. In this paper, we study inferential complexity under the concepts of epistemic irrelevance and strong independence. We show that inferences under strong independence are NP-hard even in trees with binary variables except for a single ternary one. We prove that under epistemic irrelevance the polynomial-time complexity of inferences in credal trees is not likely to extend to more general models (e.g., singly connected topologies). These results clearly distinguish networks that admit efficient inferences and those where inferences are most likely hard, and settle several open questions regarding their computational complexity. We show that these results remain valid even if we disallow the use of zero probabilities. We also show that the computation of bounds on the probability of the future state in a hidden Markov model is the same whether we assume epistemic irrelevance or strong independence, and we prove a similar result for inference in naive Bayes structures. These inferential equivalences are important for practitioners, as hidden Markov models and naive Bayes structures are used in real applications of imprecise probability.

Variable (feature, gene, model, which we use interchangeably) selections for regression with high-dimensional BIGDATA have found many applications in bioinformatics, computational biology, image processing, and engineering. One appealing approach is the L0 regularized regression which penalizes the number of nonzero features in the model directly. L0 is known as the most essential sparsity measure and has nice theoretical properties, while the popular L1 regularization is only a best convex relaxation of L0. Therefore, it is natural to expect that L0 regularized regression performs better than LASSO. However, it is well-known that L0 optimization is NP-hard and computationally challenging. Instead of solving the L0 problems directly, most publications so far have tried to solve an approximation problem that closely resembles L0 regularization. In this paper, we propose an efficient EM algorithm (L0EM) that directly solves the L0 optimization problem. $L_0$EM is efficient with high dimensional data. It also provides a natural solution to all Lp p in [0,2] problems. The regularized parameter can be either determined through cross-validation or AIC and BIC. Theoretical properties of the L0-regularized estimator are given under mild conditions that permit the number of variables to be much larger than the sample size. We demonstrate our methods through simulation and high-dimensional genomic data. The results indicate that L0 has better performance than LASSO and L0 with AIC or BIC has similar performance as computationally intensive cross-validation. The proposed algorithms are efficient in identifying the non-zero variables with less-bias and selecting biologically important genes and pathways with high dimensional BIGDATA.

In Bayesian analysis the form of the posterior distribution is often not analytically tractable. To obtain quantities of interest under such a distribution, such as moments or marginal distributions, we typically need to use Monte Carlo methods or approximate the posterior with a more convenient distribution. A popular method of obtaining such an approximation is structured or fixed-form Variational Bayes, which works by numerically minimizing the Kullback-Leibler divergence of an approximating distribution in the exponential family to the intractable target distribution (Attias, 2000; Beal and Ghahramani, 2006; Jordan et al., 1999; Wainwright and Jordan, 2008). For certain problems, algorithms exist that can solve this optimization problem in much less time than it would take to approximate the posterior using Monte Carlo methods (see e.g.

Motivation: Algorithms that discover variables which are causally related to a target may inform the design of experiments. With observational gene expression data, many methods discover causal variables by measuring each variable's degree of statistical dependence with the target using dependence measures (DMs). However, other methods measure each variable's ability to explain the statistical dependence between the target and the remaining variables in the data using conditional dependence measures (CDMs), since this strategy is guaranteed to find the target's direct causes, direct effects, and direct causes of the direct effects in the infinite sample limit. In this paper, we design a new algorithm in order to systematically compare the relative abilities of DMs and CDMs in discovering causal variables from gene expression data. Results: The proposed algorithm using a CDM is sample efficient, since it consistently outperforms other state-of-the-art local causal discovery algorithms when samples sizes are small. However, the proposed algorithm using a CDM outperforms the proposed algorithm using a DM only when sample sizes are above several hundred. These results suggest that accurate causal discovery from gene expression data using current CDM-based algorithms requires datasets with at least several hundred samples. Availability: The proposed algorithm is freely available at https://github.com/ericstrobl/DvCD.

We consider the problem of sparse coding, where each sample consists of a sparse linear combination of a set of dictionary atoms, and the task is to learn both the dictionary elements and the mixing coefficients. Alternating minimization is a popular heuristic for sparse coding, where the dictionary and the coefficients are estimated in alternate steps, keeping the other fixed. Typically, the coefficients are estimated via $\ell_1$ minimization, keeping the dictionary fixed, and the dictionary is estimated through least squares, keeping the coefficients fixed. In this paper, we establish local linear convergence for this variant of alternating minimization and establish that the basin of attraction for the global optimum (corresponding to the true dictionary and the coefficients) is $\order{1/s^2}$, where $s$ is the sparsity level in each sample and the dictionary satisfies RIP. Combined with the recent results of approximate dictionary estimation, this yields provable guarantees for exact recovery of both the dictionary elements and the coefficients, when the dictionary elements are incoherent.

We introduce kLog, a novel approach to statistical relational learning. Unlike standard approaches, kLog does not represent a probability distribution directly. It is rather a language to perform kernel-based learning on expressive logical and relational representations. kLog allows users to specify learning problems declaratively. It builds on simple but powerful concepts: learning from interpretations, entity/relationship data modeling, logic programming, and deductive databases. Access by the kernel to the rich representation is mediated by a technique we call graphicalization: the relational representation is first transformed into a graph --- in particular, a grounded entity/relationship diagram. Subsequently, a choice of graph kernel defines the feature space. kLog supports mixed numerical and symbolic data, as well as background knowledge in the form of Prolog or Datalog programs as in inductive logic programming systems. The kLog framework can be applied to tackle the same range of tasks that has made statistical relational learning so popular, including classification, regression, multitask learning, and collective classification. We also report about empirical comparisons, showing that kLog can be either more accurate, or much faster at the same level of accuracy, than Tilde and Alchemy. kLog is GPLv3 licensed and is available at http://klog.dinfo.unifi.it along with tutorials.