The term "CoRE kernel" stands for correlation-resemblance kernel. In many applications (e.g., vision), the data are often high-dimensional, sparse, and non-binary. We propose two types of (nonlinear) CoRE kernels for non-binary sparse data and demonstrate the effectiveness of the new kernels through a classification experiment. CoRE kernels are simple with no tuning parameters. However, training nonlinear kernel SVM can be (very) costly in time and memory and may not be suitable for truly large-scale industrial applications (e.g. search). In order to make the proposed CoRE kernels more practical, we develop basic probabilistic hashing algorithms which transform nonlinear kernels into linear kernels.

The causal assumptions, the study design and the data are the elements required for scientific inference in empirical research. The research is adequately communicated only if all of these elements and their relations are described precisely. Causal models with design describe the study design and the missing data mechanism together with the causal structure and allow the direct application of causal calculus in the estimation of the causal effects. The flow of the study is visualized by ordering the nodes of the causal diagram in two dimensions by their causal order and the time of the observation. Conclusions whether a causal or observational relationship can be estimated from the collected incomplete data can be made directly from the graph. Causal models with design offer a systematic and unifying view scientific inference and increase the clarity and speed of communication. Examples on the causal models for a case-control study, a nested case-control study, a clinical trial and a two-stage case-cohort study are presented.

Networks are ubiquitous in biology and computational approaches have been largely investigated for their inference. In particular, supervised machine learning methods can be used to complete a partially known network by integrating various measurements. Two main supervised frameworks have been proposed: the local approach, which trains a separate model for each network node, and the global approach, which trains a single model over pairs of nodes. Here, we systematically investigate, theoretically and empirically, the exploitation of tree-based ensemble methods in the context of these two approaches for biological network inference. We first formalize the problem of network inference as classification of pairs, unifying in the process homogeneous and bipartite graphs and discussing two main sampling schemes. We then present the global and the local approaches, extending the later for the prediction of interactions between two unseen network nodes, and discuss their specializations to tree-based ensemble methods, highlighting their interpretability and drawing links with clustering techniques. Extensive computational experiments are carried out with these methods on various biological networks that clearly highlight that these methods are competitive with existing methods.

This paper studies the relationship between resolution and conflict driven clause learning (CDCL) without restarts, and refutes some conjectured possible separations. We prove that the guarded, xor-ified pebbling tautology clauses, which Urquhart proved are hard for regular resolution, as well as the guarded graph tautology clauses of Alekhnovich, Johannsen, Pitassi, and Urquhart have polynomial size pool resolution refutations that use only input lemmas as learned clauses. For the latter set of clauses, we extend this to prove that a CDCL search without restarts can refute these clauses in polynomial time, provided it makes the right choices for decision literals and clause learning. This holds even if the CDCL search is required to greedily process conflicts arising from unit propagation. This refutes the conjecture that the guarded graph tautology clauses or the guarded xor-ified pebbling tautology clauses can be used to separate CDCL without restarts from general resolution. Together with subsequent results by Buss and Ko lodziejczyk, this means we lack any good conjectures about how to establish the exact logical strength of conflict-driven clause learning without restarts.

We propose a timed and soft extension of Concurrent Constraint Programming. The time extension is based on the hypothesis of bounded asynchrony: the computation takes a bounded period of time and is measured by a discrete global clock. Action prefixing is then considered as the syntactic marker which distinguishes a time instant from the next one. Supported by soft constraints instead of crisp ones, tell and ask agents are now equipped with a preference (or consistency) threshold which is used to determine their success or suspension. In the paper we provide a language to describe the agents behavior, together with its operational and denotational semantics, for which we also prove the compositionality and correctness properties. After presenting a semantics using maximal parallelism of actions, we also describe a version for their interleaving on a single processor (with maximal parallelism for time elapsing). Coordinating agents that need to take decisions both on preference values and time events may benefit from this language. To appear in Theory and Practice of Logic Programming (TPLP).

Mean shift clustering finds the modes of the data probability density by identifying the zero points of the density gradient. Since it does not require to fix the number of clusters in advance, the mean shift has been a popular clustering algorithm in various application fields. A typical implementation of the mean shift is to first estimate the density by kernel density estimation and then compute its gradient. However, since good density estimation does not necessarily imply accurate estimation of the density gradient, such an indirect two-step approach is not reliable. In this paper, we propose a method to directly estimate the gradient of the log-density without going through density estimation. The proposed method gives the global solution analytically and thus is computationally efficient. We then develop a mean-shift-like fixed-point algorithm to find the modes of the density for clustering. As in the mean shift, one does not need to set the number of clusters in advance. We empirically show that the proposed clustering method works much better than the mean shift especially for high-dimensional data. Experimental results further indicate that the proposed method outperforms existing clustering methods.

I think that the main reason why we do not understand the general principles of how knowledge works (and probably also the reason why we have not yet designed and built efficient machines capable of artificial intelligence), is not the excessive complexity of cognitive phenomena, but the lack of the conceptual and methodological tools to properly address the problem. It is like trying to build up Physics without the concept of number, or to understand the origin of species without including the mechanism of natural selection. In this paper I propose some new conceptual and methodological tools, which seem to offer a real opportunity to understand the logic of cognitive processes. I propose a new method to properly treat the concepts of structure and schema, and to perform on them operations of structural analysis. These operations allow to move straightforwardly from concrete to more abstract representations. With these tools I will suggest a definition for the concept of rule, of regularity and of emergent phenomena. From the analysis of some important aspects of the rules, I suggest to distinguish them in operational and associative rules. I propose that associative rules assume a dominant role in cognition. I also propose a definition for the concept of problem. At the end I will briefly illustrate a possible general model for cognitive systems.

When making decisions under uncertainty, the optimal choices are often difficult to discern, especially if not enough information has been gathered. Two key questions in this regard relate to whether one should stop the information gathering process and commit to a decision (stopping criterion), and if not, what information to gather next (selection criterion). In this paper, we show that the recently introduced notion, Same-Decision Probability (SDP), can be useful as both a stopping and a selection criterion, as it can provide additional insight and allow for robust decision making in a variety of scenarios. This query has been shown to be highly intractable, being PP^PP-complete, and is exemplary of a class of queries which correspond to the computation of certain expectations. We propose the first exact algorithm for computing the SDP, and demonstrate its effectiveness on several real and synthetic networks. Finally, we present new complexity results, such as the complexity of computing the SDP on models with a Naive Bayes structure. Additionally, we prove that computing the non-myopic value of information is complete for the same complexity class as computing the SDP.

A Dung argumentation framework (AF) is a pair (A,R): A is a set of abstract arguments and R ⊆ A×A is a binary relation, so-called the attack relation, for capturing the conflicting arguments. Labeling based algorithms for enumerating extensions (i.e. sets of acceptable arguments) have been set out such that arguments (i.e. elements of A) are the only subject for labeling. In this paper we present implemented algorithms for listing extensions by labeling attacks (i.e. elements of R) along with arguments. Specifically, these algorithms are concerned with enumerating all extensions of an AF under a number of argumentation semantics: preferred, stable, complete, semi stable, stage, ideal and grounded. Our algorithms have impact, in particular, on enumerating extensions of AF-extended models that allow attacks on attacks. To demonstrate this impact, we instantiate our algorithms for an example of such models: namely argumentation frameworks with recursive attacks (AFRA), thereby we end up with unified algorithms that enumerate extensions of any AF/AFRA.

Extracting latent low-dimensional structure from high-dimensional data is of paramount importance in timely inference tasks encountered with `Big Data' analytics. However, increasingly noisy, heterogeneous, and incomplete datasets as well as the need for {\em real-time} processing of streaming data pose major challenges to this end. In this context, the present paper permeates benefits from rank minimization to scalable imputation of missing data, via tracking low-dimensional subspaces and unraveling latent (possibly multi-way) structure from \emph{incomplete streaming} data. For low-rank matrix data, a subspace estimator is proposed based on an exponentially-weighted least-squares criterion regularized with the nuclear norm. After recasting the non-separable nuclear norm into a form amenable to online optimization, real-time algorithms with complementary strengths are developed and their convergence is established under simplifying technical assumptions. In a stationary setting, the asymptotic estimates obtained offer the well-documented performance guarantees of the {\em batch} nuclear-norm regularized estimator. Under the same unifying framework, a novel online (adaptive) algorithm is developed to obtain multi-way decompositions of \emph{low-rank tensors} with missing entries, and perform imputation as a byproduct. Simulated tests with both synthetic as well as real Internet and cardiac magnetic resonance imagery (MRI) data confirm the efficacy of the proposed algorithms, and their superior performance relative to state-of-the-art alternatives.