While graphs with continuous node attributes arise in many applications, state-of-the-art graph kernels for comparing continuous-attributed graphs suffer from a high runtime complexity; for instance, the popular shortest path kernel scales as $\mathcal{O}(n^4)$, where $n$ is the number of nodes. In this paper, we present a class of path kernels with computational complexity $\mathcal{O}(n^2 (m + \delta^2))$, where $\delta$ is the graph diameter and $m$ the number of edges. Due to the sparsity and small diameter of real-world graphs, these kernels scale comfortably to large graphs. In our experiments, the presented kernels outperform state-of-the-art kernels in terms of speed and accuracy on classification benchmark datasets.

Causal inference uses observational data to infer the causal structure of the data generating system. We study a class of restricted Structural Equation Models for time series that we call Time Series Models with Independent Noise (TiMINo). These models require independent residual time series, whereas traditional methods like Granger causality exploit the variance of residuals. This work contains two main contributions: (1) Theoretical: By restricting the model class (e.g. to additive noise) we provide more general identifiability results than existing ones. The results cover lagged and instantaneous effects that can be nonlinear and unfaithful, and non-instantaneous feedbacks between the time series. (2) Practical: If there are no feedback loops between time series, we propose an algorithm based on non-linear independence tests of time series. When the data are causally insufficient, or the data generating process does not satisfy the model assumptions, this algorithm may still give partial results, but mostly avoids incorrect answers. The Structural Equation Model point of view allows us to extend both the theoretical and the algorithmic part to situations in which the time series have been measured with different time delays (as may happen for fMRI data, for example). TiMINo outperforms existing methods on artificial and real data. Code is provided.

This paper proposes the formalization and implementation of a novel class of constraints aimed at modeling problems related to placement of multi-body systems in the 3-dimensional space. Each multi-body is a system composed of body elements, connected by joint relationships and constrained by geometric properties. The emphasis of this investigation is the use of multi-body systems to model native conformations of protein structures---where each body represents an entity of the protein (e.g., an amino acid, a small peptide) and the geometric constraints are related to the spatial properties of the composing atoms. The paper explores the use of the proposed class of constraints to support a variety of different structural analysis of proteins, such as loop modeling and structure prediction. The declarative nature of a constraint-based encoding provides elaboration tolerance and the ability to make use of any additional knowledge in the analysis studies. The filtering capabilities of the proposed constraints also allow to control the number of representative solutions that are withdrawn from the conformational space of the protein, by means of criteria driven by uniform distribution sampling principles. In this scenario it is possible to select the desired degree of precision and/or number of solutions. The filtering component automatically excludes configurations that violate the spatial and geometric properties of the composing multi-body system. The paper illustrates the implementation of a constraint solver based on the multi-body perspective and its empirical evaluation on protein structure analysis problems.

Multi-task learning has shown to significantly enhance the performance of multiple related learning tasks in a variety of situations. We present the fused logistic regression, a sparse multi-task learning approach for binary classification. Specifically, we introduce sparsity inducing penalties over parameter differences of related logistic regression models to encode similarity across related tasks. The resulting joint learning task is cast into a form that lends itself to be efficiently optimized with a recursive variant of the alternating direction method of multipliers. We show results on synthetic data and describe the regime of settings where our multi-task approach achieves significant improvements over the single task learning approach and discuss the implications on applying the fused logistic regression in different real world settings.

In this paper we define Clinical Data Intelligence as the analysis of data generated in the clinical routine with the goal of improving patient care. We define a science of a Clinical Data Intelligence as a data analysis that permits the derivation of scientific, i.e., generalizable and reliable results. We argue that a science of a Clinical Data Intelligence is sensible in the context of a Big Data analysis, i.e., with data from many patients and with complete patient information. We discuss that Clinical Data Intelligence requires the joint efforts of knowledge engineering, information extraction (from textual and other unstructured data), and statistics and statistical machine learning. We describe some of our main results as conjectures and relate them to a recently funded research project involving two major German university hospitals.

A new iterative low complexity algorithm has been presented for computing the Walsh-Hadamard transform (WHT) of an $N$ dimensional signal with a $K$-sparse WHT, where $N$ is a power of two and $K = O(N^\alpha)$, scales sub-linearly in $N$ for some $0 < \alpha < 1$. Assuming a random support model for the non-zero transform domain components, the algorithm reconstructs the WHT of the signal with a sample complexity $O(K \log_2(\frac{N}{K}))$, a computational complexity $O(K\log_2(K)\log_2(\frac{N}{K}))$ and with a very high probability asymptotically tending to 1. The approach is based on the subsampling (aliasing) property of the WHT, where by a carefully designed subsampling of the time domain signal, one can induce a suitable aliasing pattern in the transform domain. By treating the aliasing patterns as parity-check constraints and borrowing ideas from erasure correcting sparse-graph codes, the recovery of the non-zero spectral values has been formulated as a belief propagation (BP) algorithm (peeling decoding) over a sparse-graph code for the binary erasure channel (BEC). Tools from coding theory are used to analyze the asymptotic performance of the algorithm in the very sparse ($\alpha\in(0,\frac{1}{3}]$) and the less sparse ($\alpha\in(\frac{1}{3},1)$) regime.

Generalizing empirical findings to new environments, settings, or populations is essential in most scientific explorations. This article treats a particular problem of generalizability, called "transportability", defined as a license to transfer information learned in experimental studies to a different population, on which only observational studies can be conducted. Given a set of assumptions concerning commonalities and differences between the two populations, Pearl and Bareinboim (2011) derived sufficient conditions that permit such transfer to take place. This article summarizes their findings and supplements them with an effective procedure for deciding when and how transportability is feasible. It establishes a necessary and sufficient condition for deciding when causal effects in the target population are estimable from both the statistical information available and the causal information transferred from the experiments. The article further provides a complete algorithm for computing the transport formula, that is, a way of combining observational and experimental information to synthesize bias-free estimate of the desired causal relation. Finally, the article examines the differences between transportability and other variants of generalizability.

This volume contains the papers presented at the sixth workshop on Answer Set Programming and Other Computing Paradigms (ASPOCP 2013) held on August 25th, 2013 in Istanbul, co-located with the 29th International Conference on Logic Programming (ICLP 2013). It thus continues a series of previous events co-located with ICLP, aiming at facilitating the discussion about crossing the boundaries of current ASP techniques in theory, solving, and applications, in combination with or inspired by other computing paradigms.

Positive definite matrices abound in a dazzling variety of applications. This ubiquity can be in part attributed to their rich geometric structure: positive definite matrices form a self-dual convex cone whose strict interior is a Riemannian manifold. The manifold view is endowed with a "natural" distance function while the conic view is not. Nevertheless, drawing motivation from the conic view, we introduce the S-Divergence as a "natural" distance-like function on the open cone of positive definite matrices. We motivate the S-divergence via a sequence of results that connect it to the Riemannian distance. In particular, we show that (a) this divergence is the square of a distance; and (b) that it has several geometric properties similar to those of the Riemannian distance, though without being computationally as demanding. The S-divergence is even more intriguing: although nonconvex, we can still compute matrix means and medians using it to global optimality. We complement our results with some numerical experiments illustrating our theorems and our optimization algorithm for computing matrix medians.

A new approach for feature extraction from time series is proposed in this paper. This approach consists of a specific regression model incorporating a discrete hidden logistic process. The model parameters are estimated by the maximum likelihood method performed by a dedicated Expectation Maximization (EM) algorithm. The parameters of the hidden logistic process, in the inner loop of the EM algorithm, are estimated using a multi-class Iterative Reweighted Least-Squares (IRLS) algorithm. A piecewise regression algorithm and its iterative variant have also been considered for comparisons. An experimental study using simulated and real data reveals good performances of the proposed approach.