The Region Connection Calculus (RCC) is a well-known calculus for representing part-whole and topological relations. It plays an important role in qualitative spatial reasoning, geographical information science, and ontology. The computational complexity of reasoning with RCC5 and RCC8 (two fragments of RCC) as well as other qualitative spatial/temporal calculi has been investigated in depth in the literature. Most of these works focus on the consistency of qualitative constraint networks. In this paper, we consider the important problem of redundant qualitative constraints. For a set $\Gamma$ of qualitative constraints, we say a constraint $(x R y)$ in $\Gamma$ is redundant if it is entailed by the rest of $\Gamma$. A prime subnetwork of $\Gamma$ is a subset of $\Gamma$ which contains no redundant constraints and has the same solution set as $\Gamma$. It is natural to ask how to compute such a prime subnetwork, and when it is unique. In this paper, we show that this problem is in general intractable, but becomes tractable if $\Gamma$ is over a tractable subalgebra $\mathcal{S}$ of a qualitative calculus. Furthermore, if $\mathcal{S}$ is a subalgebra of RCC5 or RCC8 in which weak composition distributes over nonempty intersections, then $\Gamma$ has a unique prime subnetwork, which can be obtained in cubic time by removing all redundant constraints simultaneously from $\Gamma$. As a byproduct, we show that any path-consistent network over such a distributive subalgebra is weakly globally consistent and minimal. A thorough empirical analysis of the prime subnetwork upon real geographical data sets demonstrates the approach is able to identify significantly more redundant constraints than previously proposed algorithms, especially in constraint networks with larger proportions of partial overlap relations.

Non-orthogonal joint diagonalization (NJD) free of prewhitening has been widely studied in the context of blind source separation (BSS) and array signal processing, etc. However, NJD is used to retrieve the jointly diagonalizable structure for a single set of target matrices which are mostly formulized with a single dataset, and thus is insufficient to handle multiple datasets with inter-set dependences, a scenario often encountered in joint BSS (J-BSS) applications. As such, we present a generalized NJD (GNJD) algorithm to simultaneously perform asymmetric NJD upon multiple sets of target matrices with mutually linked loading matrices, by using LU decomposition and successive rotations, to enable J-BSS over multiple datasets with indication/exploitation of their mutual dependences. Experiments with synthetic and real-world datasets are provided to illustrate the performance of the proposed algorithm.

In view of the paradigm shift that makes science ever more data-driven, in this thesis we propose a synthesis method for encoding and managing large-scale deterministic scientific hypotheses as uncertain and probabilistic data. In the form of mathematical equations, hypotheses symmetrically relate aspects of the studied phenomena. For computing predictions, however, deterministic hypotheses can be abstracted as functions. We build upon Simon's notion of structural equations in order to efficiently extract the (so-called) causal ordering between variables, implicit in a hypothesis structure (set of mathematical equations). We show how to process the hypothesis predictive structure effectively through original algorithms for encoding it into a set of functional dependencies (fd's) and then performing causal reasoning in terms of acyclic pseudo-transitive reasoning over fd's. Such reasoning reveals important causal dependencies implicit in the hypothesis predictive data and guide our synthesis of a probabilistic database. Like in the field of graphical models in AI, such a probabilistic database should be normalized so that the uncertainty arisen from competing hypotheses is decomposed into factors and propagated properly onto predictive data by recovering its joint probability distribution through a lossless join. That is motivated as a design-theoretic principle for data-driven hypothesis management and predictive analytics. The method is applicable to both quantitative and qualitative deterministic hypotheses and demonstrated in realistic use cases from computational science.

This book is devoted to metric learning, a set of techniques to automatically learn similarity and distance functions from data that has attracted a lot of interest in machine learning and related fields in the past ten years. ISBN 9781627053655, 151 pages.

Exponential smoothers are a simple and memory efficient way to compute running averages of time series. Here we define and describe practical properties of exponential smoothers for signals observed at constant and variable intervals.

Multiple hypothesis testing is a significant problem in nearly all neuroimaging studies. In order to correct for this phenomena, we require a reliable estimate of the Family-Wise Error Rate (FWER). The well known Bonferroni correction method, while simple to implement, is quite conservative, and can substantially under-power a study because it ignores dependencies between test statistics. Permutation testing, on the other hand, is an exact, non-parametric method of estimating the FWER for a given $\alpha$-threshold, but for acceptably low thresholds the computational burden can be prohibitive. In this paper, we show that permutation testing in fact amounts to populating the columns of a very large matrix ${\bf P}$. By analyzing the spectrum of this matrix, under certain conditions, we see that ${\bf P}$ has a low-rank plus a low-variance residual decomposition which makes it suitable for highly sub--sampled --- on the order of $0.5\%$ --- matrix completion methods. Based on this observation, we propose a novel permutation testing methodology which offers a large speedup, without sacrificing the fidelity of the estimated FWER. Our evaluations on four different neuroimaging datasets show that a computational speedup factor of roughly $50\times$ can be achieved while recovering the FWER distribution up to very high accuracy. Further, we show that the estimated $\alpha$-threshold is also recovered faithfully, and is stable.

The labeled stochastic block model is a random graph model representing networks with community structure and interactions of multiple types. In its simplest form, it consists of two communities of approximately equal size, and the edges are drawn and labeled at random with probability depending on whether their two endpoints belong to the same community or not. It has been conjectured in \cite{Heimlicher12} that correlated reconstruction (i.e.\ identification of a partition correlated with the true partition into the underlying communities) would be feasible if and only if a model parameter exceeds a threshold. We prove one half of this conjecture, i.e., reconstruction is impossible when below the threshold. In the positive direction, we introduce a weighted graph to exploit the label information. With a suitable choice of weight function, we show that when above the threshold by a specific constant, reconstruction is achieved by (1) minimum bisection, (2) a semidefinite relaxation of minimum bisection, and (3) a spectral method combined with removal of edges incident to vertices of high degree. Furthermore, we show that hypothesis testing between the labeled stochastic block model and the labeled Erd\H{o}s-R\'enyi random graph model exhibits a phase transition at the conjectured reconstruction threshold.

For the challenging task of modeling multivariate time series, we propose a new class of models that use dependent Mat\'ern processes to capture the underlying structure of data, explain their interdependencies, and predict their unknown values. Although similar models have been proposed in the econometric, statistics, and machine learning literature, our approach has several advantages that distinguish it from existing methods: 1) it is flexible to provide high prediction accuracy, yet its complexity is controlled to avoid overfitting; 2) its interpretability separates it from black-box methods; 3) finally, its computational efficiency makes it scalable for high-dimensional time series. In this paper, we use several simulated and real data sets to illustrate these advantages. We will also briefly discuss some extensions of our model.

We consider a fundamental algorithmic question in spectral graph theory: Compute a spectral sparsifier of random-walk matrix-polynomial $$L_\alpha(G)=D-\sum_{r=1}^d\alpha_rD(D^{-1}A)^r$$ where $A$ is the adjacency matrix of a weighted, undirected graph, $D$ is the diagonal matrix of weighted degrees, and $\alpha=(\alpha_1...\alpha_d)$ are nonnegative coefficients with $\sum_{r=1}^d\alpha_r=1$. Recall that $D^{-1}A$ is the transition matrix of random walks on the graph. The sparsification of $L_\alpha(G)$ appears to be algorithmically challenging as the matrix power $(D^{-1}A)^r$ is defined by all paths of length $r$, whose precise calculation would be prohibitively expensive. In this paper, we develop the first nearly linear time algorithm for this sparsification problem: For any $G$ with $n$ vertices and $m$ edges, $d$ coefficients $\alpha$, and $\epsilon > 0$, our algorithm runs in time $O(d^2m\log^2n/\epsilon^{2})$ to construct a Laplacian matrix $\tilde{L}=D-\tilde{A}$ with $O(n\log n/\epsilon^{2})$ non-zeros such that $\tilde{L}\approx_{\epsilon}L_\alpha(G)$. Matrix polynomials arise in mathematical analysis of matrix functions as well as numerical solutions of matrix equations. Our work is particularly motivated by the algorithmic problems for speeding up the classic Newton's method in applications such as computing the inverse square-root of the precision matrix of a Gaussian random field, as well as computing the $q$th-root transition (for $q\geq1$) in a time-reversible Markov model. The key algorithmic step for both applications is the construction of a spectral sparsifier of a constant degree random-walk matrix-polynomials introduced by Newton's method. Our algorithm can also be used to build efficient data structures for effective resistances for multi-step time-reversible Markov models, and we anticipate that it could be useful for other tasks in network analysis.

Off-policy learning in dynamic decision problems is essential for providing strong evidence that a new policy is better than the one in use. But how can we prove superiority without testing the new policy? To answer this question, we introduce the G-SCOPE algorithm that evaluates a new policy based on data generated by the existing policy. Our algorithm is both computationally and sample efficient because it greedily learns to exploit factored structure in the dynamics of the environment. We present a finite sample analysis of our approach and show through experiments that the algorithm scales well on high-dimensional problems with few samples.