The Cover Number of a Matrix and its Algorithmic Applications

Given a matrix A, we study how many epsilon-cubes are required to cover the convex hull of the columns of A. We show bounds on this cover number in terms of VC dimension and the gamma_2 norm and give algorithms for enumerating elements of a cover. This leads to algorithms for computing approximate Nash equilibria that unify and extend several previous results in the literature. Moreover, our approximation algorithms can be applied quite generally to a family of quadratic optimization problems that also includes finding the k-by-k combinatorial rectangle of a matrix. In particular, for this problem we give the first quasi-polynomial time additive approximation algorithm that works for any matrix A in [0,1]^{m x n}

The Sample Complexity of Dictionary Learning

A large set of signals can sometimes be described sparsely using a dictionary, that is, every element can be represented as a linear combination of few elements from the dictionary. Algorithms for various signal processing applications, including classification, denoising and signal separation, learn a dictionary from a set of signals to be represented. Can we expect that the representation found by such a dictionary for a previously unseen example from the same source will have L_2 error of the same magnitude as those for the given examples? We assume signals are generated from a fixed distribution, and study this questions from a statistical learning theory perspective. We develop generalization bounds on the quality of the learned dictionary for two types of constraints on the coefficient selection, as measured by the expected L_2 error in representation when the dictionary is used. For the case of l_1 regularized coefficient selection we provide a generalization bound of the order of O(sqrt(np log(m lambda)/m)), where n is the dimension, p is the number of elements in the dictionary, lambda is a bound on the l_1 norm of the coefficient vector and m is the number of samples, which complements existing results. For the case of representing a new signal as a combination of at most k dictionary elements, we provide a bound of the order O(sqrt(np log(m k)/m)) under an assumption on the level of orthogonality of the dictionary (low Babel function). We further show that this assumption holds for most dictionaries in high dimensions in a strong probabilistic sense. Our results further yield fast rates of order 1/m as opposed to 1/sqrt(m) using localized Rademacher complexity. We provide similar results in a general setting using kernels with weak smoothness requirements

Numerical Investigation of Graph Spectra and Information Interpretability of Eigenvalues

We undertake an extensive numerical investigation of the graph spectra of thousands regular graphs, a set of random Erd\"os-R\'enyi graphs, the two most popular types of complex networks and an evolving genetic network by using novel conceptual and experimental tools. Our objective in so doing is to contribute to an understanding of the meaning of the Eigenvalues of a graph relative to its topological and information-theoretic properties. We introduce a technique for identifying the most informative Eigenvalues of evolving networks by comparing graph spectra behavior to their algorithmic complexity. We suggest that extending techniques can be used to further investigate the behavior of evolving biological networks. In the extended version of this paper we apply these techniques to seven tissue specific regulatory networks as static example and network of a na\"ive pluripotent immune cell in the process of differentiating towards a Th17 cell as evolving example, finding the most and least informative Eigenvalues at every stage.Comment: Forthcoming in 3rd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO), Lecture Notes in Bioinformatics, 201

A Tight Lower Bound for Counting Hamiltonian Cycles via Matrix Rank

For even $k$, the matchings connectivity matrix $\mathbf{M}_k$ encodes which pairs of perfect matchings on $k$ vertices form a single cycle. Cygan et al. (STOC 2013) showed that the rank of $\mathbf{M}_k$ over $\mathbb{Z}_2$ is $\Theta(\sqrt 2^k)$ and used this to give an $O^*((2+\sqrt{2})^{\mathsf{pw}})$ time algorithm for counting Hamiltonian cycles modulo $2$ on graphs of pathwidth $\mathsf{pw}$. The same authors complemented their algorithm by an essentially tight lower bound under the Strong Exponential Time Hypothesis (SETH). This bound crucially relied on a large permutation submatrix within $\mathbf{M}_k$, which enabled a "pattern propagation" commonly used in previous related lower bounds, as initiated by Lokshtanov et al. (SODA 2011). We present a new technique for a similar pattern propagation when only a black-box lower bound on the asymptotic rank of $\mathbf{M}_k$ is given; no stronger structural insights such as the existence of large permutation submatrices in $\mathbf{M}_k$ are needed. Given appropriate rank bounds, our technique yields lower bounds for counting Hamiltonian cycles (also modulo fixed primes $p$) parameterized by pathwidth. To apply this technique, we prove that the rank of $\mathbf{M}_k$ over the rationals is $4^k / \mathrm{poly}(k)$. We also show that the rank of $\mathbf{M}_k$ over $\mathbb{Z}_p$ is $\Omega(1.97^k)$ for any prime $p\neq 2$ and even $\Omega(2.15^k)$ for some primes. As a consequence, we obtain that Hamiltonian cycles cannot be counted in time $O^*((6-\epsilon)^{\mathsf{pw}})$ for any $\epsilon>0$ unless SETH fails. This bound is tight due to a $O^*(6^{\mathsf{pw}})$ time algorithm by Bodlaender et al. (ICALP 2013). Under SETH, we also obtain that Hamiltonian cycles cannot be counted modulo primes $p\neq 2$ in time $O^*(3.97^\mathsf{pw})$, indicating that the modulus can affect the complexity in intricate ways.Comment: improved lower bounds modulo primes, improved figures, to appear in SODA 201

JGraphT -- A Java library for graph data structures and algorithms

Mathematical software and graph-theoretical algorithmic packages to efficiently model, analyze and query graphs are crucial in an era where large-scale spatial, societal and economic network data are abundantly available. One such package is JGraphT, a programming library which contains very efficient and generic graph data-structures along with a large collection of state-of-the-art algorithms. The library is written in Java with stability, interoperability and performance in mind. A distinctive feature of this library is the ability to model vertices and edges as arbitrary objects, thereby permitting natural representations of many common networks including transportation, social and biological networks. Besides classic graph algorithms such as shortest-paths and spanning-tree algorithms, the library contains numerous advanced algorithms: graph and subgraph isomorphism; matching and flow problems; approximation algorithms for NP-hard problems such as independent set and TSP; and several more exotic algorithms such as Berge graph detection. Due to its versatility and generic design, JGraphT is currently used in large-scale commercial, non-commercial and academic research projects. In this work we describe in detail the design and underlying structure of the library, and discuss its most important features and algorithms. A computational study is conducted to evaluate the performance of JGraphT versus a number of similar libraries. Experiments on a large number of graphs over a variety of popular algorithms show that JGraphT is highly competitive with other established libraries such as NetworkX or the BGL.Comment: Major Revisio