Faster tuple lattice sieving using spherical locality-sensitive filters

To overcome the large memory requirement of classical lattice sieving algorithms for solving hard lattice problems, Bai-Laarhoven-Stehl\'{e} [ANTS 2016] studied tuple lattice sieving, where tuples instead of pairs of lattice vectors are combined to form shorter vectors. Herold-Kirshanova [PKC 2017] recently improved upon their results for arbitrary tuple sizes, for example showing that a triple sieve can solve the shortest vector problem (SVP) in dimension $d$ in time $2^{0.3717d + o(d)}$, using a technique similar to locality-sensitive hashing for finding nearest neighbors. In this work, we generalize the spherical locality-sensitive filters of Becker-Ducas-Gama-Laarhoven [SODA 2016] to obtain space-time tradeoffs for near neighbor searching on dense data sets, and we apply these techniques to tuple lattice sieving to obtain even better time complexities. For instance, our triple sieve heuristically solves SVP in time $2^{0.3588d + o(d)}$. For practical sieves based on Micciancio-Voulgaris' GaussSieve [SODA 2010], this shows that a triple sieve uses less space and less time than the current best near-linear space double sieve.Comment: 12 pages + references, 2 figures. Subsumed/merged into Cryptology ePrint Archive 2017/228, available at https://ia.cr/2017/122

Sparse Learning over Infinite Subgraph Features

We present a supervised-learning algorithm from graph data (a set of graphs) for arbitrary twice-differentiable loss functions and sparse linear models over all possible subgraph features. To date, it has been shown that under all possible subgraph features, several types of sparse learning, such as Adaboost, LPBoost, LARS/LASSO, and sparse PLS regression, can be performed. Particularly emphasis is placed on simultaneous learning of relevant features from an infinite set of candidates. We first generalize techniques used in all these preceding studies to derive an unifying bounding technique for arbitrary separable functions. We then carefully use this bounding to make block coordinate gradient descent feasible over infinite subgraph features, resulting in a fast converging algorithm that can solve a wider class of sparse learning problems over graph data. We also empirically study the differences from the existing approaches in convergence property, selected subgraph features, and search-space sizes. We further discuss several unnoticed issues in sparse learning over all possible subgraph features.Comment: 42 pages, 24 figures, 4 table

Combinatorial algorithm for counting small induced graphs and orbits

Graphlet analysis is an approach to network analysis that is particularly popular in bioinformatics. We show how to set up a system of linear equations that relate the orbit counts and can be used in an algorithm that is significantly faster than the existing approaches based on direct enumeration of graphlets. The algorithm requires existence of a vertex with certain properties; we show that such vertex exists for graphlets of arbitrary size, except for complete graphs and $C_4$, which are treated separately. Empirical analysis of running time agrees with the theoretical results

On the Distributed Complexity of Large-Scale Graph Computations

Motivated by the increasing need to understand the distributed algorithmic foundations of large-scale graph computations, we study some fundamental graph problems in a message-passing model for distributed computing where $k \geq 2$ machines jointly perform computations on graphs with $n$ nodes (typically, $n \gg k$). The input graph is assumed to be initially randomly partitioned among the $k$ machines, a common implementation in many real-world systems. Communication is point-to-point, and the goal is to minimize the number of communication {\em rounds} of the computation. Our main contribution is the {\em General Lower Bound Theorem}, a theorem that can be used to show non-trivial lower bounds on the round complexity of distributed large-scale data computations. The General Lower Bound Theorem is established via an information-theoretic approach that relates the round complexity to the minimal amount of information required by machines to solve the problem. Our approach is generic and this theorem can be used in a "cookbook" fashion to show distributed lower bounds in the context of several problems, including non-graph problems. We present two applications by showing (almost) tight lower bounds for the round complexity of two fundamental graph problems, namely {\em PageRank computation} and {\em triangle enumeration}. Our approach, as demonstrated in the case of PageRank, can yield tight lower bounds for problems (including, and especially, under a stochastic partition of the input) where communication complexity techniques are not obvious. Our approach, as demonstrated in the case of triangle enumeration, can yield stronger round lower bounds as well as message-round tradeoffs compared to approaches that use communication complexity techniques

ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra

Background: Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, with the goal to gain a better understanding of the system. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. Although there exist sophisticated algorithms to determine the dynamics of discrete models, their implementations usually require labor-intensive formatting of the model formulation, and they are oftentimes not accessible to users without programming skills. Efficient analysis methods are needed that are accessible to modelers and easy to use. Method: By converting discrete models into algebraic models, tools from computational algebra can be used to analyze their dynamics. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Results: A method for efficiently identifying attractors, and the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness, i.e., while the number of nodes in a biological network may be quite large, each node is affected only by a small number of other nodes, and robustness, i.e., small number of attractors