Describing the complexity of systems: multi-variable "set complexity" and the information basis of systems biology

Context dependence is central to the description of complexity. Keying on the pairwise definition of "set complexity" we use an information theory approach to formulate general measures of systems complexity. We examine the properties of multi-variable dependency starting with the concept of interaction information. We then present a new measure for unbiased detection of multi-variable dependency, "differential interaction information." This quantity for two variables reduces to the pairwise "set complexity" previously proposed as a context-dependent measure of information in biological systems. We generalize it here to an arbitrary number of variables. Critical limiting properties of the "differential interaction information" are key to the generalization. This measure extends previous ideas about biological information and provides a more sophisticated basis for study of complexity. The properties of "differential interaction information" also suggest new approaches to data analysis. Given a data set of system measurements differential interaction information can provide a measure of collective dependence, which can be represented in hypergraphs describing complex system interaction patterns. We investigate this kind of analysis using simulated data sets. The conjoining of a generalized set complexity measure, multi-variable dependency analysis, and hypergraphs is our central result. While our focus is on complex biological systems, our results are applicable to any complex system.Comment: 44 pages, 12 figures; made revisions after peer revie

Semi-Streaming Set Cover

This paper studies the set cover problem under the semi-streaming model. The underlying set system is formalized in terms of a hypergraph $G = (V, E)$ whose edges arrive one-by-one and the goal is to construct an edge cover $F \subseteq E$ with the objective of minimizing the cardinality (or cost in the weighted case) of $F$. We consider a parameterized relaxation of this problem, where given some $0 \leq \epsilon < 1$, the goal is to construct an edge $(1 - \epsilon)$-cover, namely, a subset of edges incident to all but an $\epsilon$-fraction of the vertices (or their benefit in the weighted case). The key limitation imposed on the algorithm is that its space is limited to (poly)logarithmically many bits per vertex. Our main result is an asymptotically tight trade-off between $\epsilon$ and the approximation ratio: We design a semi-streaming algorithm that on input graph $G$, constructs a succinct data structure $\mathcal{D}$ such that for every $0 \leq \epsilon < 1$, an edge $(1 - \epsilon)$-cover that approximates the optimal edge \mbox{($1$-)cover} within a factor of $f(\epsilon, n)$ can be extracted from $\mathcal{D}$ (efficiently and with no additional space requirements), where $$f(\epsilon, n) = \left\{ \begin{array}{ll} O (1 / \epsilon), & \text{if } \epsilon > 1 / \sqrt{n} \\ O (\sqrt{n}), & \text{otherwise} \end{array} \right. \, .$$ In particular for the traditional set cover problem we obtain an $O(\sqrt{n})$-approximation. This algorithm is proved to be best possible by establishing a family (parameterized by $\epsilon$) of matching lower bounds.Comment: Full version of the extended abstract that will appear in Proceedings of ICALP 2014 track