The Connectivity of Boolean Satisfiability: Dichotomies for Formulas and Circuits

For Boolean satisfiability problems, the structure of the solution space is characterized by the solution graph, where the vertices are the solutions, and two solutions are connected iff they differ in exactly one variable. In 2006, Gopalan et al. studied connectivity properties of the solution graph and related complexity issues for CSPs, motivated mainly by research on satisfiability algorithms and the satisfiability threshold. They proved dichotomies for the diameter of connected components and for the complexity of the st-connectivity question, and conjectured a trichotomy for the connectivity question. Recently, we were able to establish the trichotomy [arXiv:1312.4524]. Here, we consider connectivity issues of satisfiability problems defined by Boolean circuits and propositional formulas that use gates, resp. connectives, from a fixed set of Boolean functions. We obtain dichotomies for the diameter and the two connectivity problems: on one side, the diameter is linear in the number of variables, and both problems are in P, while on the other side, the diameter can be exponential, and the problems are PSPACE-complete. For partially quantified formulas, we show an analogous dichotomy.Comment: 20 pages, several improvement

The pharmacophore kernel for virtual screening with support vector machines

We introduce a family of positive definite kernels specifically optimized for the manipulation of 3D structures of molecules with kernel methods. The kernels are based on the comparison of the three-points pharmacophores present in the 3D structures of molecul es, a set of molecular features known to be particularly relevant for virtual screening applications. We present a computationally demanding exact implementation of these kernels, as well as fast approximations related to the classical fingerprint-based approa ches. Experimental results suggest that this new approach outperforms state-of-the-art algorithms based on the 2D structure of mol ecules for the detection of inhibitors of several drug targets

Immunity and Simplicity for Exact Counting and Other Counting Classes

Ko [RAIRO 24, 1990] and Bruschi [TCS 102, 1992] showed that in some relativized world, PSPACE (in fact, ParityP) contains a set that is immune to the polynomial hierarchy (PH). In this paper, we study and settle the question of (relativized) separations with immunity for PH and the counting classes PP, C_{=}P, and ParityP in all possible pairwise combinations. Our main result is that there is an oracle A relative to which C_{=}P contains a set that is immune to BPP^{ParityP}. In particular, this C_{=}P^A set is immune to PH^{A} and ParityP^{A}. Strengthening results of Tor\'{a}n [J.ACM 38, 1991] and Green [IPL 37, 1991], we also show that, in suitable relativizations, NP contains a C_{=}P-immune set, and ParityP contains a PP^{PH}-immune set. This implies the existence of a C_{=}P^{B}-simple set for some oracle B, which extends results of Balc\'{a}zar et al. [SIAM J.Comp. 14, 1985; RAIRO 22, 1988] and provides the first example of a simple set in a class not known to be contained in PH. Our proof technique requires a circuit lower bound for ``exact counting'' that is derived from Razborov's [Mat. Zametki 41, 1987] lower bound for majority.Comment: 20 page

Total Domishold Graphs: a Generalization of Threshold Graphs, with Connections to Threshold Hypergraphs

A total dominating set in a graph is a set of vertices such that every vertex of the graph has a neighbor in the set. We introduce and study graphs that admit non-negative real weights associated to their vertices such that a set of vertices is a total dominating set if and only if the sum of the corresponding weights exceeds a certain threshold. We show that these graphs, which we call total domishold graphs, form a non-hereditary class of graphs properly containing the classes of threshold graphs and the complements of domishold graphs, and are closely related to threshold Boolean functions and threshold hypergraphs. We present a polynomial time recognition algorithm of total domishold graphs, and characterize graphs in which the above property holds in a hereditary sense. Our characterization is obtained by studying a new family of hypergraphs, defined similarly as the Sperner hypergraphs, which may be of independent interest.Comment: 19 pages, 1 figur