A novel evolutionary formulation of the maximum independent set problem

We introduce a novel evolutionary formulation of the problem of finding a maximum independent set of a graph. The new formulation is based on the relationship that exists between a graph's independence number and its acyclic orientations. It views such orientations as individuals and evolves them with the aid of evolutionary operators that are very heavily based on the structure of the graph and its acyclic orientations. The resulting heuristic has been tested on some of the Second DIMACS Implementation Challenge benchmark graphs, and has been found to be competitive when compared to several of the other heuristics that have also been tested on those graphs

Network conduciveness with application to the graph-coloring and independent-set optimization transitions

We introduce the notion of a network's conduciveness, a probabilistically interpretable measure of how the network's structure allows it to be conducive to roaming agents, in certain conditions, from one portion of the network to another. We exemplify its use through an application to the two problems in combinatorial optimization that, given an undirected graph, ask that its so-called chromatic and independence numbers be found. Though NP-hard, when solved on sequences of expanding random graphs there appear marked transitions at which optimal solutions can be obtained substantially more easily than right before them. We demonstrate that these phenomena can be understood by resorting to the network that represents the solution space of the problems for each graph and examining its conduciveness between the non-optimal solutions and the optimal ones. At the said transitions, this network becomes strikingly more conducive in the direction of the optimal solutions than it was just before them, while at the same time becoming less conducive in the opposite direction. We believe that, besides becoming useful also in other areas in which network theory has a role to play, network conduciveness may become instrumental in helping clarify further issues related to NP-hardness that remain poorly understood

A methodology for determining amino-acid substitution matrices from set covers

We introduce a new methodology for the determination of amino-acid substitution matrices for use in the alignment of proteins. The new methodology is based on a pre-existing set cover on the set of residues and on the undirected graph that describes residue exchangeability given the set cover. For fixed functional forms indicating how to obtain edge weights from the set cover and, after that, substitution-matrix elements from weighted distances on the graph, the resulting substitution matrix can be checked for performance against some known set of reference alignments and for given gap costs. Finding the appropriate functional forms and gap costs can then be formulated as an optimization problem that seeks to maximize the performance of the substitution matrix on the reference alignment set. We give computational results on the BAliBASE suite using a genetic algorithm for optimization. Our results indicate that it is possible to obtain substitution matrices whose performance is either comparable to or surpasses that of several others, depending on the particular scenario under consideration

On the phase transitions of graph coloring and independent sets

We study combinatorial indicators related to the characteristic phase transitions associated with coloring a graph optimally and finding a maximum independent set. In particular, we investigate the role of the acyclic orientations of the graph in the hardness of finding the graph's chromatic number and independence number. We provide empirical evidence that, along a sequence of increasingly denser random graphs, the fraction of acyclic orientations that are `shortest' peaks when the chromatic number increases, and that such maxima tend to coincide with locally easiest instances of the problem. Similar evidence is provided concerning the `widest' acyclic orientations and the independence number