Structure of conflict graphs in constraint alignment problems and algorithms

We consider the constrained graph alignment problem which has applications in biological network analysis. Given two input graphs $G_1=(V_1,E_1), G_2=(V_2,E_2)$, a pair of vertex mappings induces an {\it edge conservation} if the vertex pairs are adjacent in their respective graphs. %In general terms The goal is to provide a one-to-one mapping between the vertices of the input graphs in order to maximize edge conservation. However the allowed mappings are restricted since each vertex from $V_1$ (resp. $V_2$) is allowed to be mapped to at most $m_1$ (resp. $m_2$) specified vertices in $V_2$ (resp. $V_1$). Most of results in this paper deal with the case $m_2=1$ which attracted most attention in the related literature. We formulate the problem as a maximum independent set problem in a related {\em conflict graph} and investigate structural properties of this graph in terms of forbidden subgraphs. We are interested, in particular, in excluding certain wheals, fans, cliques or claws (all terms are defined in the paper), which corresponds in excluding certain cycles, paths, cliques or independent sets in the neighborhood of each vertex. Then, we investigate algorithmic consequences of some of these properties, which illustrates the potential of this approach and raises new horizons for further works. In particular this approach allows us to reinterpret a known polynomial case in terms of conflict graph and to improve known approximation and fixed-parameter tractability results through efficiently solving the maximum independent set problem in conflict graphs. Some of our new approximation results involve approximation ratios that are function of the optimal value, in particular its square root; this kind of results cannot be achieved for maximum independent set in general graphs.Comment: 22 pages, 6 figure

Structural solutions to maximum independent set and related problems

In this thesis, we study some fundamental problems in algorithmic graph theory. Most natural problems in this area are hard from a computational point of view. However, many applications demand that we do solve such problems, even if they are intractable. There are a number of methods in which we can try to do this: 1) We may use an approximation algorithm if we do not necessarily require the best possible solution to a problem. 2) Heuristics can be applied and work well enough to be useful for many applications. 3) We can construct randomised algorithms for which the probability of failure is very small. 4) We may parameterize the problem in some way which limits its complexity. In other cases, we may also have some information about the structure of the instances of the problem we are trying to solve. If we are lucky, we may and that we can exploit this extra structure to find efficient ways to solve our problem. The question which arises is - How far must we restrict the structure of our graph to be able to solve our problem efficiently? In this thesis we study a number of problems, such as Maximum Indepen- dent Set, Maximum Induced Matching, Stable-II, Efficient Edge Domina- tion, Vertex Colouring and Dynamic Edge-Choosability. We try to solve problems on various hereditary classes of graphs and analyse the complexity of the resulting problem, both from a classical and parameterized point of view

Proceedings of the 8th Cologne-Twente Workshop on Graphs and Combinatorial Optimization

International audienceThe Cologne-Twente Workshop (CTW) on Graphs and Combinatorial Optimization started off as a series of workshops organized bi-annually by either Köln University or Twente University. As its importance grew over time, it re-centered its geographical focus by including northern Italy (CTW04 in Menaggio, on the lake Como and CTW08 in Gargnano, on the Garda lake). This year, CTW (in its eighth edition) will be staged in France for the first time: more precisely in the heart of Paris, at the Conservatoire National d’Arts et Métiers (CNAM), between 2nd and 4th June 2009, by a mixed organizing committee with members from LIX, Ecole Polytechnique and CEDRIC, CNAM