Problems and memories

I state some open problems coming from joint work with Paul Erd\H{o}sComment: This is a paper form of the talk I gave on July 5, 2013 at the centennial conference in Budapest to honor Paul Erd\H{o}

Partitioning Perfect Graphs into Stars

The partition of graphs into "nice" subgraphs is a central algorithmic problem with strong ties to matching theory. We study the partitioning of undirected graphs into same-size stars, a problem known to be NP-complete even for the case of stars on three vertices. We perform a thorough computational complexity study of the problem on subclasses of perfect graphs and identify several polynomial-time solvable cases, for example, on interval graphs and bipartite permutation graphs, and also NP-complete cases, for example, on grid graphs and chordal graphs.Comment: Manuscript accepted to Journal of Graph Theor

Assessing the Computational Complexity of Multi-Layer Subgraph Detection

Multi-layer graphs consist of several graphs (layers) over the same vertex set. They are motivated by real-world problems where entities (vertices) are associated via multiple types of relationships (edges in different layers). We chart the border of computational (in)tractability for the class of subgraph detection problems on multi-layer graphs, including fundamental problems such as maximum matching, finding certain clique relaxations (motivated by community detection), or path problems. Mostly encountering hardness results, sometimes even for two or three layers, we can also spot some islands of tractability

Graph Isomorphism for unit square graphs

In the past decades for more and more graph classes the Graph Isomorphism Problem was shown to be solvable in polynomial time. An interesting family of graph classes arises from intersection graphs of geometric objects. In this work we show that the Graph Isomorphism Problem for unit square graphs, intersection graphs of axis-parallel unit squares in the plane, can be solved in polynomial time. Since the recognition problem for this class of graphs is NP-hard we can not rely on standard techniques for geometric graphs based on constructing a canonical realization. Instead, we develop new techniques which combine structural insights into the class of unit square graphs with understanding of the automorphism group of such graphs. For the latter we introduce a generalization of bounded degree graphs which is used to capture the main structure of unit square graphs. Using group theoretic algorithms we obtain sufficient information to solve the isomorphism problem for unit square graphs.Comment: 31 pages, 6 figure

Graph classes and forbidden patterns on three vertices

This paper deals with graph classes characterization and recognition. A popular way to characterize a graph class is to list a minimal set of forbidden induced subgraphs. Unfortunately this strategy usually does not lead to an efficient recognition algorithm. On the other hand, many graph classes can be efficiently recognized by techniques based on some interesting orderings of the nodes, such as the ones given by traversals. We study specifically graph classes that have an ordering avoiding some ordered structures. More precisely, we consider what we call patterns on three nodes, and the recognition complexity of the associated classes. In this domain, there are two key previous works. Damashke started the study of the classes defined by forbidden patterns, a set that contains interval, chordal and bipartite graphs among others. On the algorithmic side, Hell, Mohar and Rafiey proved that any class defined by a set of forbidden patterns can be recognized in polynomial time. We improve on these two works, by characterizing systematically all the classes defined sets of forbidden patterns (on three nodes), and proving that among the 23 different classes (up to complementation) that we find, 21 can actually be recognized in linear time. Beyond this result, we consider that this type of characterization is very useful, leads to a rich structure of classes, and generates a lot of open questions worth investigating.Comment: Third version version. 38 page

On combinatorial optimisation in analysis of protein-protein interaction and protein folding networks

Abstract: Protein-protein interaction networks and protein folding networks represent prominent research topics at the intersection of bioinformatics and network science. In this paper, we present a study of these networks from combinatorial optimisation point of view. Using a combination of classical heuristics and stochastic optimisation techniques, we were able to identify several interesting combinatorial properties of biological networks of the COSIN project. We obtained optimal or near-optimal solutions to maximum clique and chromatic number problems for these networks. We also explore patterns of both non-overlapping and overlapping cliques in these networks. Optimal or near-optimal solutions to partitioning of these networks into non-overlapping cliques and to maximum independent set problem were discovered. Maximal cliques are explored by enumerative techniques. Domination in these networks is briefly studied, too. Applications and extensions of our findings are discussed