Recognizing Chordal-Bipartite Probe Graphs

A graph G is chordal-bipartite probe if its vertices can be partitioned into two sets P (probes) and N (non-probes) where N is a stable set and such that G can be extended to a chordal-bipartite graph by adding edges between non-probes. A bipartite graph is called chordal-bipartite if it contains no chordless cycle of length strictly greater than 5. Such probe/non-probe completion problems have been studied previously on other families of graphs, such as interval graphs and chordal graphs. In this paper, we give a characterization of chordal-bipartite probe graphs, in the case of a fixed given partition of the vertices into probes and nonprobes. Our results are obtained by solving first the more general case without assuming that N is a stable set, and then this can be applied to the more specific case. Our characterization uses an edge elimination ordering which also implies a polynomial time recognition algorithm for the class. This research was conducted in the context of a France-Israel Binational project, while the French team visited Haifa in March 2007

Relative Timing Information and Orthology in Evolutionary Scenarios

Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree $T$ to vertices and edges of a species tree $S$. The relative timing of the last common ancestors of two extant genes (leaves of $T$) and the last common ancestors of the two species (leaves of $S$) in which they reside is indicative of horizontal gene transfers (HGT) and ancient duplications. Orthologous gene pairs, on the other hand, require that their last common ancestors coincides with a corresponding speciation event. The relative timing information of gene and species divergences is captured by three colored graphs that have the extant genes as vertices and the species in which the genes are found as vertex colors: the equal-divergence-time (EDT) graph, the later-divergence-time (LDT) graph and the prior-divergence-time (PDT) graph, which together form an edge partition of the complete graph. Here we give a complete characterization in terms of informative and forbidden triples that can be read off the three graphs and provide a polynomial time algorithm for constructing an evolutionary scenario that explains the graphs, provided such a scenario exists. We show that every EDT graph is perfect. While the information about LDT and PDT graphs is necessary to recognize EDT graphs in polynomial-time for general scenarios, this extra information can be dropped in the HGT-free case. However, recognition of EDT graphs without knowledge of putative LDT and PDT graphs is NP-complete for general scenarios. In contrast, PDT graphs can be recognized in polynomial-time. We finally connect the EDT graph to the alternative definitions of orthology that have been proposed for scenarios with horizontal gene transfer. With one exception, the corresponding graphs are shown to be colored cographs

Edge Intersection Graphs of L-Shaped Paths in Grids

In this paper we continue the study of the edge intersection graphs of one (or zero) bend paths on a rectangular grid. That is, the edge intersection graphs where each vertex is represented by one of the following shapes: $\llcorner$,$\ulcorner$, $\urcorner$, $\lrcorner$, and we consider zero bend paths (i.e., | and $-$) to be degenerate $\llcorner$s. These graphs, called $B_1$-EPG graphs, were first introduced by Golumbic et al (2009). We consider the natural subclasses of $B_1$-EPG formed by the subsets of the four single bend shapes (i.e., {$\llcorner$}, {$\llcorner$,$\ulcorner$}, {$\llcorner$,$\urcorner$}, and {$\llcorner$,$\ulcorner$,$\urcorner$}) and we denote the classes by [$\llcorner$], [$\llcorner$,$\ulcorner$], [$\llcorner$,$\urcorner$], and [$\llcorner$,$\ulcorner$,$\urcorner$] respectively. Note: all other subsets are isomorphic to these up to 90 degree rotation. We show that testing for membership in each of these classes is NP-complete and observe the expected strict inclusions and incomparability (i.e., [$\llcorner$] $\subsetneq$ [$\llcorner$,$\ulcorner$], [$\llcorner$,$\urcorner$] $\subsetneq$ [$\llcorner$,$\ulcorner$,$\urcorner$] $\subsetneq$ $B_1$-EPG; also, [$\llcorner$,$\ulcorner$] is incomparable with [$\llcorner$,$\urcorner$]). Additionally, we give characterizations and polytime recognition algorithms for special subclasses of Split $\cap$ [$\llcorner$].Comment: 14 pages, to appear in DAM special issue for LAGOS'1

Parameterized Algorithms on Perfect Graphs for deletion to (r,ℓ)(r,\ell)-graphs

For fixed integers $r,\ell \geq 0$, a graph $G$ is called an {\em $(r,\ell)$-graph} if the vertex set $V(G)$ can be partitioned into $r$ independent sets and $\ell$ cliques. The class of $(r, \ell)$ graphs generalizes $r$-colourable graphs (when $\ell =0)$ and hence not surprisingly, determining whether a given graph is an $(r, \ell)$-graph is \NP-hard even when $r \geq 3$ or $\ell \geq 3$ in general graphs. When $r$ and $\ell$ are part of the input, then the recognition problem is NP-hard even if the input graph is a perfect graph (where the {\sc Chromatic Number} problem is solvable in polynomial time). It is also known to be fixed-parameter tractable (FPT) on perfect graphs when parameterized by $r$ and $\ell$. I.e. there is an f(r+\ell) \cdot n^{\Oh(1)} algorithm on perfect graphs on $n$ vertices where $f$ is some (exponential) function of $r$ and $\ell$. In this paper, we consider the parameterized complexity of the following problem, which we call {\sc Vertex Partization}. Given a perfect graph $G$ and positive integers $r,\ell,k$ decide whether there exists a set $S\subseteq V(G)$ of size at most $k$ such that the deletion of $S$ from $G$ results in an $(r,\ell)$-graph. We obtain the following results: \begin{enumerate} \item {\sc Vertex Partization} on perfect graphs is FPT when parameterized by $k+r+\ell$. \item The problem does not admit any polynomial sized kernel when parameterized by $k+r+\ell$. In other words, in polynomial time, the input graph can not be compressed to an equivalent instance of size polynomial in $k+r+\ell$. In fact, our result holds even when $k=0$. \item When $r,\ell$ are universal constants, then {\sc Vertex Partization} on perfect graphs, parameterized by $k$, has a polynomial sized kernel. \end{enumerate

A survey on algorithmic aspects of modular decomposition

The modular decomposition is a technique that applies but is not restricted to graphs. The notion of module naturally appears in the proofs of many graph theoretical theorems. Computing the modular decomposition tree is an important preprocessing step to solve a large number of combinatorial optimization problems. Since the first polynomial time algorithm in the early 70's, the algorithmic of the modular decomposition has known an important development. This paper survey the ideas and techniques that arose from this line of research