Linear-Time Algorithms for Maximum-Weight Induced Matchings and Minimum Chain Covers in Convex Bipartite Graphs

A bipartite graph $G=(U,V,E)$ is convex if the vertices in $V$ can be linearly ordered such that for each vertex $u\in U$, the neighbors of $u$ are consecutive in the ordering of $V$. An induced matching $H$ of $G$ is a matching such that no edge of $E$ connects endpoints of two different edges of $H$. We show that in a convex bipartite graph with $n$ vertices and $m$ weighted edges, an induced matching of maximum total weight can be computed in $O(n+m)$ time. An unweighted convex bipartite graph has a representation of size $O(n)$ that records for each vertex $u\in U$ the first and last neighbor in the ordering of $V$. Given such a compact representation, we compute an induced matching of maximum cardinality in $O(n)$ time. In convex bipartite graphs, maximum-cardinality induced matchings are dual to minimum chain covers. A chain cover is a covering of the edge set by chain subgraphs, that is, subgraphs that do not contain induced matchings of more than one edge. Given a compact representation, we compute a representation of a minimum chain cover in $O(n)$ time. If no compact representation is given, the cover can be computed in $O(n+m)$ time. All of our algorithms achieve optimal running time for the respective problem and model. Previous algorithms considered only the unweighted case, and the best algorithm for computing a maximum-cardinality induced matching or a minimum chain cover in a convex bipartite graph had a running time of $O(n^2)$

Polyhedral characteristics of balanced and unbalanced bipartite subgraph problems

We study the polyhedral properties of three problems of constructing an optimal complete bipartite subgraph (a biclique) in a bipartite graph. In the first problem we consider a balanced biclique with the same number of vertices in both parts and arbitrary edge weights. In the other two problems we are dealing with unbalanced subgraphs of maximum and minimum weight with nonnegative edges. All three problems are established to be NP-hard. We study the polytopes and the cone decompositions of these problems and their 1-skeletons. We describe the adjacency criterion in 1-skeleton of the polytope of the balanced complete bipartite subgraph problem. The clique number of 1-skeleton is estimated from below by a superpolynomial function. For both unbalanced biclique problems we establish the superpolynomial lower bounds on the clique numbers of the graphs of nonnegative cone decompositions. These values characterize the time complexity in a broad class of algorithms based on linear comparisons

Hitting and Harvesting Pumpkins

The "c-pumpkin" is the graph with two vertices linked by c>0 parallel edges. A c-pumpkin-model in a graph G is a pair A,B of disjoint subsets of vertices of G, each inducing a connected subgraph of G, such that there are at least c edges in G between A and B. We focus on covering and packing c-pumpkin-models in a given graph: On the one hand, we provide an FPT algorithm running in time 2^O(k) n^O(1) deciding, for any fixed c>0, whether all c-pumpkin-models can be covered by at most k vertices. This generalizes known single-exponential FPT algorithms for Vertex Cover and Feedback Vertex Set, which correspond to the cases c=1,2 respectively. On the other hand, we present a O(log n)-approximation algorithm for both the problems of covering all c-pumpkin-models with a smallest number of vertices, and packing a maximum number of vertex-disjoint c-pumpkin-models.Comment: v2: several minor change

Mod/Resc Parsimony Inference

We address in this paper a new computational biology problem that aims at understanding a mechanism that could potentially be used to genetically manipulate natural insect populations infected by inherited, intra-cellular parasitic bacteria. In this problem, that we denote by \textsc{Mod/Resc Parsimony Inference}, we are given a boolean matrix and the goal is to find two other boolean matrices with a minimum number of columns such that an appropriately defined operation on these matrices gives back the input. We show that this is formally equivalent to the \textsc{Bipartite Biclique Edge Cover} problem and derive some complexity results for our problem using this equivalence. We provide a new, fixed-parameter tractability approach for solving both that slightly improves upon a previously published algorithm for the \textsc{Bipartite Biclique Edge Cover}. Finally, we present experimental results where we applied some of our techniques to a real-life data set.Comment: 11 pages, 3 figure