Finding Biclique Partitions of Co-Chordal Graphs

The biclique partition number $(\text{bp})$ of a graph $G$ is referred to as the least number of complete bipartite (biclique) subgraphs that are required to cover the edges of the graph exactly once. In this paper, we show that the biclique partition number ($\text{bp}$) of a co-chordal (complementary graph of chordal) graph $G = (V, E)$ is less than the number of maximal cliques ($\text{mc}$) of its complementary graph: a chordal graph $G^c = (V, E^c)$. We first provide a general framework of the ``divide and conquer" heuristic of finding minimum biclique partitions of co-chordal graphs based on clique trees. Furthermore, a heuristic of complexity $O[|V|(|V|+|E^c|)]$ is proposed by applying lexicographic breadth-first search to find structures called moplexes. Either heuristic gives us a biclique partition of $G$ with size $\text{mc}(G^c)-1$. In addition, we prove that both of our heuristics can solve the minimum biclique partition problem on $G$ exactly if its complement $G^c$ is chordal and clique vertex irreducible. We also show that $\text{mc}(G^c) - 2 \leq \text{bp}(G) \leq \text{mc}(G^c) - 1$ if $G$ is a split graph

Inapproximability of Maximum Biclique Problems, Minimum kk-Cut and Densest At-Least-kk-Subgraph from the Small Set Expansion Hypothesis

The Small Set Expansion Hypothesis (SSEH) is a conjecture which roughly states that it is NP-hard to distinguish between a graph with a small subset of vertices whose edge expansion is almost zero and one in which all small subsets of vertices have expansion almost one. In this work, we prove inapproximability results for the following graph problems based on this hypothesis: - Maximum Edge Biclique (MEB): given a bipartite graph $G$, find a complete bipartite subgraph of $G$ with maximum number of edges. - Maximum Balanced Biclique (MBB): given a bipartite graph $G$, find a balanced complete bipartite subgraph of $G$ with maximum number of vertices. - Minimum $k$-Cut: given a weighted graph $G$, find a set of edges with minimum total weight whose removal partitions $G$ into $k$ connected components. - Densest At-Least-$k$-Subgraph (DAL$k$S): given a weighted graph $G$, find a set $S$ of at least $k$ vertices such that the induced subgraph on $S$ has maximum density (the ratio between the total weight of edges and the number of vertices). We show that, assuming SSEH and NP $\nsubseteq$ BPP, no polynomial time algorithm gives $n^{1 - \varepsilon}$-approximation for MEB or MBB for every constant $\varepsilon > 0$. Moreover, assuming SSEH, we show that it is NP-hard to approximate Minimum $k$-Cut and DAL$k$S to within $(2 - \varepsilon)$ factor of the optimum for every constant $\varepsilon > 0$. The ratios in our results are essentially tight since trivial algorithms give $n$-approximation to both MEB and MBB and efficient $2$-approximation algorithms are known for Minimum $k$-Cut [SV95] and DAL$k$S [And07, KS09]. Our first result is proved by combining a technique developed by Raghavendra et al. [RST12] to avoid locality of gadget reductions with a generalization of Bansal and Khot's long code test [BK09] whereas our second result is shown via elementary reductions.Comment: A preliminary version of this work will appear at ICALP 2017 under a different title "Inapproximability of Maximum Edge Biclique, Maximum Balanced Biclique and Minimum k-Cut from the Small Set Expansion Hypothesis

Clique-Stable Set separation in perfect graphs with no balanced skew-partitions

Inspired by a question of Yannakakis on the Vertex Packing polytope of perfect graphs, we study the Clique-Stable Set Separation in a non-hereditary subclass of perfect graphs. A cut (B,W) of G (a bipartition of V(G)) separates a clique K and a stable set S if $K\subseteq B$ and $S\subseteq W$. A Clique-Stable Set Separator is a family of cuts such that for every clique K, and for every stable set S disjoint from K, there exists a cut in the family that separates K and S. Given a class of graphs, the question is to know whether every graph of the class admits a Clique-Stable Set Separator containing only polynomially many cuts. It is open for the class of all graphs, and also for perfect graphs, which was Yannakakis' original question. Here we investigate on perfect graphs with no balanced skew-partition; the balanced skew-partition was introduced in the proof of the Strong Perfect Graph Theorem. Recently, Chudnovsky, Trotignon, Trunck and Vuskovic proved that forbidding this unfriendly decomposition permits to recursively decompose Berge graphs using 2-join and complement 2-join until reaching a basic graph, and they found an efficient combinatorial algorithm to color those graphs. We apply their decomposition result to prove that perfect graphs with no balanced skew-partition admit a quadratic-size Clique-Stable Set Separator, by taking advantage of the good behavior of 2-join with respect to this property. We then generalize this result and prove that the Strong Erdos-Hajnal property holds in this class, which means that every such graph has a linear-size biclique or complement biclique. This property does not hold for all perfect graphs (Fox 2006), and moreover when the Strong Erdos-Hajnal property holds in a hereditary class of graphs, then both the Erdos-Hajnal property and the polynomial Clique-Stable Set Separation hold.Comment: arXiv admin note: text overlap with arXiv:1308.644

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