Inapproximability of Maximum Weighted Edge Biclique and Its Applications (0704.0468v2)

Abstract: Given a bipartite graph $G = (V_1,V_2,E)$ where edges take on {\it both} positive and negative weights from set $\mathcal{S}$, the {\it maximum weighted edge biclique} problem, or $\mathcal{S}$-MWEB for short, asks to find a bipartite subgraph whose sum of edge weights is maximized. This problem has various applications in bioinformatics, machine learning and databases and its (in)approximability remains open. In this paper, we show that for a wide range of choices of $\mathcal{S}$, specifically when $| \frac{\min\mathcal{S}} {\max \mathcal{S}} | \in \Omega(\eta^{\delta-1/2}) \cap O(\eta^{1/2-\delta})$ (where $\eta = \max{|V_1|, |V_2|}$, and $\delta \in (0,1/2]$), no polynomial time algorithm can approximate $\mathcal{S}$-MWEB within a factor of $n^{\epsilon}$ for some $\epsilon > 0$ unless $\mathsf{RP = NP}$. This hardness result gives justification of the heuristic approaches adopted for various applied problems in the aforementioned areas, and indicates that good approximation algorithms are unlikely to exist. Specifically, we give two applications by showing that: 1) finding statistically significant biclusters in the SAMBA model, proposed in \cite{Tan02} for the analysis of microarray data, is $n^{\epsilon}$-inapproximable; and 2) no polynomial time algorithm exists for the Minimum Description Length with Holes problem \cite{Bu05} unless $\mathsf{RP=NP}$.