Mining biological interaction networks using weighted quasi-bicliques
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
Finding bicliques in digraphs: application into viral-host protein interactome
PReMI'11 Proceedings of the 4th international conference on Pattern recognition and machine intelligence
A continuous characterization of the maximum-edge biclique problem
Journal of Global Optimization
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Biclustering has many applications in text mining, web clickstream mining, and bioinformatics. When data entries are binary, the tightest biclusters become bicliques. We propose a flexible and highly efficient algorithm to compute bicliques. We first generalize the Motzkin-Straus formalism for computing the maximal clique from L_1 constraint to L_p constraint, which enables us to provide a generalized Motzkin-Straus formalism for computing maximal-edge bicliques. By adjusting parameters, the algorithm can favor biclusters with more rows less columns, or vice verse, thus increasing the flexibility of the targeted biclusters. We then propose an algorithmto solve the generalized Motzkin- Straus optimization problem. The algorithm is provably convergent and has a computational complexity of O(|E|) where |E| is the number of edges. Using this algorithm, we bicluster the yeast protein complex interaction network. We find that biclustering protein complexes at the protein level does not clearly reflect the functional linkage among protein complexes in many cases, while biclustering at protein domain level can reveal many underlying linkages. We show several new biologically significant results.