Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
The maximum edge biclique problem is NP-complete
Discrete Applied Mathematics
Consensus algorithms for the generation of all maximal bicliques
Discrete Applied Mathematics - The fourth international colloquium on graphs and optimisation (GO-IV)
Biclustering Protein Complex Interactions with a Biclique Finding Algorithm
ICDM '06 Proceedings of the Sixth International Conference on Data Mining
Statistical Analysis and Data Mining
Modeling Protein Interacting Groups by Quasi-Bicliques: Complexity, Algorithm, and Application
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Near optimal solutions for maximum quasi-bicliques
COCOON'10 Proceedings of the 16th annual international conference on Computing and combinatorics
Unraveling multiple miRNA-mRNA associations through a graph-based approach
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
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Biological network studies can provide fundamental insights into various biological tasks including the functional characterization of genes and their products, the characterization of DNA-protein interactions, and the identification of regulatory mechanisms. However, biological networks are confounded with unreliable interactions and are incomplete, and thus, their computational exploitation is fraught with algorithmic challenges. Here we introduce quasi-biclique problems to analyze biological networks when represented by bipartite graphs. In difference to previous quasi-biclique problems, we include biological interaction levels by using edge-weighted quasi-bicliques. While we prove that our problems are NP-hard, we also provide exact IP solutions that can compute moderately sized networks. We verify the effectiveness of our IP solutions using both simulation and empirical data. The simulation shows high quasi-biclique recall rates, and the empirical data corroborate the abilities of our weighted quasi-bicliques in extracting features and recovering missing interactions from the network.