To understand the organization and dynamics of cell functions, it is necessary to determine functional modules from a biological network like protein-protein interaction (PPI) networks and gene regulatory networks. A protein complex, which is one of the typical functional modules, is a group of two or more associated proteins that can operate its intrinsic function in a cell. PPIs have been experimentally identified by significant efforts like Gavin et al. [4] and Krogan et al. [6]. Those experimentally identified PPIs are accumulated into databases like HPRD [13] and BioGRID [12], which are increasing in size. Those accumulated PPI data make it more important to develop more efficient and accurate intelligent tools for the identification of protein complexes from such PPI data.
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