Allows identification of functional modules in protein-protein interaction (PPI) networks. HAM-FMD is based on ant colony optimization and multi-agent evolution (ACO-MAE). This tool focuses on the detection of densely connected subgraphs within the graphic representation of a PPI network. It proceeds to a transformation of the clustering of proteins in a PPI network into the searching of an optimization path among proteins by a neighboring distance metric. Then, some optimal paths with high quality were encoded and evolved in a multi-agent evolutionary environment.
College of Computer Science and Technology, Beijing University of Technology, Beijing Municipal Key Laboratory of Multimedia and Intelligent Software Technology, Beijing, China; Department of Computer Science and Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA