Algebraic Topological Analysis of networks
Description
Algebraic Topological Analysis of various networks, including molecular interacting networks, protein protein interaction (PPI) networks. Calculation of homology group (HG) and Betti numbers, can be performed. In addition, traditional graph parameters of the network can be calculated, including degree, cluster coefficient, betweenness, assortativity (assortativity of degree, closeness, and betweenness). Furthermore, novel parameters of the network, such as degree of involved cycles of each node, based on the Algebraic Topological Analysis, can be performed.
Files
Steps to reproduce
Code dependency: javaplex.jar, plex-viewer.jar, jung-api-2.1.1.jar, processing.core. Net construction: (file is the file pathway for network edges, the first 2 columns are node1 and node2, and the 3rd column is the weight of the edge) NetworkOfFiltration net=new NetworkOfFiltration(file); net.getFiltritionDistribution(1, NetworkOfFiltration.SERIE_CYCLE_NUM).print(true);