Algorithms for the Maximum Weight Connected k -Induced Subgraph Problem

Finding differentially regulated subgraphs in a biochemical network is an important problem in bioinformatics. We present a new model for finding such subgraphs which takes the polarity of the edges (activating or inhibiting) into account, leading to the problem of finding a connected subgraph induced by k vertices with maximum weight. We present several algorithms for this problem, including dynamic programming on tree decompositions and integer linear programming. We compare the strength of our integer linear program to previous formulations of the k-cardinality tree problem. Finally, we compare the performance of the algorithms and the quality of the results to a previous approach for finding differentially regulated subgraphs.