Identifying Biological Response Pathways

A method for operating a machine for identifying a mechanism associated with a cellular response includes identifying molecules participating in the cellular response, accessing a database containing information characterizing molecular interactions, determining pathways connecting the identified molecules participating in the response, and solving an optimization problem. The pathways comprise nodes, each representing a molecule, and edges, each connecting a pair of nodes and representing an interaction between a respective pair of molecules represented by the pair of nodes. The nodes includes a subset that represent molecules identified as participating in the cellular response. Solving an optimization problem comprises determining a subset of the molecules and interactions having a minimum aggregate cost, associating each participating node with a penalty value, associating each edge with a cost value, forming an objective function based on the penalty and cost values, and identifying the sub-network of nodes and edges that minimizes the objective function.