Method and system for analyzing biological networks

A method and associated system are provided for analyzing biological networks. The method includes obtaining data representing biological networks from one or more data stores and obtaining data representing biological pathways, such as pathways defined for the biological networks. The biological networks are defined by respective nodes representing molecules and connections representing relationships between or among the molecules. Each pathway represents any set of molecules that work in a collaborative way to produce an outcome. The method generates, in one or more processors, a computational model (e.g., a classifier) based on the data representing the biological networks and the data representing the pathways. Further, a set of molecules within or related to a given biological network is classified into pathway molecules and non-pathway molecules using the generated model.