A set of treatment data corresponding to a response of the biological system to the agent and a set of control data corresponding to a response of the biological system not exposed to the agent are received, and a first computational causal network model and a second computational causal network model that each represents a biological process in the biological system are identified. Based on the set of treatment data and the set of control data, a first score for the first computational causal network model and a second score for the second computational causal network model are computed. A factor is generated based on the first score, the second score, and an intersection between the first computational causal network model and the second computational causal network model, wherein the factor represents the perturbation of the biological system in response to the agent.