Learning biological processes with global constraints

Biological processes are complex phenomena involving a series of events that are related to one another through various relationships. Systems that can understand and reason over biological processes would dramatically improve the performance of semantic applications involving inference such as question answering (QA) - specifically "How?" and "Why?" questions. In this paper, we present the task of process extraction, in which events within a process and the relations between the events are automatically extracted from text. We represent processes by graphs whose edges describe a set of temporal, causal and co-reference event-event relations, and characterize the structural properties of these graphs (e.g., the graphs are connected). Then, we present a method for extracting relations between the events, which exploits these structural properties by performing joint inference over the set of extracted relations. On a novel dataset containing 148 descriptions of biological processes (released with this paper), we show significant improvement comparing to baselines that disregard process structure.