Fast and Robust Joint Models for Biomedical Event Extraction.

Extracting biomedical events from literature has attracted much recent attention. The best-performing systems so far have been pipelines of simple subtask-specific local classifiers. A natural drawback of such approaches are cascading errors introduced in early stages of the pipeline. We present three joint models of increasing complexity designed to overcome this problem. The first model performs joint trigger and argument extraction, and lends itself to a simple, efficient and exact inference algorithm. The second model captures correlations between events, while the third model ensures consistency between arguments of the same event. Inference in these models is kept tractable through dual decomposition. The first two models outperform the previous best joint approaches and are very competitive with respect to the current state-of-the-art. The third model yields the best results reported so far on the BioNLP 2009 shared task, the BioNLP 2011 Genia task and the BioNLP 2011 Infectious Diseases task.