We present a joint model for biomedical event extraction and apply it to four tracks of the BioNLP 2011 Shared Task. Our model decomposes into three sub-models that concern (a) event triggers and outgoing arguments, (b) event triggers and incoming arguments and (c) protein-protein bindings. For efficient decoding we employ dual decomposition. Our results are very competitive: With minimal adaptation of our model we come in second for two of the tasks-right behind a version of the system presented here that includes predictions of the Stanford event extractor as features. We also show that for the Infectious Diseases task using data from the Genia track is a very effective way to improve accuracy.
REF develop a joint model with dual decomposition.
Robust Biomedical Event Extraction with Dual Decomposition and Minimal Domain Adaptation
Proceedings of BioNLP Shared Task 2011 Workshop
Computer Science