Biomedical Event Extraction based on Knowledge-driven Tree-LSTM

Event extraction for the biomedical domain is more challenging than that in the general news domain since it requires broader acquisition of domain-specific knowledge and deeper understanding of complex contexts. To better encode contextual information and external background knowledge, we propose a novel knowledge base (KB)-driven tree-structured long short-term memory networks (Tree-LSTM) framework, incorporating two new types of features: (1) dependency structures to capture wide contexts; (2) entity properties (types and category descriptions) from external ontologies via entity linking. We evaluate our approach on the BioNLP shared task with Genia dataset and achieve a new state-of-the-art result. In addition, both quantitative and qualitative studies demonstrate the advancement of the Tree-LSTM and the external knowledge representation for biomedical event extraction.