TY - GEN
T1 - Biomedical event extraction based on knowledge-driven tree-LSTM
AU - Li, Diya
AU - Huang, Lifu
AU - Ji, Heng
AU - Han, Jiawei
N1 - Funding Information:
This work was supported by the U.S. NSF No. 1741634, Air Force No. FA8650-17-C-7715 and ARL NS-CTA No. W911NF-09-2-0053. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation here on.
Publisher Copyright:
© 2019 Association for Computational Linguistics
PY - 2019
Y1 - 2019
N2 - 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.
AB - 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.
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M3 - Conference contribution
AN - SCOPUS:85070813367
T3 - NAACL HLT 2019 - 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies - Proceedings of the Conference
SP - 1421
EP - 1430
BT - Long and Short Papers
PB - Association for Computational Linguistics (ACL)
T2 - 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, NAACL HLT 2019
Y2 - 2 June 2019 through 7 June 2019
ER -