A Search-based Neural Model for Biomedical Nested and Overlapping Event Detection

Kurt Junshean Espinosa, Makoto Miwa, Sophia Ananiadou

Abstract
We tackle the nested and overlapping event detection task and propose a novel search-based neural network (SBNN) structured prediction model that treats the task as a search problem on a relation graph of trigger-argument structures. Unlike existing structured prediction tasks such as dependency parsing, the task targets to detect DAG structures, which constitute events, from the relation graph. We define actions to construct events and use all the beams in a beam search to detect all event structures that may be overlapping and nested. The search process constructs events in a bottom-up manner while modelling the global properties for nested and overlapping structures simultaneously using neural networks. We show that the model achieves performance comparable to the state-of-the-art model Turku Event Extraction System (TEES) on the BioNLP Cancer Genetics (CG) Shared Task 2013 without the use of any syntactic and hand-engineered features. Further analyses on the development set show that our model is more computationally efficient while yielding higher F1-score performance.
Anthology ID:
D19-1381
Volume:
Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP)
Month:
November
Year:
2019
Address:
Hong Kong, China
Venues:
EMNLP | IJCNLP
SIG:
SIGDAT
Publisher:
Association for Computational Linguistics
Note:
Pages:
3679–3686
Language:
URL:
https://aclanthology.org/D19-1381
DOI:
10.18653/v1/D19-1381
Bibkey:
Cite (ACL):
Kurt Junshean Espinosa, Makoto Miwa, and Sophia Ananiadou. 2019. A Search-based Neural Model for Biomedical Nested and Overlapping Event Detection. In Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP), pages 3679–3686, Hong Kong, China. Association for Computational Linguistics.
Cite (Informal):
A Search-based Neural Model for Biomedical Nested and Overlapping Event Detection (Espinosa et al., EMNLP-IJCNLP 2019)
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