Combining relation extraction with function detection for BEL statement extraction

• Published in: Database : the journal of biological databases and curation 2019-01, Vol.2019
• Main Authors: Liu, Suwen, Cheng, Wei, Qian, Longhua, Zhou, Guodong
• Format: Article
• Language: English
• Subjects: Computational Biology - methods; Data Mining - methods; Databases, Factual; Deep Learning; Humans; Long short-term memory; Natural Language Processing; Original; Software
• ISSN: 1758-0463; 1758-0463
• DOI: 10.1093/database/bay133

Abstract The BioCreative-V community proposed a challenging task of automatic extraction of causal relation network in Biological Expression Language (BEL) from the biomedical literature. Previous studies on this task largely used models induced from other related tasks and then transformed intermediate structures to BEL statements, which left the given training corpus unexplored. To make full use of the BEL training corpus, in this work, we propose a deep learning-based approach to extract BEL statements. Specifically, we decompose the problem into two subtasks: entity relation extraction and entity function detection. First, two attention-based bidirectional long short-term memory networks models are used to extract entity relation and entity function, respectively. Then entity relation and their functions are combined into a BEL statement. In order to boost the overall performance, a strategy of threshold filtering is applied to improve the precision of identified entity functions. We evaluate our approach on the BioCreative-V Track 4 corpus with or without gold entities. The experimental results show that our method achieves the state-of-the-art performance with an overall F1-measure of 46.9% in stage 2 and 21.3% in stage 1, respectively.