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论文类型： 期刊论文

发表时间： 2019-12-01

发表刊物： COMPUTATIONAL BIOLOGY AND CHEMISTRY

收录刊物： PubMed、EI、SCIE

卷号： 83

页面范围： 107146

ISSN号： 1476-9271

关键字： PPI extraction; Knowledge selection; Mutual attention; Prior knowledge

摘要： Protein-protein interaction (PPI) extraction from published scientific literature provides additional support for precision medicine efforts. Meanwhile, knowledge bases (KBs) contain huge amounts of structured information of protein entities and their relations, which can be encoded in entity and relation embeddings to help PPI extraction. However, the prior knowledge of protein-protein pairs must be selectively used so that it is suitable for different contexts. This paper proposes a Knowledge Selection Model (KSM) to fuse the selected prior knowledge and context information for PPI extraction. Firstly, two Transformers encode the context sequence of a protein pair according to each protein embedding, respectively. Then, the two outputs are fed to a mutual attention to capture the important context features towards the protein pair. Next, the context features are used to distill the relation embedding by a knowledge selector. Finally, the selected relation embedding and the context features are concatenated for PPI extraction. Experiments on the BioCreative VI PPI dataset show that KSM achieves a new state-of-the-art performance (38.08 % F1-score) by adding knowledge selection.