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In JMIR medical informatics ; h5-index 23.0

BACKGROUND : With the rapid expansion of biomedical literature, biomedical information extraction has attracted increasing attention from researchers. In particular, relation extraction between 2 entities is a long-term research topic.

OBJECTIVE : This study aimed to perform 2 multiclass relation extraction tasks of Biomedical Natural Language Processing Workshop 2019 Open Shared Tasks: relation extraction of Bacteria-Biotope (BB-rel) task and binary relation extraction of plant seed development (SeeDev-binary) task. In essence, these 2 tasks are aimed at extracting the relation between annotated entity pairs from biomedical texts, which is a challenging problem.

METHODS : Traditional research methods adopted feature- or kernel-based methods and achieved good performance. For these tasks, we propose a deep learning model based on a combination of several distributed features, such as domain-specific word embedding, part-of-speech embedding, entity-type embedding, distance embedding, and position embedding. The multi-head attention mechanism is used to extract the global semantic features of an entire sentence. Meanwhile, we introduced a dependency-type feature and the shortest dependency path connecting 2 candidate entities in the syntactic dependency graph to enrich the feature representation.

RESULTS : Experiments show that our proposed model has excellent performance in biomedical relation extraction, achieving F1 scores of 65.56% and 38.04% on the test sets of the BB-rel and SeeDev-binary tasks. Especially in the SeeDev-binary task, the F1 score of our model is superior to that of other existing models and achieves state-of-the-art performance.

CONCLUSIONS : We demonstrated that the multi-head attention mechanism can learn relevant syntactic and semantic features in different representation subspaces and different positions to extract comprehensive feature representation. Moreover, syntactic dependency features can improve the performance of the model by learning dependency relation between the entities in biomedical texts.

Li Yongbin, Hui Linhu, Zou Liping, Li Huyang, Xu Luo, Wang Xiaohua, Chua Stephanie


additive attention, biomedical relation extraction, deep learning, feature combination, multi-head attention, shortest dependency path, syntactic dependency feature, syntactic dependency graph