Learning entity-oriented representation for biomedical relation extraction

Abstract

Biomedical Relation Extraction (BioRE) aims to automatically extract semantic relations for given entity pairs and is of great significance in biomedical research. Current popular methods often utilize pretrained language models to extract semantic features from individual input instances, which frequently suffer from overlapping semantics. Overlapping semantics refers to the situation in which a sentence contains multiple entity pairs that share the same context, leading to highly similar information between these entity pairs. In this study, we propose a model for learning Entity-oriented Representation (EoR) that aims to improve the performance of the model by enhancing the discriminability between entity pairs. It contains three modules: sentence representation, entity-oriented representation, and output. The first module learns the global semantic information of the input instance; the second module focuses on extracting the semantic information of the sentence from the target entities; and the third module enhances distinguishability among entity pairs and classifies the relation type. We evaluated our approach on four BioRE tasks with eight datasets, and the experiments showed that our EoR achieved state-of-the-art performance for PPI, DDI, CPI, and DPI tasks. Further analysis demonstrated the benefits of entity-oriented semantic information in handling multiple entity pairs in the BioRE task.

Keywords: Biomedical natural language processing; Information extraction; Overlapping semantics.