Topic-BiGRU-U-Net for Document-level Relation Extraction from Biomedical Literature

Document-level biomedical relation extraction refers to extract relationship facts from unstructured biomedical literature. Due to the fact that many relationship facts span multiple sentences and involve complex interactions between entities, it requires models with strong logical reasoning capabilities. However, previous methods have had limitations in terms of logical reasoning, such as lack logical reasoning and the entities merely based on a single granularity. Although other efforts are based on multiple granularity, including mention pairs and entity pairs, the inference mechanism is weak. In this paper, we propose a module to enhance the model’s logical reasoning capabilities from four kinds of granularity (mention, entity, mention pairs, and entity pairs). Specifically, we encode the entities and mentions separately using BiGRU to capture contextual features. Simultaneously, we employ a U-Net network to model entity pairs and mention pairs, and enhance inter-sentence reasoning abilities. Additionally, to support the model’s reasoning capabilities, we introduce topic nodes into the traditional heterogeneous graph to fully extract document information. Experimental results on CDR and GDA datasets in the biomedical field demonstrate the outstanding performance of the proposed model.