BioGSF: a graph-driven semantic feature integration framework for biomedical relation extraction

The automatic and accurate extraction of diverse biomedical relations from literature constitutes the core elements of medical knowledge graphs, which are indispensable for healthcare artificial intelligence. Currently, fine-tuning through stacking various neural networks on pre-trained language models (PLMs) represents a common framework for end-to-end resolution of the biomedical relation extraction (RE) problem. Nevertheless, sequence-based PLMs, to a certain extent, fail to fully exploit the connections between semantics and the topological features formed by these connections. In this study, we presented a graph-driven framework named BioGSF for RE from the literature by integrating shortest dependency paths (SDP) with entity-pair graph through the employment of the graph neural network model. Initially, we leveraged dependency relationships to obtain the SDP between entities and incorporated this information into the entity-pair graph. Subsequently, the graph attention network was utilized to acquire the topological information of the entity-pair graph. Ultimately, the obtained topological information was combined with the semantic features of the contextual information for relation classification. Our method was evaluated on two distinct datasets, namely S4 and BioRED. The outcomes reveal that BioGSF not only attains the superior performance among previous models with a micro-F1 score of 96.68% (S4) and 96.03% (BioRED), but also demands the shortest running times. BioGSF emerges as an efficient framework for biomedical RE.