Enhancing biomedical relation extraction with directionality

Abstract

Summary Biological relation networks contain rich information for understanding the biological mechanisms behind the relationship of entities such as genes, proteins, diseases, and chemicals. The vast growth of biomedical literature poses significant challenges in updating the network knowledge. The recent Biomedical Relation Extraction Dataset (BioRED) provides valuable manual annotations, facilitating the development of machine learning and pre-trained language model approaches for automatically identifying novel document-level (inter-sentence context) relationships. Nonetheless, its annotations lack directionality (subject/object) for the entity roles, which is essential for studying complex biological networks. Herein, we annotate the entity roles of the relationships in the BioRED corpus and subsequently propose a novel multi-task language model with soft-prompt learning to jointly identify the relationship, novel findings, and entity roles. Our results include an enriched BioRED corpus with 10 864 directionality annotations. Moreover, our proposed method outperforms existing large language models, such as the state-of-the-art GPT-4 and Llama-3, on two benchmarking tasks. Availability and implementation Our source code and dataset are available at https://github.com/ncbi-nlp/BioREDirect.