Joint Biomedical Entity and Relation Extraction with Unified Interaction Maps

Haixin Tan, Zhihao Yang, Zeyuan Ding, Zhijun Wang, Ling Luo, Lei Wang, Yin Zhang, Wei Liu, Hongfei Lin, Jian Wang

Abstract: Automatic extraction of entities and their relations from unstructured literature to form structured triples is essential for biomedical knowledge construction. Although most existing joint methods have effectively addressed some challenging problems in the biomedical corpora, i.e., the prevalent overlapping issue, they still suffer from a lack of consideration for the intrinsic correlations between entities and relations, as well as low computational efficiency. In this paper, we present a joint entity and relation extraction model with unified interaction maps. Specifically, we concatenate all relations in the natural language form with the input text to integrate the semantic information of relations through a deep Transformer-based encoder. In addition, we apply unified interaction maps to capture the correlations, which can naturally handle the overlapping issue. Extensive experiments on the CHEMPROT and DDIExtraction2013 datasets demonstrate the effectiveness of our model, achieving the state-of-the-art performance with higher efficiency.