Full-Abstract Biomedical Relation Extraction with Keyword-Attentive Domain Knowledge Infusion

Abstract

Relation extraction (RE) is an essential task in natural language processing. Given a context, RE aims to classify an entity-mention pair into a set of pre-defined relations. In the biomedical field, building an efficient and accurate RE system is critical for the construction of a domain knowledge base to support upper-level applications. Recent advances have witnessed a focus shift from sentence to document-level RE problems, which are more challenging due to the need for inter- and intra-sentence semantic reasoning. This type of distant dependency is difficult to understand and capture for a learning algorithm. To address the challenge, prior efforts either attempted to improve the cross sentence text representation or infuse domain or local knowledge into the model. Both strategies demonstrated efficacy on various datasets. In this paper, a keyword-attentive knowledge infusion strategy is proposed and integrated into BioBERT. A domain keyword collection mechanism is developed to discover the most relation-suggestive word tokens for bio-entities in a given context. By manipulating the attention masks, the model can be guided to focus on the semantic interaction between bio-entities linked by the keywords. We validated the proposed method on the Biocreative V Chemical Disease Relation dataset with an F1 of 75.6%, outperforming the state-of-the-art by 5.6%.