Relation-aware deep neural network enables more efficient biomedical knowledge acquisition from massive literature

Abstract

Biomedical knowledge is typically organized in a relational scheme, such as chemical-disease relation, gene-disease relation, and gene-pathway relation. Biomedical scientists heavily rely on search engines to acquire up-to-date relational knowledge from massive biomedical articles. The navigation efficiency of the retrieval process, however, is significantly restricted by keyword matching techniques unaware of the biomedical relations of these keywords in articles. To bridge the gap between existing retrieval techniques and practical access demands for relational knowledge, we present a novel framework, Biomedical Relation-Aware Document Ranking (BioRADR), capable of retrieving articles expressing specific relations with respect to the queried entity pair. Based on a deep neural network, BioRADR can be trained from large-scale data automatically annotated via distant supervision, and empirical evaluation reveals that it outperforms the strongest baseline by over 8 points in NDCG@1. We implement an online system (http://bioradr.ai.thunlp.org/) based on BioRADR, enabling more efficient relation-oriented retrieval of biomedical articles.

Keywords

• Biomedical knowledge retrieval
• Biomedical relation modeling
• Deep learning
• Pre-trained language model