Biomedical Information Retrieval with Positive-Unlabeled Learning and Knowledge Graphs

Abstract

The rapid growth of biomedical publications has presented significant challenges in the field of information retrieval. Most existing work focuses on document retrieval given explicit queries. However, in real applications such as curated biomedical database maintenance, explicit queries are missing. In this paper, we propose a two-step model for biomedical information retrieval in the case that only a small set of example documents is available without explicit queries. Initially, we extract keywords from the observed documents using large pre-trained language models and biomedical knowledge graphs. These keywords are then enriched with domain-specific entities. Information retrieval techniques can subsequently use the collected entities to rank the documents. Following this, we introduce an iterative Positive-Unlabeled learning method to classify all unlabeled documents. Experiments conducted on the PubMed dataset demonstrate that the proposed technique outperforms the state-of-the-art positive-unlabeled learning methods. The results underscore the effectiveness of integrating large language models and biomedical knowledge graphs in improving zero-shot information retrieval performance in the biomedical domain.