GRAPHENE: A Precise Biomedical Literature Retrieval Engine with Graph Augmented Deep Learning and External Knowledge Empowerment

TL;DR

GRAPHENE is a deep learning framework that enhances biomedical literature retrieval by integrating graph-based external knowledge, query expansion, and learning to rank, significantly improving retrieval accuracy in precision medicine applications.

Contribution

The paper introduces a novel deep learning framework combining graph-augmented document representation, query expansion, and ranking methods for precise biomedical literature retrieval.

Findings

Outperforms existing retrieval methods on TREC Precision Medicine data

Effectively captures global biomedical concepts through external knowledge integration

Improves query understanding with abbreviation and synonym expansion

Abstract

Effective biomedical literature retrieval (BLR) plays a central role in precision medicine informatics. In this paper, we propose GRAPHENE, which is a deep learning based framework for precise BLR. GRAPHENE consists of three main different modules 1) graph-augmented document representation learning; 2) query expansion and representation learning and 3) learning to rank biomedical articles. The graph-augmented document representation learning module constructs a document-concept graph containing biomedical concept nodes and document nodes so that global biomedical related concept from external knowledge source can be captured, which is further connected to a BiLSTM so both local and global topics can be explored. Query expansion and representation learning module expands the query with abbreviations and different names, and then builds a CNN-based model to convolve the expanded query and obtain a vector representation for each query. Learning to rank minimizes a ranking loss between biomedical articles with the query to learn the retrieval function. Experimental results on applying our system to TREC Precision Medicine track data are provided to demonstrate its effectiveness.