Year: 2019
Type: conference-paper
Abstract: Effective biomedical literature retrieval (BLR) plays a central role inprecision medicine informatics. In this paper, we propose GRAPHENE,which is a deep learning based framework for precise BLR. GRAPHENEconsists of three main different modules 1) graph-augmented doc-ument representation learning; 2) query expansion and represen-tation learning and 3) learning to rank biomedical articles. Thegraph-augmented document representation learning module con-structs a document-concept graph containing biomedical conceptnodes and document nodes so that global biomedical related con-cept from external knowledge source can be captured, which isfurther connected to a BiLSTM so both local and global topics canbe explored. Query expansion and representation learning moduleexpands the query with abbreviations and different names, and thenbuilds a CNN-based model to convolve the expanded query andobtain a vector representation for each query. Learning to rank min-imizes a ranking loss between biomedical articles with the queryto learn the retrieval function. Experimental results on applyingour system to TREC Precision Medicine track data are provided todemonstrate its effectiveness.
Authors: Sendong Zhao, Chang Su, Andrea Sboner, Fei Wang
Institution: Cornell University
Language: English
Subfield: Information Systems
Field: Computer Science
Domain: Physical Sciences
Open Access status: bronze
Funder: National Science Foundation
OpenAlex ID: W2986940428