Large-scale fine-grained semantic indexing of biomedical literature based on weakly-supervised deep learning

Abstract

Semantic indexing of biomedical literature is usually done at the level of MeSH descriptors, representing topics of interest for the biomedical community. Several related but distinct biomedical concepts are often grouped together in a single coarse-grained descriptor and are treated as a single topic for semantic indexing. This study proposes a new method for the automated refinement of subject annotations at the level of concepts, investigating deep learning approaches. Lacking labelled data for this task, our method relies on weak supervision based on concept occurrence in the abstract of an article. The proposed approach is evaluated on an extended large-scale retrospective scenario, taking advantage of concepts that eventually become MeSH descriptors, for which annotations become available in MEDLINE/PubMed. The results suggest that concept occurrence is a strong heuristic for automated subject annotation refinement and can be further enhanced when combined with dictionary-based heuristics. In addition, such heuristics can be useful as weak supervision for developing deep learning models that can achieve further improvement in some cases.Comment: 48 pages, 5 figures, 9 tables, 1 algorith