Large-scale investigation of weakly-supervised deep learning for the fine-grained semantic indexing of biomedical literature

OBJECTIVE Semantic indexing of biomedical literature is usually done at the level of MeSH descriptors with several related but distinct biomedical concepts often grouped together and treated as a single topic. This study proposes a new method for the automated refinement of subject annotations at the level of MeSH concepts. METHODS Lacking labelled data, we rely on weak supervision based on concept occurrence in the abstract of an article, which is also enhanced by dictionary-based heuristics. In addition, we investigate deep learning approaches, making design choices to tackle the particular challenges of this task. The new method is evaluated on a large-scale retrospective scenario, based on concepts that have been promoted to descriptors. RESULTS In our experiments concept occurrence was the strongest heuristic achieving a macro-F1 score of about 0.63 across several labels. The proposed method improved it further by more than 4pp. CONCLUSION The results suggest that concept occurrence is a strong heuristic for refining the coarse-grained labels at the level of MeSH concepts and the proposed method improves it further.