OSLAT: Open Set Label Attention Transformer for Medical Entity Retrieval and Span Extraction

Abstract: Medical entity span extraction and linking are critical steps for many healthcare NLP tasks. Most existing entity extraction methods either have a fixed vocabulary of medical entities or require span annotations. In this paper, we propose a method for linking an open set of entities that does not require any span annotations. Our method, Open Set Label Attention Transformer (OSLAT), uses the label-attention mechanism to learn candidate-entity contextualized text representations. We find that OSLAT can not only link entities but is also able to implicitly learn spans associated with entities. We evaluate OSLAT on two tasks: (1) span extraction trained without explicit span annotations, and (2) entity linking trained without span-level annotation. We test the generalizability of our method by training two separate models on two datasets with low entity overlap and comparing cross-dataset performance.