Simultaneously Linking Entities and Extracting Relations from Biomedical Text Without Mention-level Supervision

Understanding the meaning of text often involves reasoning about entities and their relationships. This requires identifying textual mentions of entities, linking them to a canonical concept, and discerning their relationships. These tasks are nearly always viewed as separate components within a pipeline, each requiring a distinct model and training data. While relation extraction can often be trained with readily available weak or distant supervision, entity linkers typically require expensive mention-level supervision -- which is not available in many domains. Instead, we propose a model which is trained to simultaneously produce entity linking and relation decisions while requiring no mention-level annotations. This approach avoids cascading errors that arise from pipelined methods and more accurately predicts entity relationships from text. We show that our model outperforms a state-of-the art entity linking and relation extraction pipeline on two biomedical datasets and can drastically improve the overall recall of the system.Comment: Accepted in AAAI 202

Extracting Multiple-Relations in One-Pass with Pre-Trained Transformers

Most approaches to extraction multiple relations from a paragraph require multiple passes over the paragraph. In practice, multiple passes are computationally expensive and this makes difficult to scale to longer paragraphs and larger text corpora. In this work, we focus on the task of multiple relation extraction by encoding the paragraph only once (one-pass). We build our solution on the pre-trained self-attentive (Transformer) models, where we first add a structured prediction layer to handle extraction between multiple entity pairs, then enhance the paragraph embedding to capture multiple relational information associated with each entity with an entity-aware attention technique. We show that our approach is not only scalable but can also perform state-of-the-art on the standard benchmark ACE 2005.Comment: 7 page

Effective Feature Representation for Clinical Text Concept Extraction

Crucial information about the practice of healthcare is recorded only in free-form text, which creates an enormous opportunity for high-impact NLP. However, annotated healthcare datasets tend to be small and expensive to obtain, which raises the question of how to make maximally efficient uses of the available data. To this end, we develop an LSTM-CRF model for combining unsupervised word representations and hand-built feature representations derived from publicly available healthcare ontologies. We show that this combined model yields superior performance on five datasets of diverse kinds of healthcare text (clinical, social, scientific, commercial). Each involves the labeling of complex, multi-word spans that pick out different healthcare concepts. We also introduce a new labeled dataset for identifying the treatment relations between drugs and diseases