Unified Medical Language System resources improve sieve-based generation and Bidirectional Encoder Representations from Transformers (BERT)-based ranking for concept normalization

Dongfang Xu, Manoj Gopale, Jiacheng Zhang, Kris Brown, Edmon Begoli, Steven Bethard

Abstract: Concept normalization, the task of linking phrases in text to concepts in an ontology, is useful for many downstream tasks including relation extraction, information retrieval, etc. We present a generate-and-rank concept normalization system based on our participation in the 2019 National NLP Clinical Challenges Shared Task Track 3 Concept Normalization.