{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/umlsbert-clinical-domain-knowledge","title":"UmlsBERT: Clinical Domain Knowledge Augmentation of Contextual Embeddings Using the Unified Medical Language System Metathesaurus","arxiv_id":"2010.10391","date":"2020-10-20","proceeding":"NAACL 2021 4","authors":["George Michalopoulos","Yuanxin Wang","Hussam Kaka","Helen Chen","Alexander Wong"],"abstract":"Contextual word embedding models, such as BioBERT and Bio_ClinicalBERT, have achieved state-of-the-art results in biomedical natural language processing tasks by focusing their pre-training process on domain-specific corpora. However, such models do not take into consideration expert domain knowledge. In this work, we introduced UmlsBERT, a contextual embedding model that integrates domain knowledge during the pre-training process via a novel knowledge augmentation strategy. More specifically, the augmentation on UmlsBERT with the Unified Medical Language System (UMLS) Metathesaurus was performed in two ways: i) connecting words that have the same underlying `concept' in UMLS, and ii) leveraging semantic group knowledge in UMLS to create clinically meaningful input embeddings. By applying these two strategies, UmlsBERT can encode clinical domain knowledge into word embeddings and outperform existing domain-specific models on common named-entity recognition (NER) and clinical natural language inference clinical NLP tasks.","url_abs":"https://arxiv.org/abs/2010.10391v5","url_pdf":"https://arxiv.org/pdf/2010.10391v5.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"umlsbert-clinical-domain-knowledge","repo_url":"https://github.com/gmichalo/UmlsBERT","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"cg","task_name":"NER"},{"task_slug":"named-entity-recognition-1","task_name":"Named Entity Recognition"},{"task_slug":"named-entity-recognition-ner","task_name":"Named Entity Recognition (NER)"},{"task_slug":"natural-language-inference","task_name":"Natural Language Inference"},{"task_slug":"word-embeddings","task_name":"Word Embeddings"},{"task_slug":"named-entity-recognition","task_name":"named-entity-recognition"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2010.10391","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}