Clinical NLP Lab

Led by Dr. Hua Xu at Biomedical Informatics and Data Science, Yale School of Medicine

Biomedical NLP Challenges

We have participated in many NLP challenges and have achieved top rankings in many of them.

NLP Challenge Tasks Ranking
Named entity recognition 2009 i2b2 medication information extraction #2
2010 i2b2 problem, treatment, test extraction #2
2013 SHARe/CLEF abbreviation recognition #1
2016 CEGS N-GRID, De-identification #2
UMLS encoding 2014 SemEval, disorder encoding #1
Relation extraction 2012 i2b2 Temporal information extraction #1
2015 SemEval Disease-modifier extraction #1
2015 BioCREATIVE Chemical-induced disease from literature #1
2016 SemEvel, temporal information extraction #1
2017 TAC ADR extraction from drug labels #1
2018 n2c2, medication and associated ADR #1
2022 LitCoin Challenge on literature mining #2

Example Software Tools

Our lab has developed a number of software tools to support clinical NLP research and applications.


Clinical Language Annotation, Modeling, and Processing Toolkit


Biomedical data index and search engine

Contact us

Contact us

Have questions or want to learn more about our lab's research and expertise? Please don't hesitate to reach out.


100 College Street, New Haven, CT 06510