The 2019 n2c2/OHNLP track on clinical semantic textual similarity: Overview

Yanshan Wang, Sunyang Fu, Feichen Shen, Sam Henry, Ozlem Uzuner, Hongfang Liu

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


Background: Semantic textual similarity is a common task in the general English domain to assess the degree to which the underlying semantics of 2 text segments are equivalent to each other. Clinical Semantic Textual Similarity (ClinicalSTS) is the semantic textual similarity task in the clinical domain that attempts to measure the degree of semantic equivalence between 2 snippets of clinical text. Due to the frequent use of templates in the Electronic Health Record system, a large amount of redundant text exists in clinical notes, making ClinicalSTS crucial for the secondary use of clinical text in downstream clinical natural language processing applications, such as clinical text summarization, clinical semantics extraction, and clinical information retrieval. Objective: Our objective was to release ClinicalSTS data sets and to motivate natural language processing and biomedical informatics communities to tackle semantic text similarity tasks in the clinical domain. Methods: We organized the first BioCreative/OHNLP ClinicalSTS shared task in 2018 by making available a real-world ClinicalSTS data set. We continued the shared task in 2019 in collaboration with National NLP Clinical Challenges (n2c2) and the Open Health Natural Language Processing (OHNLP) consortium and organized the 2019 n2c2/OHNLP ClinicalSTS track. We released a larger ClinicalSTS data set comprising 1642 clinical sentence pairs, including 1068 pairs from the 2018 shared task and 1006 new pairs from 2 electronic health record systems, GE and Epic. We released 80% (1642/2054) of the data to participating teams to develop and fine-tune the semantic textual similarity systems and used the remaining 20% (412/2054) as blind testing to evaluate their systems. The workshop was held in conjunction with the American Medical Informatics Association 2019 Annual Symposium. Results: Of the 78 international teams that signed on to the n2c2/OHNLP ClinicalSTS shared task, 33 produced a total of 87 valid system submissions. The top 3 systems were generated by IBM Research, the National Center for Biotechnology Information, and the University of Florida, with Pearson correlations of r=.9010, r=.8967, and r=.8864, respectively. Most top-performing systems used state-of-the-art neural language models, such as BERT and XLNet, and state-of-the-art training schemas in deep learning, such as pretraining and fine-tuning schema, and multitask learning. Overall, the participating systems performed better on the Epic sentence pairs than on the GE sentence pairs, despite a much larger portion of the training data being GE sentence pairs. Conclusions: The 2019 n2c2/OHNLP ClinicalSTS shared task focused on computing semantic similarity for clinical text sentences generated from clinical notes in the real world. It attracted a large number of international teams. The ClinicalSTS shared task could continue to serve as a venue for researchers in natural language processing and medical informatics communities to develop and improve semantic textual similarity techniques for clinical text.

Original languageEnglish (US)
Article numbere23375
JournalJMIR Medical Informatics
Issue number11
StatePublished - Nov 2020


  • Challenge
  • Clinical natural language processing
  • ClinicalSTS
  • Electronic health records
  • Medical natural language processing
  • N2c2
  • Natural language processing
  • Semantic textual similarity
  • Shared task

ASJC Scopus subject areas

  • Health Informatics
  • Health Information Management


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