Are synthetic clinical notes useful for real natural language processing tasks: A case study on clinical entity recognition. (17th July 2021)

• Record Type: Journal Article
• Authors: Li, Jianfu; Zhou, Yujia; Jiang, Xiaoqian; Natarajan, Karthik; Pakhomov, Serguei Vs; Liu, Hongfang; Xu, Hua
• Is Part Of: Journal of the American Medical Informatics Association. Volume 28:Number 10(2021)
• Page Start: 2193
• Page End: 2201
• Publication Date: 2021-07-17
• Subjects: natural language processing -- neural language model -- text generation -- clinical notes -- named entity recognition; Medical informatics -- Periodicals; Information Services -- Periodicals; Medical Informatics -- Periodicals; Médecine -- Informatique -- Périodiques; Informatica; Geneeskunde; Informatique médicale; Computer network resources; Electronic journals; 610.285
• DOI: 10.1093/jamia/ocab112
• Languages: English
• ISSNs: 1067-5027

Abstract

Abstract: Objective: : Developing clinical natural language processing systems often requires access to many clinical documents, which are not widely available to the public due to privacy and security concerns. To address this challenge, we propose to develop methods to generate synthetic clinical notes and evaluate their utility in real clinical natural language processing tasks. Materials and Methods: : We implemented 4 state-of-the-art text generation models, namely CharRNN, SegGAN, GPT-2, and CTRL, to generate clinical text for the History and Present Illness section. We then manually annotated clinical entities for randomly selected 500 History and Present Illness notes generated from the best-performing algorithm. To compare the utility of natural and synthetic corpora, we trained named entity recognition (NER) models from all 3 corpora and evaluated their performance on 2 independent natural corpora. Results: : Our evaluation shows GPT-2 achieved the best BLEU (bilingual evaluation understudy) score (with a BLEU-2 of 0.92). NER models trained on synthetic corpus generated by GPT-2 showed slightly better performance on 2 independent corpora: strict F1 scores of 0.709 and 0.748, respectively, when compared with the NER models trained on natural corpus (F1 scores of 0.706 and 0.737, respectively), indicating the good utility of synthetic corpora in clinical NER model development. In addition, we also demonstrated that an augmented method that combines both natural and synthetic corpora achieved better performance than that uses the natural corpus only. Conclusions: : Recent advances in text generation have made it possible to generate synthetic clinical notes that could be useful for training NER models for information extraction from natural clinical notes, thus lowering the privacy concern and increasing data availability. Further investigation is needed to apply this technology to practice.