Summarizing Patients’ Problems from Hospital Progress Notes Using Pre-trained Sequence-to-Sequence Models
Yanjun Gao, Dmitriy Dligach, Timothy Miller, Dongfang Xu, Matthew M. M. Churpek, Majid Afshar
Abstract
Automatically summarizing patients’ main problems from daily progress notes using natural language processing methods helps to battle against information and cognitive overload in hospital settings and potentially assists providers with computerized diagnostic decision support. Problem list summarization requires a model to understand, abstract, and generate clinical documentation. In this work, we propose a new NLP task that aims to generate a list of problems in a patient’s daily care plan using input from the provider’s progress notes during hospitalization. We investigate the performance of T5 and BART, two state-of-the-art seq2seq transformer architectures, in solving this problem. We provide a corpus built on top of progress notes from publicly available electronic health record progress notes in the Medical Information Mart for Intensive Care (MIMIC)-III. T5 and BART are trained on general domain text, and we experiment with a data augmentation method and a domain adaptation pre-training method to increase exposure to medical vocabulary and knowledge. Evaluation methods include ROUGE, BERTScore, cosine similarity on sentence embedding, and F-score on medical concepts. Results show that T5 with domain adaptive pre-training achieves significant performance gains compared to a rule-based system and general domain pre-trained language models, indicating a promising direction for tackling the problem summarization task.- Anthology ID:
- 2022.coling-1.264
- Volume:
- Proceedings of the 29th International Conference on Computational Linguistics
- Month:
- October
- Year:
- 2022
- Address:
- Gyeongju, Republic of Korea
- Editors:
- Nicoletta Calzolari, Chu-Ren Huang, Hansaem Kim, James Pustejovsky, Leo Wanner, Key-Sun Choi, Pum-Mo Ryu, Hsin-Hsi Chen, Lucia Donatelli, Heng Ji, Sadao Kurohashi, Patrizia Paggio, Nianwen Xue, Seokhwan Kim, Younggyun Hahm, Zhong He, Tony Kyungil Lee, Enrico Santus, Francis Bond, Seung-Hoon Na
- Venue:
- COLING
- SIG:
- Publisher:
- International Committee on Computational Linguistics
- Note:
- Pages:
- 2979–2991
- Language:
- URL:
- https://aclanthology.org/2022.coling-1.264
- DOI:
- Cite (ACL):
- Yanjun Gao, Dmitriy Dligach, Timothy Miller, Dongfang Xu, Matthew M. M. Churpek, and Majid Afshar. 2022. Summarizing Patients’ Problems from Hospital Progress Notes Using Pre-trained Sequence-to-Sequence Models. In Proceedings of the 29th International Conference on Computational Linguistics, pages 2979–2991, Gyeongju, Republic of Korea. International Committee on Computational Linguistics.
- Cite (Informal):
- Summarizing Patients’ Problems from Hospital Progress Notes Using Pre-trained Sequence-to-Sequence Models (Gao et al., COLING 2022)
- PDF:
- https://preview.aclanthology.org/emnlp-22-attachments/2022.coling-1.264.pdf