The Effectiveness of Uncased Tokeniziaion for Clinical Notes

Cory Paik, Katharina Von Der Wense


Abstract
The impact of case-sensitive tokenization on clinical notes is not well understood. While clinical notes share similarities with biomedical text in terminology, they often lack the proper casing found in polished publications. Language models, unlike humans, require a fixed vocabulary and case sensitivity is a trade-off that must be considered carefully. Improper casing can lead to sub-optimal tokenization and increased sequence length, degrading downstream performance and increasing computational costs. While most recent open-domain encoder language models use uncased tokenization for all tasks, there is no clear trend in biomedical and clinical models. In this work we (1) show that uncased models exceed the performance of cased models on clinical notes, even on traditionally case-sensitive tasks such as named entity recognition and (2) introduce independent case encoding to better balance model performance on case-sensitive and improperly-cased tasks.
Anthology ID:
2025.findings-acl.775
Volume:
Findings of the Association for Computational Linguistics: ACL 2025
Month:
July
Year:
2025
Address:
Vienna, Austria
Editors:
Wanxiang Che, Joyce Nabende, Ekaterina Shutova, Mohammad Taher Pilehvar
Venue:
Findings
SIG:
Publisher:
Association for Computational Linguistics
Note:
Pages:
14986–14992
Language:
URL:
https://preview.aclanthology.org/display_plenaries/2025.findings-acl.775/
DOI:
Bibkey:
Cite (ACL):
Cory Paik and Katharina Von Der Wense. 2025. The Effectiveness of Uncased Tokeniziaion for Clinical Notes. In Findings of the Association for Computational Linguistics: ACL 2025, pages 14986–14992, Vienna, Austria. Association for Computational Linguistics.
Cite (Informal):
The Effectiveness of Uncased Tokeniziaion for Clinical Notes (Paik & Wense, Findings 2025)
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PDF:
https://preview.aclanthology.org/display_plenaries/2025.findings-acl.775.pdf