ClinStructor: AI-Powered Structuring of Unstructured Clinical Texts

Karthikeyan K, Raghuveer Thirukovalluru, David Carlson


Abstract
Clinical notes contain valuable, context-rich information, but their unstructured format introduces several challenges, including unintended biases (e.g., gender or racial bias), and poor generalization across clinical settings (e.g., models trained on one EHR system may perform poorly on another due to format differences) and poor interpretability. To address these issues, we present ClinStructor, a pipeline that leverages large language models (LLMs) to convert clinical free-text into structured, task-specific question–answer pairs prior to predictive modeling. Our method substantially enhances transparency and controllability and only leads to a modest reduction in predictive performance (a 2–3% drop in AUC), compared to direct fine-tuning, on the ICU mortality prediction task. ClinStructor lays a strong foundation for building reliable, interpretable, and generalizable machine learning models in clinical environments.
Anthology ID:
2025.ijcnlp-long.151
Volume:
Proceedings of the 14th International Joint Conference on Natural Language Processing and the 4th Conference of the Asia-Pacific Chapter of the Association for Computational Linguistics
Month:
December
Year:
2025
Address:
Mumbai, India
Editors:
Kentaro Inui, Sakriani Sakti, Haofen Wang, Derek F. Wong, Pushpak Bhattacharyya, Biplab Banerjee, Asif Ekbal, Tanmoy Chakraborty, Dhirendra Pratap Singh
Venues:
IJCNLP | AACL
SIG:
Publisher:
The Asian Federation of Natural Language Processing and The Association for Computational Linguistics
Note:
Pages:
2822–2836
Language:
URL:
https://preview.aclanthology.org/ingest-ijcnlp-aacl/2025.ijcnlp-long.151/
DOI:
Bibkey:
Cite (ACL):
Karthikeyan K, Raghuveer Thirukovalluru, and David Carlson. 2025. ClinStructor: AI-Powered Structuring of Unstructured Clinical Texts. In Proceedings of the 14th International Joint Conference on Natural Language Processing and the 4th Conference of the Asia-Pacific Chapter of the Association for Computational Linguistics, pages 2822–2836, Mumbai, India. The Asian Federation of Natural Language Processing and The Association for Computational Linguistics.
Cite (Informal):
ClinStructor: AI-Powered Structuring of Unstructured Clinical Texts (K et al., IJCNLP-AACL 2025)
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https://preview.aclanthology.org/ingest-ijcnlp-aacl/2025.ijcnlp-long.151.pdf