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Background <p>Real-world studies based on electronic health records often require manual chart review to derive patients’ clinical phenotypes, a labor-intensive task with limited scalability. Here, we developed and compared computable phenotyping based on rules using the spaCy framework and a Large Language Model (LLM), GPT-4, for sub-phenotyping of patients with Crohn’s disease, considering age at diagnosis and disease behavior.</p> Methods <p>For our rule-based approach, we leveraged the spaCy framework and for the LLM-based approach, we used the GPT-4 model. The underlying data included 49,572 clinical notes and 2204 radiology reports from 584 Crohn’s disease patients. A test set of 280 clinical texts was labeled at sentence-level, in addition to patient-level ground truth data. The algorithms were evaluated based on their recall, precision, specificity values, and F1 scores.</p> Results <p>Overall, we observe similar or better performance using GPT-4 compared to the rules. On a note-level, the F1 score is at least 0.90 for disease behavior and 0.82 for age at diagnosis, and on patient level at least 0.66 for disease behavior and 0.71 for age at diagnosis.</p> Conclusions <p>To our knowledge, this is the first study to explore computable phenotyping algorithms based on clinical narrative text for these complex tasks, where prior inter-annotator agreements ranged from 0.54 to 0.98. There is no statistical evidence for a difference to the performance of human experts on this task. Our findings underline the potential of LLMs for computable phenotyping and may support large-scale cohort analyses from electronic health records and streamline chart review processes in the future.</p> <p></p>

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Automating clinical phenotyping using natural language processing

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年1月14日

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  • Linea Schmidt,
  • Susanne Ibing,
  • Florian Borchert,
  • Julian Hugo,
  • Allison A. Marshall,
  • Jellyana Peraza,
  • Judy H. Cho,
  • Erwin P. Böttinger,
  • Bernhard Y. Renard,
  • Ryan C. Ungaro

摘要

Background

Real-world studies based on electronic health records often require manual chart review to derive patients’ clinical phenotypes, a labor-intensive task with limited scalability. Here, we developed and compared computable phenotyping based on rules using the spaCy framework and a Large Language Model (LLM), GPT-4, for sub-phenotyping of patients with Crohn’s disease, considering age at diagnosis and disease behavior.

Methods

For our rule-based approach, we leveraged the spaCy framework and for the LLM-based approach, we used the GPT-4 model. The underlying data included 49,572 clinical notes and 2204 radiology reports from 584 Crohn’s disease patients. A test set of 280 clinical texts was labeled at sentence-level, in addition to patient-level ground truth data. The algorithms were evaluated based on their recall, precision, specificity values, and F1 scores.

Results

Overall, we observe similar or better performance using GPT-4 compared to the rules. On a note-level, the F1 score is at least 0.90 for disease behavior and 0.82 for age at diagnosis, and on patient level at least 0.66 for disease behavior and 0.71 for age at diagnosis.

Conclusions

To our knowledge, this is the first study to explore computable phenotyping algorithms based on clinical narrative text for these complex tasks, where prior inter-annotator agreements ranged from 0.54 to 0.98. There is no statistical evidence for a difference to the performance of human experts on this task. Our findings underline the potential of LLMs for computable phenotyping and may support large-scale cohort analyses from electronic health records and streamline chart review processes in the future.