Hybrid NLP–LLM framework extracts Montreal classification in IBD reports, suggesting efficient phenotyping methods.
Background The Montreal classification is fundamental for phenotyping inflammatory bowel disease (IBD), yet these descriptors are rarely structured in routine colonoscopy reports. Manual extraction is labor-intensive, and keyword-based natural language processing (NLP) often fails in complex narrative text. We developed and validated a hybrid NLP–large language model (LLM) framework to automatically extract Montreal categories from free-text reports and applied it to a large real-world cohort. Methods Colonoscopy narratives from IBD patients (2020–2025) at a tertiary center were analyzed. A 300-report test set (150 ulcerative colitis [UC], 150 Crohn’s disease [CD]) was manually annotated as gold standard. A rule-based NLP pipeline identified segmental pathology descriptors and mapped them to Montreal extent (E1–E3) and location (L1–L3). Incomplete examinations were coded as E2* or L2* to denote left-sided colitis or colonic CD in which the proximal colon could not be fully intubated. An LLM was prompted to infer Montreal classification directly from the narrative. Accuracy, macro F1-score, and Cohen’s κ were calculated. Distributional agreement between NLP and LLM outputs was evaluated using Jensen–Shannon (JS) similarity. The validated NLP pipeline was applied to 2,150 real-world reports. Results In the test set, the LLM achieved 74% accuracy, macro F1 0.76, and κ = 0.71, with expected adjacent-class drift (E2↔E3; L1/L2↔L3). In the real-world cohort, ulcerative colitis (UC, n = 844) exhibited the following distribution of Montreal extent: E1 9.6%, E2 27.4%, E2* 5.8%, E3 33.5%, and unknown (UNK) 23.7%. Crohn’s disease (CD, n = 1,306) showed the following Montreal location distribution: L1 26.7%, L2 11.7%, L2* 7.4%, L3 16.4%, and UNK 37.8%. Overall, Montreal categories were classifiable in 67.7% of reports; remaining UNK cases reflected normal mucosa or insufficient segmental information. Cross-model comparison demonstrated strong distributional agreement between LLM and NLP outputs (JS similarity 0.82), indicating convergent Montreal phenotyping across independent computational methods. Conclusion A hybrid NLP–LLM approach enables accurate and scalable extraction of the Montreal classification from routine colonoscopy narratives. This framework supports automated real-world IBD phenotyping, accelerates digital registry development, and provides a foundation for large-scale phenotypic research without relying on structured reporting. Conflict of interest: Dr. Agargun, Besim Fazil: No conflict of interest Genc Ulucecen, Sezen: No conflict of interest Dağcı, Gizem: No conflict of interest Yağlı, Mehmet Akif: No conflict of interest Gurbanov, Asım: No conflict of interest Telli, Pelin: No conflict of interest Mammadov, Sabuhi: No conflict of interest Bilgin, Ersel: No conflict of interest Cavus, Bilger: No conflict of interest Ormeci Çifcibaşi, Asli: No conflict of interest Demir, Kadir: No conflict of interest Besisik, Fatih: No conflict of interest Kaymakoglu, Sabahattin: No conflict of interest Akyüz, Filiz: No conflict of interest
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