BMJ Open Gastroenterology最新文献

{"title":"Robust comparative evaluation of 15 natural language processing algorithms to positively identify patients with inflammatory bowel disease from secondary care records.","authors":"Matt Stammers, Markus Gwiggner, Reza Nouraei, Cheryl Metcalf, James Batchelor","doi":"10.1136/bmjgast-2025-001977","DOIUrl":"https://doi.org/10.1136/bmjgast-2025-001977","url":null,"abstract":"<p><strong>Objective: </strong>Natural language processing (NLP) can identify cohorts of patients with inflammatory bowel disease (IBD) from free text. However, limited sharing of code, models, and data sets continues to hinder progress. The aim of this study was to evaluate multiple open-source NLP models for identifying IBD cohorts, reporting on document-to-patient-level classification, while exploring explainability, generalisability, fairness and cost.</p><p><strong>Methods: </strong>15 algorithms were assessed, covering all types of NLP spanning over 50 years of NLP development. Rule-based (regular expressions, spaCy with negation), and vector-based (bag-of-words (BoW), term frequency inverse document frequency (TF IDF), word-2-vector), to transformers: (two sentence-based sBERT models, three bidirectional encoder representations from transformers (BERT) models (distilBERT, BioclinicalBERT, RoBERTa), and five large language models (LLMs): (Mistral-Instruct-v0.3-7B, M42-Health/Llama-v3-8B, Deepseek-R1-Distill-Qwen-v2.5-32B, Qwen-v3-32B, and Deepseek-R1-Distill-Llama-v3-70B). Models were comparatively evaluated based on full confusion matrices, time/environmental costs, fairness, and explainability.</p><p><strong>Results: </strong>A total of 9311 labelled documents were evaluated. The fine-tuned DistilBERT_IBD model achieved the best performance overall (micro F1: 93.54%), followed by sBERT-Base (micro F1: 93.05%); however, specificity was an issue for both: (67.80-64.41%) respectively. LLMs performed well, given that they had never seen the training data (micro F1: 86.47-92.20%), but were comparatively slow (18-300 hours) and expensive. Bias was a significant issue for all effective model types.</p><p><strong>Conclusion: </strong>NLP has undergone significant advancements over the last 50 years. LLMs appear likely to solve the problem of re-identifying patients with IBD from clinical free text sources in the future. Once cost, performance and bias issues are addressed, they and their successors are likely to become the primary method of data retrieval for clinical data warehousing.</p>","PeriodicalId":9235,"journal":{"name":"BMJ Open Gastroenterology","volume":"12 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145273878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Liver fibrosis with persistently normal alanine transaminase levels exhibits a distinct treatment response in MASLD.","authors":"Ling Luo, Congxiang Shao, Long Teng, Shuyu Zhuo, Zhi Dong, Wei Wang, Junzhao Ye, Bihui Zhong","doi":"10.1136/bmjgast-2025-001895","DOIUrl":"https://doi.org/10.1136/bmjgast-2025-001895","url":null,"abstract":"<p><strong>Objective: </strong>Metabolic dysfunction-associated steatotic liver disease (MASLD) presents considerable variability in disease progression and treatment outcomes. We aimed to determine whether specific patterns of liver inflammatory flares are correlated with distinct treatment responses.</p><p><strong>Methods: </strong>We conducted an analysis of a well-characterised prospective cohort involving treatment-naïve MASLD patients from January 2015 to November 2023 at The First Affiliated Hospital of Sun Yat-sen University. Participants underwent a standardised 48-week lifestyle modification programme, with follow-up extending through December 2024. Liver fat content (LFC) was assessed using MRI-based proton density fat fraction (MRI-PDFF), whereas liver stiffness measurements (LSMs) were performed using two-dimensional shear wave elastography at baseline and after 48 weeks.</p><p><strong>Results: </strong>Participants were stratified by alanine transaminase (ALT) and liver fibrosis status: normal ALT/no fibrosis (n=149), elevated ALT/no fibrosis (n=264), normal ALT/fibrosis (n=91) and elevated ALT/fibrosis (n=178). While MRI-PDFF (≥30% LFC decline) and ALT responses (≥17 U/L decrease) did not differ between groups, the elevated ALT/fibrosis group exhibited a significantly higher probability of LSM response (≥1 fibrosis stage improvement) than in the normal ALT/ fibrosis group (53.4% vs 31.9%, p=0.001; OR=2.53, 95% CI: 1.31 to 4.85, p=0.006). Receiver operating characteristic analysis revealed that the cut-offs for weight loss (8.55% vs 4.94%, p=0.023) and LFC reduction (39.85% vs 20.57%, p=0.062) associated with LSM response were higher in patients with normal ALT/fibrosis than in those with elevated ALT/fibrosis.</p><p><strong>Conclusion: </strong>MASLD patients with liver fibrosis and persistently normal ALT levels exhibited a less favourable treatment response to fibrosis than those with elevated ALT levels, necessitating more substantial reductions in steatosis and weight to achieve the desired outcomes.</p>","PeriodicalId":9235,"journal":{"name":"BMJ Open Gastroenterology","volume":"12 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of complete colonoscopy after ischaemic colitis onset on colorectal neoplasm detection in patients without suspected coexistence of colorectal cancer on computed tomography: a retrospective analysis.","authors":"Kengo Kasuga, Yoji Takeuchi, Sakuya Katakai, Ami Hosoi, Megumi Shimizu, Fukiko Yoshinari, Tatsuya Kouga, Ayaki Isshiki, Ayako Matsui, Keisuke Iizuka, Shingo Ishihara, Takashi Ueno, Xing Hua Ma, Takashige Masuo, Toshio Uraoka","doi":"10.1136/bmjgast-2025-001990","DOIUrl":"https://doi.org/10.1136/bmjgast-2025-001990","url":null,"abstract":"<p><strong>Objective: </strong>Ischaemic colitis is the most prevalent form of ischaemic enteritis and represents a major cause of acute lower gastrointestinal bleeding. Although the American College of Gastroenterology's clinical guidelines recommend colonoscopy after ischaemic colitis to screen for colorectal cancer, the actual detection rate of neoplastic lesions in patients without suspected malignancies on CT remains unclear. This study aimed to assess the efficacy of colonoscopy in detecting colorectal neoplasms after the resolution of ischaemic colitis.</p><p><strong>Methods: </strong>This retrospective, single-centre, observational study included patients diagnosed with ischaemic colitis at the Isesaki Municipal Hospital in Japan between 2014 and 2023. Patients with CT-confirmed ischaemic colitis without a suspicion of colorectal cancer were eligible. Clinical data, colonoscopic findings and histopathological results were extracted from medical records. Comparative analyses were conducted between patients who underwent complete colonoscopy and those who did not.</p><p><strong>Results: </strong>Among the 418 patients diagnosed with ischaemic colitis, 396 underwent CT imaging, and 116 underwent subsequent complete colonoscopy. Colorectal polyps were identified in 34.5% (40/116) of the patients, with 75 lesions predominantly located in the right-sided colon. Invasive colorectal carcinoma was detected in 3.4% (4/116) of the patients, along with an additional case of intramucosal carcinoma. Notably, one invasive adenocarcinoma was located proximal to the site of the ischaemic injury. Between the complete colonoscopy and incomplete/no colonoscopy groups, the patients in the incomplete/no colonoscopy group were significantly older, had a higher proportion of poor performance status and were more likely to have used saline laxatives.</p><p><strong>Conclusion: </strong>Colonoscopy after ischaemic colitis revealed a non-negligible prevalence of colorectal neoplasms even in the absence of CT findings suggestive of malignancies. These results underscore the importance of colonoscopy after recovery, particularly in patients without a poor performance status. Further prospective, multicentre studies are warranted to validate these findings and optimise postischaemic colitis management strategies.</p>","PeriodicalId":9235,"journal":{"name":"BMJ Open Gastroenterology","volume":"12 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expression of concern: Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen.","authors":"","doi":"10.1136/bmjgast-2016-000080eoc1","DOIUrl":"https://doi.org/10.1136/bmjgast-2016-000080eoc1","url":null,"abstract":"","PeriodicalId":9235,"journal":{"name":"BMJ Open Gastroenterology","volume":"12 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effectiveness and safety of upadacitinib in a real-world cohort of patients with Crohn's disease in the UK: a multicentre retrospective cohort study.","authors":"Yaa Danso, Chandni Radia, Alex Elford, Jie Han Yeo, Thomas Morris, Chirag Patel, Kimberley Butler, Sonia Kalyanji, Katie Yeung, Chaonan Dong, Karishma Sethi-Arora, Alice Hewitt, Lushen Pillay, Susan Ritchie, Mohammed Allah-Ditta, Lucy Hicks, Phil Harvey, Fiona Rees, Emma Johnston, Ruth Rudling, Charlie Lees, Jennifer Toft, Sara Mccartney, Xinyi Choon, Richard C G Pollok, Dania Al-Zarrad, Melissa Hale, Christopher Andrew Lamb, R Alexander Speight, Jimmy Limdi, Hannah Trodden-Mittnacht, Konstantina Rosiou, Tim Raine, Anjan Dhar, Puneet Chhabra, Nick N Burr, Paul Harrow, Kamal V Patel, Mark Samaan, Polychronis Pavlidis, Alexandra Kent, Klaartje Bel Kok, Christian Selinger","doi":"10.1136/bmjgast-2025-001916","DOIUrl":"10.1136/bmjgast-2025-001916","url":null,"abstract":"<p><strong>Objective: </strong>Upadacitinib is the first Janus kinase inhibitor and oral advanced therapy licensed for Crohn's disease (CD). Following NICE approval in 2023, real-world data on outcomes are limited. The effectiveness and safety of upadacitinib in a cohort of patients with CD was assessed.</p><p><strong>Methods: </strong>A multicentre retrospective cohort analysis across 19 UK hospitals. Adult patients with active CD who started upadacitinib between April 2023 and October 2023 were included. Outcomes were reviewed over 24 weeks. The primary endpoint was clinical remission (Harvey Bradshaw Index (HBI) <4) at 12 and 24 weeks. Biochemical remission (faecal calprotectin <200 μg/g and C-reactive protein ≤5) and endoscopic remission (Simple Endoscopic Score for Crohn's Disease ≤3) were assessed at the same intervals. Adverse events (AEs) were recorded until 24 weeks or drug withdrawal.</p><p><strong>Results: </strong>312 patients were included, with a minimum follow-up of 12 weeks. The cohort had difficult-to-treat disease; 64% failing 3 or more biologics, 51% exhibiting penetrating or stricturing disease and 41% requiring prior resection. 50% (113/227) of patients achieved clinical remission at 12 weeks and 45% (77/172) at 24 weeks. Patients with colonic disease had higher remission rates at 24 weeks compared with other disease locations. At 24 weeks, 51 patients (16%) had discontinued upadacitinib. Treatment persistence was 90.3% at 12 weeks and 84.1% at 24 weeks. 28% had AEs, with 18% experiencing serious AEs and 16.6% requiring hospitalisation.</p><p><strong>Conclusion: </strong>This is a large real-world study reporting outcomes in patients with CD treated with upadacitinib. Our data demonstrated good short-term effectiveness and tolerance in a clinically refractory population.</p>","PeriodicalId":9235,"journal":{"name":"BMJ Open Gastroenterology","volume":"12 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506220/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Association between autoimmune disease and colorectal cancer: a retrospective case-control study of 120 876 patients.","authors":"Sven Heiko Loosen, Frederik Hansen, Tom Luedde, Christoph Roderburg, Karel Kostev","doi":"10.1136/bmjgast-2025-001886","DOIUrl":"10.1136/bmjgast-2025-001886","url":null,"abstract":"<p><strong>Objective: </strong>Colorectal cancer (CRC) is one of the most frequently diagnosed cancers and a leading cause of cancer-related deaths worldwide. While inflammatory bowel disease (IBD) is a well-established risk factor for CRC, the potential link between other autoimmune diseases and CRC is unclear. In light of the growing prevalence of autoimmune diseases and their recognised link to various malignancies, this study seeks to investigate whether different autoimmune diseases are associated with CRC.</p><p><strong>Methods: </strong>A total of 20 146 patients with an initial diagnosis of CRC and 100 730 propensity score-matched cancer-free individuals were identified from the Disease Analyzer database (IQVIA). Univariable conditional logistic regression models were used to examine whether each autoimmune disorder was associated with subsequent CRC diagnosis.</p><p><strong>Results: </strong>Only IBD was significantly associated with CRC (OR 1.53; 95% CI 1.33 to 1.75). Type 1 diabetes, rheumatic diseases, autoimmune thyroiditis, and multiple sclerosis did not show a significant association with CRC. Psoriasis showed a non-significant trend towards an association with CRC (OR 1.11; 95% CI 0.97 to 1.27). Coeliac disease was not associated with the development of CRC (OR 1.06; 95% CI 0.69 to 1.64). A sex-stratified analysis revealed that the association between IBD and CRC was similar in both women (OR 1.48; 95% CI 1.22 to 1.81) and men (OR 1.57; 95% CI 1.29 to 1.89). No significant sex differences for any other autoimmune disease were observed.</p><p><strong>Conclusion: </strong>The presence of IBD, but not any other autoimmune diseases, was significantly associated with a subsequent CRC. This finding serves to emphasise the significance of routine screening for patients suffering from IBD.</p>","PeriodicalId":9235,"journal":{"name":"BMJ Open Gastroenterology","volume":"12 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506172/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145237970","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine learning in gastrointestinal endoscopy: challenges and opportunities.","authors":"Sergejs Lobanovs, Jekaterina Aleksejeva, Alise Kitija Rūtiņa, Eduards Krustiņš, Jurijs Čižovs, Dmitrijs Bļizņuks","doi":"10.1136/bmjgast-2025-001923","DOIUrl":"10.1136/bmjgast-2025-001923","url":null,"abstract":"<p><p>The integration of machine learning (ML) into medical diagnostics has significantly advanced endoscopic examinations for gastrointestinal diseases. By leveraging extensive datasets and sophisticated algorithms, ML technologies enhance diagnostic precision, detect subtle abnormalities, classify diverse pathologies and predict disease progression. However, their widespread adoption is hindered by the inherent heterogeneity of gastrointestinal diseases, technical limitations, limited generalisability across different populations and ethical challenges related to patient privacy, data security and algorithmic bias.This review provides a comprehensive structural analysis of ML approaches in endoscopy, starting with an overview of the classical endoscopic methodology that relies on direct visualisation of the gastrointestinal tract for diagnosis and therapeutic interventions. Then, current ML applications that hold promise for reducing physician-dependent variability, improving diagnostic accuracy and streamlining procedural workflows were explored. Despite these advances, the effectiveness of ML models often remains constrained by the quality and diversity of training data, which can undermine both reliability and generalisability.Ethical considerations - such as safeguarding patient information, upholding data security and mitigating biases embedded in algorithms - are integral to responsibly deploying ML in clinical settings. By examining these technical and ethical barriers, this work contributes to the evolving discourse on integrating advanced ML techniques into gastroenterology. Ultimately, our goal is to pave the way for more effective and reliable ML-driven endoscopic practices that will enhance disease detection, optimise patient care and benefit healthcare providers worldwide.</p>","PeriodicalId":9235,"journal":{"name":"BMJ Open Gastroenterology","volume":"12 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12496122/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and validation of the FR-QoL-29-Dutch (Flemish) Questionnaire and assessment of clinical factors associated with food-related quality of life in a Belgian inflammatory bowel disease population: a cross-sectional study.","authors":"Judith Wellens, Livia Guadagnoli, Julie Vanderstappen, Sien Hoekx, Justine Vandaele, Bram Verstockt, Marc Ferrante, Kevin Whelan, Séverine Vermeire, João Sabino","doi":"10.1136/bmjgast-2025-001940","DOIUrl":"10.1136/bmjgast-2025-001940","url":null,"abstract":"<p><strong>Objective: </strong>Food-related quality of life (FR-QoL) is the psychosocial impact of food, nutrition, eating and drinking on QoL and can be profoundly affected by inflammatory bowel disease (IBD). We aimed to translate and validate the FR-QoL-29 Questionnaire in a Belgian IBD population and investigate associations with relevant clinical variables.</p><p><strong>Methods: </strong>The English FR-QoL-29 was translated to Dutch using the forward-backward method. Consecutive patients with IBD attending the outpatient clinic in a university hospital in Belgium completed the FR-QoL-29 Dutch (Flemish), alongside questionnaires assessing disease severity and IBD-related disability. Clinical and biochemical data were collected. Exploratory factor analysis (EFA) with promax rotation assessed the underlying factor structure. Reliability measures (internal consistency, test-retest reliability) were evaluated. Pearson and Spearman correlations assessed relationships between FR-QoL-29 Score and continuous demographic and clinical variables, while categorical parameters were analysed using independent t-tests and one-way analysis of variance with Tukey post hoc tests.</p><p><strong>Results: </strong>301 patients were included, with 31 (10.3%) completing the retest. EFA revealed a one-factor structure explaining 55% of the variance. The FR-QoL-29-Dutch (Flemish) showed excellent internal consistency (Cronbach's α=0.97) and very good test-retest reliability (intraclass correlation=0.94). Lower FR-QoL-29 Score was associated with higher serum albumin levels, younger age, disease activity and IBD-related disability. FR-QoL-29 Score was lower in females, those with Crohn's disease (CD), CD patients with a stricturing phenotype and those previously receiving IBD-related surgery.</p><p><strong>Conclusion: </strong>The FR-QoL-29-Dutch (Flemish) is valid and reliable and correlates with disease activity and IBD-related disability. Patients with CD, stricturing disease and who previously underwent IBD-related surgery have a significantly lower FR-QoL and should be targeted for support.</p>","PeriodicalId":9235,"journal":{"name":"BMJ Open Gastroenterology","volume":"12 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12481406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145191075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Endoscopic ultrasound for pancreatic cystic lesions: a narrative review.","authors":"Lucía Guilabert, Sara Nikolìc, Enrique de-Madaria, Giuseppe Vanella, Gabriele Capurso, Matteo Tacelli, Marcello Maida, Catalina Vladut, Cecilie Siggaard Knoph, Dario Quintini, Gabriele Rancatore, Giuseppe Infantino, Ilaria Tarantino, Giacomo Emanuele Maria Rizzo","doi":"10.1136/bmjgast-2025-001893","DOIUrl":"10.1136/bmjgast-2025-001893","url":null,"abstract":"<p><p>The incidence of incidental pancreatic cystic lesions (PCLs) has risen in recent years, largely due to advances in and increased use of imaging techniques. Endoscopic ultrasound (EUS) has become a crucial tool for evaluating and characterising PCLs, allowing for detailed morphological assessment and aiding in the identification of lesions with a higher risk of progression to high-grade dysplasia or invasive pancreatic carcinoma. This review aims to outline the key aspects of EUS in the evaluation of PCLs, covering a range of modalities from morphological assessment and contrast-enhanced imaging to elastography, fine-needle aspiration for biomarker analysis, cytology, DNA sequencing, histological evaluation and the emerging role of confocal laser endomicroscopy or artificial intelligence. Additionally, we address therapeutic EUS modalities for PCLs, the current limitations of EUS, anticipated technological advancements and the diverse management strategies recommended by leading scientific societies for the clinical handling of PCLs.</p>","PeriodicalId":9235,"journal":{"name":"BMJ Open Gastroenterology","volume":"12 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12481305/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Large language models for extracting histopathologic diagnoses of colorectal cancer and dysplasia from electronic health records.","authors":"Brian Johnson, Tyler Bath, Xinyi Huang, Mark Lamm, Ashley Earles, Hyrum Eddington, Anna M Dornisch, Lily J Jih, Samir Gupta, Shailja C Shah, Kit Curtius","doi":"10.1136/bmjgast-2025-001896","DOIUrl":"10.1136/bmjgast-2025-001896","url":null,"abstract":"<p><strong>Objective: </strong>Accurate data resources are essential for impactful medical research, but available structured datasets are often incomplete or inaccurate. Recent advances in open-weight large language models (LLMs) enable more accurate data extraction from unstructured text in electronic health records (EHRs), however, thorough validation of such approaches is lacking. Our objective was to create a validated approach using LLMs for identifying histopathologic diagnoses in pathology reports from the nationwide Veterans Health Administration (VHA) database, including patients with genotype data within the Million Veteran Program (MVP) biobank.</p><p><strong>Methods: </strong>Our approach utilises search term filtering followed by simple 'yes/no' question prompts for the following phenotypes of interest: any colorectal dysplasia, high-grade dysplasia and/or colorectal adenocarcinoma (HGD/CRC) and invasive CRC. We first developed the LLM prompts using example reports from patients with inflammatory bowel disease (IBD). We then validated the approach in IBD and non-IBD by applying the fixed prompts to a separate corpus of 116 373 pathology reports generated in the VHA between 1999 and 2024. We compared model outputs to blinded manual chart review of 200-300 pathology reports for each patient cohort and diagnostic task, totalling 3816 reviewed reports, and calculated F1 scores as a balanced accuracy measure.</p><p><strong>Results: </strong>In patients with IBD in MVP, we achieved F1-scores of 96.9% (95% CI 94.0% to 99.6%) for identifying dysplasia, 93.7% (88.2%-98.4%) for identifying HGD/CRC and 98% (96.3%-99.4%) for identifying CRC. In patients without IBD in MVP, we achieved F1-scores of 99.2% (98.2%-100%) for identifying any colorectal dysplasia, 96.5% (93.0%-99.2%) for identifying HGD/CRC and 95% (92.8%-97.2%) for identifying CRC using LLM Gemma-2.</p><p><strong>Conclusion: </strong>LLMs provided excellent accuracy in extracting the diagnoses of interest from EHRs. Our validated methods generalised to unstructured pathology notes, even withstanding challenges of resource-limited computing environments. This may, therefore, be a promising approach for other clinical phenotypes given the minimal human-led development required.</p>","PeriodicalId":9235,"journal":{"name":"BMJ Open Gastroenterology","volume":"12 1","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12458811/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145090837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}