Towards deep-learning based detection and quantification of intestinal metaplasia on digitized gastric biopsies: a multi-expert comparative study
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| Main Authors: | , , , , , , , , , , , |
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| Format: | Preprint |
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2025
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| author | Cano, Fabian Caviedes, Mauricio Siabatto, Andres Villarreal, Jesus Quijano, Jose Bedoya-Urresta, Álvaro Bedoya, Marino Coral Caicedo, Yomaira Yepez Cruz-Roa, Angel González, Fabio A. Viswanath, Satish E. Romero, Eduardo |
| author_facet | Cano, Fabian Caviedes, Mauricio Siabatto, Andres Villarreal, Jesus Quijano, Jose Bedoya-Urresta, Álvaro Bedoya, Marino Coral Caicedo, Yomaira Yepez Cruz-Roa, Angel González, Fabio A. Viswanath, Satish E. Romero, Eduardo |
| contents | Current gastric cancer (GCa) risk systems are prone to errors since they evaluate a visual estimation of intestinal metaplasia percentages in histopathology images of gastric mucosa to assign a risk. This study presents an automated method to detect and quantify intestinal metaplasia using deep convolutional neural networks as well as a comparative analysis with visual estimations of three pathologists. Gastric samples were collected from two different cohorts: 149 asymptomatic volunteers from a region with a high prevalence of GCa in Colombia and 56 patients from a tertiary hospital. Deep learning models were trained to classify intestinal metaplasia, and predictions were used to estimate a percentage of intestinal metaplasia and to assign an adapted OLGIM stage. Atrophy was not assessed because of the limited reproducibility among pathologists. Results were compared with independent blinded metaplastic assessments performed by three graduated pathologists. The best-performing deep learning architecture classified intestinal metaplasia with F1-Score of 0.80 +- 0.01 and AUC of 0.91 +- 0.01. Among pathologists, inter-observer agreement by a Fleiss's Kappa score ranged from 0.20 to 0.48. In comparison, agreement between the pathologists and the best-performing model ranged from 0.12 to 0.35. Deep learning models show potential to reliably detect and quantify the percentage of intestinal metaplasia, achieving high classification performance. In practice, visual estimation is still the only available method, yet it is marked by considerable inter-observer variability. Deep learning models provide consistent estimates that could help reduce this subjectivity in risk stratification. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2509_06991 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Towards deep-learning based detection and quantification of intestinal metaplasia on digitized gastric biopsies: a multi-expert comparative study Cano, Fabian Caviedes, Mauricio Siabatto, Andres Villarreal, Jesus Quijano, Jose Bedoya-Urresta, Álvaro Bedoya, Marino Coral Caicedo, Yomaira Yepez Cruz-Roa, Angel González, Fabio A. Viswanath, Satish E. Romero, Eduardo Tissues and Organs Computational Engineering, Finance, and Science Current gastric cancer (GCa) risk systems are prone to errors since they evaluate a visual estimation of intestinal metaplasia percentages in histopathology images of gastric mucosa to assign a risk. This study presents an automated method to detect and quantify intestinal metaplasia using deep convolutional neural networks as well as a comparative analysis with visual estimations of three pathologists. Gastric samples were collected from two different cohorts: 149 asymptomatic volunteers from a region with a high prevalence of GCa in Colombia and 56 patients from a tertiary hospital. Deep learning models were trained to classify intestinal metaplasia, and predictions were used to estimate a percentage of intestinal metaplasia and to assign an adapted OLGIM stage. Atrophy was not assessed because of the limited reproducibility among pathologists. Results were compared with independent blinded metaplastic assessments performed by three graduated pathologists. The best-performing deep learning architecture classified intestinal metaplasia with F1-Score of 0.80 +- 0.01 and AUC of 0.91 +- 0.01. Among pathologists, inter-observer agreement by a Fleiss's Kappa score ranged from 0.20 to 0.48. In comparison, agreement between the pathologists and the best-performing model ranged from 0.12 to 0.35. Deep learning models show potential to reliably detect and quantify the percentage of intestinal metaplasia, achieving high classification performance. In practice, visual estimation is still the only available method, yet it is marked by considerable inter-observer variability. Deep learning models provide consistent estimates that could help reduce this subjectivity in risk stratification. |
| title | Towards deep-learning based detection and quantification of intestinal metaplasia on digitized gastric biopsies: a multi-expert comparative study |
| topic | Tissues and Organs Computational Engineering, Finance, and Science |
| url | https://arxiv.org/abs/2509.06991 |