A comprehensive multimodal dataset and benchmark for ulcerative colitis scoring in endoscopy
Authors: Noha Ghatwary, Jiangbei Yue, Ahmed Elgendy, Hanna Nagdy, Ahmed Galal, Hayam Fathy, Hussein El-Amin, Venkataraman Subramanian, Noor Mohammed, Gilberto Ochoa-Ruiz, Sharib Ali
Organizations: Computer Engineering Department, Arab Academy for Science and Technology,Smart Village, Giza, Egypt · AI in Medicine and Surgery group, School of Computer Science, University of Leeds, LS2 9JT, Leeds, United Kingdom · Department of Electrical and Computer Engineering, Queen’s University, Canada · Internal Medicine Department, College of Medicine, Arab Academy for Science and Technology, Egypt · Internal medicine, Alexandria University, Egypt · Internal medicine, Division Hepatogastroenterology, Assiut university, Egypt · Leeds Teaching Hospital NHS Trust, Leeds, United Kingdom · School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Mexico
Ulcerative colitis (UC) is a chronic mucosal inflammatory condition that places patients at increased risk of colorectal cancer. Colonoscopic surveillance remains the gold standard for assessing disease activity, and reporting typically relies on standardised endoscopic scoring metrics. The most widely used is the Mayo Endoscopic Score (MES), with some centres also adopting the Ulcerative Colitis Endoscopic Index of Severity (UCEIS). Both are descriptive assessments of mucosal inflammation (MES: 0 to 3; UCEIS: 0 to 8), where higher values indicate more severe disease. However, computational methods for automatically predicting these scores remain limited, largely due to the lack of publicly available expert-annotated datasets and the absence of robust benchmarking. There is also a significant research gap in generating clinically meaningful descriptions of UC images, despite image captioning being a well-established computer vision task. Variability in endoscopic systems and procedural workflows across centres further highlights the need for multi-centre datasets to ensure algorithmic robustness and generalisability. In this work, we introduce a curated multi-centre, multi-resolution dataset that includes expert-validated MES and UCEIS labels, alongside detailed clinical descriptions. To our knowledge, this is the first comprehensive dataset that combines dual scoring metrics for classification tasks with expert-generated captions describing mucosal appearance and clinically accepted reasoning for image captioning. This resource opens new opportunities for developing clinically meaningful multimodal algorithms. In addition to the dataset, we also provide benchmarking using convolutional neural networks, vision transformers, hybrid models, and widely used multimodal vision-language captioning algorithms.
Figures & tables
UCEIS-0
UCEIS-1
UCEIS-2
UCEIS-3
UCEIS-4
UCEIS-5
UCEIS-6
UCEIS-7
UCEIS-8
Total
MES-0
285
6
3
0
0
0
0
0
0
294
MES-1
4
202
252
45
15
5
1
0
0
524
MES-2
1
0
129
319
254
124
81
0
0
908
MES-3
0
0
2
7
24
221
173
150
192
769
Total
290
208
386
371
293
350
255
150
192
2495
Table 1: Distribution of the MES and UCEIS scores for the full dataset comprised of 2945 images total from the three Subsets. Each value indicate the number of images in each score combination.
Figure 1: Distribution of MES and UCEIS scores categories across three Subsets for the full dataset. The inner ring represents the MES-score distribution while the outer ring represents the UCEIS distribution each with corresponding percentages. The total number of images per subset is shown in the center of the chart
Figure 2: Representative sample for different MES score across the three subsets. Rows presents the MES Scores (MES-0, MES-1, MES-2 and MES-3) while columns presents the three Subsets consecutively
Figure 3: Overview of annotation pipeline, illustrating features selected by gastroenterologist and the generation of descriptive caption.
Figure 4: Sample images from the dataset with captions presenting different grades of MES score with varied properties
Model
Top-1 Accuracy
F1-score
AUC
Sensitivity
Specificity
PPV
ResNet50 [ 8 ]
0.6013
0.4934
0.6798
0.5101
0.8496
0.5023
SwinTransform [ 17 ]
0.6720
0.5878
0.7339
0.5953
0.8725
0.6128
DINOv2_Large [ 22 ]
0.7138
0.6592
0.7694
0.6477
0.8911
0.6746
DINOv2 [ 22 ]
0.6945
0.5998
0.7448
0.6033
0.8863
0.6198
DINOv3 [ 25 ]
0.6881
0.6066
0.7467
0.6098
0.8837
0.6126
ViT [ 6 ]
0.6624
0.5543
0.7289
0.5839
0.8738
0.5707
Table 2: Performance evaluation of SOTA classification methods of MES scoring on 311 low-resolution test samples similar to the challenge leaderboard. Top two values are presented in bold. Results present, Top-1 Accuracy, F1-Score, AUC: Area Under Curve, Sensitivity, Specificity and PPV: positive predictive value
Model
MES-0
MES-1
MES-2
MES-3
SEN
SPE
PPV
SEN
SPE
PPV
SEN
SPE
PPV
SEN
SPE
PPV
ResNet50 [ 8 ]
0.667
0.913
0.500
0.313
0.858
0.364
0.211
0.933
0.414
0.851
0.694
0.732
SwinTransform [ 17 ]
0.806
0.942
0.644
0.375
0.955
0.686
0.298
0.886
0.370
0.903
0.707
0.751
DINOv2_Large [ 22 ]
0.722
0.975
0.788
0.547
0.915
0.625
0.439
0.898
0.490
0.883
0.777
0.795
DINOv2 [ 22 ]
0.667
0.960
0.686
0.609
0.854
0.520
0.228
0.941
0.464
0.909
0.790
0.809
DINOv3 [ 25 ]
0.750
0.949
0.659
0.453
0.915
0.580
0.333
0.894
0.413
0.903
0.777
0.799
Table 3: Performance evaluation of SOTA classification methods for each MES Category (MES-0, MES-1, MES-3 and MES-3) scoring on 311 low-resolution test samples. Top two values are presented in bold. Results present, SEN: Sensitivity, SPE: Specificity and PPV: positive predictive value
Model
Cosine Similarity
BLEU-1
BLEU-4
METEOR
ROUGE-1
ROUGE-L
BLIP-Base [ 13 ]
0.7590
0.7887
0.6573
0.8124
0.8338
0.8298
BLIP-Large [ 13 ]
0.7977
0.8210
0.6960
0.8435
0.8615
0.8574
Table 4: Performance evaluation of SOTA captioning methods on 311 low-resolution test samples.
Medical image benchmarks compare AI methods on curated clinical images, tasks, and evaluation protocols to measure accuracy, robustness, and clinical usefulness.
Synthesizing longitudinal medical images at controllable disease stages while preserving patient-specific anatomy is hindered by the entanglement of pathological textures and structural features. We address this challenge for ulcerative colitis (UC) endoscopy, where severity follows a continuous ordinal progression along the Mayo Endoscopic Score (MES). Our framework, Disentangled Anatomy-Disease Diffusion (DADD), conditions a latent diffusion model on two complementary embeddings: a pretrained image encoder for patient anatomy and a separately trained ordinal embedder for cumulative disease severity. Since image embeddings inevitably capture disease information, we introduce a Feature Purifier, a cross-attention-based erasure mechanism that identifies and suppresses disease-correlated channels, yielding purified anatomical representations. These cleaned anatomy tokens and target disease tokens are injected into the denoising network via a Triple-Pathway Cross-Attention mechanism with resolution-dependent routing gates. This architecture leverages the U-Net hierarchy, in which different network depths encode global structure versus fine-grained pathological texture. Furthermore, we introduce Delta Steering, a training-free directional signal derived from the ordinal embeddings that enables explicit, single-pass control over disease transitions at inference without requiring additional forward passes. Validated on the LIMUC dataset, our approach produces high-fidelity images across all severity levels and effectively rebalances skewed class distributions, enhancing performance for downstream classification tasks. The dataset is available at zenodo.org/records/5827695 and the code base at github.com/umutdundar99/progressive-stable-diffusion
Umut Dundar, Alptekin Temizel
Graduate School of Informatics Middle East Technical University, Turkey
Histologic assessment of ulcerative colitis (UC) activity is an important endpoint in clinical trials and routine care, but manual grading with indices such as the Nancy histological index (NHI) is time-consuming and prone to observer variability. While computational pathology methods can automate scoring, many approaches depend on dense region-level annotations, which are costly to obtain, particularly in heterogeneous, multicenter cohorts. We propose a weakly supervised multiple instance learning (MIL) approach for whole-slide images that learns from case- and slide-level NHI labels, leveraging foundation models. Our method targets clinically relevant endpoints, including neutrophilic activity and derived Nancy-low/high groupings, enabling full five-grade NHI prediction. On a multicenter dataset of H&E-stained colon biopsies from three hospitals (2019-2025), we evaluate multiple foundation model encoders and aggregation strategies. We find that foundation model choice and resolution substantially affect performance, with Virchow2 providing the most consistent gains, and that a simple ensembling rule improves five-grade NHI prediction compared to a hierarchical gating baseline. Overall, our results demonstrate that weakly supervised MIL with modern foundation-model representations can provide robust, interpretable UC histology activity assessment in realistic multicenter settings.
Adam Kukučka, Ondřej Fabián, Vít Musil +1
Masaryk University, Faculty of Informatics, Brno, Czech Republic · Institute of Clinical and Experimental Medicine, Prague, Czech Republic
Improving the reliability and completeness of colonoscopic inspection is critical for reducing missed lesions and improving colorectal cancer prevention. Reliable scene understanding is essential for navigation, reconstruction, and assessment of inspection completeness. Anatomical structures such as mucosal folds provide stable geometric cues for endoscope localization, while surgical instruments introduce dynamic occlusions that complicate visual interpretation. However, existing gastrointestinal endoscopy datasets largely focus on disease detection or artifact segmentation, leaving a gap in precise annotations of structural landmarks and instruments. We introduce SegCol, a dataset and benchmark for semantic segmentation of colon fold edges and surgical instruments derived from the EndoMapper dataset. SegCol provides manually annotated pixel-level masks for three instrument classes and thin fold-edge structures across temporally consistent image sequences. It forms the basis of the SegCol Challenge, organized as part of the EndoVis Challenge at MICCAI 2024, evaluating both supervised segmentation and annotation-efficient active learning. We further study segmentation metrics, including Dice, ODS/OIS, AP, and CLDice, under structural perturbations and different object geometries, and analyze participating methods, architectural choices, and active learning strategies. Our findings show that metric behavior strongly depends on target structure, highlighting the need for carefully selected evaluation protocols in endoscopic segmentation. Details are available at https://www.synapse.org/Synapse:syn54124209/wiki/626563, and code at https://github.com/surgical-vision/segcol_challenge.
Xinwei Ju, Rema Daher, Razvan Caramalau +7
UCL Hawkes Institute, University College London, London, UK · Department of Computer Science, University College London, London, UK · Medtronic, London, UK +3