# Predicting ulcer in H&E images of inflammatory bowel disease using domain-knowledge-driven graph neural network

arXiv: https://arxiv.org/abs/2504.09430 · HTML: https://mlsanity.com/paper/2504.09430/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 9 of its 18 references that are in the map.
- First posted on arXiv 13 Apr 2025.

## Builds on (most cited first, 9 of 9)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images](https://mlsanity.com/paper/2004.09666/) (2020)
- [TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classification](https://mlsanity.com/paper/2106.00908/) (2021)
- [DeeperGCN: All You Need to Train Deeper GCNs](https://mlsanity.com/paper/2006.07739/) (2020)
- [Whole Slide Images are 2D Point Clouds: Context-Aware Survival Prediction using Patch-based Graph Convolutional Networks](https://mlsanity.com/paper/2107.13048/) (2021)
- [MambaMIL: Enhancing Long Sequence Modeling with Sequence Reordering in Computational Pathology](https://mlsanity.com/paper/2403.06800/) (2024)
- [A graph-transformer for whole slide image classification](https://mlsanity.com/paper/2205.09671/) (2022)
- [Interpretable histopathology-based prediction of disease relevant features in Inflammatory Bowel Disease biopsies using weakly-supervised deep learning](https://mlsanity.com/paper/2303.12095/) (2023)

## Built on by (most cited first, 1 of 1)

- [IMILIA: interpretable multiple instance learning for inflammation prediction in IBD from H&E whole slide images](https://mlsanity.com/paper/2512.13440/) (2025)

## Abstract (arXiv)

Inflammatory bowel disease (IBD) involves chronic inflammation of the digestive tract, with treatment options often burdened by adverse effects. Identifying biomarkers for personalized treatment is crucial. While immune cells play a key role in IBD, accurately identifying ulcer regions in whole slide images (WSIs) is essential for characterizing these cells and exploring potential therapeutics. Multiple instance learning (MIL) approaches have advanced WSI analysis but they lack spatial context awareness. In this work, we propose a weakly-supervised model called DomainGCN that employs a graph convolution neural network (GCN) and incorporates domain-specific knowledge of ulcer features, specifically, the presence of epithelium, lymphocytes, and debris for WSI-level ulcer prediction in IBD. We demonstrate that DomainGCN outperforms various state-of-the-art (SOTA) MIL methods and show the added value of domain knowledge.