# HIEGNet: A Heterogenous Graph Neural Network Including the Immune Environment in Glomeruli Classification

arXiv: https://arxiv.org/abs/2506.02542 · HTML: https://mlsanity.com/paper/2506.02542/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 18 of its 39 references that are in the map.
- First posted on arXiv 3 Jun 2025.

## Builds on (most cited first, 18 of 18)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Modeling Relational Data with Graph Convolutional Networks](https://mlsanity.com/paper/1703.06103/) (2017)
- [EfficientNetV2: Smaller Models and Faster Training](https://mlsanity.com/paper/2104.00298/) (2021)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [Representation Learning on Graphs with Jumping Knowledge Networks](https://mlsanity.com/paper/1806.03536/) (2018)
- [How Attentive are Graph Attention Networks?](https://mlsanity.com/paper/2105.14491/) (2021)
- [SchNet: A continuous-filter convolutional neural network for modeling quantum interactions](https://mlsanity.com/paper/1706.08566/) (2017)
- [Whole-Slide Mitosis Detection in H&E Breast Histology Using PHH3 as a Reference to Train Distilled Stain-Invariant Convolutional Networks](https://mlsanity.com/paper/1808.05896/) (2018)
- [A Survey on Graph-Based Deep Learning for Computational Histopathology](https://mlsanity.com/paper/2107.00272/) (2021)
- [Towards Histopathological Stain Invariance by Unsupervised Domain Augmentation using Generative Adversarial Networks](https://mlsanity.com/paper/2012.12413/) (2020)
- [Graph Neural Networks in Histopathology: Emerging Trends and Future Directions](https://mlsanity.com/paper/2406.12808/) (2024)
- [HistoStarGAN: A Unified Approach to Stain Normalisation, Stain Transfer and Stain Invariant Segmentation in Renal Histopathology](https://mlsanity.com/paper/2210.09798/) (2022)
- [Resource Efficient Multi-stain Kidney Glomeruli Segmentation via Self-supervision](https://mlsanity.com/paper/2412.15389/) (2024)

## Abstract (arXiv)

Graph Neural Networks (GNNs) have recently been found to excel in histopathology. However, an important histopathological task, where GNNs have not been extensively explored, is the classification of glomeruli health as an important indicator in nephropathology. This task presents unique difficulties, particularly for the graph construction, i.e., the identification of nodes, edges, and informative features. In this work, we propose a pipeline composed of different traditional and machine learning-based computer vision techniques to identify nodes, edges, and their corresponding features to form a heterogeneous graph. We then proceed to propose a novel heterogeneous GNN architecture for glomeruli classification, called HIEGNet, that integrates both glomeruli and their surrounding immune cells. Hence, HIEGNet is able to consider the immune environment of each glomerulus in its classification. Our HIEGNet was trained and tested on a dataset of Whole Slide Images from kidney transplant patients. Experimental results demonstrate that HIEGNet outperforms several baseline models and generalises best between patients among all baseline models. Our implementation is publicly available at https://github.com/nklsKrmnn/HIEGNet.git.