# Context-aware Skin Cancer Epithelial Cell Classification with Scalable Graph Transformers

arXiv: https://arxiv.org/abs/2602.15783 · HTML: https://mlsanity.com/paper/2602.15783/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 27 of its 44 references that are in the map.
- First posted on arXiv 17 Feb 2026.

## Builds on (most cited first, 27 of 27)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [Simplifying Graph Convolutional Networks](https://mlsanity.com/paper/1902.07153/) (2019)
- [Recipe for a General, Powerful, Scalable Graph Transformer](https://mlsanity.com/paper/2205.12454/) (2022)
- [TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classification](https://mlsanity.com/paper/2106.00908/) (2021)
- [Nystr"omformer: A Nystr"om-Based Algorithm for Approximating Self-Attention](https://mlsanity.com/paper/2102.03902/) (2021)
- [HoVer-Net: Simultaneous Segmentation and Classification of Nuclei in Multi-Tissue Histology Images](https://mlsanity.com/paper/1812.06499/) (2018)
- [Do Transformers Really Perform Bad for Graph Representation?](https://mlsanity.com/paper/2106.05234/) (2021)
- [SIGN: Scalable Inception Graph Neural Networks](https://mlsanity.com/paper/2004.11198/) (2020)
- [NodeFormer: A Scalable Graph Structure Learning Transformer for Node Classification](https://mlsanity.com/paper/2306.08385/) (2023)
- [Pure Transformers are Powerful Graph Learners](https://mlsanity.com/paper/2207.02505/) (2022)
- [SGFormer: Simplifying and Empowering Transformers for Large-Graph Representations](https://mlsanity.com/paper/2306.10759/) (2023)
- [Whole Slide Images are 2D Point Clouds: Context-Aware Survival Prediction using Patch-based Graph Convolutional Networks](https://mlsanity.com/paper/2107.13048/) (2021)
- [CellViT: Vision Transformers for Precise Cell Segmentation and Classification](https://mlsanity.com/paper/2306.15350/) (2023)
- [DIFFormer: Scalable (Graph) Transformers Induced by Energy Constrained Diffusion](https://mlsanity.com/paper/2301.09474/) (2023)
- [A graph-transformer for whole slide image classification](https://mlsanity.com/paper/2205.09671/) (2022)
- [Hierarchical Graph Representations in Digital Pathology](https://mlsanity.com/paper/2102.11057/) (2021)
- [CGC-Net: Cell Graph Convolutional Network for Grading of Colorectal Cancer Histology Images](https://mlsanity.com/paper/1909.01068/) (2019)
- [Amazon-M2: A Multilingual Multi-locale Shopping Session Dataset for Recommendation and Text Generation](https://mlsanity.com/paper/2307.09688/) (2023)
- [HistoCartography: A Toolkit for Graph Analytics in Digital Pathology](https://mlsanity.com/paper/2107.10073/) (2021)
- [Structure Embedded Nucleus Classification for Histopathology Images](https://mlsanity.com/paper/2302.11416/) (2023)
- [Cell Graph Transformer for Nuclei Classification](https://mlsanity.com/paper/2402.12946/) (2024)
- [VOLTA: an Environment-Aware Contrastive Cell Representation Learning for Histopathology](https://mlsanity.com/paper/2303.04696/) (2023)
- [Integrative Graph-Transformer Framework for Histopathology Whole Slide Image Representation and Classification](https://mlsanity.com/paper/2403.18134/) (2024)
- [A New Graph Node Classification Benchmark: Learning Structure from Histology Cell Graphs](https://mlsanity.com/paper/2211.06292/) (2022)
- [Histo-Miner: Deep learning based tissue features extraction pipeline from H&E whole slide images of cutaneous squamous cell carcinoma](https://mlsanity.com/paper/2505.04672/) (2025)

## Abstract (arXiv)

Whole-slide images (WSIs) from cancer patients contain rich information that can be used for medical diagnosis or to follow treatment progress. To automate their analysis, numerous deep learning methods based on convolutional neural networks and Vision Transformers have been developed and have achieved strong performance in segmentation and classification tasks. However, due to the large size and complex cellular organization of WSIs, these models rely on patch-based representations, losing vital tissue-level context. We propose using scalable Graph Transformers on a full-WSI cell graph for classification. We evaluate this methodology on a challenging task: the classification of healthy versus tumor epithelial cells in cutaneous squamous cell carcinoma (cSCC), where both cell types exhibit very similar morphologies and are therefore difficult to differentiate for image-based approaches. We first compared image-based and graph-based methods on a single WSI. Graph Transformer models SGFormer and DIFFormer achieved balanced accuracies of 85.2 ± 1.5 (± standard error) and 85.1 ± 2.5 in 3-fold cross-validation, respectively, whereas the best image-based method reached 81.2 ± 3.0. By evaluating several node feature configurations, we found that the most informative representation combined morphological and texture features as well as the cell classes of non-epithelial cells, highlighting the importance of the surrounding cellular context. We then extended our work to train on several WSIs from several patients. To address the computational constraints of image-based models, we extracted four 2560 × 2560 pixel patches from each image and converted them into graphs. In this setting, DIFFormer achieved a balanced accuracy of 83.6 ± 1.9 (3-fold cross-validation), while the state-of-the-art image-based model CellViT256 reached 78.1 ± 0.5.