# SurGen: 1020 H&E-stained Whole Slide Images With Survival and Genetic Markers

arXiv: https://arxiv.org/abs/2502.04946 · HTML: https://mlsanity.com/paper/2502.04946/

## Key facts

- Cited by 8 papers in the map (data through 14 Oct 2026).
- Builds on 18 of its 91 references that are in the map.
- First posted on arXiv 7 Feb 2025.

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

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Scaling Vision Transformers to Gigapixel Images via Hierarchical Self-Supervised Learning](https://mlsanity.com/paper/2206.02647/) (2022)
- [Multimodal Whole Slide Foundation Model for Pathology](https://mlsanity.com/paper/2411.19666/) (2024)
- [Virchow2: Scaling Self-Supervised Mixed Magnification Models in Pathology](https://mlsanity.com/paper/2408.00738/) (2024)
- [Benchmarking Self-Supervised Learning on Diverse Pathology Datasets](https://mlsanity.com/paper/2212.04690/) (2022)
- [Phikon-v2, A large and public feature extractor for biomarker prediction](https://mlsanity.com/paper/2409.09173/) (2024)
- [A Multimodal Knowledge-enhanced Whole-slide Pathology Foundation Model](https://mlsanity.com/paper/2407.15362/) (2024)
- [Hibou: A Family of Foundational Vision Transformers for Pathology](https://mlsanity.com/paper/2406.05074/) (2024)
- [Molecular-driven Foundation Model for Oncologic Pathology](https://mlsanity.com/paper/2501.16652/) (2025)
- [RudolfV: A Foundation Model by Pathologists for Pathologists](https://mlsanity.com/paper/2401.04079/) (2024)
- [Computational Pathology at Health System Scale -- Self-Supervised Foundation Models from Three Billion Images](https://mlsanity.com/paper/2310.07033/) (2023)
- [Towards Large-Scale Training of Pathology Foundation Models](https://mlsanity.com/paper/2404.15217/) (2024)
- [PLUTO: Pathology-Universal Transformer](https://mlsanity.com/paper/2405.07905/) (2024)
- [PathoDuet: Foundation Models for Pathological Slide Analysis of H&E and IHC Stains](https://mlsanity.com/paper/2312.09894/) (2023)
- [Efficient Quality Control of Whole Slide Pathology Images with Human-in-the-loop Training](https://mlsanity.com/paper/2409.19587/) (2024)
- [Domain-specific optimization and diverse evaluation of self-supervised models for histopathology](https://mlsanity.com/paper/2310.13259/) (2023)

## Built on by (most cited first, 8 of 8)

- [CARE: A Molecular-Guided Foundation Model with Adaptive Region Modeling for Whole Slide Image Analysis](https://mlsanity.com/paper/2602.21637/) (2026)
- [Ensemble learning of pathology foundation models for precision oncology](https://mlsanity.com/paper/2508.16085/) (2025)
- [nnMIL: A generalizable multiple instance learning framework for computational pathology](https://mlsanity.com/paper/2511.14907/) (2025)
- [A protocol for evaluating robustness to H&E staining variation in computational pathology models](https://mlsanity.com/paper/2603.12886/) (2026)
- [INSIGHT: Spatially resolved survival modelling from routine histology crosslinked with molecular profiling reveals prognostic epithelial-immune axes in stage II/III colorectal cancer](https://mlsanity.com/paper/2512.22262/) (2025)
- [Enabling Progressive Whole-slide Image Analysis with Multi-scale Pyramidal Network](https://mlsanity.com/paper/2602.01951/) (2026)
- [S3-Diff: Structural Semantic Synergy Diffusion Model for High Fidelity Super Resolution of Pathological Images](https://mlsanity.com/paper/2608.03540/) (2026)
- [HERO: Histology Encoder for Robust Representation in Oncology](https://mlsanity.com/paper/2609.35943/) (2026)

## Abstract (arXiv)

Cancer remains one of the leading causes of morbidity and mortality worldwide. Comprehensive datasets that combine histopathological images with genetic and survival data across various tumour sites are essential for advancing computational pathology and personalised medicine. We present SurGen, a dataset comprising 1,020 H&E-stained whole-slide images (WSIs) from 843 colorectal cancer cases. The dataset includes detailed annotations for key genetic mutations (KRAS, NRAS, BRAF) and mismatch repair status, as well as survival data for 426 cases. We illustrate SurGen's utility with a proof-of-concept model that predicts mismatch repair status directly from WSIs, achieving a test area under the receiver operating characteristic curve of 0.8273. These preliminary results underscore the dataset's potential to facilitate research in biomarker discovery, prognostic modelling, and advanced machine learning applications in colorectal cancer and beyond. SurGen offers a valuable resource for the scientific community, enabling studies that require high-quality WSIs linked with comprehensive clinical and genetic information on colorectal cancer. Our initial findings affirm the dataset's capacity to advance diagnostic precision and foster the development of personalised treatment strategies in colorectal oncology. Data available online: https://doi.org/10.6019/S-BIAD1285.