# A self-supervised framework for learning whole slide representations

arXiv: https://arxiv.org/abs/2402.06188 · HTML: https://mlsanity.com/paper/2402.06188/

## Key facts

- Cited by 7 papers in the map (data through 14 Oct 2026).
- Builds on 37 of its 64 references that are in the map.
- First posted on arXiv 9 Feb 2024.

## Builds on (most cited first, 30 of 37)

- [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)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Efficient Estimation of Word Representations in Vector Space](https://mlsanity.com/paper/1301.3781/) (2013)
- [Unsupervised Learning of Visual Features by Contrasting Cluster Assignments](https://mlsanity.com/paper/2006.09882/) (2020)
- [Supervised Contrastive Learning](https://mlsanity.com/paper/2004.11362/) (2020)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [VICReg: Variance-Invariance-Covariance Regularization for Self-Supervised Learning](https://mlsanity.com/paper/2105.04906/) (2021)
- [What Makes for Good Views for Contrastive Learning?](https://mlsanity.com/paper/2005.10243/) (2020)
- [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)
- [A Survey on Contrastive Self-supervised Learning](https://mlsanity.com/paper/2011.00362/) (2020)
- [Dual-stream Multiple Instance Learning Network for Whole Slide Image Classification with Self-supervised Contrastive Learning](https://mlsanity.com/paper/2011.08939/) (2020)
- [Scaling Vision Transformers to Gigapixel Images via Hierarchical Self-Supervised Learning](https://mlsanity.com/paper/2206.02647/) (2022)
- [A Cookbook of Self-Supervised Learning](https://mlsanity.com/paper/2304.12210/) (2023)
- [Whole Slide Images based Cancer Survival Prediction using Attention Guided Deep Multiple Instance Learning Networks](https://mlsanity.com/paper/2009.11169/) (2020)
- [Patch-based Convolutional Neural Network for Whole Slide Tissue Image Classification](https://mlsanity.com/paper/1504.07947/) (2015)
- [Visual Language Pretrained Multiple Instance Zero-Shot Transfer for Histopathology Images](https://mlsanity.com/paper/2306.07831/) (2023)
- [Learnable Fourier Features for Multi-Dimensional Spatial Positional Encoding](https://mlsanity.com/paper/2106.02795/) (2021)
- [Interventional Bag Multi-Instance Learning On Whole-Slide Pathological Images](https://mlsanity.com/paper/2303.06873/) (2023)
- [Deep Learning-based Computational Pathology Predicts Origins for Cancers of Unknown Primary](https://mlsanity.com/paper/2006.13932/) (2020)
- [To Compress or Not to Compress- Self-Supervised Learning and Information Theory: A Review](https://mlsanity.com/paper/2304.09355/) (2023)

## Built on by (most cited first, 7 of 7)

- [PathAlign: A vision-language model for whole slide images in histopathology](https://mlsanity.com/paper/2406.19578/) (2024)
- [Step-Calibrated Diffusion for Biomedical Optical Image Restoration](https://mlsanity.com/paper/2403.13680/) (2024)
- [Super-resolution of biomedical volumes with 2D supervision](https://mlsanity.com/paper/2404.09425/) (2024)
- [PathVQ: Reforming Computational Pathology Foundation Model for Whole Slide Image Analysis via Vector Quantization](https://mlsanity.com/paper/2503.06482/) (2025)
- [MOOZY: A Patient-First Foundation Model for Computational Pathology](https://mlsanity.com/paper/2603.27048/) (2026)
- [Learning Spatial-Preserving Hierarchical Representations for Digital Pathology](https://mlsanity.com/paper/2406.09333/) (2024)
- [Intelligent Histology for Tumor Neurosurgery](https://mlsanity.com/paper/2507.03037/) (2025)

## Abstract (arXiv)

Whole slide imaging is fundamental to biomedical microscopy and computational pathology. Previously, learning representations for gigapixel-sized whole slide images (WSIs) has relied on multiple instance learning with weak labels, which do not annotate the diverse morphologic features and spatial heterogeneity of WSIs. A high-quality self-supervised learning method for WSIs would provide transferable visual representations for downstream computational pathology tasks, without the need for dense annotations. We present Slide Pre-trained Transformers (SPT) for gigapixel-scale self-supervision of WSIs. Treating WSI patches as tokens, SPT combines data transformation strategies from language and vision modeling into a general and unified framework to generate views of WSIs for self-supervised pretraining. SPT leverages the inherent regional heterogeneity, histologic feature variability, and information redundancy within WSIs to learn high-quality whole slide representations. We benchmark SPT visual representations on five diagnostic tasks across three biomedical microscopy datasets. SPT significantly outperforms baselines for histopathologic diagnosis, cancer subtyping, and genetic mutation prediction. Finally, we demonstrate that SPT consistently improves whole slide representations when using off-the-shelf, in-domain, and foundational patch encoders for whole slide multiple instance learning.