# Contrastive learning-based computational histopathology predict differential expression of cancer driver genes

arXiv: https://arxiv.org/abs/2204.11994 · HTML: https://mlsanity.com/paper/2204.11994/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 8 of its 49 references that are in the map.
- First posted on arXiv 25 Apr 2022.

## Builds on (most cited first, 8 of 8)

- [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)
- [Dual-stream Multiple Instance Learning Network for Whole Slide Image Classification with Self-supervised Contrastive Learning](https://mlsanity.com/paper/2011.08939/) (2020)
- [Pathomic Fusion: An Integrated Framework for Fusing Histopathology and Genomic Features for Cancer Diagnosis and Prognosis](https://mlsanity.com/paper/1912.08937/) (2019)
- [Patch-based Convolutional Neural Network for Whole Slide Tissue Image Classification](https://mlsanity.com/paper/1504.07947/) (2015)
- [AdCo: Adversarial Contrast for Efficient Learning of Unsupervised Representations from Self-Trained Negative Adversaries](https://mlsanity.com/paper/2011.08435/) (2020)
- [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)
- [MITOS-RCNN: A Novel Approach to Mitotic Figure Detection in Breast Cancer Histopathology Images using Region Based Convolutional Neural Networks](https://mlsanity.com/paper/1807.01788/) (2018)

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

- [Regression-based Deep-Learning predicts molecular biomarkers from pathology slides](https://mlsanity.com/paper/2304.05153/) (2023)

## Abstract (arXiv)

Digital pathological analysis is run as the main examination used for cancer diagnosis. Recently, deep learning-driven feature extraction from pathology images is able to detect genetic variations and tumor environment, but few studies focus on differential gene expression in tumor cells. In this paper, we propose a self-supervised contrastive learning framework, HistCode, to infer differential gene expressions from whole slide images (WSIs). We leveraged contrastive learning on large-scale unannotated WSIs to derive slide-level histopathological feature in latent space, and then transfer it to tumor diagnosis and prediction of differentially expressed cancer driver genes. Our extensive experiments showed that our method outperformed other state-of-the-art models in tumor diagnosis tasks, and also effectively predicted differential gene expressions. Interestingly, we found the higher fold-changed genes can be more precisely predicted. To intuitively illustrate the ability to extract informative features from pathological images, we spatially visualized the WSIs colored by the attentive scores of image tiles. We found that the tumor and necrosis areas were highly consistent with the annotations of experienced pathologists. Moreover, the spatial heatmap generated by lymphocyte-specific gene expression patterns was also consistent with the manually labeled WSI.