# Contrastive Learning for Predicting Cancer Prognosis Using Gene Expression Values

arXiv: https://arxiv.org/abs/2306.06276 · HTML: https://mlsanity.com/paper/2306.06276/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 7 of its 67 references that are in the map.
- First posted on arXiv 9 Jun 2023.

## Builds on (most cited first, 7 of 7)

- [XGBoost: A Scalable Tree Boosting System](https://mlsanity.com/paper/1603.02754/) (2016)
- [Model-Agnostic Meta-Learning for Fast Adaptation of Deep Networks](https://mlsanity.com/paper/1703.03400/) (2017)
- [Supervised Contrastive Learning](https://mlsanity.com/paper/2004.11362/) (2020)
- [SmoothGrad: removing noise by adding noise](https://mlsanity.com/paper/1706.03825/) (2017)
- [DeepSurv: Personalized Treatment Recommender System Using A Cox Proportional Hazards Deep Neural Network](https://mlsanity.com/paper/1606.00931/) (2016)
- [Keystroke Dynamics as Part of Lifelogging](https://mlsanity.com/paper/2010.10144/) (2020)
- [A Scalable Discrete-Time Survival Model for Neural Networks](https://mlsanity.com/paper/1805.00917/) (2018)

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

- [Deep Semi-Supervised Survival Analysis for Predicting Cancer Prognosis](https://mlsanity.com/paper/2601.20729/) (2026)

## Abstract (arXiv)

Recent advancements in image classification have demonstrated that contrastive learning (CL) can aid in further learning tasks by acquiring good feature representation from a limited number of data samples. In this paper, we applied CL to tumor transcriptomes and clinical data to learn feature representations in a low-dimensional space. We then utilized these learned features to train a classifier to categorize tumors into a high- or low-risk group of recurrence. Using data from The Cancer Genome Atlas (TCGA), we demonstrated that CL can significantly improve classification accuracy. Specifically, our CL-based classifiers achieved an area under the receiver operating characteristic curve (AUC) greater than 0.8 for 14 types of cancer, and an AUC greater than 0.9 for 2 types of cancer. We also developed CL-based Cox (CLCox) models for predicting cancer prognosis. Our CLCox models trained with the TCGA data outperformed existing methods significantly in predicting the prognosis of 19 types of cancer under consideration. The performance of CLCox models and CL-based classifiers trained with TCGA lung and prostate cancer data were validated using the data from two independent cohorts. We also show that the CLCox model trained with the whole transcriptome significantly outperforms the Cox model trained with the 21 genes of Oncotype DX that is in clinical use for breast cancer patients. CL-based classifiers and CLCox models for 19 types of cancer are publicly available and can be used to predict cancer prognosis using the RNA-seq transcriptome of an individual tumor. Python codes for model training and testing are also publicly accessible, and can be applied to train new CL-based models using gene expression data of tumors.