# Self-supervised learning on gene expression data

arXiv: https://arxiv.org/abs/2507.13912 · HTML: https://mlsanity.com/paper/2507.13912/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 14 of its 27 references that are in the map.
- First posted on arXiv 18 Jul 2025.

## Builds on (most cited first, 14 of 14)

- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [TabTransformer: Tabular Data Modeling Using Contextual Embeddings](https://mlsanity.com/paper/2012.06678/) (2020)
- [Understanding Dimensional Collapse in Contrastive Self-supervised Learning](https://mlsanity.com/paper/2110.09348/) (2021)
- [SAINT: Improved Neural Networks for Tabular Data via Row Attention and Contrastive Pre-Training](https://mlsanity.com/paper/2106.01342/) (2021)
- [A Survey on Self-supervised Learning: Algorithms, Applications, and Future Trends](https://mlsanity.com/paper/2301.05712/) (2023)
- [SCARF: Self-Supervised Contrastive Learning using Random Feature Corruption](https://mlsanity.com/paper/2106.15147/) (2021)
- [Self-Supervised Representation Learning: Introduction, Advances and Challenges](https://mlsanity.com/paper/2110.09327/) (2021)
- [LIFT: Language-Interfaced Fine-Tuning for Non-Language Machine Learning Tasks](https://mlsanity.com/paper/2206.06565/) (2022)
- [TransTab: Learning Transferable Tabular Transformers Across Tables](https://mlsanity.com/paper/2205.09328/) (2022)
- [STUNT: Few-shot Tabular Learning with Self-generated Tasks from Unlabeled Tables](https://mlsanity.com/paper/2303.00918/) (2023)
- [A Survey on Self-Supervised Learning for Non-Sequential Tabular Data](https://mlsanity.com/paper/2402.01204/) (2024)
- [Machine Learning Methods for Cancer Classification Using Gene Expression Data: A Review](https://mlsanity.com/paper/2301.12222/) (2023)

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

- [Adversarial Domain Adaptation Enables Knowledge Transfer Across Heterogeneous RNA-Seq Datasets](https://mlsanity.com/paper/2603.08062/) (2026)

## Abstract (arXiv)

Predicting phenotypes from gene expression data is a crucial task in biomedical research, enabling insights into disease mechanisms, drug responses, and personalized medicine. Traditional machine learning and deep learning rely on supervised learning, which requires large quantities of labeled data that are costly and time-consuming to obtain in the case of gene expression data. Self-supervised learning has recently emerged as a promising approach to overcome these limitations by extracting information directly from the structure of unlabeled data. In this study, we investigate the application of state-of-the-art self-supervised learning methods to bulk gene expression data for phenotype prediction. We selected three self-supervised methods, based on different approaches, to assess their ability to exploit the inherent structure of the data and to generate qualitative representations which can be used for downstream predictive tasks. By using several publicly available gene expression datasets, we demonstrate how the selected methods can effectively capture complex information and improve phenotype prediction accuracy. The results obtained show that self-supervised learning methods can outperform traditional supervised models besides offering significant advantage by reducing the dependency on annotated data. We provide a comprehensive analysis of the performance of each method by highlighting their strengths and limitations. We also provide recommendations for using these methods depending on the case under study. Finally, we outline future research directions to enhance the application of self-supervised learning in the field of gene expression data analysis. This study is the first work that deals with bulk RNA-Seq data and self-supervised learning.