# Spatially Resolved Gene Expression Prediction from Histology via Multi-view Graph Contrastive Learning with HSIC-bottleneck Regularization

arXiv: https://arxiv.org/abs/2406.12229 · HTML: https://mlsanity.com/paper/2406.12229/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 5 of its 21 references that are in the map.
- First posted on arXiv 18 Jun 2024.

## Builds on (most cited first, 5 of 5)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Deep Graph Infomax](https://mlsanity.com/paper/1809.10341/) (2018)
- [Spatially Resolved Gene Expression Prediction from H&E Histology Images via Bi-modal Contrastive Learning](https://mlsanity.com/paper/2306.01859/) (2023)
- [hist2RNA: An efficient deep learning architecture to predict gene expression from breast cancer histopathology images](https://mlsanity.com/paper/2304.04507/) (2023)

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

- [Doloris: Dual Conditional Diffusion Implicit Bridges with Sparsity Masking Strategy for Unpaired Single-Cell Perturbation Estimation](https://mlsanity.com/paper/2506.21107/) (2025)

## Abstract (arXiv)

The rapid development of spatial transcriptomics(ST) enables the measurement of gene expression at spatial resolution, making it possible to simultaneously profile the gene expression, spatial locations of spots, and the matched histopathological images. However, the cost for collecting ST data is much higher than acquiring histopathological images, and thus several studies attempt to predict the gene expression on ST by leveraging their corresponding histopathological images. Most of the existing image-based gene prediction models treat the prediction task on each spot of ST data independently, which ignores the spatial dependency among spots. In addition, while the histology images share phenotypic characteristics with the ST data, it is still challenge to extract such common information to help align paired image and expression representations. To address the above issues, we propose a Multi-view Graph Contrastive Learning framework with HSIC-bottleneck Regularization(ST-GCHB) aiming at learning shared representation to help impute the gene expression of the queried imagingspots by considering their spatial dependency.