# scGTN: Deep Siamese Graph Transformer Network for Single-cell RNA Sequencing Clustering

arXiv: https://arxiv.org/abs/2606.18672 · HTML: https://mlsanity.com/paper/2606.18672/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 10 of its 45 references that are in the map.
- First posted on arXiv 17 Jun 2026.

## Builds on (most cited first, 10 of 10)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning](https://mlsanity.com/paper/1801.07606/) (2018)
- [Unsupervised Deep Embedding for Clustering Analysis](https://mlsanity.com/paper/1511.06335/) (2015)
- [Structural Deep Clustering Network](https://mlsanity.com/paper/2002.01633/) (2020)
- [A Survey of Graph Neural Networks in Real world: Imbalance, Noise, Privacy and OOD Challenges](https://mlsanity.com/paper/2403.04468/) (2024)
- [GLCC: A General Framework for Graph-Level Clustering](https://mlsanity.com/paper/2210.11879/) (2022)
- [scCDCG: Efficient Deep Structural Clustering for single-cell RNA-seq via Deep Cut-informed Graph Embedding](https://mlsanity.com/paper/2404.06167/) (2024)
- [scSiameseClu: A Siamese Clustering Framework for Interpreting single-cell RNA Sequencing Data](https://mlsanity.com/paper/2505.12626/) (2025)
- [CMGL: Confidence-guided Multi-omics Graph Learning for Cancer Subtype Classification](https://mlsanity.com/paper/2604.24201/) (2026)

## Abstract (arXiv)

Single-cell RNA sequencing (scRNA-seq) serves a pivotal role in characterizing gene expression at the cellular level, enabling the identification of cell types and advancing the understanding of cellular heterogeneity. Despite the significant progress in scRNA-seq data clustering, we argue that current methods always ignore the sparsity and noise, as well as the complex intercellular structural information inherent in scRNA-seq data. Toward this end, in this paper, we propose a novel single-cell RNA-seq clustering framework via deep Siamese Graph Transformer Network (termed scGTN), which explicitly integrates gene expression profile and intercellular structural dependencies for cell clustering. In particular, we formulate scRNA-seq data as a graph and construct two augmented graph views that serve as dual views to capture complementary intercellular information. Then, a Siamese graph transformer network is employed to explicitly incorporate shortest-path information and node-wise distances for capturing richer structural relationships between cells. Finally, we employ an optimal transport strategy to guide the cell clustering in a self-supervised manner. Extensive experiments on multiple benchmark scRNA-seq datasets demonstrate that our scGTN consistently outperforms existing methods. Our code is available at https://github.com/W-RMSL/scGTN.