# Global Context-aware Representation Learning for Spatially Resolved Transcriptomics

arXiv: https://arxiv.org/abs/2506.15698 · HTML: https://mlsanity.com/paper/2506.15698/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 11 of its 45 references that are in the map.
- First posted on arXiv 28 May 2025.

## Builds on (most cited first, 11 of 11)

- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Unsupervised Learning of Visual Features by Contrasting Cluster Assignments](https://mlsanity.com/paper/2006.09882/) (2020)
- [Deep Graph Infomax](https://mlsanity.com/paper/1809.10341/) (2018)
- [Unsupervised Deep Embedding for Clustering Analysis](https://mlsanity.com/paper/1511.06335/) (2015)
- [Prototypical Contrastive Learning of Unsupervised Representations](https://mlsanity.com/paper/2005.04966/) (2020)
- [Deep Graph Contrastive Representation Learning](https://mlsanity.com/paper/2006.04131/) (2020)
- [Large-Scale Representation Learning on Graphs via Bootstrapping](https://mlsanity.com/paper/2102.06514/) (2021)
- [From Canonical Correlation Analysis to Self-supervised Graph Neural Networks](https://mlsanity.com/paper/2106.12484/) (2021)

## Abstract (arXiv)

Spatially Resolved Transcriptomics (SRT) is a cutting-edge technique that captures the spatial context of cells within tissues, enabling the study of complex biological networks. Recent graph-based methods leverage both gene expression and spatial information to identify relevant spatial domains. However, these approaches fall short in obtaining meaningful spot representations, especially for spots near spatial domain boundaries, as they heavily emphasize adjacent spots that have minimal feature differences from an anchor node. To address this, we propose Spotscape, a novel framework that introduces the Similarity Telescope module to capture global relationships between multiple spots. Additionally, we propose a similarity scaling strategy to regulate the distances between intra- and inter-slice spots, facilitating effective multi-slice integration. Extensive experiments demonstrate the superiority of Spotscape in various downstream tasks, including single-slice and multi-slice scenarios. Our code is available at the following link: https: //github.com/yunhak0/Spotscape.