Global Context-aware Representation Learning for Spatially Resolved Transcriptomics

TL;DR

Spotscape is a new framework for spatially resolved transcriptomics that captures global relationships between spots, improving the quality of spatial domain representations especially near boundaries.

Contribution

It introduces the Similarity Telescope module and a similarity scaling strategy to enhance multi-slice integration and spatial domain detection.

Findings

Outperforms existing methods in downstream tasks

Effective in single-slice and multi-slice scenarios

Improves spot representations near domain boundaries

Abstract

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.