Graspot: a graph attention network for spatial transcriptomics data integration with optimal transport.

ABSTRACT:

Summary

Spatial transcriptomics (ST) technologies enable the measurement of mRNA expression while simultaneously capturing spot locations. By integrating ST data, the 3D structure of a tissue can be reconstructed, yielding a comprehensive understanding of the tissue's intricacies. Nevertheless, a computational challenge persists: how to remove batch effects while preserving genuine biological structure variations across ST data. To address this, we introduce Graspot, a graph attention network designed for spatial transcriptomics data integration with unbalanced optimal transport. Graspot adeptly harnesses both gene expression and spatial information to align common structures across multiple ST datasets. It embeds multiple ST datasets into a unified latent space, facilitating the p

SUBMITTER: Gao Z 

PROVIDER: S-EPMC11520409 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature