stFormer: a foundation model for spatial transcriptomics

Abstract excerpt

Recent foundation models for single-cell transcriptomics data generate informative, context-aware representations for genes and cells. The S patial T ranscriptomics (ST) data offer extra positional insights, which were not considered by these single-cell models. Here, we introduce stFormer, a transformer model tailored for ST data. stFormer employs the cross-attention module to incorporate spatial ligand genes i...

Topics

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• Brain
• COVID-19
• Mice
• Neural Networks, Computer
• Sequence Analysis, RNA
• Single-Cell Analysis
• Single-Cell Gene Expression Analysis
• Transcriptome

Identifiers and source

Literature Corpus work

b52fa3c9-12e8-54cd-9c84-8d61ccf66da8

DOI

10.1101/2024.09.27.615337