stFormer integrates spatial ligand signaling into a foundation model for spatial transcriptomics

Cao et al. (Cell Reports Methods 2026): stFormer, a transformer for spatial transcriptomics that adds spatial ligand genes via cross-attention; pretrained on ~4.1 million spatial samples from public human Visium data; the abstract reports gains over scFoundation on clustering, batch correction, cell-type and gene-function prediction, and in silico perturbation of ligand-receptor signalling, plus two case studies.

Authors / organisation

Cao S, Yang K, Cheng J, Li J, Shen H-B, Pan X, Yuan Y.

Venue

Cell Reports Methods

Date

2026-09-30

Type

paper

Year

2026

DOI

10.1016/j.crmeth.2026.101612

PMID

42815472

Verification

Crossref (title, 7 authors, 2026-09, article 101612) + Europe PMC (PMID 42815472, first publication 2026-09-30, abstract); Technology Networks 2026-10-13 (CAS press story) used only as lead; full text not read

Foundation modelIn-silico perturbationspatial-transcriptomicsligand-receptor

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