Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies
biorxiv(2024)
摘要
Recent advances in spatially-resolved single-omics and multi-omics technologies have led to the emergence of computational tools to detect or predict spatial domains. Additionally, histological images and immunofluorescence (IF) staining of proteins and cell types provide multiple perspectives and a more complete understanding of tissue architecture. Here, we introduce Proust, a scalable tool to predict discrete domains using spatial multi-omics data by combining the low-dimensional representation of biological profiles based on graph-based contrastive self-supervised learning. Our scalable method integrates multiple data modalities, such as RNA, protein, and H&E images, and predicts spatial domains within tissue samples. Through the integration of multiple modalities, Proust consistently demonstrates enhanced accuracy in detecting spatial domains, as evidenced across various benchmark datasets and technological platforms.
### Competing Interest Statement
The authors have declared no competing interest.
* Abeta
: amyloid- beta
AD
: Alzheimer’s disease
ARI
: adjusted Rand index
DLPFC
: dorsolateral prefrontal cortex
H&E
: hematoxylin and eosin
IF
: immunofluorescence
PCA
: Principal component analysis
pTau
: hyperphosphorylated tau
SRT
: spatially-resolved transcriptomics
Visium SPG
: 10x Genomics Visium Spatial Proteogenomics platform
UMAP
: uniform manifold approximation and projection
WM
: white matter
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