1. Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data
- Author
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Jiayu Su, Jean-Baptiste Reynier, Xi Fu, Guojie Zhong, Jiahao Jiang, Rydberg Supo Escalante, Yiping Wang, Luis Aparicio, Benjamin Izar, David A. Knowles, and Raul Rabadan
- Subjects
Spatial omics ,Spatial prior ,Data imputation ,Cell-type deconvolution ,Dimensionality reduction ,Reference mapping ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Abstract Spatial omics technologies can help identify spatially organized biological processes, but existing computational approaches often overlook structural dependencies in the data. Here, we introduce Smoother, a unified framework that integrates positional information into non-spatial models via modular priors and losses. In simulated and real datasets, Smoother enables accurate data imputation, cell-type deconvolution, and dimensionality reduction with remarkable efficiency. In colorectal cancer, Smoother-guided deconvolution reveals plasma cell and fibroblast subtype localizations linked to tumor microenvironment restructuring. Additionally, joint modeling of spatial and single-cell human prostate data with Smoother allows for spatial mapping of reference populations with significantly reduced ambiguity.
- Published
- 2023
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