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DOT: a flexible multi-objective optimization framework for transferring features across single-cell and spatial omics

Single-cell transcriptomics and spatially-resolved imaging/sequencing technologies have revolutionized biomedical research. However, they suffer from lack of spatial information and a trade-off of resolution and gene coverage, respectively. We propose DOT, a multi-objective optimization framework fo...

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Bibliographic Details
Main Authors: Rahimi, Arezou (Author) , Vale Silva, Luis A. (Author) , Fälth Savitski, Maria (Author) , Tanevski, Jovan (Author) , Sáez Rodríguez, Julio (Author)
Format: Article (Journal)
Language:English
Published: 11 June 2024
In: Nature Communications
Year: 2024, Volume: 15, Pages: 1-15
ISSN:2041-1723
DOI:10.1038/s41467-024-48868-z
Online Access:Verlag, kostenfrei, Volltext: https://doi.org/10.1038/s41467-024-48868-z
Verlag, kostenfrei, Volltext: https://www.nature.com/articles/s41467-024-48868-z
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Author Notes:Arezou Rahimi, Luis A. Vale-Silva, Maria Fälth Savitski, Jovan Tanevski & Julio Saez-Rodriguez
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Summary:Single-cell transcriptomics and spatially-resolved imaging/sequencing technologies have revolutionized biomedical research. However, they suffer from lack of spatial information and a trade-off of resolution and gene coverage, respectively. We propose DOT, a multi-objective optimization framework for transferring cellular features across these data modalities, thus integrating their complementary information. DOT uses genes beyond those common to the data modalities, exploits the local spatial context, transfers spatial features beyond cell-type information, and infers absolute/relative abundance of cell populations at tissue locations. Thus, DOT bridges single-cell transcriptomics data with both high- and low-resolution spatially-resolved data. Moreover, DOT combines practical aspects related to cell composition, heterogeneity, technical effects, and integration of prior knowledge. Our fast implementation based on the Frank-Wolfe algorithm achieves state-of-the-art or improved performance in localizing cell features in high- and low-resolution spatial data and estimating the expression of unmeasured genes in low-coverage spatial data.
Item Description:Gesehen am 20.01.2025
Physical Description:Online Resource
ISSN:2041-1723
DOI:10.1038/s41467-024-48868-z

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