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© Research
Publication : Bioinformatics (Oxford, England)

Optimal Transport improves cell-cell similarity inference in single-cell omics data.

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Bioinformatics (Oxford, England) - 14 Feb 2022

Huizing GJ, Peyré G, Cantini L,

Link to Pubmed [PMID] – 35157031

Link to DOI – btac08410.1093/bioinformatics/btac084

Bioinformatics 2022 Feb; 38(8): 2169-77

High-throughput single-cell molecular profiling is revolutionizing biology and medicine by unveiling the diversity of cell types and states contributing to development and disease. The identification and characterization of cellular heterogeneity is typically achieved through unsupervised clustering, which crucially relies on a similarity metric.We here propose the use of Optimal Transport (OT) as a cell-cell similarity metric for single-cell omics data. OT defines distances to compare high-dimensional data represented as probability distributions. To speed up computations and cope with the high-dimensionality of single-cell data, we consider the entropic regularization of the classical OT distance. We then extensively benchmark OT against state-of-the-art metrics over thirteen independent datasets, including simulated, scRNA-seq, scATAC-seq and single-cell DNA methylation data. First, we test the ability of the metrics to detect the similarity between cells belonging to the same groups (e.g. cell types, cell lines of origin). Then, we apply unsupervised clustering and test the quality of the resulting clusters. OT is found to improve cell-cell similarity inference and cell clustering in all simulated and real scRNA-seq data, as well as in scATAC-seq and single-cell DNA methylation data.All our analyses are reproducible through the OT-scOmics Jupyter notebook available at https://github.com/ComputationalSystemsBiology/OT-scOmics.Supplementary data are available at Bioinformatics online.

https://pubmed.ncbi.nlm.nih.gov/35157031