Evaluation of UMAP as an alternative to t-SNE for single-cell data

Becht, E.; Dutertre, C.-A.; Kwok, I. W. H.; Ng, L. G.; Ginhoux, F.; Newell, E. W.

doi:10.1101/298430

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bioRxiv · 10.1101/298430

Evaluation of UMAP as an alternative to t-SNE for single-cell data

Becht, E.·Dutertre, C.-A.·Kwok, I. W. H.·Ng, L. G.·Ginhoux, F.·Newell, E. W.

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Abstract

Uniform Manifold Approximation and Projection (UMAP) is a recently-published non-linear dimensionality reduction technique. Another such algorithm, t-SNE, has been the default method for such task in the past years. Herein we comment on the usefulness of UMAP high-dimensional cytometry and single-cell RNA sequencing, notably highlighting faster runtime and consistency, meaningful organization of cell clusters and preservation of continuums in UMAP compared to t-SNE.

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Becht, E., Dutertre, C.-A., Kwok, I. W. H., Ng, L. G., Ginhoux, F., Newell, E. W.. 2018-04-10. Evaluation of UMAP as an alternative to t-SNE for single-cell data. https://doi.org/10.1101/298430

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