The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense.

A recent paper claimed that t-SNE and UMAP embeddings of single-cell datasets are "specious" and fail to capture true biological structure. The authors argued that such embeddings are as arbitrary and as misleading as forcing the data into an elephant shape. Here we show that this conclusion was based on inadequate and limited metrics of embedding quality. More appropriate metrics quantifying neighborhood and class preservation reveal the elephant in the room: while t-SNE and UMAP embeddings of single-cell data do not preserve high-dimensional distances, they can nevertheless provide biologically relevant information.

Informations de copyright

Copyright: © 2024 Lause et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. All used datasets are publicly available (see Table A in S1 Text). Our code in Python is available at https://github.com/berenslab/elephant-in-the-room.

Déclaration de conflit d'intérêts

The authors have declared that no competing interests exist.