Ontology highlight
ABSTRACT:
SUBMITTER: Lause J
PROVIDER: S-EPMC10996625 | biostudies-literature | 2024 Mar
REPOSITORIES: biostudies-literature
Lause Jan J Kobak Dmitry D Berens Philipp P
bioRxiv : the preprint server for biology 20240731
A recent paper in <i>PLOS Computational Biology</i> (Chari and Pachter, 2023) claimed that <i>t</i> -SNE and UMAP embeddings of single-cell datasets 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 eleph ...[more]