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 conclusi...
Saved in:
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2024-10-01
|
| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1012403 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850034321997430784 |
|---|---|
| author | Jan Lause Philipp Berens Dmitry Kobak |
| author_facet | Jan Lause Philipp Berens Dmitry Kobak |
| author_sort | Jan Lause |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-008163fc2bc04c30bab1b28d2920cf1f |
| institution | DOAJ |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2024-10-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-008163fc2bc04c30bab1b28d2920cf1f2025-08-20T02:57:52ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582024-10-012010e101240310.1371/journal.pcbi.1012403The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense.Jan LausePhilipp BerensDmitry KobakA 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.https://doi.org/10.1371/journal.pcbi.1012403 |
| spellingShingle | Jan Lause Philipp Berens Dmitry Kobak The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense. PLoS Computational Biology |
| title | The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense. |
| title_full | The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense. |
| title_fullStr | The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense. |
| title_full_unstemmed | The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense. |
| title_short | The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense. |
| title_sort | art of seeing the elephant in the room 2d embeddings of single cell data do make sense |
| url | https://doi.org/10.1371/journal.pcbi.1012403 |
| work_keys_str_mv | AT janlause theartofseeingtheelephantintheroom2dembeddingsofsinglecelldatadomakesense AT philippberens theartofseeingtheelephantintheroom2dembeddingsofsinglecelldatadomakesense AT dmitrykobak theartofseeingtheelephantintheroom2dembeddingsofsinglecelldatadomakesense AT janlause artofseeingtheelephantintheroom2dembeddingsofsinglecelldatadomakesense AT philippberens artofseeingtheelephantintheroom2dembeddingsofsinglecelldatadomakesense AT dmitrykobak artofseeingtheelephantintheroom2dembeddingsofsinglecelldatadomakesense |