Joshua Shapiro
@josh.shapiro.foo
2.9K followers 547 following 402 posts
not ‘Eureka’ but ‘That’s funny…’ Current projects: Biological data and Childhood cancer at ccdatalab.org, part of alexslemonade.org Not governor.
not ‘Eureka’ but ‘That’s funny…’ Current projects: Biological data and Childhood cancer at ccdatalab.org, part of alexslemonade.org Not governor.
![Visualizing how this large number of cellstates relates to another is difficult because the GESs are objects in a very high-dimensional space. The approach that is currently by far most popular in the field is to use stochastic embedding methods that attempt to place cells that are close in gene expression space near each other in a 2-dimensional plane, in particular UMAP
[37] and t-SNE [38]. However, it is well appreciated that proper application of these tools is challenging [39], and that beyond a very rough approximate conservation of nearest neighbor relationships, all other structures in these visualizations are virtually meaningless. In fact, we share the opinion of some in the field that the current usage of t-SNE and UMAP visualizations may be doing more harm than good. Nonetheless, since such visualizations have become the de facto standard in the field, and anticipating the request to see where cells from identical cellstates map in such a visualization, we decided prov](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:7ciou2drgyn5vco6rwojwey5/bafkreiczhbts5bccr24m3zyl52aoeixfgybqi2exk3agunoi5vdrnki67i)
