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onkus t1_jbwftny wrote

Doesn’t this also make it essentially impossible to compare the two figures you’ve shown?

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Thog78 t1_jbyh4w1 wrote

What you're looking for when comparing UMAPs is if the local relationships are the same. Try to recognize clusters and see their neighbors, or whether they are distinct or not. A much finer colored clustering based on another reduction (typically PCA) helps with that. Without clustering, you can only try to recognize landmarks from their size and shape.

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