Custom embedding initialization

Looking at the embedding initialization options, I see ‘random’ and ‘spectral’. Would it be possible to initialize with a custom embedding? And if so, would this embedding be at all preserved?

In trying to compare the effect of different parameter changes, it could be helpful to use the embedding of a previous run as the initialization to a new UMAP instance with slightly different parameters. For example, these two min_dist values result in embeddings with different global orientations but similar local relationships.

[kylemcdonald]

great! it works!

the only hurdle i had to get across: t-SNE tends towards larger embeddings than umap. for example, t-SNE with default parameters embeds MNIST into a +/-35 range while UMAP is closer to +/-15. so initializing with the raw output of t-SNE produces some minor artifacts. once i scale the t-SNE output closer to the UMAP output it works better.

some gifs for your trouble:

https://www.dropbox.com/s/wbv73swh6qlrexg/mnist-all-init-0.8.gif?dl=0

this one is UMAP with min_dist=0.8 and initialized with a t-SNE embedding scaled by 0.4.

https://www.dropbox.com/s/cufrbjsbm79a3kh/mnist-all-init.gif?dl=0

this one is UMAP with default parameters also initialized with a t-SNE embedding scaled by 0.4.

the final embeddings of both are normalized uniformly across both axes to fill the screen with a little padding.

[lmcinnes]

That’s a great idea for making the comparison clear. It certainly raises the priority on getting the custom initialisation done!