UMAP fixes

[viclafargue]

No description provided.

[viclafargue]

I also reviewed the smooth_knn_dist_kernel kernel and noticed that one of the loops doesn't account for the first element. Is this because the first distance is expected to be zero (self) in a pairwise search? If so, is this safe for transformations? Despite this, the membership strength values seem to be reasonably in accordance with the KNN dists. However, it might be worth addressing if this turns out to be a genuine issue.

[cjnolet]

I'm still curious about this change- I want to make sure we're not sacrificing the numerical stability by changing this based on limited evidence. What is the reason for changing this?

[viclafargue]

This is a clear mistake here.
Here is the reference implementation : https://github.com/lmcinnes/umap/blob/a012b9d8751d98b94935ca21f278a54b3c3e1b7f/umap/layouts.py#L181

[cjnolet]

Is this because the first distance is expected to be zero (self) in a pairwise search? If so, is this safe for transformations?

Yes, that's exactly why. I've verified this many times in the past and it should be equivalent w/ this logic. We don't remove the self-loop until later to save memory.

[codecov-commenter]

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