Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

Bug: NaN result with projection to 1D latent space

See original GitHub issue

Hi,

thanks for publishing and maintaining this cool project! I played around with UMAP a bit and encountered an oddity: I have a small (n=178) distance matrix that I want to project onto a 1D space. If I run UMAP in version 0.3.0 with the default parameters, sometimes the resulting low-dimensional data consists of NaNs exclusively while sometimes the result seems perfectly fine.

I narrowed it down to the random_state being used, which seems a bit fishy. To reproduce: I call

res = umap.UMAP(
    n_components=1,
    random_state=8, 
    metric='precomputed'
).fit_transform(high_dim_data)

print(numpy.count_nonzero(numpy.isnan(res)))

where high_dim_data is as defined in https://gist.github.com/rmitsch/cd99fcacf6a8f3c0d41af6f903735251.

I didn’t observe this behaviour with n_components > 1, but haven’t checked thoroughly yet. I just tried various values for random_state until I could reproduce the NaN result.

Is this a known problem? I couldn’t find any related issues.

Issue Analytics

State:
Created 5 years ago
Reactions:2
Comments:12 (7 by maintainers)

Top GitHub Comments

2reactions

lmcinnescommented, Aug 17, 2018

I wanted to verify this fixes the issue for others before releasing an update to PyPI (which should be on version 0.3.2 by now anyway – note that you need umap-learn on PyPI). Will try to get an update rolled out soon. Thanks for the feedback and the reproducer everytone – it helped a lot.

On Fri, Aug 17, 2018 at 8:43 AM Raphael Mitsch notifications@github.com wrote:

Fixes my problem. The version currently available on pip (0.1.1) does not contain the fix though, does it? I just copied the changes in your commit by hand for now.

Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lmcinnes/umap/issues/85#issuecomment-413853449, or mute the thread https://github.com/notifications/unsubscribe-auth/ALaKBQyzIqFgIik7z46-pUO_3_NGxnmFks5uRrpVgaJpZM4VS04v .

2reactions

lmcinnescommented, Aug 9, 2018

Fine suggestion. I set a loop running until I got a failure, which is now reproducible with that seed. I’ll try to dig into this soon and see what the actual underlying issues is. Thanks!