topic Re: Problem with the new built-in UMAP feature in Discussions

Problem with the new built-in UMAP feature

Biominer_17 — Sun, 11 Jun 2023 11:31:17 GMT

Hi, I've testing both t-SNE and UMAP embedding features in Jmp Pro 17.1 release. t-SNE performs flawlessly, but UMAP just makes the program closes inmediatly as I run the analysis. Jmp closes suddenly without any error prompt or log, no matter the number of samples analyzed (50, 100, 300, etc) or settled parameters. I actually use the MNIST sample data provided in the former UMAP ADD-in dependent on R. Why does it happen? And how can I fix it? Thanks in advance

Re: Problem with the new built-in UMAP feature

Victor_G — Fri, 07 Apr 2023 10:08:46 GMT

Hi @Biominer_17,

Welcome in the Community !

I tried to reproduce the same analysis on the same dataset (attached) with JMP PRO 17.1, and I got the same results as yours with UMAP : calculations are in progress, and then everything is closed.
Can someone from JMP look at this technical bug ? @MJ ?

In the meantime, I didn't try it, but an add-in has been created in 2019 by @MJ to realize t-SNE and UMAP, perhaps the add-in will be more "robust" and reliable :

Re: Problem with the new built-in UMAP feature

Jeff_Perkinson — Fri, 07 Apr 2023 12:31:19 GMT

I’m sorry to hear that you’re experiencing this crash. Please reach out to Tech Support (support@jmp.com) to ensure this is fully investigated and reported to our development team for correction in a future version.

Re: Problem with the new built-in UMAP feature

MeichenDong — Fri, 07 Apr 2023 15:11:53 GMT

Hi @Biominer_17 ! Thank you for the question! There is a quick solution for this:

on the Multivariate Embedding platform, click UMAP Options, then you will be able to see a set of UMAP-specific parameters. Please check if the parameter "Local Connectivity" has a missing value . there. You could specify the number 1 for "Local Connectivity". Just like the screenshot below.

Please let me know if you still encounter errors/crashes after trying this.

Thank you, @Victor_G and @Jeff_Perkinson ! This issue is fixed for JMP PRO 17.2.

Re: Problem with the new built-in UMAP feature

Biominer_17 — Fri, 07 Apr 2023 16:45:11 GMT

Many thanks for the suggestion

Re: Problem with the new built-in UMAP feature

Biominer_17 — Fri, 07 Apr 2023 16:50:57 GMT

Indeed, I've used the ADD-in many times and worked well. Nevertheless I'm unable to run a R environment in this machine, so I tried the new built-in UMAP to perform some analysis. Thanks for your kindness

Re: Problem with the new built-in UMAP feature

Biominer_17 — Fri, 07 Apr 2023 19:45:21 GMT

Now the issue is gone. For some reason I've omitted that parameter, setting it to 1 has solved the problem. Many thanks to all for your kindness and attention. Thanks for an efficient and quick solution