continuous UMAP latent space

[spagliarini]

Hi,

I have been using UMAP for cluster visualization for long time now. I would like now to build continuous trajectories using UMAP (what I am trying to represent are words). I have seen this done in some works, and I have been checking the documentation and the paper, but couldn't find the reference to how to build such a representation? Could you give any?

I am talking about something like Fig. 18 here: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008228

Thank you so much!

[lmcinnes]

I think you will want to look into ParametricUMAP (included in this package) by Tim Sainburg (@timsainb). The documentation has some basic mentions of it, but you way also want to look into the paper on Parametric UMAP, and possibly even reach out to Tim directly.

[timsainb]

Hi Silvia,

This is the code for the figure you mentioned: https://github.com/timsainb/avgn_paper/blob/V2/notebooks/05.0-viz-transitions-continuous/english-traj/english-say-day-way-4ms.ipynb https://github.com/timsainb/avgn_paper/blob/V2/notebooks/05.0-viz-transitions-continuous/english-traj/english-words-latent-trajectory.ipynb

All of the figures in that paper are produced by notebooks in that repo. It's a little messy, feel free to email me if you have questions. That code predates parametric umap, but parametric umap would also be a good way of creating the continuous trajectories as Leland mentioned. Those figures are just produced by dragging a sliding window along the spectrogram and projecting each frame in the sliding window.

[spagliarini]

Thank you so much to both of you for the references, and the availability! I will look into them.