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Add LSE-OMNI #550

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bdpedigo opened this issue Oct 20, 2020 · 5 comments · Fixed by #835
Closed

Add LSE-OMNI #550

bdpedigo opened this issue Oct 20, 2020 · 5 comments · Fixed by #835
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enhancement New feature or request
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Neuro Data Design

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@bdpedigo
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bdpedigo commented Oct 20, 2020 •
edited

Should be able to run OMNI where each individual matrix that is input is the Laplacian of each.

Theory/papers on it have not been published (to my knowledge) but has definitely been used successfully in the wild.

Maybe we want to include R-LSE as an option?
@bdpedigo bdpedigo added the enhancement New feature or request label Oct 20, 2020
@bdpedigo
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@nyecarr fair to say this is desired, right?

@bdpedigo bdpedigo added this to New implementations in Neuro Data Design Oct 20, 2020
@daxpryce
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Yeah, this is desired - we do use it semi-frequently.

@nicaurvi
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Yes, we use both LSE/ASE omni in several of our projects. After digging in and comparing topologic vs graspy, we reached out to Carey and it was confirmed that he agrees with our experience that it is useful but it hasn't been published yet.

It brings up some questions of LSE normalization and how to effectively do it as well as how to perform graph augmentations (ptr/cvec) in a reasonable way.

@zeou1
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zeou1 commented Oct 30, 2020

I am interested in working on this issue for sprint 2

@zeou1
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zeou1 commented Nov 16, 2020

Definition of Done:

  1. Implement OMNI with Laplacian matrices as the input
  2. Run experiments to visualize the difference between ASE and LSE OMNI?
  3. Add LSE-OMNI to the current OMNI tutorial

@zeou1 zeou1 mentioned this issue Mar 2, 2021
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@nicaurvi nicaurvi linked a pull request Sep 14, 2021 that will close this issue
LSE Omnibus embedding #835
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enhancement New feature or request
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LSE Omnibus embedding graspologic-org/graspologic
LSE-OMNI zeou1/graspy
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@daxpryce @nicaurvi @bdpedigo @zeou1