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DiagVI tutorials #508

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1a3683b
diagvi tutorial
WinterHannah Feb 12, 2026
848eac4
tutorial update
WinterHannah Feb 15, 2026
fa28822
Add DiagVI spatial proteomics tutorial
michelta00 Feb 20, 2026
7a0ba42
tutorial update
WinterHannah Feb 21, 2026
97ccf3c
Merge branch 'diagvi-tutorials' of https://github.com/quadbio/scvi-tu…
michelta00 Feb 21, 2026
7b26cd5
spatial transcriptomics tutorial update
WinterHannah Feb 21, 2026
2ea3606
delete duplicate
WinterHannah Feb 21, 2026
6fc4678
Refactor rsc import and usage
michelta00 Feb 21, 2026
8435b04
Merge branch 'main' into diagvi-tutorials
michelta00 Feb 21, 2026
367b9a9
Resolve pre-commit issues
michelta00 Feb 21, 2026
f0a94e5
Remove pcr comparison metric
michelta00 Feb 22, 2026
9133f69
Merge branch 'scverse:main' into diagvi-tutorials
michelta00 Feb 24, 2026
3e2edbb
Add scVI and scANVI comparison
michelta00 Feb 26, 2026
89ecb39
Remove duplications and make code more concise
michelta00 Feb 27, 2026
36ca7ef
text update
WinterHannah Mar 8, 2026
cad2f45
cell type classifier and hvg selection
WinterHannah Mar 13, 2026
4fe1497
removed comments
WinterHannah Mar 13, 2026
fd11914
parameter correction
Mar 13, 2026
4ac53c2
fix pre-commit
Mar 18, 2026
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1,471 changes: 1,471 additions & 0 deletions multimodal/DiagVI_spatial_proteomics.ipynb
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@ori-kron-wis ori-kron-wis Mar 23, 2026

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A few things:

  1. I wouldn't commit with warnings.filterwarnings("ignore")
  2. See other comments from the scvi-tools diagvi PR. e.g : compute_foscttm into a different location
  3. Add convergence curves
  4. Validate with the most recent scvi-tools/scib-metrics versions (from main branch)
  5. Validate both CPU/GPU runs (even a few epochs to see it works logically)

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1,656 changes: 1,656 additions & 0 deletions multimodal/DiagVI_spatial_transcriptomics.ipynb
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