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feat: MULTIVI Mudata Minification#3039

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ori-kron-wis wants to merge 96 commits intomainscverse/scvi-tools:mainfrom Ori-MultiVI-TotalVi-Minification-MuDatascverse/scvi-tools:Ori-MultiVI-TotalVi-Minification-MuDataCopy head branch name to clipboard

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Commits on Jun 26, 2024

• wip

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Commits on Jul 2, 2024

• Merge branch 'main' into minified-mode

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Commits on Jul 3, 2024

• wip

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• keep empty layers for registry

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Commits on Jul 26, 2024

• Merge branch 'main' into minified-mode

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Commits on Sep 15, 2024

• Merge branch 'main' into minified-mode

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Commits on Nov 6, 2024

• Merge branch 'main' into minified-mode

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• updated conflics during merge

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• Added mudata support for MULTIVI as well as tests

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• needed muon

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• Merge remote-tracking branch 'origin/Ori-MultiVI-MuData' into Ori-MultiVI-MuData

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Commits on Nov 7, 2024

• Added ATC/PROTEIN + RNA capability for MultiVI + more tests like in totalvi

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• small fix

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• small fix

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• small fix

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• small fix

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Commits on Nov 12, 2024

• Added mudata minification models for MULTIVI & TOTALVI as well as tests

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• fix typos

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Commits on Nov 13, 2024

• Merge remote-tracking branch 'origin/main' into Ori-MultiVI-MuData

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• fixed comments

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Commits on Nov 14, 2024

• Merge remote-tracking branch 'origin/main' into Ori-MultiVI-TotalVi-Minification-MuData

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• Merge remote-tracking branch 'origin/main' into Ori-MultiVI-MuData

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• fixed typos

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• Merge remote-tracking branch 'origin/Ori-MultiVI-MuData' into Ori-MultiVI-TotalVi-Minification-MuData

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Commits on Nov 18, 2024

• fix comments

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• fix some tests

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Commits on Nov 19, 2024

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• Merge branch 'main' into minified-mode

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• Merge remote-tracking branch 'origin/minified-mode' into minified-mode

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• added atac registry field

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• merged with the minification refactor branch

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• Refactored minified models

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• added adata minification for multi/total vi and fixed several tests

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• Fixed loss computation for keep count models

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Commits on Nov 20, 2024

• Increase tolerance

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• Merge branch 'minified-mode' of https://github.com/scverse/scvi-tools into minified-mode

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• Typo

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• Changed keep adata when keep_counts

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• Fixed multiVI mudata

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• following can's fixes

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• Merge remote-tracking branch 'origin/Ori-MultiVI-TotalVi-Minification-MuData' into Ori-MultiVI-TotalVi-Minification-MuData

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• update branch

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• Merge remote-tracking branch 'origin/main' into minified-mode

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• fix get_accessibility was using gene indices, should have used regions instead

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• Merge remote-tracking branch 'origin/minified-mode' into Ori-MultiVI-TotalVi-Minification-MuData

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• some fixes

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• update tests

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• fix tests, save/load

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• more fixes.

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Commits on Nov 21, 2024

• Refactor code and add tests

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• updated multivi tutorials with mudata and minification

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• Merge branch 'Ori-MultiVI-TotalVi-Minification-MuData' of https://github.com/scverse/scvi-tools into Ori-MultiVI-TotalVi-Minification-MuData

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Commits on Nov 22, 2024

• Fixed multiVI

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Commits on Nov 27, 2024

• Merge branch 'main' into Ori-MultiVI-TotalVi-Minification-MuData

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Commits on Dec 30, 2024

• merged with main

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Commits on Dec 31, 2024

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• updates

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• updates

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Commits on Jan 8, 2025

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• update with main

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