All pull requests

Pull requests

• fix(cytovi): honor DE test mode without clipping

  #4037·sofoklis326 opened Sep 23, 2026·

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• fix(cytovi): preserve DA cell and sample alignment

  #4036·sofoklis326 opened Sep 23, 2026·

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• fix(cytovi): use supplied AnnData for posterior and sample scores

  #4035·sofoklis326 opened Sep 23, 2026·

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• fix(cytovi): use standard deviation for aggregated posterior scale

  #4034·sofoklis326 opened Sep 23, 2026·

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• fix(totalvi): apply protein capture efficiency in posterior predictive samples

  on-merge: backport to 1.5.x
  #4033·ori-kron-wis opened Sep 23, 2026Collaborator·

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• fix: store NegativeBinomialMixture's theta2 as a tensor

  #4028·VishnuR23 opened Sep 21, 2026·

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• fix: draw a mixture component per sample in NegativeBinomialMixture.sample

  #4027·VishnuR23 opened Sep 21, 2026·

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• fix: honor the registry passed to SCANVI.from_scvi_model

  #4026·VishnuR23 opened Sep 21, 2026·

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• fix: forward deeply_inject_covariates to MULTIVAE's protein decoder

  #4025·VishnuR23 opened Sep 21, 2026·

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• fix: only warn about dataloader-redundant args the caller actually set

  #4024·VishnuR23 opened Sep 21, 2026·

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• feat: Extract some methods of DRVI for easier extention + code improvement

  #4020·moinfar opened Sep 14, 2026Contributor·

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• feat: FCLayers residual and forward kwargs

  #4019·moinfar opened Sep 14, 2026Contributor·

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• perf: sample cells before the forward pass in get_normalized_expression(n_samples_overall=...)

  #4018·JESUSROYETH opened Sep 14, 2026·

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• perf: remove per-minibatch overhead from the data path and the inference forward

  on-merge: backport to 1.5.x
  #4017·JESUSROYETH opened Sep 13, 2026·

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• build: drop Python 3.12 support, add Python 3.15 support

  on-merge: backport to 1.5.x
  #3997·ori-kron-wis opened Sep 6, 2026Collaborator·

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• Refactor [WIP]: Removed the spatial models from scvi-tools in v1.6 and move them to scVIVA-Tools

  cuda testson-merge: backport to 1.5.x
  #3908·ori-kron-wis opened Jul 9, 2026Collaborator·

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• feat: supporting sparse mode in DataSplitter

  cuda testson-merge: backport to 1.5.x
  #3840·ori-kron-wis opened Jun 11, 2026Collaborator·

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• feat: scvix reformat

  on-merge: backport to 1.5.x
  #3827·ori-kron-wis opened May 28, 2026Collaborator·

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  3

  

• feat: First draft of scPoli

  on-merge: backport to 1.5.x
  #3824·canergen opened May 23, 2026Member·

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• feat: scVI-X release

  on-merge: backport to 1.5.x
  #3823·canergen opened May 22, 2026Member·

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  28

• feat: Add RESOLVI graph dataloader integration and benchmark CI

  on-merge: backport to 1.5.x
  #3798·ori-kron-wis opened May 5, 2026Collaborator·

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• feat: add shared memory for DDP data deduplication

  on-merge: backport to 1.5.x
  #3754·ori-kron-wis opened Mar 19, 2026Collaborator·

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  1

  

• Feat: Asymmetric n_layers for encoder/decoder

  on-merge: backport to 1.5.x
  #3702·ori-kron-wis opened Feb 8, 2026Collaborator·

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• model: SENAVAE

  on-merge: backport to 1.5.x
  #3571·ori-kron-wis opened Oct 22, 2025Collaborator·

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• Fixes to pyro model initialisation & sampling [WIP]

  P1
  #2695·vitkl opened Apr 7, 2024Contributor·

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  9