Issues

• SCBASSET training crashes on MPS: torchmetrics binary AUROC is broken for batches >= 65,536 logits

  scverse/scvi-tools#4071 · Filter by author AqibHasnain opened on Oct 23, 2026

• Integration Testing CI Install Failure on python 3.14 with prerelease dependencies

  scverse/scvi-tools#4070 · Filter by author scverse-issue-creator opened on Oct 23, 2026

• Integration Testing CI Install Failure on python 3.13

  scverse/scvi-tools#4069 · Filter by author scverse-issue-creator opened on Oct 23, 2026

• Integration Testing CI Install Failure on python 3.14

  scverse/scvi-tools#4068 · Filter by author scverse-issue-creator opened on Oct 23, 2026

• TOTALVI.get_normalized_expression omits learned protein capture efficiency

  bug
  scverse/scvi-tools#4022 · Filter by author arberqoku opened on Sep 16, 2026
  1

• RESOLVI._prepare_data stores incorrect spatial neighbors due to sparse matrix power and CSR row ordering

  scverse/scvi-tools#3977 · Filter by author kwangdol opened on Aug 30, 2026
  2

• Model request: scPhere (hyperspherical / hyperbolic latent embedding for scRNA-seq)

  enhancement
  scverse/scvi-tools#3839 · Filter by author nataliaMalicka opened on Jun 9, 2026
  1

• MultiVI MuData setup rejects unpaired observations despite model supporting missing modalities

  bug
  scverse/scvi-tools#3834 · Filter by author catheriz opened on Jun 7, 2026
  4

• Direct csr sparse ops support

  enhancement
  scverse/scvi-tools#3759 · Filter by author ilan-gold opened on Mar 23, 2026
  3

• Allow custom label_key for scib-metrics in scvi.autotune

  enhancement
  scverse/scvi-tools#3647 · Filter by author catheriz opened on Dec 14, 2025
  1

• Training models with torch.Tensor input

  enhancementP1
  scverse/scvi-tools#2736 · Filter by author j-bac opened on Apr 22, 2024 · scvi-tools 1.2
  4

  

• PyroModelGuideWarmup fails on GPU - probably need to be manually run before trainer.fit()

  bugP0
  scverse/scvi-tools#2616 · Filter by author vitkl opened on Mar 18, 2024
  4

  

• MultiVI with Poisson/NB likelihood for ATAC?

  enhancementP1
  scverse/scvi-tools#2257 · Filter by author vitkl opened on Sep 6, 2023
  8

• Model request: non-negative spatial factorization (NSF)

  backlogenhancementnew model
  scverse/scvi-tools#1859 · Filter by author aribenjamin opened on Jan 18, 2023
  4

  

• Finalize scBasset

  backlogenhancementhelp wanted
  scverse/scvi-tools#1840 · Filter by author adamgayoso opened on Jan 9, 2023
  4

• Some suggestion about GNN

  dataenhancementP2
  scverse/scvi-tools#1789 · Filter by author HuangDDU opened on Nov 16, 2022 · scvi-tools 2.0
  3

• Faster NB LL computation if data is known to be sparse

  enhancementP2
  scverse/scvi-tools#1038 · Filter by author adamgayoso opened on Apr 26, 2021
  6