Model

scVI

scVI models single-cell RNA counts with a probabilistic latent-variable model that accounts for observed covariates.

Sources (2)

scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations

2 evaluations · 24 metric rows · 2 evaluated configurations using this model

How it worksscVI workflow

Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.

Sources (2)

scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations

Overview

Model type

Variational autoencoder for count data

Sources (2)

scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations

Inputs

Cell-by-gene count matrix, optionally with batch, donor or other covariates.

Sources (2)

scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations

Outputs

Low-dimensional cell representations, normalized expression and probabilistic downstream quantities.

Sources (2)

scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations

Access

Official project documentation and implementation: https://github.com/scverse/scvi-tools

Sources (2)

scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations

Source reviewed · Automated source review, 2026-09-16. All specifications and missing details

Evaluations and results

2 evaluations · 24 metric rows. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: scvi_embed · hvg, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.9492497974437232 ARI_cluster/label score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 230, column 3 (ARI_cluster/label)
Configuration: scvi_embed · full_feature, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.3348520347498182 kBET score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 231, column 11 (kBET)
Configuration: scvi_embed · hvg, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.4372361330169315 kBET score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 230, column 11 (kBET)
Configuration: scvi_embed · hvg, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.999587635359695 cLISI score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 230, column 13 (cLISI)
Configuration: scvi_embed · full_feature, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.5760091468691826 isolated_label_silhouette score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 231, column 9 (isolated_label_silhouette)
Configuration: scvi_embed · full_feature, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.9685477617391932 graph_conn score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 231, column 10 (graph_conn)
Configuration: scvi_embed · hvg, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.098591549295775 isolated_label_F1 score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 230, column 8 (isolated_label_F1)
Configuration: scvi_embed · full_feature, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.097902097902098 isolated_label_F1 score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 231, column 8 (isolated_label_F1)
Configuration: scvi_embed · hvg, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.4862182342249621 cell_cycle_conservation score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 230, column 7 (cell_cycle_conservation)
Configuration: scvi_embed · full_feature, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.924531301553261 ARI_cluster/label score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 231, column 3 (ARI_cluster/label)
Configuration: scvi_embed · full_feature, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.874482888741797 NMI_cluster/label score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 231, column 2 (NMI_cluster/label)
Configuration: scvi_embed · full_feature, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.998845172330768 cLISI score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 231, column 13 (cLISI)
Configuration: scvi_embed · hvg, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.929525587174975 PCR_batch score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 230, column 6 (PCR_batch)
Configuration: scvi_embed · full_feature, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.862350614009722 PCR_batch score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 231, column 6 (PCR_batch)
Configuration: scvi_embed · full_feature, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.856719623267588 ASW_label/batch score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 231, column 5 (ASW_label/batch)
Configuration: scvi_embed · hvg, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.304252237012593 iLISI score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 230, column 12 (iLISI)
Configuration: scvi_embed · hvg, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.863945401459413 ASW_label/batch score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 230, column 5 (ASW_label/batch)
Configuration: scvi_embed · hvg, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.9144647104516592 NMI_cluster/label score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 230, column 2 (NMI_cluster/label)
Configuration: scvi_embed · full_feature, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.670155438154198 cell_cycle_conservation score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 231, column 7 (cell_cycle_conservation)
Configuration: scvi_embed · hvg, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.990548145030244 graph_conn score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 230, column 10 (graph_conn)
Configuration: scvi_embed · hvg, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.5838454514741898 isolated_label_silhouette score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 230, column 9 (isolated_label_silhouette)
Configuration: scvi_embed · full_feature, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.5826019421219829 ASW_label score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 231, column 4 (ASW_label)
Configuration: scvi_embed · full_feature, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.18144840479935 iLISI score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 231, column 12 (iLISI)
Configuration: scvi_embed · hvg, unscaled	Protocol: scIB official RNA metrics export · pancreas Dataset subset: pancreas	0.595530979335308 ASW_label score · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source scvi_embed · scIB official RNA metrics export · pancreas scIB official RNA metrics export Aggregation: unreported scIB: 3afbffd3674726e5146797be21cf6bd7470a2c5f · data/metrics.csv row 230, column 4 (ASW_label)

Source checking is not independent reproduction. Release 2026-09-23-2b89723c6dd9.

Related configurations, pipelines and services

These configurations, services and pipelines use this model within their own configurations. Their results, where available, are not assigned to the underlying model.

scVI + scANVI Pipeline · 1 metric rows
scVI Configuration · 1 metric rows

Use this model

How it works, versions and access

Versions and evaluated configurations

scvi_embed · full_feature, unscaled · family
scvi_embed · hvg, unscaled · family
scVI · alias of

How it works

scVI models single-cell RNA counts with a probabilistic latent-variable model that accounts for observed covariates. Variational autoencoder with a count likelihood and neural encoder/decoder; likelihood and batch/dispersion settings are configurable. The documented inputs are cell-by-gene count matrix, optionally with batch, donor or other covariates. The output consists of low-dimensional cell representations, normalized expression and probabilistic downstream quantities.

Sources (2)

scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations

Versions and reproducibility

scVI model within scvi-tools; package version, likelihood, covariates and checkpoint are evaluation-specific. Gene-feature matrix rather than a fixed sequence-token window.

Sources (2)

scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths supported by sources

Models count observations directly and supports batch-conditioned expression estimates and reference-to-query transfer.
Sources (2)
scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations

Limitations and conditions

The documentation notes that the latent space is less interpretable than a linear method and efficient inference generally benefits from a GPU. Covariates and likelihood must be reported.
Sources (2)
scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations

Profile review details

Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied.

Stable record: catalog-model-scvi

Specifications

Inputs, training, access and other details

Explanatory profile: source reviewed · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Inputs, outputs and configuration
Property	Description and evidence
Model type	Variational autoencoder for count data Sources (2) scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations
Architecture	Variational autoencoder with a count likelihood and neural encoder/decoder; likelihood and batch/dispersion settings are configurable. Sources (2) scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations
Inputs	Cell-by-gene count matrix, optionally with batch, donor or other covariates. Sources (2) scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations
Outputs	Low-dimensional cell representations, normalized expression and probabilistic downstream quantities. Sources (2) scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations
Parameters	Configuration-dependent, including gene count and encoder/decoder dimensions. Sources (2) scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations
Known versions	scVI model within scvi-tools; package version, likelihood, covariates and checkpoint are evaluation-specific. Sources (2) scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations
Training data	Fitted to the user-selected count matrix or a specified pretrained reference; scVI is not one universal checkpoint. Sources (2) scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations
Training cutoff	Inapplicable as one universal pretraining date: scVI is fitted to the supplied dataset, whose collection date and train/test split belong to the evaluation. · Not applicable Sources (2) scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations
Context limits	Gene-feature matrix rather than a fixed sequence-token window. Sources (2) scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations
Weights licence	No universal weights release applies to a model fitted on each dataset; any reused checkpoint requires its own licence. Sources (2) scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations
Access	Official project documentation and implementation: https://github.com/scverse/scvi-tools Sources (2) scverse/scvi-tools: README.md; scverse/scvi-tools: docs/user_guide/models/scvi.md · docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations
Code licence	BSD-3-Clause Sources scverse/scvi-tools: LICENSE · LICENSE: licence text

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

39 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-23-2b89723c6dd9
Property and statement	Original source and location	Review and provenance
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	scverse/scvi-tools: docs/user_guide/models/scvi.md Original source ↗ docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 73b28e44223621470e582a81a102c107bb22678b Retrieved: 2026-09-16T19:46:20.137176+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `c81a5cfb30db1eca8c03af3d0db1a36a447a1bb5a27b270de5633ba73ebeeeef` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	scverse/scvi-tools: README.md Original source ↗ docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 73b28e44223621470e582a81a102c107bb22678b Retrieved: 2026-09-16T19:46:20.137176+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `eb46b8a54e60643ca0cd8cb375ede05b01dcbd2380ca17ce8027a92ba13cebbb` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps RNA counts and covariates Variational encoder Latent cell state Count decoder and estimates Individual claims	scverse/scvi-tools: docs/user_guide/models/scvi.md Original source ↗ docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 73b28e44223621470e582a81a102c107bb22678b Retrieved: 2026-09-16T19:46:20.137176+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `c81a5cfb30db1eca8c03af3d0db1a36a447a1bb5a27b270de5633ba73ebeeeef` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps RNA counts and covariates Variational encoder Latent cell state Count decoder and estimates Individual claims	scverse/scvi-tools: README.md Original source ↗ docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 73b28e44223621470e582a81a102c107bb22678b Retrieved: 2026-09-16T19:46:20.137176+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `eb46b8a54e60643ca0cd8cb375ede05b01dcbd2380ca17ce8027a92ba13cebbb` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title scVI workflow Individual claims	scverse/scvi-tools: docs/user_guide/models/scvi.md Original source ↗ docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 73b28e44223621470e582a81a102c107bb22678b Retrieved: 2026-09-16T19:46:20.137176+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `c81a5cfb30db1eca8c03af3d0db1a36a447a1bb5a27b270de5633ba73ebeeeef` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title scVI workflow Individual claims	scverse/scvi-tools: README.md Original source ↗ docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 73b28e44223621470e582a81a102c107bb22678b Retrieved: 2026-09-16T19:46:20.137176+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `eb46b8a54e60643ca0cd8cb375ede05b01dcbd2380ca17ce8027a92ba13cebbb` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Model type Variational autoencoder for count data Individual claims	scverse/scvi-tools: docs/user_guide/models/scvi.md Original source ↗ docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 73b28e44223621470e582a81a102c107bb22678b Retrieved: 2026-09-16T19:46:20.137176+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `c81a5cfb30db1eca8c03af3d0db1a36a447a1bb5a27b270de5633ba73ebeeeef` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Model type Variational autoencoder for count data Individual claims	scverse/scvi-tools: README.md Original source ↗ docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 73b28e44223621470e582a81a102c107bb22678b Retrieved: 2026-09-16T19:46:20.137176+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `eb46b8a54e60643ca0cd8cb375ede05b01dcbd2380ca17ce8027a92ba13cebbb` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Architecture Variational autoencoder with a count likelihood and neural encoder/decoder; likelihood and batch/dispersion settings are configurable. Individual claims	scverse/scvi-tools: docs/user_guide/models/scvi.md Original source ↗ docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 73b28e44223621470e582a81a102c107bb22678b Retrieved: 2026-09-16T19:46:20.137176+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `c81a5cfb30db1eca8c03af3d0db1a36a447a1bb5a27b270de5633ba73ebeeeef` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Architecture Variational autoencoder with a count likelihood and neural encoder/decoder; likelihood and batch/dispersion settings are configurable. Individual claims	scverse/scvi-tools: README.md Original source ↗ docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 73b28e44223621470e582a81a102c107bb22678b Retrieved: 2026-09-16T19:46:20.137176+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `eb46b8a54e60643ca0cd8cb375ede05b01dcbd2380ca17ce8027a92ba13cebbb` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

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Release 2026-09-23-2b89723c6dd9 · Record review: discovered

4 source records and release history

scVI official resource · Original source · Not reported
scverse/scvi-tools: README.md · Original source · 73b28e44223621470e582a81a102c107bb22678b
scverse/scvi-tools: docs/user_guide/models/scvi.md · Original source · 73b28e44223621470e582a81a102c107bb22678b
scverse/scvi-tools: LICENSE · Original source · 73b28e44223621470e582a81a102c107bb22678b

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Technical metadata and extraction receipts

Stable ID: catalog-model-scvi

areas: cells-tissues
method types: baseline
entity level: family
version: scvi-tools
reported name: scVI
access: Public software; train a task-specific model on the permitted split.
method type: baseline
historical missing metadata: checkpoint revision: not_yet_extracted; training data: not_yet_extracted; licence: not_yet_extracted
metadata review scope: historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
entity classification: review date: 2026-09-17; rationale: The cited profile describes a named learned biological predictor or representation model/family. Preserve this identity separately from task-specific fitting, individual checkpoints, pipelines and hosted access.; source ids: evidence-official-550f6719c2f22f4d57b3; evidence-official-0cbab80c2d1769287a1f; source locator: docs/user_guide/models/scvi.md: Preliminaries, Generative process, Inference and Limitations; ambiguities: None recorded

Related records

family: scvi_embed · full_feature, unscaled
family: scvi_embed · hvg, unscaled
model: scVI
alias of: scVI
uses model: scVI + scANVI
uses model: scVI

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