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 results

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

Inputs

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

Outputs

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

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 results. Different protocols are not a single leaderboard.

Protocol: scIB official RNA metrics export · pancreas · Dataset subset: pancreas

Sorted by Adjusted rand index (clusters vs cell-type labels) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Adjusted rand index (clusters vs cell-type labels)	Normalized mutual information (clusters vs cell-type labels)	Scib asw batch	Scib asw label	Scib cell cycle conservation	Scib clisi	Scib graph connectivity	Scib ilisi	Scib isolated label F1	Scib isolated label silhouette	Scib kbet	Scib pcr batch
scvi_embed · hvg, unscaledEvaluation	0.949 (best in column)	0.914 (best in column)	0.864 (best in column)	0.596 (best in column)	0.486	1 (best in column)	0.991 (best in column)	0.304 (best in column)	0.0986 (best in column)	0.584 (best in column)	0.437 (best in column)	0.93 (best in column)
scvi_embed · full_feature, unscaledEvaluation	0.925	0.874	0.857	0.583	0.67 (best in column)	0.999	0.969	0.181	0.0979	0.576	0.335	0.862

All 24 result rows with coverage, uncertainty and sources

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	0.949 Adjusted rand index (clusters vs cell-type labels) unitless · higher Uncertainty: Not reported by the source 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	0.335 Scib kbet unitless · higher Uncertainty: Not reported by the source 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	0.437 Scib kbet unitless · higher Uncertainty: Not reported by the source 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	1 Scib clisi unitless · higher Uncertainty: Not reported by the source 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	0.576 Scib isolated label silhouette unitless · higher Uncertainty: Not reported by the source 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	0.969 Scib graph connectivity unitless · higher Uncertainty: Not reported by the source 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	0.0986 Scib isolated label F1 unitless · higher Uncertainty: Not reported by the source 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	0.0979 Scib isolated label F1 unitless · higher Uncertainty: Not reported by the source 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	0.486 Scib cell cycle conservation unitless · higher Uncertainty: Not reported by the source 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	0.925 Adjusted rand index (clusters vs cell-type labels) unitless · higher Uncertainty: Not reported by the source 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	0.874 Normalized mutual information (clusters vs cell-type labels) unitless · higher Uncertainty: Not reported by the source 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	0.999 Scib clisi unitless · higher Uncertainty: Not reported by the source 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	0.93 Scib pcr batch unitless · higher Uncertainty: Not reported by the source 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	0.862 Scib pcr batch unitless · higher Uncertainty: Not reported by the source 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	0.857 Scib asw batch unitless · higher Uncertainty: Not reported by the source 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	0.304 Scib ilisi unitless · higher Uncertainty: Not reported by the source 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	0.864 Scib asw batch unitless · higher Uncertainty: Not reported by the source 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	0.914 Normalized mutual information (clusters vs cell-type labels) unitless · higher Uncertainty: Not reported by the source 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	0.67 Scib cell cycle conservation unitless · higher Uncertainty: Not reported by the source 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	0.991 Scib graph connectivity unitless · higher Uncertainty: Not reported by the source 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	0.584 Scib isolated label silhouette unitless · higher Uncertainty: Not reported by the source 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	0.583 Scib asw label unitless · higher Uncertainty: Not reported by the source 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	0.181 Scib ilisi unitless · higher Uncertainty: Not reported by the source 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	0.596 Scib asw label unitless · higher Uncertainty: Not reported by the source 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 2026-11-02-a7f03c9e55a5.

Use this model

How it works, versions and access

Related profile: scVI. This page retains the exact record and its evaluation context.

How it works

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: discovery-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

Applicable tests and references

Applicability is distinct from a completed evaluation.

scIB · Proposed association

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.

40 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
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

How to read the evidence

Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: discovered

4 source records and release history

scverse/scvi-tools official source · Original source · 73b28e44223621470e582a81a102c107bb22678b
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: discovery-model-scvi

areas: single-cell
access: official_source_linked
candidate benchmark ids: discovery-benchmark-scib
entity level: family
reported name: scVI
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
missing metadata: version: reason: unextracted

Related records

applicable to: scIB
alias of: scVI
subject: scVI: alias of scVI

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