Donor-held-out reference mapping asks whether a reference learned from some donors remains useful for cells from a new donor.
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.
| Property | Description and evidence |
|---|---|
| Entity type | Task guide; concrete protocol identities remain separate.Sources (2)scverse/scvi-tools: docs/user_guide/models/scvi.md; theislab/scib official source · scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. |
| Datasets | No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. · Not applicableSources (2)scverse/scvi-tools: docs/user_guide/models/scvi.md; theislab/scib official source · scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. |
| Organisms | No shared organism population is defined at this guide level. Record it for each selected dataset. · Not applicableSources (2)scverse/scvi-tools: docs/user_guide/models/scvi.md; theislab/scib official source · scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. |
| Assays | No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. · Not applicableSources (2)scverse/scvi-tools: docs/user_guide/models/scvi.md; theislab/scib official source · scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. |
| Splits | This proposed guide requires donor separation; no particular donor assignment or cohort is fixed here. · Not applicableSources (2)scverse/scvi-tools: docs/user_guide/models/scvi.md; theislab/scib official source · scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. |
| Allowed inputs | Reference and query molecular measurements, compatible feature identities, donor metadata and labels reserved for assessment.Sources (2)scverse/scvi-tools: docs/user_guide/models/scvi.md; theislab/scib official source · scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. |
| Adaptation | No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. · Not applicableSources (2)scverse/scvi-tools: docs/user_guide/models/scvi.md; theislab/scib official source · scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. |
| Metrics | Choose label-transfer metrics for annotations and biological-conservation metrics for representations. The exact metric, averaging and unknown-cell handling belong to the concrete protocol.Sources (2)scverse/scvi-tools: docs/user_guide/models/scvi.md; theislab/scib official source · scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. |
| Baselines | Specify a reference-only comparator with the same available labels and features. No measured baseline is assigned here.Sources (2)scverse/scvi-tools: docs/user_guide/models/scvi.md; theislab/scib official source · scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. |
Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol.
Keep donor identity visible throughout the evaluation. The reference and any fitted annotation rules belong to the training data; a query donor supplies the held-out assessment. Cell representations and transferred labels are different outputs and require different scoring. This is a proposed task definition, not a claim that every reference-mapping paper uses donor holdout.
This is a task guide, not a single versioned benchmark protocol. The connected resources provide examples or concrete procedures. A candidate method or proposed control is not evidence that an evaluation has been completed.
Release 2026-09-17-d277315f7d76 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.
No evaluations linked in this release.
Last literature check: 2026-09-17. Primary-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.
| Paper or primary resource | Version | Reference |
|---|---|---|
| Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models | PMC full-text XML snapshot PMC7829634 at retrieval; byte-pinned by SHA-256 | Read source DOI: 10.15252/msb.20209620 |
| Defining and benchmarking open problems in single-cell analysis | PMC full-text XML snapshot PMC11030530 at retrieval; byte-pinned by SHA-256 | Read source DOI: 10.21203/rs.3.rs-4181617/v1 |
| openproblems-label primary benchmark evidence | v1.0.0 | Read source |
broad task primary protocol linked
Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol.
Stable record: catalog-task-cell-reference-mappingApplicability is distinct from a completed evaluation.
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.
34 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol. Individual claims | scverse/scvi-tools: docs/user_guide/models/scvi.md scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 73b28e44223621470e582a81a102c107bb22678b | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram caption Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol. Individual claims | theislab/scib official source scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: cd67913396b4c0430710b3d90f1d1841f5fa4468 | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Define reference and query donors","Fit reference using permitted data","Map held-out query cells","Score labels and biological structure"] Individual claims | scverse/scvi-tools: docs/user_guide/models/scvi.md scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 73b28e44223621470e582a81a102c107bb22678b | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram steps ["Define reference and query donors","Fit reference using permitted data","Map held-out query cells","Score labels and biological structure"] Individual claims | theislab/scib official source scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: cd67913396b4c0430710b3d90f1d1841f5fa4468 | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Conceptual evaluation workflow Individual claims | scverse/scvi-tools: docs/user_guide/models/scvi.md scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 73b28e44223621470e582a81a102c107bb22678b | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram title Conceptual evaluation workflow Individual claims | theislab/scib official source scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: cd67913396b4c0430710b3d90f1d1841f5fa4468 | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Entity type Task guide; concrete protocol identities remain separate. Individual claims | scverse/scvi-tools: docs/user_guide/models/scvi.md scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 73b28e44223621470e582a81a102c107bb22678b | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Entity type Task guide; concrete protocol identities remain separate. Individual claims | theislab/scib official source scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: cd67913396b4c0430710b3d90f1d1841f5fa4468 | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. Individual claims | scverse/scvi-tools: docs/user_guide/models/scvi.md scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 73b28e44223621470e582a81a102c107bb22678b | inapplicable automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Datasets No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. Individual claims | theislab/scib official source scVI model guide: generative model and latent representation; scIB README: biological-conservation metrics. Donor holdout is this guide’s evaluation requirement, not an asserted scVI default. Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: cd67913396b4c0430710b3d90f1d1841f5fa4468 | inapplicable automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-09-17-d277315f7d76 · Record review: discovered
Stable ID: catalog-task-cell-reference-mapping