scTab Table 1a: seeded model fits
Macro F1 on donor-held-out known cell labels, ontology-adjusted. No whole-study, disease-shift or universal unknown-type conclusion.
Overview
Macro F1 on donor-held-out known cell labels, ontology-adjusted. No whole-study, disease-shift or universal unknown-type conclusion.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
11 recorded evaluations, 11 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
11 evaluations · 11 results. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: celltypist default parameters — scTab Table 6 | Protocol: scTab Table 1a: seeded model fits Dataset: scTab processed CELLxGENE 2023-05-15 donor holdouts | 0.6258 ± 0.0036 macro-f1 fraction · higher Uncertainty: type: standard_deviation; value: 0.0036; n: 4 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNot reported Aggregation: Not reported scTab supplementary comparison tables · Supplementary Table 6, celltypist, default parameters |
| Configuration: xgboost default parameters — scTab Table 6 | Protocol: scTab Table 1a: seeded model fits Dataset: scTab processed CELLxGENE 2023-05-15 donor holdouts | 0.5855 ± 0.0112 macro-f1 fraction · higher Uncertainty: type: standard_deviation; value: 0.0112; n: 4 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNot reported Aggregation: Not reported scTab supplementary comparison tables · Supplementary Table 6, xgboost, default parameters |
| Configuration: CellTypist — scTab Table 1 | Protocol: scTab Table 1a: seeded model fits Dataset: scTab processed CELLxGENE 2023-05-15 donor holdouts | 0.7304 ± 0.0015 macro-f1 fraction · higher Uncertainty: type: standard_deviation; value: 0.0015; n: 4 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNot reported Aggregation: Not reported scTab supplementary comparison tables · Supplementary Table 1a, CellTypist row, macro F1 and number-of-runs columns |
| Configuration: CIForm — scTab Table 1 | Protocol: scTab Table 1a: seeded model fits Dataset: scTab processed CELLxGENE 2023-05-15 donor holdouts | 0.766 macro-f1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNot reported Aggregation: Not reported scTab supplementary comparison tables · Supplementary Table 1a, CIForm row, macro F1 and number-of-runs columns |
| Configuration: Optimized linear logistic regression — scTab Table 1 | Protocol: scTab Table 1a: seeded model fits Dataset: scTab processed CELLxGENE 2023-05-15 donor holdouts | 0.7848 ± 0.0001 macro-f1 fraction · higher Uncertainty: type: standard_deviation; value: 0.0001; n: 4 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNot reported Aggregation: Not reported scTab supplementary comparison tables · Supplementary Table 1a, Optimized linear logistic regression row, macro F1 and number-of-runs columns |
| Configuration: MLP — scTab Table 1 | Protocol: scTab Table 1a: seeded model fits Dataset: scTab processed CELLxGENE 2023-05-15 donor holdouts | 0.7971 ± 0.0012 macro-f1 fraction · higher Uncertainty: type: standard_deviation; value: 0.0012; n: 5 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNot reported Aggregation: Not reported scTab supplementary comparison tables · Supplementary Table 1a, MLP row, macro F1 and number-of-runs columns |
| Configuration: scGPT fine-tuned — scTab Table 1 | Protocol: scTab Table 1a: seeded model fits Dataset: scTab processed CELLxGENE 2023-05-15 donor holdouts | 0.749 macro-f1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNot reported Aggregation: Not reported scTab supplementary comparison tables · Supplementary Table 1a, scGPT fine-tuned row, macro F1 and number-of-runs columns |
| Configuration: scGPT frozen embeddings + logistic regression — scTab Table 1 | Protocol: scTab Table 1a: seeded model fits Dataset: scTab processed CELLxGENE 2023-05-15 donor holdouts | 0.7301 ± 0.0035 macro-f1 fraction · higher Uncertainty: type: standard_deviation; value: 0.0035; n: 5 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNot reported Aggregation: Not reported scTab supplementary comparison tables · Supplementary Table 1a, scGPT frozen embeddings + logistic regression row, macro F1 and number-of-runs columns |
| Configuration: scTab — scTab Table 1 | Protocol: scTab Table 1a: seeded model fits Dataset: scTab processed CELLxGENE 2023-05-15 donor holdouts | 0.8295 ± 0.0007 macro-f1 fraction · higher Uncertainty: type: standard_deviation; value: 0.0007; n: 5 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNot reported Aggregation: Not reported scTab supplementary comparison tables · Supplementary Table 1a, scTab row, macro F1 and number-of-runs columns |
| Configuration: UCE frozen embeddings + classifier — scTab Table 1 | Protocol: scTab Table 1a: seeded model fits Dataset: scTab processed CELLxGENE 2023-05-15 donor holdouts | 0.7611 ± 0.0018 macro-f1 fraction · higher Uncertainty: type: standard_deviation; value: 0.0018; n: 4 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNot reported Aggregation: Not reported scTab supplementary comparison tables · Supplementary Table 1a, UCE frozen embeddings + classifier row, macro F1 and number-of-runs columns |
| Configuration: XGBoost — scTab Table 1 | Protocol: scTab Table 1a: seeded model fits Dataset: scTab processed CELLxGENE 2023-05-15 donor holdouts | 0.8127 ± 0.0005 macro-f1 fraction · higher Uncertainty: type: standard_deviation; value: 0.0005; n: 5 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNot reported Aggregation: Not reported scTab supplementary comparison tables · Supplementary Table 1a, XGBoost row, macro F1 and number-of-runs columns |
Source checking is not independent reproduction. Release 2026-09-30-e37e3ab1284d.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Benchmarks
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- Author-reported evaluations
- 11
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Select a task-valid null control after reviewing inputs and metric
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Select an upstream conventional reference after reviewing the full protocol
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-09-30-e37e3ab1284d. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Applicable tests and references
Applicability is distinct from a completed evaluation.
- CellTypist baseline · source_supported
- celltypist default-parameter baseline · source_supported
- Optimized linear logistic regression baseline · source_supported
- XGBoost baseline · source_supported
- xgboost default-parameter baseline · source_supported
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.
3 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: part of ucc-research-benchmark-sctab Individual claims | scTab official reproducibility repository Supplementary Tables 1,2,6 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 5ede7f2ba1f9618b86924f2ff587931de18f4ada | source checked automated source review · 2026-09-30T21:43:56Z Audit detailsPrimary-source table transcription and scope review; no independent reproduction or human scientific review. Field: Claim: ucc-research-membership-sctab-seed Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Relationship: part of ucc-research-benchmark-sctab Individual claims | scTab: Scaling cross-tissue single-cell annotation models Supplementary Tables 1,2,6 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 10.1038/s41467-024-51059-5; published article XML retrieved 2026-09-30 | source checked automated source review · 2026-09-30T21:43:56Z Audit detailsPrimary-source table transcription and scope review; no independent reproduction or human scientific review. Field: Claim: ucc-research-membership-sctab-seed Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Relationship: part of ucc-research-benchmark-sctab Individual claims | scTab supplementary comparison tables Supplementary Tables 1,2,6 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Information to 10.1038/s41467-024-51059-5 | source checked automated source review · 2026-09-30T21:43:56Z Audit detailsPrimary-source table transcription and scope review; no independent reproduction or human scientific review. Field: Claim: ucc-research-membership-sctab-seed Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
View linked audit checks and correction history
Release 2026-09-30-e37e3ab1284d · Record review: source checked
2 source records and release history
- scTab: Scaling cross-tissue single-cell annotation models · Original source · 10.1038/s41467-024-51059-5; published article XML retrieved 2026-09-30
- scTab supplementary comparison tables · Original source · Supplementary Information to 10.1038/s41467-024-51059-5
Technical metadata and extraction receipts
Stable ID: ucc-research-protocol-sctab-seed
- review
- method: automated_source_review; actor: Codex research coverage worker; reviewed at: 2026-09-30T21:43:56Z; note: Primary-source table transcription and scope review; no independent reproduction or human scientific review.
- source locator
- Supplementary Table 1a
- uncertainty note
- Heading calls these confidence intervals; column explicitly calls them standard deviation. Main article explicitly defines Table 1a ± as SD. Table 1b uncertainty left semantically unresolved.
Related records
- dataset: scTab processed CELLxGENE 2023-05-15 donor holdouts
- part of: scTab published annotation evaluation
- applicable to: CellTypist baseline
- applicable to: celltypist default-parameter baseline
- applicable to: Optimized linear logistic regression baseline
- applicable to: XGBoost baseline
- applicable to: xgboost default-parameter baseline
- protocol: sctab default celltypist
- protocol: sctab default xgboost
- protocol: sctab seed celltypist
- protocol: sctab seed ciform
- protocol: sctab seed linear
- protocol: sctab seed mlp
- protocol: sctab seed scgpt ft
- protocol: sctab seed scgpt zero
- protocol: sctab seed sctab
- protocol: sctab seed uce
- protocol: sctab seed xgboost
- subject: Source membership: ucc-research-protocol-sctab-seed