Scanpy on scFoundation cell-type annotation comparison Zheng68K: Zheng68K cell-type annotation
scFoundation cell-type annotation comparison evaluation of Scanpy on Zheng68K cell-type annotation, scored with Macro F1.
Evaluation results
1 evaluation · 1 metric rows. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Pipeline: Scanpy | Protocol: scFoundation cell-type annotation comparison Zheng68K: Zheng68K cell-type annotation Dataset subset: Zheng68K subset used in scFoundation Supplementary Table4 (scFoundation cell-type annotation comparison split) | 0.547 macro_f1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · source checkedMethods, coverage and sourceScanpy on scFoundation cell-type annotation comparison Zheng68K: Zheng68K cell-type annotation Cell-type annotation evaluated by unweighted mean of cell-type F1 scores. Each class F1=TP/(TP+0.5*(FP+FN)), defined in Supplementary Note3. Exact dataset release, split manifest, fitting and preprocessing remain unextracted. Aggregation: Not reported scFoundation primary supplement, Table4 · Supplementary Table4, PDF p16, row Scanpy, column Zheng68K |
Source checking is not independent reproduction. Release 2026-09-23-2b89723c6dd9.
Evaluation procedure
Cell-type annotation evaluated by unweighted mean of cell-type F1 scores. Each class F1=TP/(TP+0.5*(FP+FN)), defined in Supplementary Note3. Exact dataset release, split manifest, fitting and preprocessing remain unextracted.
- Pipeline
- Scanpy
- Protocol
- scFoundation cell-type annotation comparison Zheng68K: Zheng68K cell-type annotation
- Dataset subset
- Zheng68K subset used in scFoundation Supplementary Table4 (scFoundation cell-type annotation comparison split)
- origin
- Evaluation origin not reported
- configuration
- Not reported
- protocol id
- scfoundation-2024-supp-table4-task-zheng68k
- metric implementation
- Macro F1
Metadata review: source checked. Unreported conditions prevent automatic comparisons.
Reproduction
- Split
- Not reported
- Adaptation
- Not reported
- Scoring implementation
- Macro F1
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
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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.
14 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.adaptation Cell-type annotation methods as evaluated by the paper; exact training and fitting details remain unextracted. This is not claimed to be a zero-shot foundation-model comparison. Context-only references | scFoundation primary supplement, Table4 Supplementary Table4, PDF p16, row Scanpy, column Zheng68K Version: 10.1038/s41592-024-02305-7 publisher supplement | not individually reviewed No individual claim review recorded unreported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.metric_implementation Macro F1 Context-only references | scFoundation primary supplement, Table4 Supplementary Table4, PDF p16, row Scanpy, column Zheng68K Version: 10.1038/s41592-024-02305-7 publisher supplement | not individually reviewed No individual claim review recorded unreported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.protocol_id scfoundation-2024-supp-table4-task-zheng68k Context-only references | scFoundation primary supplement, Table4 Supplementary Table4, PDF p16, row Scanpy, column Zheng68K Version: 10.1038/s41592-024-02305-7 publisher supplement | not individually reviewed No individual claim review recorded unreported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.evidence_overlap Complete Table4, one cell-type classification score per method/dataset. scFoundation Zheng68K 0.736 is also Table2 scale-100M; no additional independent run implied. Context-only references | scFoundation primary supplement, Table4 Supplementary Table4, PDF p16, row Scanpy, column Zheng68K Version: 10.1038/s41592-024-02305-7 publisher supplement | not individually reviewed No individual claim review recorded unreported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.origin unreported Context-only references | scFoundation primary supplement, Table4 Supplementary Table4, PDF p16, row Scanpy, column Zheng68K Version: 10.1038/s41592-024-02305-7 publisher supplement | missing or unspecified No individual claim review recorded unreported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.protocol Cell-type annotation evaluated by unweighted mean of cell-type F1 scores. Each class F1=TP/(TP+0.5*(FP+FN)), defined in Supplementary Note3. Exact dataset release, split manifest, fitting and preprocessing remain unextracted. Context-only references | scFoundation primary supplement, Table4 Supplementary Table4, PDF p16, row Scanpy, column Zheng68K Version: 10.1038/s41592-024-02305-7 publisher supplement | not individually reviewed No individual claim review recorded unreported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.published_score_reproduction false Context-only references | scFoundation primary supplement, Table4 Supplementary Table4, PDF p16, row Scanpy, column Zheng68K Version: 10.1038/s41592-024-02305-7 publisher supplement | not individually reviewed No individual claim review recorded unreported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.source_locator Supplementary Table4, PDF p16, row Scanpy, column Zheng68K Context-only references | scFoundation primary supplement, Table4 Supplementary Table4, PDF p16, row Scanpy, column Zheng68K Version: 10.1038/s41592-024-02305-7 publisher supplement | not individually reviewed No individual claim review recorded unreported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.suite_complete false Context-only references | scFoundation primary supplement, Table4 Supplementary Table4, PDF p16, row Scanpy, column Zheng68K Version: 10.1038/s41592-024-02305-7 publisher supplement | not individually reviewed No individual claim review recorded unreported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| description scFoundation cell-type annotation comparison evaluation of Scanpy on Zheng68K cell-type annotation, scored with Macro F1. Context-only references | scFoundation primary supplement, Table4 Supplementary Table4, PDF p16, row Scanpy, column Zheng68K Version: 10.1038/s41592-024-02305-7 publisher supplement | not individually reviewed No individual claim review recorded unreported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
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Release 2026-09-23-2b89723c6dd9 · Record review: source checked
1 source records and release history
- scFoundation primary supplement, Table4 · Original source · 10.1038/s41592-024-02305-7 publisher supplement
Technical metadata and extraction receipts
Stable ID: scfoundation-2024-supp-table4-evaluation-scanpy-zheng68k
- areas
- cells-spatial-multiomics
- tasks
- Zheng68K cell-type annotation
- origin
- unreported
- protocol
- Cell-type annotation evaluated by unweighted mean of cell-type F1 scores. Each class F1=TP/(TP+0.5*(FP+FN)), defined in Supplementary Note3. Exact dataset release, split manifest, fitting and preprocessing remain unextracted.
- comparison
- protocol id: scfoundation-2024-supp-table4-task-zheng68k; metric implementation: Macro F1
- missing metadata
- checkpoint revision: unreported; seeds: unreported; budget: unreported; split manifest: unextracted
- source locator
- Supplementary Table4, PDF p16, row Scanpy, column Zheng68K
- adaptation
- Cell-type annotation methods as evaluated by the paper; exact training and fitting details remain unextracted. This is not claimed to be a zero-shot foundation-model comparison.
- evidence overlap
- Complete Table4, one cell-type classification score per method/dataset. scFoundation Zheng68K 0.736 is also Table2 scale-100M; no additional independent run implied.
- published score reproduction
- false
- suite complete
- false
Related records
- benchmark: scFoundation cell-type annotation comparison Zheng68K: Zheng68K cell-type annotation
- model: Scanpy
- dataset: Zheng68K subset used in scFoundation Supplementary Table4 (scFoundation cell-type annotation comparison split)
- evaluation: Scanpy · scFoundation cell-type annotation comparison Zheng68K · Macro F1