scFoundation cell-type annotation comparison evaluation of Scanpy on Zheng68K cell-type annotation, scored with Macro F1.
1 evaluation · 1 result. 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 yet extracted 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 |
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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.
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12 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Source location 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 |
| 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 |
| Relationship: assessment 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 |
| Relationship: data scfoundation-2024-supp-table4-dataset-zheng68k-subset-used-in-scfoundation-supplementary-table4 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 |
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
Stable ID: scfoundation-2024-supp-table4-evaluation-scanpy-zheng68k