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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Harmony (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring after UMAP projection Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025) | 2 Rank (overall average ranking across datasets, based on mean biological-conservation and batch-mixing scores (1 = best); UMAP projection of the embedding) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHarmony UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-umap-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS5' cell B4, row 'Harmony', column 'Average ranking' |
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Kedzierska et al. 2025 cell embedding scoring after UMAP projection
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36 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Comparison: adaptation scGPT and Geneformer zero-shot from pretrained weights (scGPT random: no pretraining); scVI and Harmony fitted on each dataset with batch labels; HVG computed from each dataset Context-only references | Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Additional file 1, sheet 'TableS5', column 'Average ranking' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: adaptation scGPT and Geneformer zero-shot from pretrained weights (scGPT random: no pretraining); scVI and Harmony fitted on each dataset with batch labels; HVG computed from each dataset Context-only references | Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Additional file 1, sheet 'TableS5', column 'Average ranking' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Genome Biology 26:101, published 2025-04-18 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: aggregation Across the evaluated datasets; each result states its ranking basis (Table S3: median score per metric; Tables S4 and S5: average ranking from mean scores) Context-only references | Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Additional file 1, sheet 'TableS5', column 'Average ranking' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: aggregation Across the evaluated datasets; each result states its ranking basis (Table S3: median score per metric; Tables S4 and S5: average ranking from mean scores) Context-only references | Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Additional file 1, sheet 'TableS5', column 'Average ranking' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Genome Biology 26:101, published 2025-04-18 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: budget Not reported Context-only references | Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Additional file 1, sheet 'TableS5', column 'Average ranking' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: budget Not reported Context-only references | Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Additional file 1, sheet 'TableS5', column 'Average ranking' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Genome Biology 26:101, published 2025-04-18 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: dataset version Not reported Context-only references | Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Additional file 1, sheet 'TableS5', column 'Average ranking' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: dataset version Not reported Context-only references | Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Additional file 1, sheet 'TableS5', column 'Average ranking' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Genome Biology 26:101, published 2025-04-18 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: inputs Each dataset's expression matrix with cell-type and batch labels; 2,000 HVG standard across experiments Context-only references | Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Additional file 1, sheet 'TableS5', column 'Average ranking' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: inputs Each dataset's expression matrix with cell-type and batch labels; 2,000 HVG standard across experiments Context-only references | Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Additional file 1, sheet 'TableS5', column 'Average ranking' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Genome Biology 26:101, published 2025-04-18 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-10-23-5347695500ed · Record review: source checked
Stable ID: gfm-guides-20261014-kedzierska2025-eval-umap-evaluated-datasets-harmony