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1 evaluation · 8 results. Different protocols are not a single leaderboard.
Protocol: Kedzierska et al. 2025 cell embedding scoring after UMAP projection · Dataset subset: PBMC (12k) (Kedzierska et al. 2025)
Sorted by Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; UMAP projection of the embedding) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; UMAP projection of the embedding) | Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; UMAP projection of the embedding) | Avg bio (AvgBIO (mean of cell-type ASW, NMI and ARI; NMI and ARI on Louvain clusters at the best-NMI resolution); whole dataset; UMAP projection of the embedding) | Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; UMAP projection of the embedding) | Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (1 = best); UMAP projection of the embedding) | Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; UMAP projection of the embedding) | Scib asw label (cell-type ASW; whole dataset; UMAP projection of the embedding) | Scib pcr batch (principal component regression on batch; whole dataset; UMAP projection of the embedding) |
|---|---|---|---|---|---|---|---|---|
| Harmony (Kedzierska et al. 2025)Evaluation | 0.5 | 0.94 | 0.66 | 0.73 | 2 | 0.91 | 0.75 | 0.96 |
Applied filters: All linked evaluations
| 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: PBMC (12k) (Kedzierska et al. 2025) | 0.5 Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; UMAP projection of the embedding) unitless · higher 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 PBMC (12k) (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 'TableS7' cell E17, metric block 'ARI', row 'PBMC (12k)', column 'Harmony' (single-value column) |
| Configuration: Harmony (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring after UMAP projection Dataset subset: PBMC (12k) (Kedzierska et al. 2025) | 0.75 Scib asw label (cell-type ASW; whole dataset; UMAP projection of the embedding) unitless · higher 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 PBMC (12k) (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 'TableS7' cell E5, metric block 'ASW', row 'PBMC (12k)', column 'Harmony' (single-value column) |
| Configuration: Harmony (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring after UMAP projection Dataset subset: PBMC (12k) (Kedzierska et al. 2025) | 0.94 Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; UMAP projection of the embedding) unitless · higher 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 PBMC (12k) (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 'TableS7' cell E39, metric block 'Average batch', row 'PBMC (12k)', column 'Harmony' (single-value column) |
| Configuration: Harmony (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring after UMAP projection Dataset subset: PBMC (12k) (Kedzierska et al. 2025) | 0.66 Avg bio (AvgBIO (mean of cell-type ASW, NMI and ARI; NMI and ARI on Louvain clusters at the best-NMI resolution); whole dataset; UMAP projection of the embedding) unitless · higher 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 PBMC (12k) (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 'TableS7' cell E23, metric block 'AvgBIO', row 'PBMC (12k)', column 'Harmony' (single-value column) |
| Configuration: Harmony (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring after UMAP projection Dataset subset: PBMC (12k) (Kedzierska et al. 2025) | 0.91 Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; UMAP projection of the embedding) unitless · higher 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 PBMC (12k) (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 'TableS7' cell E29, metric block 'Batch integration', row 'PBMC (12k)', column 'Harmony' (single-value column) |
| Configuration: Harmony (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring after UMAP projection Dataset subset: PBMC (12k) (Kedzierska et al. 2025) | 0.73 Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; UMAP projection of the embedding) unitless · higher 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 PBMC (12k) (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 'TableS7' cell E11, metric block 'NMI', row 'PBMC (12k)', column 'Harmony' (single-value column) |
| Configuration: Harmony (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring after UMAP projection Dataset subset: PBMC (12k) (Kedzierska et al. 2025) | 0.96 Scib pcr batch (principal component regression on batch; whole dataset; UMAP projection of the embedding) unitless · higher 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 PBMC (12k) (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 'TableS7' cell E34, metric block 'PCR', row 'PBMC (12k)', column 'Harmony' (single-value column) |
| Configuration: Harmony (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring after UMAP projection Dataset subset: PBMC (12k) (Kedzierska et al. 2025) | 2 Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (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 PBMC (12k) (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 D4, row 'Harmony', column 'PBMC (12k)' |
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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 'TableS7', column 'Harmony', row 'PBMC (12k)' 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 'TableS7', column 'Harmony', row 'PBMC (12k)' 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 Single dataset; whole-dataset score Context-only references | Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Additional file 1, sheet 'TableS7', column 'Harmony', row 'PBMC (12k)' 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 Single dataset; whole-dataset score 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 'TableS7', column 'Harmony', row 'PBMC (12k)' 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 'TableS7', column 'Harmony', row 'PBMC (12k)' 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 'TableS7', column 'Harmony', row 'PBMC (12k)' 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 'TableS7', column 'Harmony', row 'PBMC (12k)' 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 'TableS7', column 'Harmony', row 'PBMC (12k)' 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 'TableS7', column 'Harmony', row 'PBMC (12k)' 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 'TableS7', column 'Harmony', row 'PBMC (12k)' 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-pbmc-12k-harmony