scVI (Kedzierska et al. 2025)
Configuration of scVI: Trained on each target dataset using its batch labels; scVI latent embedding.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
14 evaluations · 97 results. Different protocols are not a single leaderboard.
Sorted by Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) (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 | Protocol and dataset | Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) | Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; 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; full embedding dimensions) | 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; full embedding dimensions) | Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; UMAP projection of the embedding) | Scib asw label (cell-type ASW; whole dataset; full embedding dimensions) | Scib asw label (cell-type ASW; whole dataset; UMAP projection of the embedding) | Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; full embedding dimensions) | Average batch score (average batch score (mean of batch integration score and PCR batch score); 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); full embedding dimensions) | 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; full embedding dimensions) | Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; UMAP projection of the embedding) | Scib pcr batch (principal component regression on batch; whole dataset; full embedding dimensions) | Scib pcr batch (principal component regression on batch; whole dataset; UMAP projection of the embedding) | Rank (overall average ranking across datasets, based on mean biological-conservation and batch-mixing scores (1 = best); full embedding dimensions) | Rank (overall average ranking across datasets, based on mean biological-conservation and batch-mixing scores (1 = best); UMAP projection of the embedding) | Rank (rank of the median ARI score across datasets among the eight representations (1 = best); full embedding dimensions) | Rank (rank of the median ASW score across datasets among the eight representations (1 = best); full embedding dimensions) | Rank (rank of the median Average batch score across datasets among the eight representations (1 = best); full embedding dimensions) | Rank (rank of the median Average BIO score across datasets among the eight representations (1 = best); full embedding dimensions) | Rank (rank of the median Batch integration score across datasets among the eight representations (1 = best); full embedding dimensions) | Rank (rank of the median NMI score across datasets among the eight representations (1 = best); full embedding dimensions) | Rank (rank of the median PCR score across datasets among the eight representations (1 = best); full embedding dimensions) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| scVI (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, Pancreas (16k) (Kedzierska et al. 2025) | 0.94 (best in column) | Not reported | 0.8 (best in column) | Not reported | 0.9 (best in column) | Not reported | 0.57 (best in column) | Not reported | 0.86 (best in column) | Not reported | 1 (best in column) | Not reported | 0.85 | Not reported | 0.87 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| scVI (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, Pancreas (8k) (Kedzierska et al. 2025) | 0.94 (best in column) | Not reported | 0.8 (best in column) | Not reported | 0.9 (best in column) | Not reported | 0.56 | Not reported | 0.77 | Not reported | Not reported | Not reported | 0.78 | Not reported | 0.76 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| scVI (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, PBMC (12k) (Kedzierska et al. 2025) | 0.86 | Not reported | 0.74 | Not reported | 0.81 | Not reported | 0.56 | Not reported | 0.86 (best in column) | Not reported | 1 (best in column) | Not reported | 0.98 (best in column) | Not reported | 0.73 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| scVI (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, PBMC (95k) (Kedzierska et al. 2025) | 0.68 | Not reported | 0.67 | Not reported | 0.8 | Not reported | 0.53 | Not reported | Not reported | Not reported | 1 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| scVI (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, Tabula Sapiens (483k) (Kedzierska et al. 2025) | 0.47 | Not reported | 0.57 | Not reported | 0.74 | Not reported | 0.49 | Not reported | 0.61 | Not reported | 1 (best in column) | Not reported | 0.77 | Not reported | 0.45 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| scVI (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, Immune (330k) (Kedzierska et al. 2025) | 0.38 | Not reported | 0.53 | Not reported | 0.65 | Not reported | 0.54 | Not reported | 0.43 | Not reported | 7 | Not reported | 0.86 | Not reported | 0 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| scVI (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, Evaluated datasets, aggregated (Kedzierska et al. 2025) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 1 | Not reported | 1 | 2 | 3 | 1 | 5 | 1 | 3 |
| scVI (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring after UMAP projection, Evaluated datasets, aggregated (Kedzierska et al. 2025) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 1 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| scVI (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring after UMAP projection, Immune (330k) (Kedzierska et al. 2025) | Not reported | 0.4 | Not reported | 0.52 | Not reported | 0.66 | Not reported | 0.51 | Not reported | 0.24 | Not reported | 4 | Not reported | 0.48 | Not reported | 0 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| scVI (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring after UMAP projection, Pancreas (16k) (Kedzierska et al. 2025) | Not reported | 0.46 | Not reported | 0.64 | Not reported | 0.73 | Not reported | 0.71 | Not reported | 0.77 | Not reported | 1 (best in column) | Not reported | 0.68 | Not reported | 0.86 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| scVI (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring after UMAP projection, Pancreas (8k) (Kedzierska et al. 2025) | Not reported | 0.5 | Not reported | 0.66 | Not reported | 0.74 | Not reported | 0.74 (best in column) | Not reported | 0.61 | Not reported | Not reported | Not reported | 0.64 | Not reported | 0.58 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| scVI (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring after UMAP projection, PBMC (12k) (Kedzierska et al. 2025) | Not reported | 0.59 | Not reported | 0.69 (best in column) | Not reported | 0.75 (best in column) | Not reported | 0.73 | Not reported | 0.95 (best in column) | Not reported | 1 (best in column) | Not reported | 0.91 (best in column) | Not reported | 1 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| scVI (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring after UMAP projection, PBMC (95k) (Kedzierska et al. 2025) | Not reported | 0.62 (best in column) | Not reported | 0.69 (best in column) | Not reported | 0.75 (best in column) | Not reported | 0.7 | Not reported | Not reported | Not reported | 1 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| scVI (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring after UMAP projection, Tabula Sapiens (483k) (Kedzierska et al. 2025) | Not reported | 0.44 | Not reported | 0.52 | Not reported | 0.74 | Not reported | 0.38 | Not reported | 0.61 | Not reported | 1 (best in column) | Not reported | 0.58 | Not reported | 0.63 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
All 97 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025) | 1 Rank (overall average ranking across datasets, based on mean biological-conservation and batch-mixing scores (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS4' cell B3, row 'scVI', column 'Average ranking' |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025) | 1 Rank (rank of the median ARI score across datasets among the eight representations (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS3' cell D3, row 'scVI', column 'ARI' |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025) | 2 Rank (rank of the median ASW score across datasets among the eight representations (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS3' cell C3, row 'scVI', column 'ASW' |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025) | 3 Rank (rank of the median Average batch score across datasets among the eight representations (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS3' cell F3, row 'scVI', column 'Average batch' |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025) | 1 Rank (rank of the median Average BIO score across datasets among the eight representations (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS3' cell B3, row 'scVI', column 'Average BIO' |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025) | 5 Rank (rank of the median Batch integration score across datasets among the eight representations (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS3' cell G3, row 'scVI', column 'Batch integration' |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025) | 1 Rank (rank of the median NMI score across datasets among the eight representations (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS3' cell E3, row 'scVI', column 'NMI' |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025) | 3 Rank (rank of the median PCR score across datasets among the eight representations (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS3' cell H3, row 'scVI', column 'PCR' |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025) | 0.38 Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell G19, metric block 'ARI', row 'Immune (330k)', column 'scVI' (single-value column) |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025) | 0.54 Scib asw label (cell-type ASW; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell G7, metric block 'ASW', row 'Immune (330k)', column 'scVI' (single-value column) |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025) | 0.43 Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell G40, metric block 'Average batch', row 'Immune (330k)', column 'scVI' (single-value column) |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025) | 0.53 Avg bio (AvgBIO (mean of cell-type ASW, NMI and ARI; NMI and ARI on Louvain clusters at the best-NMI resolution); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell G25, metric block 'AvgBIO', row 'Immune (330k)', column 'scVI' (single-value column) |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025) | 0.86 Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell G30, metric block 'Batch integration', row 'Immune (330k)', column 'scVI' (single-value column) |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025) | 0.65 Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell G13, metric block 'NMI', row 'Immune (330k)', column 'scVI' (single-value column) |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025) | 0 Scib pcr batch (principal component regression on batch; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell G35, metric block 'PCR', row 'Immune (330k)', column 'scVI' (single-value column) |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025) | 7 Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS4' cell F3, row 'scVI', column 'Immune (330k)' |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025) | 0.94 Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on Pancreas (16k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell G15, metric block 'ARI', row 'Pancreas (16k)', column 'scVI' (single-value column) |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025) | 0.57 Scib asw label (cell-type ASW; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on Pancreas (16k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell G3, metric block 'ASW', row 'Pancreas (16k)', column 'scVI' (single-value column) |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025) | 0.86 Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on Pancreas (16k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell G37, metric block 'Average batch', row 'Pancreas (16k)', column 'scVI' (single-value column) |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025) | 0.8 Avg bio (AvgBIO (mean of cell-type ASW, NMI and ARI; NMI and ARI on Louvain clusters at the best-NMI resolution); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on Pancreas (16k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell G21, metric block 'AvgBIO', row 'Pancreas (16k)', column 'scVI' (single-value column) |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025) | 0.85 Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on Pancreas (16k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell G27, metric block 'Batch integration', row 'Pancreas (16k)', column 'scVI' (single-value column) |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025) | 0.9 Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on Pancreas (16k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell G9, metric block 'NMI', row 'Pancreas (16k)', column 'scVI' (single-value column) |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025) | 0.87 Scib pcr batch (principal component regression on batch; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on Pancreas (16k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell G32, metric block 'PCR', row 'Pancreas (16k)', column 'scVI' (single-value column) |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025) | 1 Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on Pancreas (16k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS4' cell C3, row 'scVI', column 'Pancreas (16k)' |
| Configuration: scVI (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (8k) (Kedzierska et al. 2025) | 0.94 Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescVI cell embedding on Pancreas (8k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell G16, metric block 'ARI', row 'Pancreas (8k)', column 'scVI' (single-value column) |
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Sources and history
Release 2026-10-23-5347695500ed · Record review: source checked
1 source record and release history
- Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) · Original source · Version of record, Genome Biology 26:101, published 2025-04-18
Technical metadata and extraction receipts
Stable ID: gfm-guides-20261014-kedzierska2025-config-scvi
- areas
- single-cell
- contexts
- research
- method types
- specialist
- reported name
- scVI
- foundation model eligible
- false
- training setting
- Trained on each target dataset using its batch labels
- representation
- scVI latent embedding
- missing metadata
- hyperparameters: reason: unreported; version: reason: unreported
- source locator
- Pages 7-8 'Models and baselines'; page 11 'Code availability'
- provenance note
- scVI baseline as run by Kedzierska et al. 2025.
Related records
- configuration of: scVI
- system: scVI cell embedding on evaluated datasets (Kedzierska et al. 2025)
- system: scVI cell embedding on Immune (330k) (Kedzierska et al. 2025)
- system: scVI cell embedding on Pancreas (16k) (Kedzierska et al. 2025)
- system: scVI cell embedding on Pancreas (8k) (Kedzierska et al. 2025)
- system: scVI cell embedding on PBMC (12k) (Kedzierska et al. 2025)
- system: scVI cell embedding on PBMC (95k) (Kedzierska et al. 2025)
- system: scVI cell embedding on Tabula Sapiens (483k) (Kedzierska et al. 2025)
- system: scVI UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025)
- system: scVI UMAP-projected embedding on Immune (330k) (Kedzierska et al. 2025)
- system: scVI UMAP-projected embedding on Pancreas (16k) (Kedzierska et al. 2025)
- system: scVI UMAP-projected embedding on Pancreas (8k) (Kedzierska et al. 2025)
- system: scVI UMAP-projected embedding on PBMC (12k) (Kedzierska et al. 2025)
- system: scVI UMAP-projected embedding on PBMC (95k) (Kedzierska et al. 2025)
- system: scVI UMAP-projected embedding on Tabula Sapiens (483k) (Kedzierska et al. 2025)