Configuration
2,000 highly variable genes (Kedzierska et al. 2025)
2,000 highly variable genes, a configuration of Highly variable gene selection: No training; 2,000 HVG of the log-normalised data; Log-normalised expression of 2,000 highly variable genes.
Overview
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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) |
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| 2,000 highly variable genes (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, Pancreas (16k) (Kedzierska et al. 2025) | 0.71 (best in column) | Not reported | 0.68 (best in column) | Not reported | 0.78 (best in column) | Not reported | 0.55 | Not reported | 0.77 (best in column) | Not reported | 3 (best in column) | Not reported | 0.93 | Not reported | 0.61 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| 2,000 highly variable genes (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, PBMC (12k) (Kedzierska et al. 2025) | 0.67 | Not reported | 0.63 | Not reported | 0.71 | Not reported | 0.51 | Not reported | 0.65 | Not reported | 5 | Not reported | 0.99 (best in column) | Not reported | 0.3 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| 2,000 highly variable genes (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, Pancreas (8k) (Kedzierska et al. 2025) | 0.49 | Not reported | 0.61 | Not reported | 0.76 | Not reported | 0.57 (best in column) | Not reported | 0.69 | Not reported | Not reported | Not reported | 0.9 | Not reported | 0.49 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| 2,000 highly variable genes (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, PBMC (95k) (Kedzierska et al. 2025) | 0.46 | Not reported | 0.53 | Not reported | 0.64 | Not reported | 0.5 | Not reported | Not reported | Not reported | 4 | 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 |
| 2,000 highly variable genes (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, Immune (330k) (Kedzierska et al. 2025) | 0.41 | Not reported | 0.53 | Not reported | 0.68 | Not reported | 0.51 | Not reported | 0.5 | Not reported | 4 | Not reported | 0.95 | Not reported | 0.05 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| 2,000 highly variable genes (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, Tabula Sapiens (483k) (Kedzierska et al. 2025) | 0.28 | Not reported | 0.45 | Not reported | 0.58 | Not reported | 0.48 | Not reported | 0.47 | Not reported | 3 (best in column) | Not reported | 0.93 | Not reported | 0 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| 2,000 highly variable genes (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 | 3 | Not reported | 3 | 5 | 4 | 3 | 1 | 3 | 4 |
| 2,000 highly variable genes (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 | 3 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| 2,000 highly variable genes (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring after UMAP projection, Immune (330k) (Kedzierska et al. 2025) | Not reported | 0.34 | Not reported | 0.48 | Not reported | 0.62 | Not reported | 0.48 | Not reported | 0.33 | Not reported | 2 (best in column) | Not reported | 0.55 | Not reported | 0.12 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| 2,000 highly variable genes (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring after UMAP projection, Pancreas (16k) (Kedzierska et al. 2025) | Not reported | 0.4 | Not reported | 0.58 (best in column) | Not reported | 0.69 | Not reported | 0.64 (best in column) | Not reported | 0.64 (best in column) | Not reported | 5 | Not reported | 0.53 | Not reported | 0.75 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| 2,000 highly variable genes (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring after UMAP projection, Pancreas (8k) (Kedzierska et al. 2025) | Not reported | 0.42 (best in column) | Not reported | 0.55 | Not reported | 0.73 (best in column) | Not reported | 0.49 | Not reported | 0.29 | Not reported | Not reported | Not reported | 0.58 | Not reported | 0 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| 2,000 highly variable genes (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring after UMAP projection, PBMC (12k) (Kedzierska et al. 2025) | Not reported | 0.42 (best in column) | Not reported | 0.55 | Not reported | 0.62 | Not reported | 0.63 | Not reported | 0.39 | Not reported | 3 | Not reported | 0.79 (best in column) | Not reported | 0 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| 2,000 highly variable genes (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring after UMAP projection, PBMC (95k) (Kedzierska et al. 2025) | Not reported | 0.4 | Not reported | 0.52 | Not reported | 0.56 | Not reported | 0.6 | Not reported | Not reported | Not reported | 5 | 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 |
| 2,000 highly variable genes (Kedzierska et al. 2025)Evaluation | Kedzierska et al. 2025 cell embedding scoring after UMAP projection, Tabula Sapiens (483k) (Kedzierska et al. 2025) | Not reported | 0.26 | Not reported | 0.39 | Not reported | 0.56 | Not reported | 0.36 | Not reported | 0.29 | Not reported | 2 (best in column) | Not reported | 0.57 | Not reported | 0 | 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
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Evidence
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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-hvg
- areas
- single-cell
- contexts
- research
- method types
- conventional_pipeline
- reported name
- HVG
- foundation model eligible
- false
- training setting
- No training; 2,000 HVG of the log-normalised data
- representation
- Log-normalised expression of 2,000 highly variable genes
- missing metadata
- version: reason: unreported; note: HVG selection flavour and software version not stated
- source locator
- Pages 7-8 'Models and baselines'; page 11 'Code availability'
- provenance note
- 2,000 highly variable genes baseline as run by Kedzierska et al. 2025.
Related records
- configuration of: Highly variable gene selection
- system: HVG cell embedding on evaluated datasets (Kedzierska et al. 2025)
- system: HVG cell embedding on Immune (330k) (Kedzierska et al. 2025)
- system: HVG cell embedding on Pancreas (16k) (Kedzierska et al. 2025)
- system: HVG cell embedding on Pancreas (8k) (Kedzierska et al. 2025)
- system: HVG cell embedding on PBMC (12k) (Kedzierska et al. 2025)
- system: HVG cell embedding on PBMC (95k) (Kedzierska et al. 2025)
- system: HVG cell embedding on Tabula Sapiens (483k) (Kedzierska et al. 2025)
- system: HVG UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025)
- system: HVG UMAP-projected embedding on Immune (330k) (Kedzierska et al. 2025)
- system: HVG UMAP-projected embedding on Pancreas (16k) (Kedzierska et al. 2025)
- system: HVG UMAP-projected embedding on Pancreas (8k) (Kedzierska et al. 2025)
- system: HVG UMAP-projected embedding on PBMC (12k) (Kedzierska et al. 2025)
- system: HVG UMAP-projected embedding on PBMC (95k) (Kedzierska et al. 2025)
- system: HVG UMAP-projected embedding on Tabula Sapiens (483k) (Kedzierska et al. 2025)