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1 evaluation · 2 results. Different protocols are not a single leaderboard.
Protocol: Kedzierska et al. 2025 Geneformer pretraining-objective reconstruction · Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025)
Sorted by Pearson (Geneformer input versus predicted gene ranking, all genes unmasked; best value across datasets) (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 | Pearson (Geneformer input versus predicted gene ranking, all genes unmasked; best value across datasets) | Pearson (Geneformer input versus predicted gene ranking, all genes unmasked; median across datasets) |
|---|---|---|
| Geneformer (Kedzierska et al. 2025)Evaluation | 0.95 | 0.56 |
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Geneformer (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 Geneformer pretraining-objective reconstruction Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025) | 0.95 Pearson (Geneformer input versus predicted gene ranking, all genes unmasked; best value across datasets) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGeneformer pretraining reconstruction on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-geneformer-reconstruction Aggregation: Not reported Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) · Page 5, 'Results and discussion', paragraph beginning 'Notably, scGPT without embeddings', sentence 2 ('median and best correlations of 0.56 and 0.95, respectively, across datasets') |
| Configuration: Geneformer (Kedzierska et al. 2025) | Protocol: Kedzierska et al. 2025 Geneformer pretraining-objective reconstruction Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025) | 0.56 Pearson (Geneformer input versus predicted gene ranking, all genes unmasked; median across datasets) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGeneformer pretraining reconstruction on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-geneformer-reconstruction Aggregation: Not reported Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) · Page 5, 'Results and discussion', paragraph beginning 'Notably, scGPT without embeddings', sentence 2 ('median and best correlations of 0.56 and 0.95, respectively, across datasets') |
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Kedzierska et al. 2025 Geneformer pretraining-objective reconstruction
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18 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 | Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Page 5, paragraph before Fig. 2 caption 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 Median and best value across datasets Context-only references | Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Page 5, paragraph before Fig. 2 caption 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 | Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Page 5, paragraph before Fig. 2 caption 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 | Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Page 5, paragraph before Fig. 2 caption 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 | Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Page 5, paragraph before Fig. 2 caption 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: metric implementation Pearson correlation of true and predicted scaled gene rankings (Methods page 10) Context-only references | Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Page 5, paragraph before Fig. 2 caption 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: population Not reported Context-only references | Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Page 5, paragraph before Fig. 2 caption 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: protocol id gfm-guides-20261014-kedzierska2025-protocol-geneformer-reconstruction Context-only references | Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Page 5, paragraph before Fig. 2 caption 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: split No split; each whole dataset embedded and scored Context-only references | Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Page 5, paragraph before Fig. 2 caption 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 |
| Origin independent_paper Context-only references | Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Page 5, paragraph before Fig. 2 caption 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-recon-evaluated-datasets-geneformer