Benchmark run by the paper's authors. The per-model mean is computed by Rewire from the authors' Source Data rows; not reproduced.
1 evaluation · 1 result. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: No change (Ahlmann-Eltze et al. 2025) | Protocol: Norman double perturbations: expression prediction for held-out double perturbations (Ahlmann-Eltze et al. 2025 Fig. 1a and Extended Data Fig. 2a) Dataset: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations (scFoundation reprocessing, Ahlmann-Eltze et al. 2025) | 5.62 L2 distance (1,000 most highly expressed control genes; mean over held-out perturbations and splits)Computed by Rewire from the authors' source data unit-unreported · lower Uncertainty: Not reported by the source: No spread of the mean is stated; Rewire did not compute one Coverage: 310/310 perturbation-split rows scored | Author-reported evaluation · Source checkedMethods, coverage and sourceNo change on Norman doubles (Ahlmann-Eltze et al. 2025) perturbation-ahlmann-20261011-protocol-norman-double Aggregation: Not reported Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines; Source Data Fig. 1, Ahlmann-Eltze et al. 2025 · Source Data Fig. 1 (MOESM3), sheet "Panel A", rows with dataset_name "norman_from_scfoundation" and method "no_change", column "l2"; plotted as the red line in Fig. 1a |
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
38 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Comparison: adaptation Fine-tuned, fitted or applied per split by the paper's authors with default parameters where possible Context-only references | Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines Fig. 1a and Extended Data Fig. 2a; Source Data method "no_change" Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Methods 22(8):1657, published online 2025-08-04; PMC12328236 full-text XML | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: adaptation Fine-tuned, fitted or applied per split by the paper's authors with default parameters where possible Context-only references | Source Data Fig. 1, Ahlmann-Eltze et al. 2025 Fig. 1a and Extended Data Fig. 2a; Source Data method "no_change" Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data Fig. 1 (41592_2025_2772_MOESM3_ESM.xlsx) as published with the article | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: aggregation Arithmetic mean per model over held-out perturbations, pooling test and val rows and all splits Context-only references | Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines Fig. 1a and Extended Data Fig. 2a; Source Data method "no_change" Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Methods 22(8):1657, published online 2025-08-04; PMC12328236 full-text XML | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: aggregation Arithmetic mean per model over held-out perturbations, pooling test and val rows and all splits Context-only references | Source Data Fig. 1, Ahlmann-Eltze et al. 2025 Fig. 1a and Extended Data Fig. 2a; Source Data method "no_change" Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data Fig. 1 (41592_2025_2772_MOESM3_ESM.xlsx) as published with the article | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: budget Not reported Context-only references | Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines Fig. 1a and Extended Data Fig. 2a; Source Data method "no_change" Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Methods 22(8):1657, published online 2025-08-04; PMC12328236 full-text XML | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: budget Not reported Context-only references | Source Data Fig. 1, Ahlmann-Eltze et al. 2025 Fig. 1a and Extended Data Fig. 2a; Source Data method "no_change" Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data Fig. 1 (41592_2025_2772_MOESM3_ESM.xlsx) as published with the article | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: dataset version scFoundation reprocessing, figshare file 44477939 Context-only references | Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines Fig. 1a and Extended Data Fig. 2a; Source Data method "no_change" Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Methods 22(8):1657, published online 2025-08-04; PMC12328236 full-text XML | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: dataset version scFoundation reprocessing, figshare file 44477939 Context-only references | Source Data Fig. 1, Ahlmann-Eltze et al. 2025 Fig. 1a and Extended Data Fig. 2a; Source Data method "no_change" Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data Fig. 1 (41592_2025_2772_MOESM3_ESM.xlsx) as published with the article | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: inputs Expression of training perturbations and control; identity of the perturbed genes Context-only references | Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines Fig. 1a and Extended Data Fig. 2a; Source Data method "no_change" Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Methods 22(8):1657, published online 2025-08-04; PMC12328236 full-text XML | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: inputs Expression of training perturbations and control; identity of the perturbed genes Context-only references | Source Data Fig. 1, Ahlmann-Eltze et al. 2025 Fig. 1a and Extended Data Fig. 2a; Source Data method "no_change" Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Source Data Fig. 1 (41592_2025_2772_MOESM3_ESM.xlsx) as published with the article | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: perturbation-ahlmann-20261011-eval-norman-no-change