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1 evaluation · 1 result. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Geneformer V2-316M attention edges, layer 15 (Kendiukhov 2026) | Protocol: Perturbation-first AUROC, RPE1 CRISPRi (Kendiukhov 2026) Dataset subset: Replogle genome-scale CRISPRi, RPE1, 1,251 evaluable perturbations (Kendiukhov 2026) | 0.748 AUROC (per-perturbation AUROC for DE targets, summarised over perturbations; RPE1 CRISPRi) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcegfm-guides-20261014-kendiukhov2026-protocol-pf-rpe1-crispri Aggregation: Not reported Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) · Page 10, 'Context-dependent attention-correlation relationship', sentence 4: '(L15: 0.748 vs. 0.658' |
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Perturbation-first AUROC, RPE1 CRISPRi (Kendiukhov 2026)
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18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Comparison: adaptation Foundation-model attention read out zero-shot; correlation and gene-level statistics computed from the same control cells; logistic regression fitted under GroupKFold Context-only references | Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) Page 10, 'Context-dependent attention-correlation relationship' Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) | 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 Summary over perturbations; statistic not stated Context-only references | Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) Page 10, 'Context-dependent attention-correlation relationship' Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) | 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 | Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) Page 10, 'Context-dependent attention-correlation relationship' Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) | 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 | Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) Page 10, 'Context-dependent attention-correlation relationship' Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) | 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 Control-cell expression and DE labels of the perturbation dataset; N_ctrl = 2,000, HVG = 3,309 with perturbation genes forced in (Methods); the LFC threshold for the reported RPE1 values is not restated Context-only references | Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) Page 10, 'Context-dependent attention-correlation relationship' Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) | 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 Per-perturbation AUROC for classifying differentially expressed targets (Mann-Whitney U test with Benjamini-Hochberg correction and an LFC threshold define DE hits); summary across perturbations not stated Context-only references | Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) Page 10, 'Context-dependent attention-correlation relationship' Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) | 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 | Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) Page 10, 'Context-dependent attention-correlation relationship' Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) | 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-kendiukhov2026-protocol-pf-rpe1-crispri Context-only references | Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) Page 10, 'Context-dependent attention-correlation relationship' Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) | 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 train/test split; scores computed from control cells and compared with DE labels Context-only references | Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) Page 10, 'Context-dependent attention-correlation relationship' Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) | 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 | Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) Page 10, 'Context-dependent attention-correlation relationship' Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) | 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 2026-11-02-a7f03c9e55a5 · Record review: source checked
Stable ID: gfm-guides-20261014-kendiukhov2026-eval-pf-rpe1-crispri-rpe1-crispri-1251-geneformer-v2-316m-attention-l15