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Replogle genome-scale CRISPRi, K562, 280 evaluable perturbations (Kendiukhov 2026)

The 280 evaluable K562 CRISPRi perturbations used for the attention versus correlation comparison and the 280 x 1,999 perturbation-gene incremental-value dataset (559,720 pairs, 2.8% positive).

Evaluation results

6 evaluations · 6 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Gene-level logistic regression (Kendiukhov 2026)	Protocol: Gene-level logistic regression under 5-fold GroupKFold by perturbation (Kendiukhov 2026) Dataset subset: Replogle genome-scale CRISPRi, K562, 280 evaluable perturbations (Kendiukhov 2026)	0.895 AUROC (cross-validated AUROC over perturbation-gene pairs, 5-fold GroupKFold by perturbation) unitless · higher Uncertainty: 95% CI 0.884 to 0.905. Methods: bootstrap CIs use 200 iterations with perturbation-level resampling unless otherwise noted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Gene-level logistic regression on Replogle genome-scale CRISPRi, K562, 280 evaluable perturbations gfm-guides-20261014-kendiukhov2026-protocol-incremental-value-lr 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 8, 'No incremental pairwise value on the perturbation-target prediction task', paragraph 1, sentence 2: 'Gene-level features alone achieve AUROC = 0.895 [bootstrap 95% CI: 0.884, 0.905]'
Configuration: Gene-level logistic regression plus attention edge (Kendiukhov 2026)	Protocol: Gene-level logistic regression under 5-fold GroupKFold by perturbation (Kendiukhov 2026) Dataset subset: Replogle genome-scale CRISPRi, K562, 280 evaluable perturbations (Kendiukhov 2026)	−0.0004 AUROC difference (Gene-level features plus attention edge minus gene-level features only (gene-level logistic regression); cross-validated AUROC over perturbation-gene pairs, 5-fold GroupKFold by perturbation) unitless · higher Uncertainty: 95% CI -0.001 to 0.000. Methods 'Statistical framework': bootstrap CIs use 200 iterations with perturbation-level resampling unless otherwise noted; Fig. 4B caption: 'Bootstrap ∆AUROC distribution (n = 100)' Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Gene-level logistic regression plus attention edge on Replogle genome-scale CRISPRi, K562, 280 evaluable perturbations gfm-guides-20261014-kendiukhov2026-protocol-incremental-value-lr 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 8, 'No incremental pairwise value on the perturbation-target prediction task', paragraph 1, sentence 2: 'adding attention yields ∆AUROC = −0.0004 [−0.001, 0.000]'
Configuration: Gene-level logistic regression plus correlation edge (Kendiukhov 2026)	Protocol: Gene-level logistic regression under 5-fold GroupKFold by perturbation (Kendiukhov 2026) Dataset subset: Replogle genome-scale CRISPRi, K562, 280 evaluable perturbations (Kendiukhov 2026)	−0.002 AUROC difference (Gene-level features plus correlation edge minus gene-level features only (gene-level logistic regression); cross-validated AUROC over perturbation-gene pairs, 5-fold GroupKFold by perturbation) unitless · higher Uncertainty: 95% CI -0.005 to 0.000. Methods 'Statistical framework': bootstrap CIs use 200 iterations with perturbation-level resampling unless otherwise noted; Fig. 4B caption: 'Bootstrap ∆AUROC distribution (n = 100)' Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Gene-level logistic regression plus correlation edge on Replogle genome-scale CRISPRi, K562, 280 evaluable perturbations gfm-guides-20261014-kendiukhov2026-protocol-incremental-value-lr 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 8, 'No incremental pairwise value on the perturbation-target prediction task', paragraph 1, sentence 2: 'adding correlation yields ∆AUROC = −0.002 [−0.005, 0.000]'
Configuration: Geneformer V2-316M attention edges, layer 13 (Kendiukhov 2026)	Protocol: Perturbation-first AUROC, K562 CRISPRi (Kendiukhov 2026) Dataset subset: Replogle genome-scale CRISPRi, K562, 280 evaluable perturbations (Kendiukhov 2026)	0.704 AUROC (per-perturbation AUROC for DE targets (LFC > 0.5), summarised over perturbations; K562 CRISPRi) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer V2-316M attention edges, layer 13 on Replogle genome-scale CRISPRi, K562, 280 evaluable perturbations gfm-guides-20261014-kendiukhov2026-protocol-pf-k562-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 7, 'Perturbation-first validation reveals gene-level dominance', paragraph 2, sentence 1: 'AUROC = 0.704 at L13 (n = 280 evaluable perturbations)'
Configuration: Geneformer V2-316M attention edges, layer 15 (Kendiukhov 2026)	Protocol: Perturbation-first AUROC, K562 CRISPRi (Kendiukhov 2026) Dataset subset: Replogle genome-scale CRISPRi, K562, 280 evaluable perturbations (Kendiukhov 2026)	0.743 AUROC (per-perturbation AUROC for DE targets (LFC > 0.5), summarised over perturbations; K562 CRISPRi) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer V2-316M attention edges, layer 15 on Replogle genome-scale CRISPRi, K562, 280 evaluable perturbations gfm-guides-20261014-kendiukhov2026-protocol-pf-k562-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 7, 'Perturbation-first validation reveals gene-level dominance', paragraph 2, sentence 5 (nested cross-validation over 18 layers): 'identifies L15 as the best layer (AUROC = 0.743'
Configuration: Absolute Spearman correlation edges (Kendiukhov 2026)	Protocol: Perturbation-first AUROC, K562 CRISPRi (Kendiukhov 2026) Dataset subset: Replogle genome-scale CRISPRi, K562, 280 evaluable perturbations (Kendiukhov 2026)	0.703 AUROC (per-perturbation AUROC for DE targets (LFC > 0.5), summarised over perturbations; K562 CRISPRi) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Absolute Spearman correlation edges on Replogle genome-scale CRISPRi, K562, 280 evaluable perturbations gfm-guides-20261014-kendiukhov2026-protocol-pf-k562-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 7, 'Perturbation-first validation reveals gene-level dominance', paragraph 2, sentence 1: '(0.703; Wilcoxon p = 0.73'

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Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Scored count 280 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) Original source ↗ Page 7 paragraph 2; page 8 'No incremental pairwise value' Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.scored_count` Source artifact SHA-256: `4c1699cb964ae588117a6737f5e9e189eb9a5ef5ff78568d2a99e7a13d6608fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source dataset label Replogle genome-scale CRISPRi (K562) 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) Original source ↗ Page 7 paragraph 2; page 8 'No incremental pairwise value' Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_dataset_label` Source artifact SHA-256: `4c1699cb964ae588117a6737f5e9e189eb9a5ef5ff78568d2a99e7a13d6608fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Page 7 paragraph 2; page 8 'No incremental pairwise value' 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) Original source ↗ Page 7 paragraph 2; page 8 'No incremental pairwise value' Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `4c1699cb964ae588117a6737f5e9e189eb9a5ef5ff78568d2a99e7a13d6608fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Split No train/test split for edge AUROC; cross-validation where stated by the protocol 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) Original source ↗ Page 7 paragraph 2; page 8 'No incremental pairwise value' Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `4c1699cb964ae588117a6737f5e9e189eb9a5ef5ff78568d2a99e7a13d6608fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description The 280 evaluable K562 CRISPRi perturbations used for the attention versus correlation comparison and the 280 x 1,999 perturbation-gene incremental-value dataset (559,720 pairs, 2.8% positive). 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) Original source ↗ Page 7 paragraph 2; page 8 'No incremental pairwise value' Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `4c1699cb964ae588117a6737f5e9e189eb9a5ef5ff78568d2a99e7a13d6608fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Name Replogle genome-scale CRISPRi, K562, 280 evaluable perturbations (Kendiukhov 2026) 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) Original source ↗ Page 7 paragraph 2; page 8 'No incremental pairwise value' Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `4c1699cb964ae588117a6737f5e9e189eb9a5ef5ff78568d2a99e7a13d6608fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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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) · Original source · Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14)

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Technical metadata and extraction receipts

Stable ID: gfm-guides-20261014-kendiukhov2026-data-k562-crispri-280

areas: single-cell; biological-networks
contexts: research
split: No train/test split for edge AUROC; cross-validation where stated by the protocol
source dataset label: Replogle genome-scale CRISPRi (K562)
scored count: 280
source locator: Page 7 paragraph 2; page 8 'No incremental pairwise value'
missing metadata: version: reason: unreported

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