Dataset subset

Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery (Kendiukhov 2026)

1,167 evaluated RPE1 perturbations and 3,838,263 gene-pair observations used for the RPE1 confound-decomposition battery.

Evaluation results

8 evaluations · 8 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, RPE1, 1,167 perturbations, confound battery (Kendiukhov 2026)	0.942 AUROC (cross-validated AUROC over perturbation-gene pairs, 5-fold GroupKFold by perturbation) unitless · higher Uncertainty: Not reported by the source 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, RPE1, 1,167 perturbations, confound battery 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 10, 'Cross-cell-type generalisation of confound pattern', item (ii): 'Gene-level features alone achieve AUROC = 0.942 under 5-fold GroupKFold CV'
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, RPE1, 1,167 perturbations, confound battery (Kendiukhov 2026)	0.0001 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 0.0001 to 0.0001. Interval type printed as '95% CI' without naming bootstrap; Methods 'Statistical framework': 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 plus attention edge on Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery 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 10, 'Cross-cell-type generalisation of confound pattern', item (ii): 'adding attention yields ∆AUROC = +0.0001 [95% CI: +0.0001, +0.0001]'
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, RPE1, 1,167 perturbations, confound battery (Kendiukhov 2026)	−0.0006 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: Not reported by the source 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, RPE1, 1,167 perturbations, confound battery 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 10, 'Cross-cell-type generalisation of confound pattern', item (ii): 'while adding correlation yields ∆AUROC = −0.0006'
Configuration: Target-gene dropout rate baseline (Kendiukhov 2026)	Protocol: Perturbation-first AUROC, RPE1 CRISPRi (Kendiukhov 2026) Dataset subset: Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery (Kendiukhov 2026)	0.797 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 checked Methods, coverage and source Target-gene dropout rate baseline on Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery gfm-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, 'Cross-cell-type generalisation of confound pattern', item (i): 'variance AUROC = 0.866, mean expression = 0.851, dropout = 0.797 vs. attention = 0.747 and correlation = 0.658'
Configuration: Target-gene mean expression baseline (Kendiukhov 2026)	Protocol: Perturbation-first AUROC, RPE1 CRISPRi (Kendiukhov 2026) Dataset subset: Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery (Kendiukhov 2026)	0.851 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 checked Methods, coverage and source Target-gene mean expression baseline on Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery gfm-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, 'Cross-cell-type generalisation of confound pattern', item (i): 'variance AUROC = 0.866, mean expression = 0.851, dropout = 0.797 vs. attention = 0.747 and correlation = 0.658'
Configuration: Target-gene variance baseline (Kendiukhov 2026)	Protocol: Perturbation-first AUROC, RPE1 CRISPRi (Kendiukhov 2026) Dataset subset: Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery (Kendiukhov 2026)	0.866 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 checked Methods, coverage and source Target-gene variance baseline on Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery gfm-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, 'Cross-cell-type generalisation of confound pattern', item (i): 'variance AUROC = 0.866, mean expression = 0.851, dropout = 0.797 vs. attention = 0.747 and correlation = 0.658'
Configuration: Geneformer V2-316M attention edges, layer not stated (Kendiukhov 2026)	Protocol: Perturbation-first AUROC, RPE1 CRISPRi (Kendiukhov 2026) Dataset subset: Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery (Kendiukhov 2026)	0.747 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 checked Methods, coverage and source Geneformer V2-316M attention edges, layer not stated on Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery gfm-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, 'Cross-cell-type generalisation of confound pattern', item (i): 'variance AUROC = 0.866, mean expression = 0.851, dropout = 0.797 vs. attention = 0.747 and correlation = 0.658'
Configuration: Absolute Spearman correlation edges (Kendiukhov 2026)	Protocol: Perturbation-first AUROC, RPE1 CRISPRi (Kendiukhov 2026) Dataset subset: Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery (Kendiukhov 2026)	0.658 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 checked Methods, coverage and source Absolute Spearman correlation edges on Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery gfm-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, 'Cross-cell-type generalisation of confound pattern', item (i): 'variance AUROC = 0.866, mean expression = 0.851, dropout = 0.797 vs. attention = 0.747 and correlation = 0.658'

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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 1167 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 10, 'Cross-cell-type generalisation of confound pattern' 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 CRISPRi (RPE1) 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 10, 'Cross-cell-type generalisation of confound pattern' 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 10, 'Cross-cell-type generalisation of confound pattern' 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 10, 'Cross-cell-type generalisation of confound pattern' 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 10, 'Cross-cell-type generalisation of confound pattern' 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 1,167 evaluated RPE1 perturbations and 3,838,263 gene-pair observations used for the RPE1 confound-decomposition battery. 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 10, 'Cross-cell-type generalisation of confound pattern' 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, RPE1, 1,167 perturbations, confound battery (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 10, 'Cross-cell-type generalisation of confound pattern' 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-rpe1-crispri-1167

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 CRISPRi (RPE1)
scored count: 1167
source locator: Page 10, 'Cross-cell-type generalisation of confound pattern'
missing metadata: version: reason: unreported

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