Perturbation-first AUROC, RPE1 CRISPRi (Kendiukhov 2026)
As the K562 CRISPRi protocol, on Replogle RPE1 CRISPRi, with 3,309 HVGs (perturbation genes forced into the HVG set).
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
9 recorded evaluations, 9 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
9 evaluations · 9 results. Different protocols are not a single leaderboard.
Protocol: Perturbation-first AUROC, RPE1 CRISPRi (Kendiukhov 2026)
Sorted by AUROC (per-perturbation AUROC for DE targets, summarised over perturbations; RPE1 CRISPRi) (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.
All 9 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- Target-gene dropout rate baseline on Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery
- Target-gene mean expression baseline on Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery
- Target-gene variance baseline on Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery
- Geneformer V2-316M attention edges, layer not stated on Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery
- Absolute Spearman correlation edges on Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery
- Geneformer V2-316M attention edges, layer 15 on Replogle genome-scale CRISPRi, RPE1, 1,251 evaluable perturbations
- Geneformer V2-316M attention edges, layer 6 on Replogle genome-scale CRISPRi, RPE1, 1,251 evaluable perturbations
- Geneformer V2-316M attention edges, layer not stated on Replogle genome-scale CRISPRi, RPE1, 1,251 evaluable perturbations
- Absolute Spearman correlation edges on Replogle genome-scale CRISPRi, RPE1, 1,251 evaluable perturbations
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- External evaluations
- 9
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
No-change prediction under matched control conditions
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Training-only mean-effect or linear prediction
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-11-02-a7f03c9e55a5. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Evidence
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Evidence table
Inspect claims, sources and review details
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Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record and release history
- 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)
Technical metadata and extraction receipts
Stable ID: gfm-guides-20261014-kendiukhov2026-protocol-pf-rpe1-crispri
- areas
- single-cell; biological-networks
- contexts
- research
- protocol
- As the K562 CRISPRi protocol, on Replogle RPE1 CRISPRi, with 3,309 HVGs (perturbation genes forced into the HVG set).
- version
- BMC Genomics 27:634
- metric
- auroc
- metric direction
- higher
- unit
- unitless
- 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
- source locator
- Page 10; page 14 'Perturbation-first validation'
- limitations
- Single run; no repeat across seeds reported for these values.
Related records
- part of: Perturbation-target prediction from attention-derived edge scores (Kendiukhov 2026, Objective B)
- assessment: Target-gene dropout rate baseline on Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery
- assessment: Target-gene mean expression baseline on Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery
- assessment: Target-gene variance baseline on Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery
- assessment: Geneformer V2-316M attention edges, layer not stated on Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery
- assessment: Absolute Spearman correlation edges on Replogle genome-scale CRISPRi, RPE1, 1,167 perturbations, confound battery
- assessment: Geneformer V2-316M attention edges, layer 15 on Replogle genome-scale CRISPRi, RPE1, 1,251 evaluable perturbations
- assessment: Geneformer V2-316M attention edges, layer 6 on Replogle genome-scale CRISPRi, RPE1, 1,251 evaluable perturbations
- assessment: Geneformer V2-316M attention edges, layer not stated on Replogle genome-scale CRISPRi, RPE1, 1,251 evaluable perturbations
- assessment: Absolute Spearman correlation edges on Replogle genome-scale CRISPRi, RPE1, 1,251 evaluable perturbations