Propensity-matched edge AUROC (Kendiukhov 2026)
Each DE-positive target matched to k = 5 DE-negative targets with similar expression mean, variance and dropout rate by propensity-score nearest-neighbour matching; edge-score AUROC on the matched pairs.
Overview
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3 recorded evaluations, 3 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
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All evaluations
3 evaluations · 3 results. Different protocols are not a single leaderboard.
Protocol: Propensity-matched edge AUROC (Kendiukhov 2026)
Sorted by AUROC (AUROC over propensity-matched perturbation-gene pairs (k = 5 negatives per positive)) (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.
| Tested configuration | Protocol and dataset | AUROC (AUROC over propensity-matched perturbation-gene pairs (k = 5 negatives per positive)) |
|---|---|---|
| Geneformer V2-316M attention edges, layer not stated (Kendiukhov 2026)Evaluation | Replogle CRISPRi K562, propensity-matched pairs (Kendiukhov 2026) | 0.609 (best in column) |
| Geneformer V2-316M attention edges, layer not stated (Kendiukhov 2026)Evaluation | Replogle CRISPRi RPE1, propensity-matched pairs (Kendiukhov 2026) | 0.568 |
| Absolute Spearman correlation edges (Kendiukhov 2026)Evaluation | Replogle CRISPRi RPE1, propensity-matched pairs (Kendiukhov 2026) | 0.561 |
All 3 result rows with coverage, uncertainty and sources
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Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
Methods and evaluation design
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Recorded evaluations
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Baseline coverage
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- External evaluations
- 3
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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
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Evidence
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Evidence table
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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-propensity-matched
- areas
- single-cell; biological-networks
- contexts
- research
- protocol
- Each DE-positive target matched to k = 5 DE-negative targets with similar expression mean, variance and dropout rate by propensity-score nearest-neighbour matching; edge-score AUROC on the matched pairs.
- version
- BMC Genomics 27:634
- metric
- auroc
- metric direction
- higher
- unit
- unitless
- metric implementation
- AUROC over propensity-matched perturbation-gene pairs
- source locator
- Page 9 paragraph 1; page 10 'Cross-cell-type generalisation of confound pattern'; page 14 'Confound decomposition'
- 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: Geneformer V2-316M attention edges, layer not stated on Replogle CRISPRi K562, propensity-matched pairs
- assessment: Geneformer V2-316M attention edges, layer not stated on Replogle CRISPRi RPE1, propensity-matched pairs
- assessment: Absolute Spearman correlation edges on Replogle CRISPRi RPE1, propensity-matched pairs