rewirebio.iobenchmarks
Dataset subset

Replogle CRISPRi RPE1, propensity-matched pairs (Kendiukhov 2026)

Propensity-matched pairs from the RPE1 confound battery; the matched count is not printed.

Evaluation results

2 evaluations · 2 results. Different protocols are not a single leaderboard.

Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: Geneformer V2-316M attention edges, layer not stated (Kendiukhov 2026)Protocol: Propensity-matched edge AUROC (Kendiukhov 2026)
Dataset subset: Replogle CRISPRi RPE1, propensity-matched pairs (Kendiukhov 2026)
0.568 AUROC (AUROC over propensity-matched perturbation-gene pairs (k = 5 negatives per positive))
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 CRISPRi RPE1, propensity-matched pairs

gfm-guides-20261014-kendiukhov2026-protocol-propensity-matched

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 (iii): '(attention = 0.568, correlation = 0.561)'
Configuration: Absolute Spearman correlation edges (Kendiukhov 2026)Protocol: Propensity-matched edge AUROC (Kendiukhov 2026)
Dataset subset: Replogle CRISPRi RPE1, propensity-matched pairs (Kendiukhov 2026)
0.561 AUROC (AUROC over propensity-matched perturbation-gene pairs (k = 5 negatives per positive))
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 CRISPRi RPE1, propensity-matched pairs

gfm-guides-20261014-kendiukhov2026-protocol-propensity-matched

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 (iii): '(attention = 0.568, correlation = 0.561)'

Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.

Research readiness

0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

Release 2026-11-02-a7f03c9e55a5 · Evidence verified: Not verified

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified
  • Sample annotations are recorded: not yet verified
  • Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • A pinned run recipe exists: not yet verified
  • Compute requirements are estimated: not yet verified

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Independent validation data exist: not yet verified
  • Overlap with training data is checked: not yet verified

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Subset and evaluation context

This record describes a particular subset or cohort used in an evaluation. Its results do not describe the full dataset.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

5 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statementOriginal source and locationReview and provenance
Source dataset label
Replogle CRISPRi (RPE1), propensity-matched
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', item (iii)

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', item (iii)
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', item (iii)

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', item (iii)

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
Propensity-matched pairs from the RPE1 confound battery; the matched count is not printed.
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', item (iii)

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 CRISPRi RPE1, propensity-matched pairs (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', item (iii)

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

Sources and history

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

1 source record and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: gfm-guides-20261014-kendiukhov2026-data-rpe1-crispri-propensity-matched

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), propensity-matched
source locator
Page 10, 'Cross-cell-type generalisation of confound pattern', item (iii)
missing metadata
version: reason: unreported
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