Result

0.919 pearson-correlation

RF_scFoundation on Replogle_RPE1 pearson-correlation (raw expression, top 20 DE genes (t-test, GEARS list))

Tested configuration: RF_scFoundation (Csendes et al. 2025)
Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, RPE1 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2)
Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, RPE1 CRISPRi (GEARS processing, Csendes et al. 2025)
Procedure: perturbation-response-20261009-protocol-csendes2025-replogle-rpe1-pex
Evaluation: RF_scFoundation on Replogle_RPE1 (Csendes et al. 2025)
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Author-reported evaluation · source checkedCsendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell D49, row 'Replogle_RPE1 / RF_scFoundation', column 'Pearson DE'

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.

Reproduction

Split: GEARS perturbation-exclusive split
Adaptation: Fine-tuned or trained per dataset with validation-set selection
Scoring implementation: Pseudo-bulk Pearson correlations as in the scGPT publication

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

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.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-10-10-6e93f504adfc
Property and statement	Original source and location	Review and provenance
Reported result 0.919001 Individual claims	Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) Original source ↗ Supplementary Table 2, cell D49, row 'Replogle_RPE1 / RF_scFoundation', column 'Pearson DE' Version: 12864_2025_11600_MOESM4_ESM.xlsx from the Europe PMC supplementary bundle (hash is of the workbook; the bundle zip is rebuilt per request) Retrieved: 2026-10-09T20:58:56Z	source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 author reported Audit details Extracted by deterministic parse of the pinned XLSX cell XML (extract/extract_perturbation.py), with row and column labels asserted. printed_value is the shortest decimal that round-trips to the stored number; display formatting was not applied. Pending independent review. Independent review 2026-10-09: value and identity match the source. Field: `attributes.printed_value` Source artifact SHA-256: `b5bfcb633921a642de077a39fcb015c6d36bc36a52d9c5e9ceca33be483d3261` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `b5bfcb633921a642de077a39fcb015c6d36bc36a52d9c5e9ceca33be483d3261` Extraction artifact

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Sources and history

Release 2026-10-10-6e93f504adfc · Record review: source checked

2 source records and release history

Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Original source · 12864_2025_11600_MOESM4_ESM.xlsx from the Europe PMC supplementary bundle (hash is of the workbook; the bundle zip is rebuilt per request)
Benchmarking foundation cell models for post-perturbation RNA-seq prediction · Original source · BMC Genomics 26:393, published 2025-04-23; PMC12016270 full-text XML

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Technical metadata and extraction receipts

Stable ID: perturbation-response-20261009-result-csendes2025-replogle-rpe1-rf-scfoundation-pearson-de

metric: pearson-correlation
metric direction: higher
unit: unitless
printed value: 0.919001
numeric value: 0.919001
source locator: Supplementary Table 2, cell D49, row 'Replogle_RPE1 / RF_scFoundation', column 'Pearson DE'
missing metadata: uncertainty: reason: unreported
review: method: source-hash-verification; deterministic-table-parse; independent-cell-check; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-09; artifact sha256: b5bfcb633921a642de077a39fcb015c6d36bc36a52d9c5e9ceca33be483d3261; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12016270/supplementaryFiles; method note: Re-downloaded the workbook and matched its SHA-256. Read Supplementary Table 2 with a separate OOXML reader written for this review (the extractor's script was not run). Checked printed and numeric value, locator, metric, qualifier, unit and direction, the evaluation's configuration, protocol and dataset, and its origin. Checked the 24 Pearson Delta values quoted in Results paragraphs 6 and 7.; note: Extracted by deterministic parse of the pinned XLSX cell XML (extract/extract_perturbation.py), with row and column labels asserted. printed_value is the shortest decimal that round-trips to the stored number; display formatting was not applied. Pending independent review. Independent review 2026-10-09: value and identity match the source.
metric qualifier: raw expression, top 20 DE genes (t-test, GEARS list)

Related records

evaluation: RF_scFoundation on Replogle_RPE1 (Csendes et al. 2025)

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