Configuration

RF_scGPT (Csendes et al. 2025)

RF regression with scGPT features of the perturbed gene.

Overview

RF regression with scGPT features of the perturbed gene.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

4 evaluations · 24 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: RF_scGPT (Csendes et al. 2025)	Protocol: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS processing, Csendes et al. 2025)	0.993 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Adamson (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-adamson-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell C5, row 'Adamson / RF_scGPT', column 'Pearson'
Configuration: RF_scGPT (Csendes et al. 2025)	Protocol: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS processing, Csendes et al. 2025)	0.97 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Adamson (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-adamson-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell D5, row 'Adamson / RF_scGPT', column 'Pearson DE'
Configuration: RF_scGPT (Csendes et al. 2025)	Protocol: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS processing, Csendes et al. 2025)	0.727 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Adamson (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-adamson-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell E5, row 'Adamson / RF_scGPT', column 'Pearson Delta'
Configuration: RF_scGPT (Csendes et al. 2025)	Protocol: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS processing, Csendes et al. 2025)	0.735 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Adamson (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-adamson-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell F5, row 'Adamson / RF_scGPT', column 'Pearson Delta DE'
Configuration: RF_scGPT (Csendes et al. 2025)	Protocol: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS processing, Csendes et al. 2025)	0.79 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Adamson (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-adamson-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell H5, row 'Adamson / RF_scGPT', column 'Pearson Delta DE without KOd gene'
Configuration: RF_scGPT (Csendes et al. 2025)	Protocol: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS processing, Csendes et al. 2025)	0.732 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Adamson (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-adamson-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell G5, row 'Adamson / RF_scGPT', column 'Pearson Delta DE (based on Wilcoxon)'
Configuration: RF_scGPT (Csendes et al. 2025)	Protocol: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations (GEARS processing, Csendes et al. 2025)	0.988 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Norman (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-norman-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell C20, row 'Norman / RF_scGPT', column 'Pearson'
Configuration: RF_scGPT (Csendes et al. 2025)	Protocol: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations (GEARS processing, Csendes et al. 2025)	0.914 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Norman (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-norman-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell D20, row 'Norman / RF_scGPT', column 'Pearson DE'
Configuration: RF_scGPT (Csendes et al. 2025)	Protocol: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations (GEARS processing, Csendes et al. 2025)	0.583 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Norman (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-norman-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell E20, row 'Norman / RF_scGPT', column 'Pearson Delta'
Configuration: RF_scGPT (Csendes et al. 2025)	Protocol: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations (GEARS processing, Csendes et al. 2025)	0.647 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Norman (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-norman-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell F20, row 'Norman / RF_scGPT', column 'Pearson Delta DE'
Configuration: RF_scGPT (Csendes et al. 2025)	Protocol: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations (GEARS processing, Csendes et al. 2025)	0.685 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Norman (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-norman-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell H20, row 'Norman / RF_scGPT', column 'Pearson Delta DE without KOd gene'
Configuration: RF_scGPT (Csendes et al. 2025)	Protocol: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations (GEARS processing, Csendes et al. 2025)	0.71 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Norman (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-norman-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell G20, row 'Norman / RF_scGPT', column 'Pearson Delta DE (based on Wilcoxon)'
Configuration: RF_scGPT (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.988 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell C35, row 'Replogle_K562 / RF_scGPT', column 'Pearson'
Configuration: RF_scGPT (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.958 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell D35, row 'Replogle_K562 / RF_scGPT', column 'Pearson DE'
Configuration: RF_scGPT (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.421 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell E35, row 'Replogle_K562 / RF_scGPT', column 'Pearson Delta'
Configuration: RF_scGPT (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.52 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell F35, row 'Replogle_K562 / RF_scGPT', column 'Pearson Delta DE'
Configuration: RF_scGPT (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.545 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell H35, row 'Replogle_K562 / RF_scGPT', column 'Pearson Delta DE without KOd gene'
Configuration: RF_scGPT (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.538 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell G35, row 'Replogle_K562 / RF_scGPT', column 'Pearson Delta DE (based on Wilcoxon)'
Configuration: RF_scGPT (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)	0.978 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Replogle_RPE1 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-rpe1-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell C50, row 'Replogle_RPE1 / RF_scGPT', column 'Pearson'
Configuration: RF_scGPT (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)	0.918 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Replogle_RPE1 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-rpe1-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell D50, row 'Replogle_RPE1 / RF_scGPT', column 'Pearson DE'
Configuration: RF_scGPT (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)	0.635 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Replogle_RPE1 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-rpe1-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell E50, row 'Replogle_RPE1 / RF_scGPT', column 'Pearson Delta'
Configuration: RF_scGPT (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)	0.646 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Replogle_RPE1 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-rpe1-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell F50, row 'Replogle_RPE1 / RF_scGPT', column 'Pearson Delta DE'
Configuration: RF_scGPT (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)	0.647 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Replogle_RPE1 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-rpe1-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell H50, row 'Replogle_RPE1 / RF_scGPT', column 'Pearson Delta DE without KOd gene'
Configuration: RF_scGPT (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)	0.725 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RF_scGPT on Replogle_RPE1 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-rpe1-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell G50, row 'Replogle_RPE1 / RF_scGPT', column 'Pearson Delta DE (based on Wilcoxon)'

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Benchmarking foundation cell models for post-perturbation RNA-seq prediction · Original source · BMC Genomics 26:393, published 2025-04-23; PMC12016270 full-text XML
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)

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Technical metadata and extraction receipts

Stable ID: perturbation-response-20261009-config-csendes2025-rf-scgpt

areas: cells-tissues
contexts: research
method types: conventional_pipeline
reported name: RF_scGPT
source locator: Supplementary Table 2 column 'model'; Methods 'Foundation models' and 'Baseline models'
foundation model eligible: false
parameters: Features: scGPT pretrained gene embeddings reduced to 256 principal components of the perturbed gene (summed for combinations); target: pseudo-bulk expression; n_estimators tuned on the validation set
version: scikit-learn 1.5.2

Related records

configuration of: Random forest regression on perturbed-gene features
system: RF_scGPT on Adamson (Csendes et al. 2025)
system: RF_scGPT on Norman (Csendes et al. 2025)
system: RF_scGPT on Replogle_K562 (Csendes et al. 2025)
system: RF_scGPT on Replogle_RPE1 (Csendes et al. 2025)

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