Configuration

KNN_scGPT (Csendes et al. 2025)

KNN regression with scGPT features of the perturbed gene.

Overview

KNN regression with scGPT features of the perturbed gene.

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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: KNN_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)	0.994 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 KNN_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 C13, row 'Adamson / KNN_scGPT', column 'Pearson'
Configuration: KNN_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)	0.976 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 KNN_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 D13, row 'Adamson / KNN_scGPT', column 'Pearson DE'
Configuration: KNN_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)	0.753 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 KNN_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 E13, row 'Adamson / KNN_scGPT', column 'Pearson Delta'
Configuration: KNN_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)	0.778 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 KNN_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 F13, row 'Adamson / KNN_scGPT', column 'Pearson Delta DE'
Configuration: KNN_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)	0.834 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 KNN_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 H13, row 'Adamson / KNN_scGPT', column 'Pearson Delta DE without KOd gene'
Configuration: KNN_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)	0.782 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 KNN_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 G13, row 'Adamson / KNN_scGPT', column 'Pearson Delta DE (based on Wilcoxon)'
Configuration: KNN_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)	0.989 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 KNN_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 C28, row 'Norman / KNN_scGPT', column 'Pearson'
Configuration: KNN_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)	0.935 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 KNN_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 D28, row 'Norman / KNN_scGPT', column 'Pearson DE'
Configuration: KNN_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)	0.603 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 KNN_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 E28, row 'Norman / KNN_scGPT', column 'Pearson Delta'
Configuration: KNN_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)	0.643 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 KNN_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 F28, row 'Norman / KNN_scGPT', column 'Pearson Delta DE'
Configuration: KNN_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)	0.681 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 KNN_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 H28, row 'Norman / KNN_scGPT', column 'Pearson Delta DE without KOd gene'
Configuration: KNN_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)	0.705 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 KNN_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 G28, row 'Norman / KNN_scGPT', column 'Pearson Delta DE (based on Wilcoxon)'
Configuration: KNN_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)	0.987 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 KNN_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 C43, row 'Replogle_K562 / KNN_scGPT', column 'Pearson'
Configuration: KNN_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)	0.959 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 KNN_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 D43, row 'Replogle_K562 / KNN_scGPT', column 'Pearson DE'
Configuration: KNN_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)	0.374 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 KNN_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 E43, row 'Replogle_K562 / KNN_scGPT', column 'Pearson Delta'
Configuration: KNN_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)	0.476 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 KNN_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 F43, row 'Replogle_K562 / KNN_scGPT', column 'Pearson Delta DE'
Configuration: KNN_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)	0.503 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 KNN_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 H43, row 'Replogle_K562 / KNN_scGPT', column 'Pearson Delta DE without KOd gene'
Configuration: KNN_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)	0.494 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 KNN_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 G43, row 'Replogle_K562 / KNN_scGPT', column 'Pearson Delta DE (based on Wilcoxon)'
Configuration: KNN_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)	0.975 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 KNN_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 C58, row 'Replogle_RPE1 / KNN_scGPT', column 'Pearson'
Configuration: KNN_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)	0.911 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 KNN_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 D58, row 'Replogle_RPE1 / KNN_scGPT', column 'Pearson DE'
Configuration: KNN_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)	0.581 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 KNN_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 E58, row 'Replogle_RPE1 / KNN_scGPT', column 'Pearson Delta'
Configuration: KNN_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)	0.59 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 KNN_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 F58, row 'Replogle_RPE1 / KNN_scGPT', column 'Pearson Delta DE'
Configuration: KNN_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)	0.598 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 KNN_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 H58, row 'Replogle_RPE1 / KNN_scGPT', column 'Pearson Delta DE without KOd gene'
Configuration: KNN_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)	0.68 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 KNN_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 G58, row 'Replogle_RPE1 / KNN_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-knn-scgpt

areas: cells-tissues
contexts: research
method types: conventional_pipeline
reported name: KNN_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; k neighbours tuned on the validation set
version: scikit-learn 1.5.2

Related records

configuration of: k-nearest-neighbours regression on perturbed-gene features
system: KNN_scGPT on Adamson (Csendes et al. 2025)
system: KNN_scGPT on Norman (Csendes et al. 2025)
system: KNN_scGPT on Replogle_K562 (Csendes et al. 2025)
system: KNN_scGPT on Replogle_RPE1 (Csendes et al. 2025)

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