Configuration

KNN_scElmo (Csendes et al. 2025)

KNN regression with scElmo features of the perturbed gene.

Overview

KNN regression with scElmo 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_scElmo (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)	0.99 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_scElmo 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 C11, row 'Adamson / KNN_scElmo', column 'Pearson'
Configuration: KNN_scElmo (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)	0.964 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_scElmo 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 D11, row 'Adamson / KNN_scElmo', column 'Pearson DE'
Configuration: KNN_scElmo (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)	0.642 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_scElmo 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 E11, row 'Adamson / KNN_scElmo', column 'Pearson Delta'
Configuration: KNN_scElmo (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)	0.651 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_scElmo 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 F11, row 'Adamson / KNN_scElmo', column 'Pearson Delta DE'
Configuration: KNN_scElmo (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)	0.706 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_scElmo 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 H11, row 'Adamson / KNN_scElmo', column 'Pearson Delta DE without KOd gene'
Configuration: KNN_scElmo (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)	0.671 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_scElmo 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 G11, row 'Adamson / KNN_scElmo', column 'Pearson Delta DE (based on Wilcoxon)'
Configuration: KNN_scElmo (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_scElmo 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 C26, row 'Norman / KNN_scElmo', column 'Pearson'
Configuration: KNN_scElmo (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_scElmo 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 D26, row 'Norman / KNN_scElmo', column 'Pearson DE'
Configuration: KNN_scElmo (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)	0.638 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_scElmo 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 E26, row 'Norman / KNN_scElmo', column 'Pearson Delta'
Configuration: KNN_scElmo (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)	0.73 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_scElmo 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 F26, row 'Norman / KNN_scElmo', column 'Pearson Delta DE'
Configuration: KNN_scElmo (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)	0.768 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_scElmo 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 H26, row 'Norman / KNN_scElmo', column 'Pearson Delta DE without KOd gene'
Configuration: KNN_scElmo (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)	0.756 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_scElmo 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 G26, row 'Norman / KNN_scElmo', column 'Pearson Delta DE (based on Wilcoxon)'
Configuration: KNN_scElmo (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)	0.989 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_scElmo 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 C41, row 'Replogle_K562 / KNN_scElmo', column 'Pearson'
Configuration: KNN_scElmo (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)	0.968 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_scElmo 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 D41, row 'Replogle_K562 / KNN_scElmo', column 'Pearson DE'
Configuration: KNN_scElmo (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)	0.453 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_scElmo 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 E41, row 'Replogle_K562 / KNN_scElmo', column 'Pearson Delta'
Configuration: KNN_scElmo (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)	0.577 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_scElmo 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 F41, row 'Replogle_K562 / KNN_scElmo', column 'Pearson Delta DE'
Configuration: KNN_scElmo (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)	0.609 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_scElmo 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 H41, row 'Replogle_K562 / KNN_scElmo', column 'Pearson Delta DE without KOd gene'
Configuration: KNN_scElmo (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)	0.576 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_scElmo 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 G41, row 'Replogle_K562 / KNN_scElmo', column 'Pearson Delta DE (based on Wilcoxon)'
Configuration: KNN_scElmo (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)	0.979 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_scElmo 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 C56, row 'Replogle_RPE1 / KNN_scElmo', column 'Pearson'
Configuration: KNN_scElmo (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_scElmo 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 D56, row 'Replogle_RPE1 / KNN_scElmo', column 'Pearson DE'
Configuration: KNN_scElmo (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)	0.62 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_scElmo 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 E56, row 'Replogle_RPE1 / KNN_scElmo', column 'Pearson Delta'
Configuration: KNN_scElmo (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)	0.639 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_scElmo 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 F56, row 'Replogle_RPE1 / KNN_scElmo', column 'Pearson Delta DE'
Configuration: KNN_scElmo (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 KNN_scElmo 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 H56, row 'Replogle_RPE1 / KNN_scElmo', column 'Pearson Delta DE without KOd gene'
Configuration: KNN_scElmo (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)	0.729 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_scElmo 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 G56, row 'Replogle_RPE1 / KNN_scElmo', 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-scelmo

areas: cells-tissues
contexts: research
method types: conventional_pipeline
reported name: KNN_scElmo
source locator: Supplementary Table 2 column 'model'; Methods 'Foundation models' and 'Baseline models'
foundation model eligible: false
parameters: Features: scELMO GPT-3.5 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_scElmo on Adamson (Csendes et al. 2025)
system: KNN_scElmo on Norman (Csendes et al. 2025)
system: KNN_scElmo on Replogle_K562 (Csendes et al. 2025)
system: KNN_scElmo on Replogle_RPE1 (Csendes et al. 2025)

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