| Configuration: GEARS, trained once on a downsampled set | Protocol: Combination phenotype prediction from small training sets: test RMSE at fixed average gene frequency
Dataset: Horlbeck et al. 2018 combinatorial CRISPRi in Jurkat T cells, gene-level viability (as processed by Qin et al. 2025) | 24.2 (28.5) RMSE (test RMSE of pair viability, training set with each gene seen about 10 times on average) unitless · lower Uncertainty: SE 28.5. Caption: error is SE across three cross-fold replicates Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGEARS, trained once on a downsampled set on Horlbeck Jurkat (Tables 1 and 6, RMSE at fixed gene frequency) pheno-20261022-qin2025-protocol-downsampling-rmse Aggregation: Not reported Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) · Table 6, Gene Frequency 10 block, row "GEARS", column "Horlbeck Jurkat" |
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| Configuration: GEARS, trained once on a downsampled set | Protocol: Combination phenotype prediction from small training sets: test RMSE at fixed average gene frequency
Dataset: Horlbeck et al. 2018 combinatorial CRISPRi in Jurkat T cells, gene-level viability (as processed by Qin et al. 2025) | 20.7 (24.0) RMSE (test RMSE of pair viability, training set with each gene seen about 20 times on average) unitless · lower Uncertainty: SE 24.0. Caption: error is SE across three cross-fold replicates Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGEARS, trained once on a downsampled set on Horlbeck Jurkat (Tables 1 and 6, RMSE at fixed gene frequency) pheno-20261022-qin2025-protocol-downsampling-rmse Aggregation: Not reported Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) · Table 1, Gene Frequency 20 block, row "GEARS", column "Horlbeck Jurkat" |
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| Configuration: GEARS, trained once on a downsampled set | Protocol: Combination phenotype prediction from small training sets: test RMSE at fixed average gene frequency
Dataset: Horlbeck et al. 2018 combinatorial CRISPRi in Jurkat T cells, gene-level viability (as processed by Qin et al. 2025) | 13.5 (16.1) RMSE (test RMSE of pair viability, training set with each gene seen about 4 times on average) unitless · lower Uncertainty: SE 16.1. Caption: error is SE across three cross-fold replicates Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGEARS, trained once on a downsampled set on Horlbeck Jurkat (Tables 1 and 6, RMSE at fixed gene frequency) pheno-20261022-qin2025-protocol-downsampling-rmse Aggregation: Not reported Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) · Table 1, Gene Frequency 4 block, row "GEARS", column "Horlbeck Jurkat" |
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| Configuration: GEARS, trained once on a downsampled set | Protocol: Combination phenotype prediction from small training sets: test RMSE at fixed average gene frequency
Dataset: Horlbeck et al. 2018 combinatorial CRISPRi in K562, gene-level viability (as processed by Qin et al. 2025) | 12.0 (9.6) RMSE (test RMSE of pair viability, training set with each gene seen about 10 times on average) unitless · lower Uncertainty: SE 9.6. Caption: error is SE across three cross-fold replicates Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGEARS, trained once on a downsampled set on Horlbeck K562 (Tables 1 and 6, RMSE at fixed gene frequency) pheno-20261022-qin2025-protocol-downsampling-rmse Aggregation: Not reported Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) · Table 6, Gene Frequency 10 block, row "GEARS", column "Horlbeck K562" |
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| Configuration: GEARS, trained once on a downsampled set | Protocol: Combination phenotype prediction from small training sets: test RMSE at fixed average gene frequency
Dataset: Horlbeck et al. 2018 combinatorial CRISPRi in K562, gene-level viability (as processed by Qin et al. 2025) | 14.0 (14.0) RMSE (test RMSE of pair viability, training set with each gene seen about 20 times on average) unitless · lower Uncertainty: SE 14.0. Caption: error is SE across three cross-fold replicates Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGEARS, trained once on a downsampled set on Horlbeck K562 (Tables 1 and 6, RMSE at fixed gene frequency) pheno-20261022-qin2025-protocol-downsampling-rmse Aggregation: Not reported Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) · Table 1, Gene Frequency 20 block, row "GEARS", column "Horlbeck K562" |
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| Configuration: GEARS, trained once on a downsampled set | Protocol: Combination phenotype prediction from small training sets: test RMSE at fixed average gene frequency
Dataset: Horlbeck et al. 2018 combinatorial CRISPRi in K562, gene-level viability (as processed by Qin et al. 2025) | 13.0 (11.6) RMSE (test RMSE of pair viability, training set with each gene seen about 4 times on average) unitless · lower Uncertainty: SE 11.6. Caption: error is SE across three cross-fold replicates Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGEARS, trained once on a downsampled set on Horlbeck K562 (Tables 1 and 6, RMSE at fixed gene frequency) pheno-20261022-qin2025-protocol-downsampling-rmse Aggregation: Not reported Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) · Table 1, Gene Frequency 4 block, row "GEARS", column "Horlbeck K562" |
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| Configuration: GEARS, trained once on a downsampled set | Protocol: Combination phenotype prediction from small training sets: test RMSE at fixed average gene frequency
Dataset: Norman et al. 2019 combinatorial CRISPRa in K562, gene-level viability (as processed by Qin et al. 2025) | 15.5 (12.8) RMSE (test RMSE of pair viability, training set with each gene seen about 10 times on average) unitless · lower Uncertainty: SE 12.8. Caption: error is SE across three cross-fold replicates Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGEARS, trained once on a downsampled set on Norman (Tables 1 and 6, RMSE at fixed gene frequency) pheno-20261022-qin2025-protocol-downsampling-rmse Aggregation: Not reported Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) · Table 6, Gene Frequency 10 block, row "GEARS", column "Norman" |
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| Configuration: GEARS, trained once on a downsampled set | Protocol: Combination phenotype prediction from small training sets: test RMSE at fixed average gene frequency
Dataset: Norman et al. 2019 combinatorial CRISPRa in K562, gene-level viability (as processed by Qin et al. 2025) | 10.7 (12.1) RMSE (test RMSE of pair viability, training set with each gene seen about 20 times on average) unitless · lower Uncertainty: SE 12.1. Caption: error is SE across three cross-fold replicates Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGEARS, trained once on a downsampled set on Norman (Tables 1 and 6, RMSE at fixed gene frequency) pheno-20261022-qin2025-protocol-downsampling-rmse Aggregation: Not reported Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) · Table 1, Gene Frequency 20 block, row "GEARS", column "Norman" |
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| Configuration: GEARS, trained once on a downsampled set | Protocol: Combination phenotype prediction from small training sets: test RMSE at fixed average gene frequency
Dataset: Norman et al. 2019 combinatorial CRISPRa in K562, gene-level viability (as processed by Qin et al. 2025) | 16.6 (19.8) RMSE (test RMSE of pair viability, training set with each gene seen about 4 times on average) unitless · lower Uncertainty: SE 19.8. Caption: error is SE across three cross-fold replicates Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGEARS, trained once on a downsampled set on Norman (Tables 1 and 6, RMSE at fixed gene frequency) pheno-20261022-qin2025-protocol-downsampling-rmse Aggregation: Not reported Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) · Table 1, Gene Frequency 4 block, row "GEARS", column "Norman" |
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| Configuration: GEARS, trained once on a downsampled set | Protocol: Combination phenotype prediction from small training sets: test RMSE at fixed average gene frequency
Dataset: Simpson et al. 2023 combinatorial CRISPRi in K562, gene-level viability (as processed by Qin et al. 2025) | 8.7 (10.3) RMSE (test RMSE of pair viability, training set with each gene seen about 10 times on average) unitless · lower Uncertainty: SE 10.3. Caption: error is SE across three cross-fold replicates Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGEARS, trained once on a downsampled set on Simpson (Tables 1 and 6, RMSE at fixed gene frequency) pheno-20261022-qin2025-protocol-downsampling-rmse Aggregation: Not reported Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) · Table 6, Gene Frequency 10 block, row "GEARS", column "Simpson" |
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| Configuration: GEARS, trained once on a downsampled set | Protocol: Combination phenotype prediction from small training sets: test RMSE at fixed average gene frequency
Dataset: Simpson et al. 2023 combinatorial CRISPRi in K562, gene-level viability (as processed by Qin et al. 2025) | 3.5 (2.0) RMSE (test RMSE of pair viability, training set with each gene seen about 20 times on average) unitless · lower Uncertainty: SE 2.0. Caption: error is SE across three cross-fold replicates Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGEARS, trained once on a downsampled set on Simpson (Tables 1 and 6, RMSE at fixed gene frequency) pheno-20261022-qin2025-protocol-downsampling-rmse Aggregation: Not reported Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) · Table 1, Gene Frequency 20 block, row "GEARS", column "Simpson" |
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| Configuration: GEARS, trained once on a downsampled set | Protocol: Combination phenotype prediction from small training sets: test RMSE at fixed average gene frequency
Dataset: Simpson et al. 2023 combinatorial CRISPRi in K562, gene-level viability (as processed by Qin et al. 2025) | 5.4 (3.4) RMSE (test RMSE of pair viability, training set with each gene seen about 4 times on average) unitless · lower Uncertainty: SE 3.4. Caption: error is SE across three cross-fold replicates Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGEARS, trained once on a downsampled set on Simpson (Tables 1 and 6, RMSE at fixed gene frequency) pheno-20261022-qin2025-protocol-downsampling-rmse Aggregation: Not reported Qin et al. 2025, Active Learning for Efficient Discovery of Optimal Combinatorial Perturbations (ICML 2025, PMLR 267) · Table 1, Gene Frequency 4 block, row "GEARS", column "Simpson" |
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