Configuration: Scouter (Sun et al. 2026) Protocol: Sun et al. 2026 unseen-perturbation DE classification (within cell line) Dataset subset: K562, RPE1, HepG2 and Jurkat test sets (Sun et al. 2026) 64.1% Proportion (share of perturbation-gene pairs predicted as differentially expressed (compare with the printed true DE prevalence))percent · unknown
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Methods describe results on both the full data and a PerturbQA-downsampled subset ('We annotate our results to distinguish between these two settings'), but the captions of Tables 1-4 do not say which setting they report. The printed true DE prevalence (1.75-4.41%) matches the full data's 95-98% non-DE share (Table 5), not the downsampled set; this is an inference, not a printed statement.Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Section 3.2 'Full vs. Curated Dataset'; Tables 1-5
Methods, coverage and source Scouter on Sun et al. 2026 within-cell-line DE classification, four cell lines
lit-cells-networks-20261011-sun2026de-protocol-within-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 1, row 'Scouter', column 'Average' Configuration: Scouter (Sun et al. 2026) Protocol: Sun et al. 2026 unseen-perturbation DE classification (within cell line) Dataset subset: HepG2 essential-gene Perturb-seq, 40% test perturbations (Sun et al. 2026) 55.1% Proportion (share of perturbation-gene pairs predicted as differentially expressed (compare with the printed true DE prevalence))percent · unknown
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Methods describe results on both the full data and a PerturbQA-downsampled subset ('We annotate our results to distinguish between these two settings'), but the captions of Tables 1-4 do not say which setting they report. The printed true DE prevalence (1.75-4.41%) matches the full data's 95-98% non-DE share (Table 5), not the downsampled set; this is an inference, not a printed statement.Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Section 3.2 'Full vs. Curated Dataset'; Tables 1-5
Methods, coverage and source Scouter on Sun et al. 2026 within-cell-line DE classification, HepG2
lit-cells-networks-20261011-sun2026de-protocol-within-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 1, row 'Scouter', column 'HepG2' Configuration: Scouter (Sun et al. 2026) Protocol: Sun et al. 2026 unseen-perturbation DE classification (within cell line) Dataset subset: Jurkat essential-gene Perturb-seq, 40% test perturbations (Sun et al. 2026) 67.1% Proportion (share of perturbation-gene pairs predicted as differentially expressed (compare with the printed true DE prevalence))percent · unknown
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Methods describe results on both the full data and a PerturbQA-downsampled subset ('We annotate our results to distinguish between these two settings'), but the captions of Tables 1-4 do not say which setting they report. The printed true DE prevalence (1.75-4.41%) matches the full data's 95-98% non-DE share (Table 5), not the downsampled set; this is an inference, not a printed statement.Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Section 3.2 'Full vs. Curated Dataset'; Tables 1-5
Methods, coverage and source Scouter on Sun et al. 2026 within-cell-line DE classification, Jurkat
lit-cells-networks-20261011-sun2026de-protocol-within-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 1, row 'Scouter', column 'Jurkat' Configuration: Scouter (Sun et al. 2026) Protocol: Sun et al. 2026 unseen-perturbation DE classification (within cell line) Dataset subset: K562 essential-gene Perturb-seq, 40% test perturbations (Sun et al. 2026) 67.1% Proportion (share of perturbation-gene pairs predicted as differentially expressed (compare with the printed true DE prevalence))percent · unknown
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Methods describe results on both the full data and a PerturbQA-downsampled subset ('We annotate our results to distinguish between these two settings'), but the captions of Tables 1-4 do not say which setting they report. The printed true DE prevalence (1.75-4.41%) matches the full data's 95-98% non-DE share (Table 5), not the downsampled set; this is an inference, not a printed statement.Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Section 3.2 'Full vs. Curated Dataset'; Tables 1-5
Methods, coverage and source Scouter on Sun et al. 2026 within-cell-line DE classification, K562
lit-cells-networks-20261011-sun2026de-protocol-within-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 1, row 'Scouter', column 'K562' Configuration: Scouter (Sun et al. 2026) Protocol: Sun et al. 2026 unseen-perturbation DE classification (within cell line) Dataset subset: RPE1 essential-gene Perturb-seq, 40% test perturbations (Sun et al. 2026) 67.2% Proportion (share of perturbation-gene pairs predicted as differentially expressed (compare with the printed true DE prevalence))percent · unknown
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Methods describe results on both the full data and a PerturbQA-downsampled subset ('We annotate our results to distinguish between these two settings'), but the captions of Tables 1-4 do not say which setting they report. The printed true DE prevalence (1.75-4.41%) matches the full data's 95-98% non-DE share (Table 5), not the downsampled set; this is an inference, not a printed statement.Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Section 3.2 'Full vs. Curated Dataset'; Tables 1-5
Methods, coverage and source Scouter on Sun et al. 2026 within-cell-line DE classification, RPE1
lit-cells-networks-20261011-sun2026de-protocol-within-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 1, row 'Scouter', column 'RPE1' Configuration: Scouter (Sun et al. 2026) Protocol: Sun et al. 2026 unseen-perturbation DE classification (within cell line) Dataset subset: K562, RPE1, HepG2 and Jurkat test sets (Sun et al. 2026) 22.6% Accuracy (3-class (non-DE, up, down) accuracy within true |log2 FC| quantile Q1 (0–0.016); quantile bins per cell line, averaged over four cell lines)percent · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Methods describe results on both the full data and a PerturbQA-downsampled subset ('We annotate our results to distinguish between these two settings'), but the captions of Tables 1-4 do not say which setting they report. The printed true DE prevalence (1.75-4.41%) matches the full data's 95-98% non-DE share (Table 5), not the downsampled set; this is an inference, not a printed statement.Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Section 3.2 'Full vs. Curated Dataset'; Tables 1-5
Methods, coverage and source Scouter on Sun et al. 2026 within-cell-line DE classification, four cell lines
lit-cells-networks-20261011-sun2026de-protocol-within-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 2, row 'Scouter', column 'Q1 (0–0.016)' Configuration: Scouter (Sun et al. 2026) Protocol: Sun et al. 2026 unseen-perturbation DE classification (within cell line) Dataset subset: K562, RPE1, HepG2 and Jurkat test sets (Sun et al. 2026) 24.9% Accuracy (3-class (non-DE, up, down) accuracy within true |log2 FC| quantile Q2 (0.016–0.034); quantile bins per cell line, averaged over four cell lines)percent · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Methods describe results on both the full data and a PerturbQA-downsampled subset ('We annotate our results to distinguish between these two settings'), but the captions of Tables 1-4 do not say which setting they report. The printed true DE prevalence (1.75-4.41%) matches the full data's 95-98% non-DE share (Table 5), not the downsampled set; this is an inference, not a printed statement.Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Section 3.2 'Full vs. Curated Dataset'; Tables 1-5
Methods, coverage and source Scouter on Sun et al. 2026 within-cell-line DE classification, four cell lines
lit-cells-networks-20261011-sun2026de-protocol-within-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 2, row 'Scouter', column 'Q2 (0.016–0.034)' Configuration: Scouter (Sun et al. 2026) Protocol: Sun et al. 2026 unseen-perturbation DE classification (within cell line) Dataset subset: K562, RPE1, HepG2 and Jurkat test sets (Sun et al. 2026) 30.5% Accuracy (3-class (non-DE, up, down) accuracy within true |log2 FC| quantile Q3 (0.034–0.060); quantile bins per cell line, averaged over four cell lines)percent · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Methods describe results on both the full data and a PerturbQA-downsampled subset ('We annotate our results to distinguish between these two settings'), but the captions of Tables 1-4 do not say which setting they report. The printed true DE prevalence (1.75-4.41%) matches the full data's 95-98% non-DE share (Table 5), not the downsampled set; this is an inference, not a printed statement.Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Section 3.2 'Full vs. Curated Dataset'; Tables 1-5
Methods, coverage and source Scouter on Sun et al. 2026 within-cell-line DE classification, four cell lines
lit-cells-networks-20261011-sun2026de-protocol-within-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 2, row 'Scouter', column 'Q3 (0.034–0.060)' Configuration: Scouter (Sun et al. 2026) Protocol: Sun et al. 2026 unseen-perturbation DE classification (within cell line) Dataset subset: K562, RPE1, HepG2 and Jurkat test sets (Sun et al. 2026) 42% Accuracy (3-class (non-DE, up, down) accuracy within true |log2 FC| quantile Q4 (0.060–0.108); quantile bins per cell line, averaged over four cell lines)percent · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Methods describe results on both the full data and a PerturbQA-downsampled subset ('We annotate our results to distinguish between these two settings'), but the captions of Tables 1-4 do not say which setting they report. The printed true DE prevalence (1.75-4.41%) matches the full data's 95-98% non-DE share (Table 5), not the downsampled set; this is an inference, not a printed statement.Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Section 3.2 'Full vs. Curated Dataset'; Tables 1-5
Methods, coverage and source Scouter on Sun et al. 2026 within-cell-line DE classification, four cell lines
lit-cells-networks-20261011-sun2026de-protocol-within-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 2, row 'Scouter', column 'Q4 (0.060–0.108)' Configuration: Scouter (Sun et al. 2026) Protocol: Sun et al. 2026 unseen-perturbation DE classification (within cell line) Dataset subset: K562, RPE1, HepG2 and Jurkat test sets (Sun et al. 2026) 63% Accuracy (3-class (non-DE, up, down) accuracy within true |log2 FC| quantile Q5 (>0.108); quantile bins per cell line, averaged over four cell lines)percent · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Methods describe results on both the full data and a PerturbQA-downsampled subset ('We annotate our results to distinguish between these two settings'), but the captions of Tables 1-4 do not say which setting they report. The printed true DE prevalence (1.75-4.41%) matches the full data's 95-98% non-DE share (Table 5), not the downsampled set; this is an inference, not a printed statement.Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Section 3.2 'Full vs. Curated Dataset'; Tables 1-5
Methods, coverage and source Scouter on Sun et al. 2026 within-cell-line DE classification, four cell lines
lit-cells-networks-20261011-sun2026de-protocol-within-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 2, row 'Scouter', column 'Q5 (>0.108)'