Configuration: TranScouter (Sun et al. 2026) Protocol: Sun et al. 2026 cellular-context DE classification (cross cell line) Dataset subset: K562, RPE1, HepG2 and Jurkat test sets (Sun et al. 2026) 72.2% 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 TranScouter on Sun et al. 2026 cross-cell-line DE classification, four cell lines
lit-cells-networks-20261011-sun2026de-protocol-cross-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 3, row 'TranScouter', column 'Average' Configuration: TranScouter (Sun et al. 2026) Protocol: Sun et al. 2026 cellular-context DE classification (cross cell line) Dataset subset: HepG2 essential-gene Perturb-seq, 40% test perturbations (Sun et al. 2026) 62.1% 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 TranScouter on Sun et al. 2026 cross-cell-line DE classification, HepG2
lit-cells-networks-20261011-sun2026de-protocol-cross-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 3, row 'TranScouter', column 'HepG2' Configuration: TranScouter (Sun et al. 2026) Protocol: Sun et al. 2026 cellular-context DE classification (cross cell line) Dataset subset: Jurkat essential-gene Perturb-seq, 40% test perturbations (Sun et al. 2026) 73.3% 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 TranScouter on Sun et al. 2026 cross-cell-line DE classification, Jurkat
lit-cells-networks-20261011-sun2026de-protocol-cross-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 3, row 'TranScouter', column 'Jurkat' Configuration: TranScouter (Sun et al. 2026) Protocol: Sun et al. 2026 cellular-context DE classification (cross cell line) Dataset subset: K562 essential-gene Perturb-seq, 40% test perturbations (Sun et al. 2026) 79.7% 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 TranScouter on Sun et al. 2026 cross-cell-line DE classification, K562
lit-cells-networks-20261011-sun2026de-protocol-cross-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 3, row 'TranScouter', column 'K562' Configuration: TranScouter (Sun et al. 2026) Protocol: Sun et al. 2026 cellular-context DE classification (cross cell line) Dataset subset: RPE1 essential-gene Perturb-seq, 40% test perturbations (Sun et al. 2026) 73.6% 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 TranScouter on Sun et al. 2026 cross-cell-line DE classification, RPE1
lit-cells-networks-20261011-sun2026de-protocol-cross-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 3, row 'TranScouter', column 'RPE1' Configuration: TranScouter (Sun et al. 2026) Protocol: Sun et al. 2026 cellular-context DE classification (cross cell line) Dataset subset: K562, RPE1, HepG2 and Jurkat test sets (Sun et al. 2026) 19.7% Accuracy (3-class (non-DE, up, down) accuracy within true |log2 FC| quantile Q1 (0–0.017); 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 TranScouter on Sun et al. 2026 cross-cell-line DE classification, four cell lines
lit-cells-networks-20261011-sun2026de-protocol-cross-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 4, row 'TranScouter', column 'Q1 (0–0.017)' Configuration: TranScouter (Sun et al. 2026) Protocol: Sun et al. 2026 cellular-context DE classification (cross cell line) Dataset subset: K562, RPE1, HepG2 and Jurkat test sets (Sun et al. 2026) 21.4% Accuracy (3-class (non-DE, up, down) accuracy within true |log2 FC| quantile Q2 (0.017–0.037); 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 TranScouter on Sun et al. 2026 cross-cell-line DE classification, four cell lines
lit-cells-networks-20261011-sun2026de-protocol-cross-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 4, row 'TranScouter', column 'Q2 (0.017–0.037)' Configuration: TranScouter (Sun et al. 2026) Protocol: Sun et al. 2026 cellular-context DE classification (cross cell line) Dataset subset: K562, RPE1, HepG2 and Jurkat test sets (Sun et al. 2026) 25.2% Accuracy (3-class (non-DE, up, down) accuracy within true |log2 FC| quantile Q3 (0.037–0.065); 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 TranScouter on Sun et al. 2026 cross-cell-line DE classification, four cell lines
lit-cells-networks-20261011-sun2026de-protocol-cross-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 4, row 'TranScouter', column 'Q3 (0.037–0.065)' Configuration: TranScouter (Sun et al. 2026) Protocol: Sun et al. 2026 cellular-context DE classification (cross cell line) Dataset subset: K562, RPE1, HepG2 and Jurkat test sets (Sun et al. 2026) 32.3% Accuracy (3-class (non-DE, up, down) accuracy within true |log2 FC| quantile Q4 (0.065–0.116); 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 TranScouter on Sun et al. 2026 cross-cell-line DE classification, four cell lines
lit-cells-networks-20261011-sun2026de-protocol-cross-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 4, row 'TranScouter', column 'Q4 (0.065–0.116)' Configuration: TranScouter (Sun et al. 2026) Protocol: Sun et al. 2026 cellular-context DE classification (cross cell line) Dataset subset: K562, RPE1, HepG2 and Jurkat test sets (Sun et al. 2026) 46.2% Accuracy (3-class (non-DE, up, down) accuracy within true |log2 FC| quantile Q5 (>0.116); 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 TranScouter on Sun et al. 2026 cross-cell-line DE classification, four cell lines
lit-cells-networks-20261011-sun2026de-protocol-cross-cell-line
Aggregation: Not reported
Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Table 4, row 'TranScouter', column 'Q5 (>0.116)'