Configuration: bindSC (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.506 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source bindSC on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G5 (row 'bindSC', column 'Overall') Configuration: Cobolt (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.533 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source Cobolt on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G7 (row 'Cobolt', column 'Overall') Configuration: Deepmaps (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.355 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source Deepmaps on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G16 (row 'Deepmaps', column 'Overall') Configuration: FM-scVI (SCMBench adapter) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.423 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source FM-scVI on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G23 (row 'FM-scVI', column 'Overall') Configuration: GLUE (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.599 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source GLUE on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G2 (row 'GLUE', column 'Overall') Configuration: Harmony (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.394 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source Harmony on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G22 (row 'Harmony', column 'Overall') Configuration: iNMF (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.165 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source iNMF on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G21 (row 'iNMF', column 'Overall') Configuration: LIGER (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.457 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source LIGER on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G11 (row 'LIGER', column 'Overall') Configuration: MMD-MA (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.346 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source MMD-MA on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G17 (row 'MMD-MA', column 'Overall') Configuration: MOFA (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.479 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source MOFA on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G10 (row 'MOFA', column 'Overall') Configuration: Pamona (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.316 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source Pamona on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G19 (row 'Pamona', column 'Overall') Configuration: PCA (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.389 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source PCA on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G14 (row 'PCA', column 'Overall') Configuration: scGPT (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.591 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; across-dataset mean over 10x-Multiome-Pbmc10k only)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source scGPT on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20 (row 'scGPT', column 'Overall') Configuration: scJoint (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.559 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source scJoint on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G4 (row 'scJoint', column 'Overall') Configuration: scMDC (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.56 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source scMDC on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G3 (row 'scMDC', column 'Overall') Configuration: scMoMaT (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.484 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source scMoMaT on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G9 (row 'scMoMaT', column 'Overall') Configuration: scVI (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.384 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source scVI on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G15 (row 'scVI', column 'Overall') Configuration: Seurat4 (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.534 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source Seurat4 on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G6 (row 'Seurat4', column 'Overall') Configuration: Seurat5 (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.504 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source Seurat5 on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G8 (row 'Seurat5', column 'Overall') Configuration: TotalVI (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.416 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source TotalVI on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G13 (row 'TotalVI', column 'Overall') Configuration: UCE (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.332 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source UCE on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G18 (row 'UCE', column 'Overall') Configuration: UnionCom (SCMBench) Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: paired-overall (SCMBench) 0.432 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)unitless · higher
Uncertainty: Not reported by the source
Coverage: Not reported scored / Not reported eligible
Independent external evaluation · Source checked Evidence concern: excluded from comparisons Sheet 'unpaired_inte_overall' has no header for column H. Each H cell is the formula =AVERAGE(Bn:Gn), the mean of the dataset cells with values. Rows with a blank Yao cell (bindSC, scMoMaT, scGPT_zero, Pamona, scFoundation, Geneformer) average five datasets and the other rows six, so column H values are not comparable across all rows.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
'FM-scVI' is a different foundation model per dataset ('the best-performing foundation model combined with scVI, which varies across datasets', Fig. 2 legend), so its rows do not describe one fixed configuration.SCMBench Supplementary Data 2 (integration results) · Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
In sheet 'paired_inte_overall' the scGPT row is scored on 10x-Multiome-Pbmc10k only; its Overall cell G20 (=AVERAGE(B20:F20)) is that single value, not a five-dataset mean, so it is not comparable with the other Overall values.SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G20
Methods, coverage and source UnionCom on SCMBench paired integration, paired-overall
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
Aggregation: Not reported
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration ; SCMBench Supplementary Data 2 (integration results) · Supplementary Data 2, sheet 'paired_inte_overall', cell G12 (row 'UnionCom', column 'Overall')