Dataset subset

Muto-2021-batch-3 (SCMBench)

Muto-2021 human kidney snRNA-seq and snATAC-seq, batch 3 (unpaired, the Methods sample each batch to 2,500 cells for the batch-effect experiments and do not say whether this sheet uses the sampled batches).

Evaluation results

17 evaluations · 17 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: bindSC (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-3 (SCMBench)	0.711 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI) 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 unpaired integration, Muto-2021-batch-3 lit-cells-networks-20261011-scmbench-protocol-unpaired-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 'unpaired_inte_overall', cell E6 (row 'bindSC', column 'Muto-2021-batch-3')
Configuration: Cobolt (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-3 (SCMBench)	0.289 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI) 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 unpaired integration, Muto-2021-batch-3 lit-cells-networks-20261011-scmbench-protocol-unpaired-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 'unpaired_inte_overall', cell E14 (row 'Cobolt', column 'Muto-2021-batch-3')
Configuration: FM-scVI (SCMBench adapter)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-3 (SCMBench)	0.603 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI) 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 unpaired integration, Muto-2021-batch-3 lit-cells-networks-20261011-scmbench-protocol-unpaired-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 'unpaired_inte_overall', cell E18 (row 'FM-scVI', column 'Muto-2021-batch-3')
Configuration: Geneformer (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-3 (SCMBench)	0.348 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI) 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 Geneformer on SCMBench unpaired integration, Muto-2021-batch-3 lit-cells-networks-20261011-scmbench-protocol-unpaired-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 'unpaired_inte_overall', cell E15 (row 'Geneformer', column 'Muto-2021-batch-3')
Configuration: GLUE (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-3 (SCMBench)	0.705 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI) 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 unpaired integration, Muto-2021-batch-3 lit-cells-networks-20261011-scmbench-protocol-unpaired-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 'unpaired_inte_overall', cell E4 (row 'GLUE', column 'Muto-2021-batch-3')
Configuration: Harmony (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-3 (SCMBench)	0.614 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI) 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 unpaired integration, Muto-2021-batch-3 lit-cells-networks-20261011-scmbench-protocol-unpaired-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 'unpaired_inte_overall', cell E17 (row 'Harmony', column 'Muto-2021-batch-3')
Configuration: iNMF (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-3 (SCMBench)	0.302 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI) 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 unpaired integration, Muto-2021-batch-3 lit-cells-networks-20261011-scmbench-protocol-unpaired-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 'unpaired_inte_overall', cell E16 (row 'iNMF', column 'Muto-2021-batch-3')
Configuration: LIGER (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-3 (SCMBench)	0.766 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI) 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 unpaired integration, Muto-2021-batch-3 lit-cells-networks-20261011-scmbench-protocol-unpaired-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 'unpaired_inte_overall', cell E5 (row 'LIGER', column 'Muto-2021-batch-3')
Configuration: Pamona (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-3 (SCMBench)	0.556 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI) 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 unpaired integration, Muto-2021-batch-3 lit-cells-networks-20261011-scmbench-protocol-unpaired-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 'unpaired_inte_overall', cell E11 (row 'Pamona', column 'Muto-2021-batch-3')
Configuration: PCA (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-3 (SCMBench)	0.58 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI) 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 unpaired integration, Muto-2021-batch-3 lit-cells-networks-20261011-scmbench-protocol-unpaired-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 'unpaired_inte_overall', cell E12 (row 'PCA', column 'Muto-2021-batch-3')
Configuration: scFoundation (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-3 (SCMBench)	0.417 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI) 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 scFoundation on SCMBench unpaired integration, Muto-2021-batch-3 lit-cells-networks-20261011-scmbench-protocol-unpaired-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 'unpaired_inte_overall', cell E13 (row 'scFoundation', column 'Muto-2021-batch-3')
Configuration: scGPT_zero (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-3 (SCMBench)	0.545 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI) 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_zero on SCMBench unpaired integration, Muto-2021-batch-3 lit-cells-networks-20261011-scmbench-protocol-unpaired-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 'unpaired_inte_overall', cell E10 (row 'scGPT_zero', column 'Muto-2021-batch-3')
Configuration: scJoint (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-3 (SCMBench)	0.828 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI) 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 unpaired integration, Muto-2021-batch-3 lit-cells-networks-20261011-scmbench-protocol-unpaired-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 'unpaired_inte_overall', cell E2 (row 'scJoint', column 'Muto-2021-batch-3')
Configuration: scMoMaT (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-3 (SCMBench)	0.678 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI) 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 unpaired integration, Muto-2021-batch-3 lit-cells-networks-20261011-scmbench-protocol-unpaired-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 'unpaired_inte_overall', cell E8 (row 'scMoMaT', column 'Muto-2021-batch-3')
Configuration: scVI (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-3 (SCMBench)	0.55 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI) 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 unpaired integration, Muto-2021-batch-3 lit-cells-networks-20261011-scmbench-protocol-unpaired-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 'unpaired_inte_overall', cell E9 (row 'scVI', column 'Muto-2021-batch-3')
Configuration: Seurat4 (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-3 (SCMBench)	0.756 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI) 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 unpaired integration, Muto-2021-batch-3 lit-cells-networks-20261011-scmbench-protocol-unpaired-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 'unpaired_inte_overall', cell E3 (row 'Seurat4', column 'Muto-2021-batch-3')
Configuration: UCE (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-3 (SCMBench)	0.611 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI) 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 unpaired integration, Muto-2021-batch-3 lit-cells-networks-20261011-scmbench-protocol-unpaired-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 'unpaired_inte_overall', cell E7 (row 'UCE', column 'Muto-2021-batch-3')

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8 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-23-5347695500ed
Property and statement	Original source and location	Review and provenance
Source dataset label Muto-2021-batch-3 Context-only references	SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration Original source ↗ Fig. 1b; Supplementary Data 1, sheet 'Dataset' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Published article, Nature Communications 2026 (PMC13342640.1) Retrieved: 2026-10-11T21:38:51Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_dataset_label` Source artifact SHA-256: `7aa2dbf1fc26bd602bf26e52c1061f91358a1c6cb389f57edc0ebfb0edc64f57` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source dataset label Muto-2021-batch-3 Context-only references	SCMBench Supplementary Data 1 (methods and datasets) Original source ↗ Fig. 1b; Supplementary Data 1, sheet 'Dataset' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Data 1 (MOESM3) of the published article Retrieved: 2026-10-11T21:38:51Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_dataset_label` Source artifact SHA-256: `7287a457b1e856742a90043e96dc57b667210b28a8228d4d9a6de5d7156ecfb9` Hash scope: Hash scope not separately documented; inspect source record
Source location Fig. 1b; Supplementary Data 1, sheet 'Dataset' Context-only references	SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration Original source ↗ Fig. 1b; Supplementary Data 1, sheet 'Dataset' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Published article, Nature Communications 2026 (PMC13342640.1) Retrieved: 2026-10-11T21:38:51Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `7aa2dbf1fc26bd602bf26e52c1061f91358a1c6cb389f57edc0ebfb0edc64f57` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Fig. 1b; Supplementary Data 1, sheet 'Dataset' Context-only references	SCMBench Supplementary Data 1 (methods and datasets) Original source ↗ Fig. 1b; Supplementary Data 1, sheet 'Dataset' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Data 1 (MOESM3) of the published article Retrieved: 2026-10-11T21:38:51Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `7287a457b1e856742a90043e96dc57b667210b28a8228d4d9a6de5d7156ecfb9` Hash scope: Hash scope not separately documented; inspect source record
Description Muto-2021 human kidney snRNA-seq and snATAC-seq, batch 3 (unpaired, the Methods sample each batch to 2,500 cells for the batch-effect experiments and do not say whether this sheet uses the sampled batches). Context-only references	SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration Original source ↗ Fig. 1b; Supplementary Data 1, sheet 'Dataset' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Published article, Nature Communications 2026 (PMC13342640.1) Retrieved: 2026-10-11T21:38:51Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `7aa2dbf1fc26bd602bf26e52c1061f91358a1c6cb389f57edc0ebfb0edc64f57` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Muto-2021 human kidney snRNA-seq and snATAC-seq, batch 3 (unpaired, the Methods sample each batch to 2,500 cells for the batch-effect experiments and do not say whether this sheet uses the sampled batches). Context-only references	SCMBench Supplementary Data 1 (methods and datasets) Original source ↗ Fig. 1b; Supplementary Data 1, sheet 'Dataset' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Data 1 (MOESM3) of the published article Retrieved: 2026-10-11T21:38:51Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `7287a457b1e856742a90043e96dc57b667210b28a8228d4d9a6de5d7156ecfb9` Hash scope: Hash scope not separately documented; inspect source record
Name Muto-2021-batch-3 (SCMBench) Context-only references	SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration Original source ↗ Fig. 1b; Supplementary Data 1, sheet 'Dataset' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Published article, Nature Communications 2026 (PMC13342640.1) Retrieved: 2026-10-11T21:38:51Z	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `7aa2dbf1fc26bd602bf26e52c1061f91358a1c6cb389f57edc0ebfb0edc64f57` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Name Muto-2021-batch-3 (SCMBench) Context-only references	SCMBench Supplementary Data 1 (methods and datasets) Original source ↗ Fig. 1b; Supplementary Data 1, sheet 'Dataset' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Data 1 (MOESM3) of the published article Retrieved: 2026-10-11T21:38:51Z	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `7287a457b1e856742a90043e96dc57b667210b28a8228d4d9a6de5d7156ecfb9` Hash scope: Hash scope not separately documented; inspect source record

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Release 2026-10-23-5347695500ed · Record review: source checked

2 source records and release history

SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration · Original source · Published article, Nature Communications 2026 (PMC13342640.1)
SCMBench Supplementary Data 1 (methods and datasets) · Original source · Supplementary Data 1 (MOESM3) of the published article

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Stable ID: lit-cells-networks-20261011-scmbench-data-muto-2021-batch-3

areas: single-cell
contexts: research
source dataset label: Muto-2021-batch-3
source locator: Fig. 1b; Supplementary Data 1, sheet 'Dataset'
missing metadata: version: reason: unreported

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