Configuration

scMoMaT (SCMBench)

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

Configuration of scMoMaT: default or tuned hyperparameters per the SCMBench setup; Defaults for R methods and methods without explicit hyperparameters; tuned otherwise.

12 evaluations · 12 results

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

12 evaluations · 12 results. Different protocols are not a single leaderboard.

Sorted by Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)	Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)	Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across the five Muto-2021 batches (Yao not scored))
scMoMaT (SCMBench)Evaluation	SCMBench unpaired RNA-ATAC integration accuracy, Muto-2021-batch-3 (SCMBench)	0.678 (best in column)	Not reported	Not reported
scMoMaT (SCMBench)Evaluation	SCMBench paired RNA-ATAC integration accuracy, 10x-Multiome-Pbmc10k (SCMBench)	0.628	Not reported	Not reported
scMoMaT (SCMBench)Evaluation	SCMBench unpaired RNA-ATAC integration accuracy, Muto-2021-batch-4 (SCMBench)	0.585	Not reported	Not reported
scMoMaT (SCMBench)Evaluation	SCMBench paired RNA-ATAC integration accuracy, Chen-2019 (SCMBench)	0.562	Not reported	Not reported
scMoMaT (SCMBench)Evaluation	SCMBench unpaired RNA-ATAC integration accuracy, Muto-2021-batch-2 (SCMBench)	0.56	Not reported	Not reported
scMoMaT (SCMBench)Evaluation	SCMBench unpaired RNA-ATAC integration accuracy, Muto-2021-batch-1 (SCMBench)	0.544	Not reported	Not reported
scMoMaT (SCMBench)Evaluation	SCMBench unpaired RNA-ATAC integration accuracy, Muto-2021-batch-5 (SCMBench)	0.521	Not reported	Not reported
scMoMaT (SCMBench)Evaluation	SCMBench paired RNA-ATAC integration accuracy, Ma-2020-batch-53 (SCMBench)	0.426	Not reported	Not reported
scMoMaT (SCMBench)Evaluation	SCMBench paired RNA-ATAC integration accuracy, Ma-2020-batch-54 (SCMBench)	0.408	Not reported	Not reported
scMoMaT (SCMBench)Evaluation	SCMBench paired RNA-ATAC integration accuracy, Ma-2020-batch-55 (SCMBench)	0.398	Not reported	Not reported
scMoMaT (SCMBench)Evaluation	SCMBench paired RNA-ATAC integration accuracy, paired-overall (SCMBench)	Not reported	0.484	Not reported
scMoMaT (SCMBench)Evaluation	SCMBench unpaired RNA-ATAC integration accuracy, unpaired-overall (SCMBench)	Not reported	Not reported	0.578

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: scMoMaT (SCMBench)	Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: 10x-Multiome-Pbmc10k (SCMBench)	0.628 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 paired integration, 10x-Multiome-Pbmc10k 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 B9 (row 'scMoMaT', column '10x-Multiome-Pbmc10k')
Configuration: scMoMaT (SCMBench)	Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: Chen-2019 (SCMBench)	0.562 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 paired integration, Chen-2019 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 C9 (row 'scMoMaT', column 'Chen-2019')
Configuration: scMoMaT (SCMBench)	Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: Ma-2020-batch-53 (SCMBench)	0.426 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 paired integration, Ma-2020-batch-53 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 D9 (row 'scMoMaT', column 'Ma-2020-batch-53')
Configuration: scMoMaT (SCMBench)	Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: Ma-2020-batch-54 (SCMBench)	0.408 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 paired integration, Ma-2020-batch-54 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 E9 (row 'scMoMaT', column 'Ma-2020-batch-54')
Configuration: scMoMaT (SCMBench)	Protocol: SCMBench paired RNA-ATAC integration accuracy Dataset subset: Ma-2020-batch-55 (SCMBench)	0.398 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 paired integration, Ma-2020-batch-55 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 F9 (row 'scMoMaT', column 'Ma-2020-batch-55')
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: scMoMaT (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-1 (SCMBench)	0.544 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-1 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 C8 (row 'scMoMaT', column 'Muto-2021-batch-1')
Configuration: scMoMaT (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-2 (SCMBench)	0.56 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-2 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 D8 (row 'scMoMaT', column 'Muto-2021-batch-2')
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: scMoMaT (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-4 (SCMBench)	0.585 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-4 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 F8 (row 'scMoMaT', column 'Muto-2021-batch-4')
Configuration: scMoMaT (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: Muto-2021-batch-5 (SCMBench)	0.521 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-5 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 G8 (row 'scMoMaT', column 'Muto-2021-batch-5')
Configuration: scMoMaT (SCMBench)	Protocol: SCMBench unpaired RNA-ATAC integration accuracy Dataset subset: unpaired-overall (SCMBench)	0.578 Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across the five Muto-2021 batches (Yao not scored)) 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, unpaired-overall 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 H8 (row 'scMoMaT', column 'unlabelled column H')

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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 2 (integration results) · Original source · Supplementary Data 2 (MOESM4) of the published article

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Stable ID: lit-cells-networks-20261011-scmbench-config-scmomat

areas: single-cell
contexts: research
method types: specialist
reported name: scMoMaT
foundation model eligible: false
hyperparameters: Defaults for R methods and methods without explicit hyperparameters; tuned otherwise (Methods 'Hyperparameter tuning')
source locator: Supplementary Data 2 method rows; Methods 'Benchmarking setup'
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provenance note: scMoMaT as run in SCMBench: default or tuned hyperparameters per the SCMBench setup.

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system: scMoMaT on SCMBench paired integration, paired-overall
system: scMoMaT on SCMBench unpaired integration, Muto-2021-batch-1
system: scMoMaT on SCMBench unpaired integration, Muto-2021-batch-2
system: scMoMaT on SCMBench unpaired integration, Muto-2021-batch-3
system: scMoMaT on SCMBench unpaired integration, Muto-2021-batch-4
system: scMoMaT on SCMBench unpaired integration, Muto-2021-batch-5
system: scMoMaT on SCMBench unpaired integration, unpaired-overall

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