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SCMBench Supplementary Data 2 (integration results)

Nature Communications · 2026 · Supplementary Data 2 (MOESM4) of the published article · Peer-reviewed

DOI: 10.1038/s41467-026-72570-xOriginal source

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Results

Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.

Model or configurationMetricValueDatasetEvaluation
bindSC (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.6603 unitless10x-Multiome-Pbmc10k (SCMBench)bindSC on SCMBench paired integration, 10x-Multiome-Pbmc10k
bindSC (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.352475 unitlessChen-2019 (SCMBench)bindSC on SCMBench paired integration, Chen-2019
bindSC (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.5579 unitlessMa-2020-batch-53 (SCMBench)bindSC on SCMBench paired integration, Ma-2020-batch-53
bindSC (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.474975 unitlessMa-2020-batch-54 (SCMBench)bindSC on SCMBench paired integration, Ma-2020-batch-54
bindSC (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.4826 unitlessMa-2020-batch-55 (SCMBench)bindSC on SCMBench paired integration, Ma-2020-batch-55
bindSC (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)0.50565 unitlesspaired-overall (SCMBench)bindSC on SCMBench paired integration, paired-overall
bindSC (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.6708 unitlessMuto-2021-batch-1 (SCMBench)bindSC on SCMBench unpaired integration, Muto-2021-batch-1
bindSC (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.7157 unitlessMuto-2021-batch-2 (SCMBench)bindSC on SCMBench unpaired integration, Muto-2021-batch-2
bindSC (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.711375 unitlessMuto-2021-batch-3 (SCMBench)bindSC on SCMBench unpaired integration, Muto-2021-batch-3
bindSC (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.76825 unitlessMuto-2021-batch-4 (SCMBench)bindSC on SCMBench unpaired integration, Muto-2021-batch-4
bindSC (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.68975 unitlessMuto-2021-batch-5 (SCMBench)bindSC on SCMBench unpaired integration, Muto-2021-batch-5
bindSC (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across the five Muto-2021 batches (Yao not scored))0.711175 unitlessunpaired-overall (SCMBench)bindSC on SCMBench unpaired integration, unpaired-overall
Cobolt (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.630875 unitless10x-Multiome-Pbmc10k (SCMBench)Cobolt on SCMBench paired integration, 10x-Multiome-Pbmc10k
Cobolt (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.546175 unitlessChen-2019 (SCMBench)Cobolt on SCMBench paired integration, Chen-2019
Cobolt (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.495775 unitlessMa-2020-batch-53 (SCMBench)Cobolt on SCMBench paired integration, Ma-2020-batch-53
Cobolt (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.496125 unitlessMa-2020-batch-54 (SCMBench)Cobolt on SCMBench paired integration, Ma-2020-batch-54
Cobolt (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.495475 unitlessMa-2020-batch-55 (SCMBench)Cobolt on SCMBench paired integration, Ma-2020-batch-55
Cobolt (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)0.532885 unitlesspaired-overall (SCMBench)Cobolt on SCMBench paired integration, paired-overall
Cobolt (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.314775 unitlessMuto-2021-batch-1 (SCMBench)Cobolt on SCMBench unpaired integration, Muto-2021-batch-1
Cobolt (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.372825 unitlessMuto-2021-batch-2 (SCMBench)Cobolt on SCMBench unpaired integration, Muto-2021-batch-2
Cobolt (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.2894 unitlessMuto-2021-batch-3 (SCMBench)Cobolt on SCMBench unpaired integration, Muto-2021-batch-3
Cobolt (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.408275 unitlessMuto-2021-batch-4 (SCMBench)Cobolt on SCMBench unpaired integration, Muto-2021-batch-4
Cobolt (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.315825 unitlessMuto-2021-batch-5 (SCMBench)Cobolt on SCMBench unpaired integration, Muto-2021-batch-5
Cobolt (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)0.3692375 unitlessunpaired-overall (SCMBench)Cobolt on SCMBench unpaired integration, unpaired-overall
Cobolt (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.514325 unitlessYao (SCMBench)Cobolt on SCMBench unpaired integration, Yao
Deepmaps (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.56745 unitless10x-Multiome-Pbmc10k (SCMBench)Deepmaps on SCMBench paired integration, 10x-Multiome-Pbmc10k
Deepmaps (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.48425 unitlessChen-2019 (SCMBench)Deepmaps on SCMBench paired integration, Chen-2019
Deepmaps (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.272475 unitlessMa-2020-batch-53 (SCMBench)Deepmaps on SCMBench paired integration, Ma-2020-batch-53
Deepmaps (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.232325 unitlessMa-2020-batch-54 (SCMBench)Deepmaps on SCMBench paired integration, Ma-2020-batch-54
Deepmaps (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.216375 unitlessMa-2020-batch-55 (SCMBench)Deepmaps on SCMBench paired integration, Ma-2020-batch-55
Deepmaps (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)0.354575 unitlesspaired-overall (SCMBench)Deepmaps on SCMBench paired integration, paired-overall
FM-scVI (SCMBench adapter)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.673625 unitless10x-Multiome-Pbmc10k (SCMBench)FM-scVI on SCMBench paired integration, 10x-Multiome-Pbmc10k
FM-scVI (SCMBench adapter)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.56805 unitlessChen-2019 (SCMBench)FM-scVI on SCMBench paired integration, Chen-2019
FM-scVI (SCMBench adapter)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.278275 unitlessMa-2020-batch-53 (SCMBench)FM-scVI on SCMBench paired integration, Ma-2020-batch-53
FM-scVI (SCMBench adapter)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.2949 unitlessMa-2020-batch-54 (SCMBench)FM-scVI on SCMBench paired integration, Ma-2020-batch-54
FM-scVI (SCMBench adapter)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.29955 unitlessMa-2020-batch-55 (SCMBench)FM-scVI on SCMBench paired integration, Ma-2020-batch-55
FM-scVI (SCMBench adapter)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)0.42288 unitlesspaired-overall (SCMBench)FM-scVI on SCMBench paired integration, paired-overall
FM-scVI (SCMBench adapter)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.57645 unitlessMuto-2021-batch-1 (SCMBench)FM-scVI on SCMBench unpaired integration, Muto-2021-batch-1
FM-scVI (SCMBench adapter)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.5988 unitlessMuto-2021-batch-2 (SCMBench)FM-scVI on SCMBench unpaired integration, Muto-2021-batch-2
FM-scVI (SCMBench adapter)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.6026 unitlessMuto-2021-batch-3 (SCMBench)FM-scVI on SCMBench unpaired integration, Muto-2021-batch-3
FM-scVI (SCMBench adapter)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.580025 unitlessMuto-2021-batch-4 (SCMBench)FM-scVI on SCMBench unpaired integration, Muto-2021-batch-4
FM-scVI (SCMBench adapter)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.550475 unitlessMuto-2021-batch-5 (SCMBench)FM-scVI on SCMBench unpaired integration, Muto-2021-batch-5
FM-scVI (SCMBench adapter)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across datasets)0.569729166666667 unitlessunpaired-overall (SCMBench)FM-scVI on SCMBench unpaired integration, unpaired-overall
FM-scVI (SCMBench adapter)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.510025 unitlessYao (SCMBench)FM-scVI on SCMBench unpaired integration, Yao
Geneformer (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.3564 unitlessMuto-2021-batch-1 (SCMBench)Geneformer on SCMBench unpaired integration, Muto-2021-batch-1
Geneformer (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.3817 unitlessMuto-2021-batch-2 (SCMBench)Geneformer on SCMBench unpaired integration, Muto-2021-batch-2
Geneformer (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.347925 unitlessMuto-2021-batch-3 (SCMBench)Geneformer on SCMBench unpaired integration, Muto-2021-batch-3
Geneformer (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.36815 unitlessMuto-2021-batch-4 (SCMBench)Geneformer on SCMBench unpaired integration, Muto-2021-batch-4
Geneformer (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI)0.335775 unitlessMuto-2021-batch-5 (SCMBench)Geneformer on SCMBench unpaired integration, Muto-2021-batch-5
Geneformer (SCMBench)Scmbench integration accuracy (mean of MAP, NMI, ASW and ARI; mean across the five Muto-2021 batches (Yao not scored))0.35799 unitlessunpaired-overall (SCMBench)Geneformer on SCMBench unpaired integration, unpaired-overall

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Evaluations (241)

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Claims, original sources and review scope · Release 2026-10-23-5347695500ed
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77582bcc906fed343de12c2b2ed7443e94f5d11bf93b7f3862a37c5099015443
Source metadata		SCMBench Supplementary Data 2 (integration results)

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10.1038/s41467-026-72570-x
Source metadata		SCMBench Supplementary Data 2 (integration results)

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3 values
  • source id
    lit-cells-networks-20261011-scmbench-source-sd2
    message
    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.
    source locator
    Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H
    artifact sha256
    77582bcc906fed343de12c2b2ed7443e94f5d11bf93b7f3862a37c5099015443
    review date
    2026-10-12
  • source id
    lit-cells-networks-20261011-scmbench-source-sd2
    message
    '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.
    source locator
    Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows
    artifact sha256
    7aa2dbf1fc26bd602bf26e52c1061f91358a1c6cb389f57edc0ebfb0edc64f57
    review date
    2026-10-11
  • source id
    lit-cells-networks-20261011-scmbench-source-sd2
    message
    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.
    source locator
    Supplementary Data 2, sheet 'paired_inte_overall', cell G20
    artifact sha256
    77582bcc906fed343de12c2b2ed7443e94f5d11bf93b7f3862a37c5099015443
    review date
    2026-10-12
Source metadata		SCMBench Supplementary Data 2 (integration results)

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application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
Source metadata		SCMBench Supplementary Data 2 (integration results)

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Source metadata		SCMBench Supplementary Data 2 (integration results)

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2026-10-12
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Artifact re-downloaded and SHA-256 matched; the archived gzip copy matches.
Source metadata		SCMBench Supplementary Data 2 (integration results)

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Version: Supplementary Data 2 (MOESM4) of the published article
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Source metadata		SCMBench Supplementary Data 2 (integration results)

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

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Stable ID: lit-cells-networks-20261011-scmbench-source-sd2

areas
single-cell
contexts
research
doi
10.1038/s41467-026-72570-x
publication status
peer_reviewed
licence
CC-BY-4.0
retrieved at
2026-10-11T21:38:51Z
year
2026
venue
Nature Communications
url
https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-026-72570-x/MediaObjects/41467_2026_72570_MOESM4_ESM.xlsx
version
Supplementary Data 2 (MOESM4) of the published article
artifact sha256
77582bcc906fed343de12c2b2ed7443e94f5d11bf93b7f3862a37c5099015443
media type
application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
evidence concerns
source id: lit-cells-networks-20261011-scmbench-source-sd2; message: 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.; source locator: Supplementary Data 2, sheet 'unpaired_inte_overall', row 1 and column H; artifact sha256: 77582bcc906fed343de12c2b2ed7443e94f5d11bf93b7f3862a37c5099015443; review date: 2026-10-12; source id: lit-cells-networks-20261011-scmbench-source-sd2; message: '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.; source locator: Article Fig. 2 legend; Supplementary Data 2 'FM-scVI' rows; artifact sha256: 7aa2dbf1fc26bd602bf26e52c1061f91358a1c6cb389f57edc0ebfb0edc64f57; review date: 2026-10-11; source id: lit-cells-networks-20261011-scmbench-source-sd2; message: 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.; source locator: Supplementary Data 2, sheet 'paired_inte_overall', cell G20; artifact sha256: 77582bcc906fed343de12c2b2ed7443e94f5d11bf93b7f3862a37c5099015443; review date: 2026-10-12
review
method: source-hash-verification; method note: Artifact re-downloaded and SHA-256 matched; the archived gzip copy matches.; reviewer: claude; reviewer note: Claude review agent reviewer-cn-2, independent of the extractor lit-cells-networks; no human review claimed; date: 2026-10-12
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