rewirebio.iobenchmarks
Evaluation

scMDC on SCMBench paired integration, 10x-Multiome-Pbmc10k

Published comparison transcribed from the pinned source; not reproduced.

Evaluation results

1 evaluation · 1 result. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: scMDC (SCMBench)Protocol: SCMBench paired RNA-ATAC integration accuracy
Dataset subset: 10x-Multiome-Pbmc10k (SCMBench)
0.739 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
Methods, coverage and source

scMDC 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 B3 (row 'scMDC', column '10x-Multiome-Pbmc10k')

Source checking is not independent reproduction. Release 2026-10-23-5347695500ed.

Research readiness

0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

Release 2026-10-23-5347695500ed · Evidence verified: Not verified

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified
  • Sample annotations are recorded: not yet verified
  • Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • A pinned run recipe exists: not yet verified
  • Compute requirements are estimated: not yet verified

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Independent validation data exist: not yet verified
  • Overlap with training data is checked: not yet verified

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Evaluation procedure

SCMBench paired RNA-ATAC integration accuracy

Configuration
scMDC (SCMBench)
Protocol
SCMBench paired RNA-ATAC integration accuracy
Dataset subset
10x-Multiome-Pbmc10k (SCMBench)
origin
Independent external evaluation
configuration
Primary source as retrieved 2026-10-11
protocol id
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
dataset version
Not reported
split
Per dataset or batch as in Supplementary Data 2; whether batch splits use the 2,500-cell samples is not stated
population
Not reported
inputs
scRNA-seq counts and scATAC-seq peaks (gene activity scores for foundation models)
adaptation
Not reported
metric implementation
SCMBench integration accuracy (MAP, NMI, ASW, ARI)
aggregation
Mean of four metrics
budget
Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split
Per dataset or batch as in Supplementary Data 2; whether batch splits use the 2,500-cell samples is not stated
Adaptation
Not reported
Scoring implementation
SCMBench integration accuracy (MAP, NMI, ASW, ARI)

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

36 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-23-5347695500ed
Property and statementOriginal source and locationReview and provenance
Comparison: adaptation
Not reported
Context-only references
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration

Original source ↗

Supplementary Data 2, sheet 'paired_inte_overall', row 3 'scMDC'

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

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: 7aa2dbf1fc26bd602bf26e52c1061f91358a1c6cb389f57edc0ebfb0edc64f57

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: adaptation
Not reported
Context-only references
SCMBench Supplementary Data 2 (integration results)

Original source ↗

Supplementary Data 2, sheet 'paired_inte_overall', row 3 'scMDC'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Supplementary Data 2 (MOESM4) of the published article
Retrieved: 2026-10-11T21:38:51Z

missing or unspecified

No individual claim review recorded

independent paper

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: 77582bcc906fed343de12c2b2ed7443e94f5d11bf93b7f3862a37c5099015443

Hash scope: Hash scope not separately documented; inspect source record

Comparison: aggregation
Mean of four metrics
Context-only references
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration

Original source ↗

Supplementary Data 2, sheet 'paired_inte_overall', row 3 'scMDC'

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

independent paper

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: 7aa2dbf1fc26bd602bf26e52c1061f91358a1c6cb389f57edc0ebfb0edc64f57

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: aggregation
Mean of four metrics
Context-only references
SCMBench Supplementary Data 2 (integration results)

Original source ↗

Supplementary Data 2, sheet 'paired_inte_overall', row 3 'scMDC'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Supplementary Data 2 (MOESM4) of the published article
Retrieved: 2026-10-11T21:38:51Z

not individually reviewed

No individual claim review recorded

independent paper

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: 77582bcc906fed343de12c2b2ed7443e94f5d11bf93b7f3862a37c5099015443

Hash scope: Hash scope not separately documented; inspect source record

Comparison: budget
Not reported
Context-only references
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration

Original source ↗

Supplementary Data 2, sheet 'paired_inte_overall', row 3 'scMDC'

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

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.budget

Source artifact SHA-256: 7aa2dbf1fc26bd602bf26e52c1061f91358a1c6cb389f57edc0ebfb0edc64f57

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: budget
Not reported
Context-only references
SCMBench Supplementary Data 2 (integration results)

Original source ↗

Supplementary Data 2, sheet 'paired_inte_overall', row 3 'scMDC'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Supplementary Data 2 (MOESM4) of the published article
Retrieved: 2026-10-11T21:38:51Z

missing or unspecified

No individual claim review recorded

independent paper

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.comparison.budget

Source artifact SHA-256: 77582bcc906fed343de12c2b2ed7443e94f5d11bf93b7f3862a37c5099015443

Hash scope: Hash scope not separately documented; inspect source record

Comparison: dataset version
Not reported
Context-only references
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration

Original source ↗

Supplementary Data 2, sheet 'paired_inte_overall', row 3 'scMDC'

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

missing or unspecified

No individual claim review recorded

independent paper

Audit details

Field: attributes.comparison.dataset_version

Source artifact SHA-256: 7aa2dbf1fc26bd602bf26e52c1061f91358a1c6cb389f57edc0ebfb0edc64f57

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: dataset version
Not reported
Context-only references
SCMBench Supplementary Data 2 (integration results)

Original source ↗

Supplementary Data 2, sheet 'paired_inte_overall', row 3 'scMDC'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Supplementary Data 2 (MOESM4) of the published article
Retrieved: 2026-10-11T21:38:51Z

missing or unspecified

No individual claim review recorded

independent paper

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.comparison.dataset_version

Source artifact SHA-256: 77582bcc906fed343de12c2b2ed7443e94f5d11bf93b7f3862a37c5099015443

Hash scope: Hash scope not separately documented; inspect source record

Comparison: inputs
scRNA-seq counts and scATAC-seq peaks (gene activity scores for foundation models)
Context-only references
SCMBench: benchmarking domain-specific and foundation models for single-cell multi-omics data integration

Original source ↗

Supplementary Data 2, sheet 'paired_inte_overall', row 3 'scMDC'

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

independent paper

Audit details

Field: attributes.comparison.inputs

Source artifact SHA-256: 7aa2dbf1fc26bd602bf26e52c1061f91358a1c6cb389f57edc0ebfb0edc64f57

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: inputs
scRNA-seq counts and scATAC-seq peaks (gene activity scores for foundation models)
Context-only references
SCMBench Supplementary Data 2 (integration results)

Original source ↗

Supplementary Data 2, sheet 'paired_inte_overall', row 3 'scMDC'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Supplementary Data 2 (MOESM4) of the published article
Retrieved: 2026-10-11T21:38:51Z

not individually reviewed

No individual claim review recorded

independent paper

Source has a recorded evidence concern. Consult its source page before using the claim.

Audit details

Field: attributes.comparison.inputs

Source artifact SHA-256: 77582bcc906fed343de12c2b2ed7443e94f5d11bf93b7f3862a37c5099015443

Hash scope: Hash scope not separately documented; inspect source record

How to read the evidence

Sources and history

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

2 source records and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: lit-cells-networks-20261011-scmbench-eval-paired-10x-multiome-pbmc10k-scmdc

areas
single-cell
contexts
research
origin
independent_paper
protocol
lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy
version
Primary source as retrieved 2026-10-11
comparison
protocol id: lit-cells-networks-20261011-scmbench-protocol-paired-integration-accuracy; dataset version: Not reported; split: Per dataset or batch as in Supplementary Data 2; whether batch splits use the 2,500-cell samples is not stated; population: Not reported; inputs: scRNA-seq counts and scATAC-seq peaks (gene activity scores for foundation models); adaptation: Not reported; metric implementation: SCMBench integration accuracy (MAP, NMI, ASW, ARI); aggregation: Mean of four metrics; budget: Not reported
source locator
Supplementary Data 2, sheet 'paired_inte_overall', row 3 'scMDC'
missing metadata
comparison.adaptation: reason: unreported; comparison.budget: reason: unreported; comparison.dataset version: reason: unreported; comparison.population: reason: unreported
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