Dataset subset

PBMC (12k) (Kedzierska et al. 2025)

PBMCs from a healthy donor, from scvi-tools data.pbmc_dataset: 12k cells, 9 labels, 2 batches.

Evaluation results

16 evaluations · 128 results. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.6 Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q17, metric block 'ARI', row 'PBMC (12k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.51 Scib asw label (cell-type ASW; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q5, metric block 'ASW', row 'PBMC (12k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.48 Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q39, metric block 'Average batch', row 'PBMC (12k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.59 Avg bio (AvgBIO (mean of cell-type ASW, NMI and ARI; NMI and ARI on Louvain clusters at the best-NMI resolution); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q23, metric block 'AvgBIO', row 'PBMC (12k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.97 Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q29, metric block 'Batch integration', row 'PBMC (12k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.65 Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q11, metric block 'NMI', row 'PBMC (12k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0 Scib pcr batch (principal component regression on batch; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q34, metric block 'PCR', row 'PBMC (12k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	8 Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS4' cell D10, row 'Geneformer', column 'PBMC (12k)'
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.72 Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Harmony cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell E17, metric block 'ARI', row 'PBMC (12k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.62 Scib asw label (cell-type ASW; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Harmony cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell E5, metric block 'ASW', row 'PBMC (12k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.89 Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Harmony cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell E39, metric block 'Average batch', row 'PBMC (12k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.72 Avg bio (AvgBIO (mean of cell-type ASW, NMI and ARI; NMI and ARI on Louvain clusters at the best-NMI resolution); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Harmony cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell E23, metric block 'AvgBIO', row 'PBMC (12k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.97 Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Harmony cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell E29, metric block 'Batch integration', row 'PBMC (12k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.82 Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Harmony cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell E11, metric block 'NMI', row 'PBMC (12k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.82 Scib pcr batch (principal component regression on batch; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Harmony cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell E34, metric block 'PCR', row 'PBMC (12k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	1 Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Harmony cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS4' cell D4, row 'Harmony', column 'PBMC (12k)'
Configuration: 2,000 highly variable genes (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.67 Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HVG cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell C17, metric block 'ARI', row 'PBMC (12k)', column 'HVG' (single-value column)
Configuration: 2,000 highly variable genes (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.51 Scib asw label (cell-type ASW; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HVG cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell C5, metric block 'ASW', row 'PBMC (12k)', column 'HVG' (single-value column)
Configuration: 2,000 highly variable genes (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.65 Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HVG cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell C39, metric block 'Average batch', row 'PBMC (12k)', column 'HVG' (single-value column)
Configuration: 2,000 highly variable genes (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.63 Avg bio (AvgBIO (mean of cell-type ASW, NMI and ARI; NMI and ARI on Louvain clusters at the best-NMI resolution); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HVG cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell C23, metric block 'AvgBIO', row 'PBMC (12k)', column 'HVG' (single-value column)
Configuration: 2,000 highly variable genes (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.99 Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HVG cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell C29, metric block 'Batch integration', row 'PBMC (12k)', column 'HVG' (single-value column)
Configuration: 2,000 highly variable genes (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.71 Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HVG cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell C11, metric block 'NMI', row 'PBMC (12k)', column 'HVG' (single-value column)
Configuration: 2,000 highly variable genes (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.3 Scib pcr batch (principal component regression on batch; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HVG cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell C34, metric block 'PCR', row 'PBMC (12k)', column 'HVG' (single-value column)
Configuration: 2,000 highly variable genes (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	5 Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HVG cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS4' cell D5, row 'HVG', column 'PBMC (12k)'
Configuration: scGPT blood (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: PBMC (12k) (Kedzierska et al. 2025)	0.87 Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source scGPT blood cell embedding on PBMC (12k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell M17, metric block 'ARI', row 'PBMC (12k)', column 'scGPT blood' (single-value column)

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.

Subset and evaluation context

This record describes a particular subset or cohort used in an evaluation. Its results do not describe the full dataset.

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.

14 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 PBMC (12k) Context-only references	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_dataset_label` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source dataset label PBMC (12k) Context-only references	Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Genome Biology 26:101, published 2025-04-18 Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_dataset_label` Source artifact SHA-256: `8efcc5fcb2e35b9a04b1ee9e03581e20fffeb5521a4a4c748a6f9b34f7d3c47f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Context-only references	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Context-only references	Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Genome Biology 26:101, published 2025-04-18 Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `8efcc5fcb2e35b9a04b1ee9e03581e20fffeb5521a4a4c748a6f9b34f7d3c47f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Split No split; each whole dataset is embedded and scored Context-only references	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Split No split; each whole dataset is embedded and scored Context-only references	Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Genome Biology 26:101, published 2025-04-18 Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `8efcc5fcb2e35b9a04b1ee9e03581e20fffeb5521a4a4c748a6f9b34f7d3c47f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description PBMCs from a healthy donor, from scvi-tools data.pbmc_dataset: 12k cells, 9 labels, 2 batches. Context-only references	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description PBMCs from a healthy donor, from scvi-tools data.pbmc_dataset: 12k cells, 9 labels, 2 batches. Context-only references	Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Genome Biology 26:101, published 2025-04-18 Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `8efcc5fcb2e35b9a04b1ee9e03581e20fffeb5521a4a4c748a6f9b34f7d3c47f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: used in gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Context-only references	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	not individually reviewed No individual claim review recorded Audit details Field: `links:used_in:gfm-guides-20261014-kedzierska2025-protocol-cell-embedding` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: used in gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Context-only references	Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) Original source ↗ Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Genome Biology 26:101, published 2025-04-18 Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `links:used_in:gfm-guides-20261014-kedzierska2025-protocol-cell-embedding` Source artifact SHA-256: `8efcc5fcb2e35b9a04b1ee9e03581e20fffeb5521a4a4c748a6f9b34f7d3c47f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

How to read the evidence

Sources and history

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

2 source records and release history

Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) · Original source · Version of record, Genome Biology 26:101, published 2025-04-18
Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Original source · Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: gfm-guides-20261014-kedzierska2025-data-pbmc-12k

areas: single-cell
contexts: research
source dataset label: PBMC (12k)
split: No split; each whole dataset is embedded and scored
source locator: Additional file 1 sheet TableS1 (dataset overview) and TableS2 (sources); page 8-9 'Datasets'; page 11 'Data availability'
missing metadata: version: reason: unreported

Related records

Suggest a correction