Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2)
Classifier trained on the Tabula Sapiens reference applied to all HLCA cells of the 14 cell types shared by both atlases.
Overview
Classifier trained on the Tabula Sapiens reference applied to all HLCA cells of the 14 cell types shared by both atlases.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
23 recorded evaluations, 46 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
23 evaluations · 46 results. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Ensemble Geneformer + LangCell (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.75 top-1-accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGeneformer + LangCell: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell B22, row 'Geneformer + LangCell', column 'Accuracy@1' |
| Configuration: Ensemble Geneformer + LangCell (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.162 macro-f1 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGeneformer + LangCell: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell C22, row 'Geneformer + LangCell', column 'Macro-F1' |
| Configuration: Ensemble Geneformer + scCello (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.76 top-1-accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGeneformer + scCello: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell B24, row 'Geneformer + scCello', column 'Accuracy@1' |
| Configuration: Ensemble Geneformer + scCello (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.164 macro-f1 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGeneformer + scCello: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell C24, row 'Geneformer + scCello', column 'Macro-F1' |
| Configuration: Ensemble Geneformer + scFoundation (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.744 top-1-accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGeneformer + scFoundation: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell B19, row 'Geneformer + scFoundation', column 'Accuracy@1' |
| Configuration: Ensemble Geneformer + scFoundation (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.156 macro-f1 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGeneformer + scFoundation: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell C19, row 'Geneformer + scFoundation', column 'Macro-F1' |
| Configuration: Ensemble Geneformer + scGPT (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.756 top-1-accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGeneformer + scGPT: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell B23, row 'Geneformer + scGPT', column 'Accuracy@1' |
| Configuration: Ensemble Geneformer + scGPT (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.161 macro-f1 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGeneformer + scGPT: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell C23, row 'Geneformer + scGPT', column 'Macro-F1' |
| Configuration: Ensemble Geneformer + UCE (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.747 top-1-accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGeneformer + UCE: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell B21, row 'Geneformer + UCE', column 'Accuracy@1' |
| Configuration: Ensemble Geneformer + UCE (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.161 macro-f1 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGeneformer + UCE: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell C21, row 'Geneformer + UCE', column 'Macro-F1' |
| Configuration: Ensemble LangCell + scCello (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.747 top-1-accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLangCell + scCello: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell B20, row 'LangCell + scCello', column 'Accuracy@1' |
| Configuration: Ensemble LangCell + scCello (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.125 macro-f1 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLangCell + scCello: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell C20, row 'LangCell + scCello', column 'Macro-F1' |
| Configuration: Ensemble LangCell + scFoundation (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.708 top-1-accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLangCell + scFoundation: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell B12, row 'LangCell + scFoundation', column 'Accuracy@1' |
| Configuration: Ensemble LangCell + scFoundation (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.111 macro-f1 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLangCell + scFoundation: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell C12, row 'LangCell + scFoundation', column 'Macro-F1' |
| Configuration: Ensemble LangCell + scGPT (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.719 top-1-accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescGPT + LangCell: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell B15, row 'scGPT + LangCell', column 'Accuracy@1' |
| Configuration: Ensemble LangCell + scGPT (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.112 macro-f1 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescGPT + LangCell: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell C15, row 'scGPT + LangCell', column 'Macro-F1' |
| Configuration: Ensemble LangCell + UCE (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.713 top-1-accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceUCE + LangCell: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell B13, row 'UCE + LangCell', column 'Accuracy@1' |
| Configuration: Ensemble LangCell + UCE (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.111 macro-f1 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceUCE + LangCell: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell C13, row 'UCE + LangCell', column 'Macro-F1' |
| Configuration: Ensemble Logit aggregation (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.753 top-1-accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLogit aggregation: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell B27, row 'Logit aggregation', column 'Accuracy@1' |
| Configuration: Ensemble Logit aggregation (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.163 macro-f1 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLogit aggregation: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell C27, row 'Logit aggregation', column 'Macro-F1' |
| Configuration: Ensemble Majority voting (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.758 top-1-accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceMajority voting: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell B28, row 'Majority voting', column 'Accuracy@1' |
| Configuration: Ensemble Majority voting (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.119 macro-f1 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceMajority voting: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell C28, row 'Majority voting', column 'Macro-F1' |
| Configuration: Ensemble scCello + scFoundation (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.731 top-1-accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescFoundation + scCello: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell B17, row 'scFoundation + scCello', column 'Accuracy@1' |
| Configuration: Ensemble scCello + scFoundation (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.128 macro-f1 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescFoundation + scCello: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell C17, row 'scFoundation + scCello', column 'Macro-F1' |
| Configuration: Ensemble scCello + scGPT (Wu et al. 2025) | Protocol: Cross-atlas annotation transfer, Tabula Sapiens to HLCA, 14 shared cell types (Wu et al. 2025 Table S2) Dataset: HLCA core (CELLxGENE), 37 leaf cell types after processing | 0.775 top-1-accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcescGPT + scCello: Tabula Sapiens to HLCA transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-ts-to-hlca Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S2, cell B25, row 'scGPT + scCello', column 'Accuracy@1' |
Source checking is not independent reproduction. Release 2026-10-10-6e93f504adfc.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- Geneformer + LangCell: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- Geneformer + scCello: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- Geneformer + scFoundation: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- Geneformer + scGPT: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- Geneformer + UCE: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- LangCell + scCello: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- LangCell + scFoundation: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- scGPT + LangCell: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- UCE + LangCell: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- Logit aggregation: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- Majority voting: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- scFoundation + scCello: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
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- External evaluations
- 23
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Training-set class prior where supervised fitting is permitted
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Regularised classifier on simple permitted features, or protocol's conventional reference
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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Sources and history
Release 2026-10-10-6e93f504adfc · Record review: source checked
2 source records and release history
- Biology-driven insights into the power of single-cell foundation models · Original source · Genome Biology 26:334, published 2025-10-03; PMC12492631 full-text XML
- Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Original source · 13059_2025_3781_MOESM3_ESM.xlsx (38,926 bytes), as linked from the article XML <supplementary-material id="MOESM3">
Technical metadata and extraction receipts
Stable ID: cell-type-20261009-protocol-wu2025-ts-to-hlca
- areas
- cells-tissues
- contexts
- research
- protocol
- Zero-shot cell embeddings from each scFM feed an OnClass classifier trained on the Tabula Sapiens intra-dataset split; the trained model is applied unchanged to every HLCA cell of the 14 shared leaf cell types. Accuracy@1 is the share of cells whose top label is correct; macro-F1 averages F1 over cell types. Labels are the atlases' own annotations.
- version
- Table S2
- source locator
- Results 'Cross-dataset validation'; Methods 'Batch integration and cell type annotation' paragraph 3; 'Standard benchmarking metrics'
- limitations
- Atlas annotations are the truth labels; they are not independent of curation choices.; Only the 14 shared cell types are scored; no rejection of unshared types is measured in these tables.; Baselines (logistic regression, scVI, HVG) are reported only in Fig. 3b, not in the tables.; Macro-F1 is much lower than accuracy (0.08-0.28), reflecting poor transfer to rare types (Results).
- missing metadata
- uncertainty: reason: unreported; note: One run per configuration printed
Related records
- uses data: HLCA core (CELLxGENE), 37 leaf cell types after processing
- subject: accuracy_versus_macro_f1: cell-type-20261009-protocol-wu2025-ts-to-hlca
- subject: baseline_gene_overlap: cell-type-20261009-protocol-wu2025-ts-to-hlca
- assessment: Geneformer + LangCell: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: Geneformer + scCello: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: Geneformer + scFoundation: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: Geneformer + scGPT: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: Geneformer + UCE: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: LangCell + scCello: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: LangCell + scFoundation: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: scGPT + LangCell: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: UCE + LangCell: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: Logit aggregation: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: Majority voting: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: scFoundation + scCello: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: scGPT + scCello: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: UCE + scCello: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: scGPT + scFoundation: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: UCE + scFoundation: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: scGPT + UCE: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: Geneformer: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: LangCell: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: scCello: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: scFoundation: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: scGPT: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessment: UCE: Tabula Sapiens to HLCA transfer (Wu et al. 2025)
- assessed by: Transfer cell-type annotations to a new dataset