Public atlas used as reference or query for annotation transfer; labels are the atlas annotations.
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23 evaluations · 46 results. Different protocols are not a single leaderboard.
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.
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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.
6 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.population 585 K cells from healthy lung across 107 individuals; label column 'cell_type'; 37 leaf cell types kept after removing non-leaf terms and types with fewer than 10 cells Context-only references | Biology-driven insights into the power of single-cell foundation models Table 2; Methods 'Batch integration and cell type annotation' paragraphs 1-3 Version: Genome Biology 26:334, published 2025-10-03; PMC12492631 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.source_locator Table 2; Methods 'Batch integration and cell type annotation' paragraphs 1-3 Context-only references | Biology-driven insights into the power of single-cell foundation models Table 2; Methods 'Batch integration and cell type annotation' paragraphs 1-3 Version: Genome Biology 26:334, published 2025-10-03; PMC12492631 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.split Reference model trained on a 20% stratified split; query test set is every cell of the 14 cell types shared by the two atlases Context-only references | Biology-driven insights into the power of single-cell foundation models Table 2; Methods 'Batch integration and cell type annotation' paragraphs 1-3 Version: Genome Biology 26:334, published 2025-10-03; PMC12492631 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.version CELLxGENE collection as downloaded by the authors (Table 2) Context-only references | Biology-driven insights into the power of single-cell foundation models Table 2; Methods 'Batch integration and cell type annotation' paragraphs 1-3 Version: Genome Biology 26:334, published 2025-10-03; PMC12492631 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| description Public atlas used as reference or query for annotation transfer; labels are the atlas annotations. Context-only references | Biology-driven insights into the power of single-cell foundation models Table 2; Methods 'Batch integration and cell type annotation' paragraphs 1-3 Version: Genome Biology 26:334, published 2025-10-03; PMC12492631 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| name HLCA core (CELLxGENE), 37 leaf cell types after processing Context-only references | Biology-driven insights into the power of single-cell foundation models Table 2; Methods 'Batch integration and cell type annotation' paragraphs 1-3 Version: Genome Biology 26:334, published 2025-10-03; PMC12492631 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-10-10-6e93f504adfc · Record review: source checked
Stable ID: cell-type-20261009-data-wu2025-hlca-core