rewirebio.iobenchmarks
Protocol

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.

23 evaluations · 46 results

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.

View coverage and remaining gaps across all benchmarks

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

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence 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 checked
Methods, coverage and source

Geneformer + 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 checked
Methods, coverage and source

Geneformer + 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 checked
Methods, coverage and source

Geneformer + 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 checked
Methods, coverage and source

Geneformer + 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 checked
Methods, coverage and source

Geneformer + 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 checked
Methods, coverage and source

Geneformer + 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 checked
Methods, coverage and source

Geneformer + 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 checked
Methods, coverage and source

Geneformer + 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 checked
Methods, coverage and source

Geneformer + 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 checked
Methods, coverage and source

Geneformer + 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 checked
Methods, coverage and source

LangCell + 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 checked
Methods, coverage and source

LangCell + 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 checked
Methods, coverage and source

LangCell + 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 checked
Methods, coverage and source

LangCell + 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 checked
Methods, coverage and source

scGPT + 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 checked
Methods, coverage and source

scGPT + 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 checked
Methods, coverage and source

UCE + 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 checked
Methods, coverage and source

UCE + 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 checked
Methods, coverage and source

Logit 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 checked
Methods, coverage and source

Logit 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 checked
Methods, coverage and source

Majority 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 checked
Methods, coverage and source

Majority 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 checked
Methods, coverage and source

scFoundation + 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 checked
Methods, coverage and source

scFoundation + 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 checked
Methods, coverage and source

scGPT + 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.

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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.

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Evidence

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Evidence table

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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
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