Configuration

Ensemble scGPT + UCE (Wu et al. 2025)

Ensemble of OnClass classifiers: scGPT + UCE.

Overview

Ensemble of OnClass classifiers: scGPT + UCE.

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Evaluations and results

2 evaluations · 4 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Ensemble scGPT + UCE (Wu et al. 2025)	Protocol: Cross-atlas annotation transfer, HLCA to Tabula Sapiens, 14 shared cell types (Wu et al. 2025 Table S3) Dataset: Tabula Sapiens (CELLxGENE), 120 leaf cell types after processing	0.802 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 + UCE: HLCA to Tabula Sapiens transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-hlca-to-ts Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S3, cell B15, row 'scGPT + UCE', column 'Accuracy@1'
Configuration: Ensemble scGPT + UCE (Wu et al. 2025)	Protocol: Cross-atlas annotation transfer, HLCA to Tabula Sapiens, 14 shared cell types (Wu et al. 2025 Table S3) Dataset: Tabula Sapiens (CELLxGENE), 120 leaf cell types after processing	0.27 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 + UCE: HLCA to Tabula Sapiens transfer (Wu et al. 2025) cell-type-20261009-protocol-wu2025-hlca-to-ts Aggregation: Not reported Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S3, cell C15, row 'scGPT + UCE', column 'Macro-F1'
Configuration: Ensemble scGPT + 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	0.725 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 + 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 B16, row 'scGPT + UCE', column 'Accuracy@1'
Configuration: Ensemble scGPT + 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	0.118 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 + 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 C16, row 'scGPT + UCE', column 'Macro-F1'

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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">

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Technical metadata and extraction receipts

Stable ID: cell-type-20261009-config-wu2025-ensemble-scgpt-uce

areas: cells-tissues
contexts: research
method types: foundation_model
reported name: scGPT + UCE
source locator: Supplementary Tables S2-S3 column 'Model' Results 'Cross-dataset validation' paragraphs 3-4
foundation model eligible: true
parameters: Sum of the output logits of the scGPT and UCE OnClass classifiers, then softmax
missing metadata: version: reason: inapplicable; note: An ensemble of the listed configurations

Related records

configuration of: Ensemble of scFM embedding classifiers
uses model: scGPT
uses model: UCE (Universal Cell Embeddings)
system: scGPT + UCE: HLCA to Tabula Sapiens transfer (Wu et al. 2025)
system: scGPT + UCE: Tabula Sapiens to HLCA transfer (Wu et al. 2025)

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