Result

0.816 top-1-accuracy

Geneformer + scGPT HLCA to Tabula Sapiens top-1-accuracy

Tested configuration: Ensemble Geneformer + scGPT (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
Procedure: cell-type-20261009-protocol-wu2025-hlca-to-ts
Evaluation: Geneformer + scGPT: HLCA to Tabula Sapiens transfer (Wu et al. 2025)
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Independent external evaluation · source checkedWu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) · Table S3, cell B20, row 'Geneformer + scGPT', column 'Accuracy@1'

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.

Reproduction

Split: Reference 20% stratified training split; query all shared-type cells
Adaptation: OnClass classifier trained on the reference; scFM frozen
Scoring implementation: Accuracy@1 and macro-F1 over shared types

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

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.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-10-10-6e93f504adfc
Property and statement	Original source and location	Review and provenance
Reported result 0.816 Individual claims	Wu et al. 2025, Additional file 3 (Supplementary Tables S1-S13) Original source ↗ Table S3, cell B20, row 'Geneformer + scGPT', column 'Accuracy@1' Version: 13059_2025_3781_MOESM3_ESM.xlsx (38,926 bytes), as linked from the article XML <supplementary-material id="MOESM3"> Retrieved: 2026-10-09T21:22:24Z	source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 independent paper Audit details Extracted by deterministic parse of the pinned XLSX cell XML (extract/extract_cell_type.py), with row and column labels asserted. printed_value is the shortest decimal that round-trips to the stored number. Pending independent review. Independent review 2026-10-09: value and identity match the source. Field: `attributes.printed_value` Source artifact SHA-256: `51ecea4318178dfb7dc6b51eae23303d68f25e83641809c95429b082353dc99d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `51ecea4318178dfb7dc6b51eae23303d68f25e83641809c95429b082353dc99d` Extraction artifact

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Sources and history

Release 2026-10-10-6e93f504adfc · Record review: source checked

2 source records and release history

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">
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

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Technical metadata and extraction receipts

Stable ID: cell-type-20261009-result-wu2025-hlca-to-ts-ensemble-geneformer-scgpt-accuracy-at-1

metric: top-1-accuracy
metric direction: higher
unit: fraction
printed value: 0.816
numeric value: 0.816
metric qualifier: Accuracy@1 over cells of the 14 shared cell types
source locator: Table S3, cell B20, row 'Geneformer + scGPT', column 'Accuracy@1'
missing metadata: uncertainty: reason: unreported
review: method: source-hash-verification; deterministic-table-parse; independent-cell-check; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-09; artifact sha256: 51ecea4318178dfb7dc6b51eae23303d68f25e83641809c95429b082353dc99d; retrieval url: https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-025-03781-6/MediaObjects/13059_2025_3781_MOESM3_ESM.xlsx; method note: Re-downloaded the workbook and matched its SHA-256. Read Supplementary Tables S2 and S3 only, with a separate OOXML reader written for this review (the extractor's script was not run). Checked value, locator, metric, unit, direction, the evaluation's protocol and dataset, and that the configuration's model links match the row.; note: Extracted by deterministic parse of the pinned XLSX cell XML (extract/extract_cell_type.py), with row and column labels asserted. printed_value is the shortest decimal that round-trips to the stored number. Pending independent review. Independent review 2026-10-09: value and identity match the source.

Related records

evaluation: Geneformer + scGPT: HLCA to Tabula Sapiens transfer (Wu et al. 2025)

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