scFoundation cell-type annotation comparison
Source-specific reported comparison. Protocol details, fitted configurations and limitations are retained separately from other evaluations.
Overview
Source-specific reported comparison. Protocol details, fitted configurations and limitations are retained separately from other evaluations.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
scFoundation cell-type annotation comparison Segerstolpe: Segerstolpe cell-type annotation
macro_f1 (fraction) · Higher values are better.
Every method scFoundation cell-type annotation comparison reports on Segerstolpe cell-type annotation, scored with Macro F1 on Segerstolpe subset used in scFoundation Supplementary Table4.
scFoundation cell-type annotation comparison Segerstolpe: Segerstolpe cell-type annotation · Segerstolpe subset used in scFoundation Supplementary Table4 (scFoundation cell-type annotation comparison split)
Evidence origin: Author-reported evaluation, Evaluation origin not reported. Numerical source review does not establish independent reproduction.
scFoundation primary supplement, Table4 · Supplementary Table4, PDF p16; Supplementary Note3, Macro F1 score.Complete seven-method by two-dataset comparison. Macro F1 is the unweighted mean of class-level F1 scores (Supplementary Note3).
All comparison limitations (5)
- Complete seven-method by two-dataset comparison. Macro F1 is the unweighted mean of class-level F1 scores (Supplementary Note3).
- No uncertainty, seeds or scored denominators printed in this table.
- Exact training/fine-tuning procedure and split manifests are unextracted; do not assume zero-shot evaluation or matched training data.
- Comparator executor provenance remains unreported from the inspected supplement; the table is the source, not an independent reproduction.
- The scFoundation Zheng68K score also appears as the scale-100M result in Table2; do not count these as independent evidence.
Automated source review: 2026-09-23.
No unavailable values; missing scores remain labelled and are never plotted as zero.
Showing 7 of 7 matching rows.
Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Evaluation design
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Protocols
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Baseline coverage
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0 of 4 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
Baseline status by linked protocol
Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-09-23-2b89723c6dd9. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
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Run this benchmark
The supplementary table reports this evaluation. Rewire has not run it and has no maintained reproduction recipe. Exact evaluator and split revisions remain unextracted.
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scFoundation primary supplement, Table4 · Supplementary Table4, PDF p16; Supplementary Note3, Macro F1 score.Strengths, limitations and unresolved questions
Evidence
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Evidence table
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Sources and history
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Release 2026-09-23-2b89723c6dd9 · Record review: source checked
1 source records and release history
- scFoundation primary supplement, Table4 · Original source · 10.1038/s41592-024-02305-7 publisher supplement
Technical metadata and extraction receipts
Stable ID: model-coverage-scfoundation-cell-annotation
- areas
- cells-spatial-multiomics
- run documentation
- record id: model-coverage-scfoundation-cell-annotation; status: source_reviewed_not_executed; source ids: coverage-source-scfoundation-supp; source locator: Supplementary Table4, PDF p16; Supplementary Note3, Macro F1 score.; summary: The supplementary table reports this evaluation. Rewire has not run it and has no maintained reproduction recipe. Exact evaluator and split revisions remain unextracted.
- entity level
- suite