scFoundation
Cell-type annotation with scFoundation, a model that produces contextual cell and gene representations from gene-expression measurements.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
2 evaluations · 2 results. Different protocols are not a single leaderboard.
Sorted by Macro F1 (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
All 2 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Pipeline: scFoundation | Protocol: scFoundation cell-type annotation comparison Segerstolpe: Segerstolpe cell-type annotation Dataset subset: Segerstolpe subset used in scFoundation Supplementary Table4 (scFoundation cell-type annotation comparison split) | 0.914 Macro F1 fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCell-type annotation evaluated by unweighted mean of cell-type F1 scores. Each class F1=TP/(TP+0.5*(FP+FN)), defined in Supplementary Note3. Exact dataset release, split manifest, fitting and preprocessing remain unextracted. Aggregation: Not reported scFoundation primary supplement, Table4 · Supplementary Table4, PDF p16, row scFoundation, column Segerstolpe |
| Pipeline: scFoundation | Protocol: scFoundation cell-type annotation comparison Zheng68K: Zheng68K cell-type annotation Dataset subset: Zheng68K subset used in scFoundation Supplementary Table4 (scFoundation cell-type annotation comparison split) | 0.736 Macro F1 fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcescFoundation on scFoundation cell-type annotation comparison Zheng68K: Zheng68K cell-type annotation Cell-type annotation evaluated by unweighted mean of cell-type F1 scores. Each class F1=TP/(TP+0.5*(FP+FN)), defined in Supplementary Note3. Exact dataset release, split manifest, fitting and preprocessing remain unextracted. Aggregation: Not reported scFoundation primary supplement, Table4 · Supplementary Table4, PDF p16, row scFoundation, column Zheng68K |
Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
Use this pipeline
How it works, versions and access
Underlying model: scFoundation. Results on this page belong to this pipeline and its evaluated settings.
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.
3 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Description Cell-type annotation with scFoundation, a model that produces contextual cell and gene representations from gene-expression measurements. Individual claims | scFoundation primary supplement, Table4 catalog-model-scfoundation profile summary (evidence-official-9863509ad10b824dc96b: Results pre-training framework; Methods Embedding, Encoder, Decoder); coverage-source-scfoundation-supp: Supplementary Table 4 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 10.1038/s41592-024-02305-7 publisher supplement | source checked ["automated-source-review","ai-assisted-source-review"] · 2026-10-11 Audit detailsApproved. Checked the new sources' licences against the arXiv abstract pages and Europe PMC, the 7 scFoundation pipeline descriptions against their abstracts, the language-model descriptions against their model cards and reports, and the TAPE architecture figures against the TAPE paper; all correct. The catalogue entries reuse reviewed profile summaries. Field: Claim: metadata-correction-8b6504e69f84d0dcf1bb Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Description Cell-type annotation with scFoundation, a model that produces contextual cell and gene representations from gene-expression measurements. Individual claims | scfoundation-preprint: Primary paper PDF catalog-model-scfoundation profile summary (evidence-official-9863509ad10b824dc96b: Results pre-training framework; Methods Embedding, Encoder, Decoder); coverage-source-scfoundation-supp: Supplementary Table 4 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv manuscript posted 2023-06-15 | source checked ["automated-source-review","ai-assisted-source-review"] · 2026-10-11 Audit detailsApproved. Checked the new sources' licences against the arXiv abstract pages and Europe PMC, the 7 scFoundation pipeline descriptions against their abstracts, the language-model descriptions against their model cards and reports, and the TAPE architecture figures against the TAPE paper; all correct. The catalogue entries reuse reviewed profile summaries. Field: Claim: metadata-correction-8b6504e69f84d0dcf1bb Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Relationship: uses model catalog-model-scfoundation Individual claims | scFoundation primary supplement, Table4 Supplementary Table4, PDF p16, row scFoundation Version: 10.1038/s41592-024-02305-7 publisher supplement | source checked ["automated-source-review"] · 2026-09-23 Audit detailsSource-backed evaluated identity only; no independent reproduction. Field: Claim: scfoundation-2024-supp-table4-method-scfoundation-catalog-model-scfoundation-identity-claim Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
2 source records and release history
- scFoundation primary supplement, Table4 · Original source · 10.1038/s41592-024-02305-7 publisher supplement
- scfoundation-preprint: Primary paper PDF · Original source · bioRxiv manuscript posted 2023-06-15
Technical metadata and extraction receipts
Stable ID: scfoundation-2024-supp-table4-method-scfoundation
- areas
- single-cell
- source locator
- Supplementary Table4, PDF p16, row scFoundation
- missing metadata
- checkpoint revision: reason: unreported; parameters: reason: unextracted
Related records
- uses model: scFoundation
- subject: scFoundation: description
- system: scFoundation on scFoundation cell-type annotation comparison Segerstolpe: Segerstolpe cell-type annotation
- system: scFoundation on scFoundation cell-type annotation comparison Zheng68K: Zheng68K cell-type annotation
- subject: scFoundation: uses model catalog-model-scfoundation