Evidence claim

scFoundation: description

scFoundation produces contextual cell and gene representations from gene-expression measurements.

Replace a placeholder description with a sourced functional description (issue #88). Historical releases retain the original value.

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.

28 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Claimed field description Context-only references	scFoundation official resource Original source ↗ Reviewed profile summary (2026-09-16): evidence-official-bfbc8babf3630ddb3ed7, evidence-official-7972ce2bdd6a5e40d8ad, evidence-official-9863509ad10b824dc96b: June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Not recorded Retrieved: 2026-09-16T10:50:02Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `Not recorded` Hash scope: Hash scope not separately documented; inspect source record
Claimed field description Context-only references	biomap-research/scFoundation: model/README.md Original source ↗ Reviewed profile summary (2026-09-16): evidence-official-bfbc8babf3630ddb3ed7, evidence-official-7972ce2bdd6a5e40d8ad, evidence-official-9863509ad10b824dc96b: June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 397631c495eddf9ad6644fc00c6ea8139e651245 Retrieved: 2026-09-16T19:46:18.581063+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `f62879233ecf5fac407cd516aca2ddb3df20370523cb111c9d057676b4721d5d` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Claimed field description Context-only references	scfoundation-preprint: Primary paper PDF Original source ↗ Reviewed profile summary (2026-09-16): evidence-official-bfbc8babf3630ddb3ed7, evidence-official-7972ce2bdd6a5e40d8ad, evidence-official-9863509ad10b824dc96b: June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv manuscript posted 2023-06-15 Retrieved: 2026-09-16T20:35:33.635910+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `e2ce9d623a09b53eb863ae6ca359fe2956b7b0a7c3ebe7de6911aca3a660f737` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Claimed field description Context-only references	biomap-research/scFoundation: README.md Original source ↗ Reviewed profile summary (2026-09-16): evidence-official-bfbc8babf3630ddb3ed7, evidence-official-7972ce2bdd6a5e40d8ad, evidence-official-9863509ad10b824dc96b: June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 397631c495eddf9ad6644fc00c6ea8139e651245 Retrieved: 2026-09-16T19:46:18.581063+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `02a7ae44cf2cc9948b5c1520b18a261b45abf9f17e3149e37d9f48072184f376` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Previous value Existing candidate catalogue entry; exact checkpoint and metadata require primary-source review. Context-only references	scFoundation official resource Original source ↗ Reviewed profile summary (2026-09-16): evidence-official-bfbc8babf3630ddb3ed7, evidence-official-7972ce2bdd6a5e40d8ad, evidence-official-9863509ad10b824dc96b: June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Not recorded Retrieved: 2026-09-16T10:50:02Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `Not recorded` Hash scope: Hash scope not separately documented; inspect source record
Previous value Existing candidate catalogue entry; exact checkpoint and metadata require primary-source review. Context-only references	biomap-research/scFoundation: model/README.md Original source ↗ Reviewed profile summary (2026-09-16): evidence-official-bfbc8babf3630ddb3ed7, evidence-official-7972ce2bdd6a5e40d8ad, evidence-official-9863509ad10b824dc96b: June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 397631c495eddf9ad6644fc00c6ea8139e651245 Retrieved: 2026-09-16T19:46:18.581063+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `f62879233ecf5fac407cd516aca2ddb3df20370523cb111c9d057676b4721d5d` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Previous value Existing candidate catalogue entry; exact checkpoint and metadata require primary-source review. Context-only references	scfoundation-preprint: Primary paper PDF Original source ↗ Reviewed profile summary (2026-09-16): evidence-official-bfbc8babf3630ddb3ed7, evidence-official-7972ce2bdd6a5e40d8ad, evidence-official-9863509ad10b824dc96b: June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv manuscript posted 2023-06-15 Retrieved: 2026-09-16T20:35:33.635910+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `e2ce9d623a09b53eb863ae6ca359fe2956b7b0a7c3ebe7de6911aca3a660f737` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Previous value Existing candidate catalogue entry; exact checkpoint and metadata require primary-source review. Context-only references	biomap-research/scFoundation: README.md Original source ↗ Reviewed profile summary (2026-09-16): evidence-official-bfbc8babf3630ddb3ed7, evidence-official-7972ce2bdd6a5e40d8ad, evidence-official-9863509ad10b824dc96b: June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 397631c495eddf9ad6644fc00c6ea8139e651245 Retrieved: 2026-09-16T19:46:18.581063+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `02a7ae44cf2cc9948b5c1520b18a261b45abf9f17e3149e37d9f48072184f376` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Source location Reviewed profile summary (2026-09-16): evidence-official-bfbc8babf3630ddb3ed7, evidence-official-7972ce2bdd6a5e40d8ad, evidence-official-9863509ad10b824dc96b: June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README Context-only references	scFoundation official resource Original source ↗ Reviewed profile summary (2026-09-16): evidence-official-bfbc8babf3630ddb3ed7, evidence-official-7972ce2bdd6a5e40d8ad, evidence-official-9863509ad10b824dc96b: June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Not recorded Retrieved: 2026-09-16T10:50:02Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `Not recorded` Hash scope: Hash scope not separately documented; inspect source record
Source location Reviewed profile summary (2026-09-16): evidence-official-bfbc8babf3630ddb3ed7, evidence-official-7972ce2bdd6a5e40d8ad, evidence-official-9863509ad10b824dc96b: June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README Context-only references	biomap-research/scFoundation: model/README.md Original source ↗ Reviewed profile summary (2026-09-16): evidence-official-bfbc8babf3630ddb3ed7, evidence-official-7972ce2bdd6a5e40d8ad, evidence-official-9863509ad10b824dc96b: June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 397631c495eddf9ad6644fc00c6ea8139e651245 Retrieved: 2026-09-16T19:46:18.581063+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `f62879233ecf5fac407cd516aca2ddb3df20370523cb111c9d057676b4721d5d` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

How to read the evidence

Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

4 source records and release history

scFoundation official resource · Original source · Not reported
biomap-research/scFoundation: README.md · Original source · 397631c495eddf9ad6644fc00c6ea8139e651245
biomap-research/scFoundation: model/README.md · Original source · 397631c495eddf9ad6644fc00c6ea8139e651245
scfoundation-preprint: Primary paper PDF · Original source · bioRxiv manuscript posted 2023-06-15

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Technical metadata and extraction receipts

Stable ID: metadata-correction-e06094525270bddf8338

areas: cells-tissues
method types: foundation_model
field: description
previous value: Existing candidate catalogue entry; exact checkpoint and metadata require primary-source review.
value: scFoundation produces contextual cell and gene representations from gene-expression measurements.
source locator: Reviewed profile summary (2026-09-16): evidence-official-bfbc8babf3630ddb3ed7, evidence-official-7972ce2bdd6a5e40d8ad, evidence-official-9863509ad10b824dc96b: June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README
review: method: automated-source-review; ai-assisted-source-review; reviewer: claude; reviewer note: Extractor: Claude integrator agent for issue #88. Reviewer: a separate Claude review agent, independent of the extractor; no human review claimed.; date: 2026-10-11; method note: Compared the store diff with origin/main, read each new description against its cited source passage and checked the licence of each new source record.; note: Approved. 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.; receipt: data/omics/qa-descriptions-20261011-b/review.json

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subject: scFoundation

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