Model

scFoundation

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

Sources (3)

biomap-research/scFoundation: README.md; biomap-research/scFoundation: model/README.md; scfoundation-preprint: Primary paper PDF · June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README

Results are available for configurations using this model. Their fitted heads, extra inputs and evaluation settings are kept separate below.

1 evaluated configuration using this model

How it worksscFoundation workflow

Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.

Sources (3)

Overview

Model type

Transcriptomic representation model

Sources (3)

Inputs

Single-cell or bulk expression aligned to the documented 19,264-gene vocabulary.

Sources (3)

Outputs

Cell embeddings, contextual gene embeddings and outputs of separately configured downstream models.

Sources (3)

Access

Official project documentation and implementation: https://github.com/biomap-research/scFoundation

Sources (3)

limited source coverage · Automated source review, 2026-09-16. All specifications and missing details

Related configurations, pipelines and services

These configurations, services and pipelines use this model within their own configurations. Their results, where available, are not assigned to the underlying model.

scFoundation Pipeline · 2 metric rows

Use this model

How it works, versions and access

How it works

scFoundation embeds gene identity and continuous expression together with source and target read-depth indicators. Its encoder processes only nonzero, unmasked genes. Those contextual embeddings are combined with zero and mask embeddings before a Performer decoder predicts expression across the full gene vocabulary. Pooled encoder outputs represent cells; decoder outputs provide gene-level context.

Sources (3)

Versions and reproducibility

scFoundation / xTrimoscFoundation-alpha; the repository exposes separately configured embedding, enhancement and downstream prediction workflows. Fixed input gene vocabulary of 19,264 genes; not a nucleotide token context.

Sources (3)

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

The released workflow includes embedding extraction, read-depth enhancement and integration with downstream predictors.
Sources (3)
biomap-research/scFoundation: README.md; biomap-research/scFoundation: model/README.md; scfoundation-preprint: Primary paper PDF · June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README

Limitations and conditions

Gene identifiers must be aligned to the supplied gene index. Source-code licensing does not grant the separate model-weight rights.
Sources (3)
biomap-research/scFoundation: README.md; biomap-research/scFoundation: model/README.md; scfoundation-preprint: Primary paper PDF · June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README

Profile review details

Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied.

Stable record: catalog-model-scfoundation

Specifications

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Inputs, outputs and configuration
Property	Description and evidence
Model type	Transcriptomic representation model Sources (3) biomap-research/scFoundation: README.md; biomap-research/scFoundation: model/README.md; scfoundation-preprint: Primary paper PDF · June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README
Architecture	An asymmetric transformer encoder-decoder: learned continuous-expression embeddings enter a transformer encoder for nonzero, unmasked genes, then a Performer decoder reconstructs the full gene set. Sources (3) biomap-research/scFoundation: README.md; biomap-research/scFoundation: model/README.md; scfoundation-preprint: Primary paper PDF · June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README
Inputs	Single-cell or bulk expression aligned to the documented 19,264-gene vocabulary. Sources (3) biomap-research/scFoundation: README.md; biomap-research/scFoundation: model/README.md; scfoundation-preprint: Primary paper PDF · June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README
Outputs	Cell embeddings, contextual gene embeddings and outputs of separately configured downstream models. Sources (3) biomap-research/scFoundation: README.md; biomap-research/scFoundation: model/README.md; scfoundation-preprint: Primary paper PDF · June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README
Parameters	100 million. Sources (3) biomap-research/scFoundation: README.md; biomap-research/scFoundation: model/README.md; scfoundation-preprint: Primary paper PDF · June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README
Known versions	scFoundation / xTrimoscFoundation-alpha; the repository exposes separately configured embedding, enhancement and downstream prediction workflows. Sources (3) biomap-research/scFoundation: README.md; biomap-research/scFoundation: model/README.md; scfoundation-preprint: Primary paper PDF · June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README
Training data	The June 2023 manuscript describes more than 50M human cells collected from GEO, Single Cell Portal, HCA and EMBL-EBI, aligned to 19,264 genes after quality control. Sources (3) biomap-research/scFoundation: README.md; biomap-research/scFoundation: model/README.md; scfoundation-preprint: Primary paper PDF · June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README
Training cutoff	The June 2023 manuscript lists GEO, Single Cell Portal, HCA and EMBL-EBI as collection sources; its data-collection section does not give a shared last-included-study date. · Not reported in inspected sources Sources (3) biomap-research/scFoundation: README.md; biomap-research/scFoundation: model/README.md; scfoundation-preprint: Primary paper PDF · 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 limits	Fixed input gene vocabulary of 19,264 genes; not a nucleotide token context. Sources (3) biomap-research/scFoundation: README.md; biomap-research/scFoundation: model/README.md; scfoundation-preprint: Primary paper PDF · June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README
Weights licence	Separate Model License; the Apache source-code notice explicitly excludes model-weight rights. Sources (3) biomap-research/scFoundation: README.md; biomap-research/scFoundation: model/README.md; scfoundation-preprint: Primary paper PDF · June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README
Access	Official project documentation and implementation: https://github.com/biomap-research/scFoundation Sources (3) biomap-research/scFoundation: README.md; biomap-research/scFoundation: model/README.md; scfoundation-preprint: Primary paper PDF · June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README
Code licence	Apache-2.0 Sources biomap-research/scFoundation: LICENSE · LICENSE: licence text

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.

58 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-23-2b89723c6dd9
Property and statement	Original source and location	Review and provenance
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	biomap-research/scFoundation: model/README.md Original source ↗ 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	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `f62879233ecf5fac407cd516aca2ddb3df20370523cb111c9d057676b4721d5d` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	scfoundation-preprint: Primary paper PDF Original source ↗ 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	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `e2ce9d623a09b53eb863ae6ca359fe2956b7b0a7c3ebe7de6911aca3a660f737` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	biomap-research/scFoundation: README.md Original source ↗ 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	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `02a7ae44cf2cc9948b5c1520b18a261b45abf9f17e3149e37d9f48072184f376` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps Expression and read-depth indicators Gene and continuous-value embeddings Sparse-input transformer encoder Full-gene Performer decoder Cell/gene embeddings or expression Individual claims	biomap-research/scFoundation: model/README.md Original source ↗ 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	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `f62879233ecf5fac407cd516aca2ddb3df20370523cb111c9d057676b4721d5d` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps Expression and read-depth indicators Gene and continuous-value embeddings Sparse-input transformer encoder Full-gene Performer decoder Cell/gene embeddings or expression Individual claims	scfoundation-preprint: Primary paper PDF Original source ↗ 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	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `e2ce9d623a09b53eb863ae6ca359fe2956b7b0a7c3ebe7de6911aca3a660f737` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps Expression and read-depth indicators Gene and continuous-value embeddings Sparse-input transformer encoder Full-gene Performer decoder Cell/gene embeddings or expression Individual claims	biomap-research/scFoundation: README.md Original source ↗ 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	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `02a7ae44cf2cc9948b5c1520b18a261b45abf9f17e3149e37d9f48072184f376` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title scFoundation workflow Individual claims	biomap-research/scFoundation: model/README.md Original source ↗ 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	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `f62879233ecf5fac407cd516aca2ddb3df20370523cb111c9d057676b4721d5d` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title scFoundation workflow Individual claims	scfoundation-preprint: Primary paper PDF Original source ↗ 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	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `e2ce9d623a09b53eb863ae6ca359fe2956b7b0a7c3ebe7de6911aca3a660f737` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title scFoundation workflow Individual claims	biomap-research/scFoundation: README.md Original source ↗ 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	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `02a7ae44cf2cc9948b5c1520b18a261b45abf9f17e3149e37d9f48072184f376` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Model type Transcriptomic representation model Individual claims	biomap-research/scFoundation: model/README.md Original source ↗ 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	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `f62879233ecf5fac407cd516aca2ddb3df20370523cb111c9d057676b4721d5d` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

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Release 2026-09-23-2b89723c6dd9 · Record review: discovered

5 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
biomap-research/scFoundation: LICENSE · Original source · 397631c495eddf9ad6644fc00c6ea8139e651245

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Technical metadata and extraction receipts

Stable ID: catalog-model-scfoundation

areas: cells-tissues
method types: foundation model
entity level: family
version: 100M
reported name: scFoundation
access: Public code; model weights have separate terms that must be checked.
method type: foundation model
historical missing metadata: checkpoint revision: not_yet_extracted; training data: not_yet_extracted; licence: not_yet_extracted
metadata review scope: historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
entity classification: review date: 2026-09-17; rationale: The cited profile describes a named learned biological predictor or representation model/family. Preserve this identity separately from task-specific fitting, individual checkpoints, pipelines and hosted access.; source ids: evidence-official-bfbc8babf3630ddb3ed7; evidence-official-7972ce2bdd6a5e40d8ad; evidence-official-9863509ad10b824dc96b; source locator: June 15 2023 scFoundation manuscript: Results pre-training framework; Methods Data collection, Embedding, Encoder, Decoder and Read-depth-aware pre-training; official model README; ambiguities: None recorded

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