Source

Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility

2025 · version of record · Peer-reviewed

DOI: 10.1371/journal.pgen.1011420 Original source

What this source contributed

Records in this release that cite this source. A record can cite several sources.

2 configurations
1 task
1 dataset
2 evaluations
2 results
4 evidence claims

Results

Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.

Model or configuration	Metric	Value	Dataset	Evaluation
Human-Geneformer	F1	74.48 percent	Human thymus scRNA-seq	Human-Geneformer: Human thymus cell-type classification
Mouse-Geneformer	F1	48.57 percent	Human thymus scRNA-seq	Mouse-Geneformer: Human thymus cell-type classification

Claims

Statements this source supports, each with where in the source it was checked.

Human-Geneformer: variant of Geneformer: Configuration of Geneformer (Human cell type classification using mouse-Geneformer; paragraph describing human Geneformer pretrained by these authors on Genecorpus-30M; Table 4)
Mouse-Geneformer: variant of Geneformer: Configuration of Geneformer (Abstract; Construction of mouse-Geneformer / Pretraining / Architecture; Tables 1 and 4)
Reported F1 for Human-Geneformer: Printed value 74.48 (Table 4, h/ Thymus row, Human-Geneformer Zero-shot F1 column)
Reported F1 for Mouse-Geneformer: Printed value 48.57 (Table 4, h/ Thymus row, Mouse-Geneformer Zero-shot F1 column)

Models, benchmarks and other records

Configurations (2)

Tasks (1)

Human thymus cell-type classification

Datasets (1)

Human thymus scRNA-seq

Evaluations (2)

Evidence

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Evidence table

Inspect claims, sources and review details

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18 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
Artifact retrieved at 2026-09-16T10:44:03.392488+00:00 Source metadata	Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:44:03.392488+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_retrieved_at` Source artifact SHA-256: `ef6c68f5c9b47c2f89598ddf647f05b72e4155e8b33609ebff23936a84bbd41d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Artifact SHA-256 ef6c68f5c9b47c2f89598ddf647f05b72e4155e8b33609ebff23936a84bbd41d Source metadata	Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:44:03.392488+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_sha256` Source artifact SHA-256: `ef6c68f5c9b47c2f89598ddf647f05b72e4155e8b33609ebff23936a84bbd41d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11964219/fullTextXML Source metadata	Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:44:03.392488+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_url` Source artifact SHA-256: `ef6c68f5c9b47c2f89598ddf647f05b72e4155e8b33609ebff23936a84bbd41d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Doi 10.1371/journal.pgen.1011420 Source metadata	Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:44:03.392488+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.doi` Source artifact SHA-256: `ef6c68f5c9b47c2f89598ddf647f05b72e4155e8b33609ebff23936a84bbd41d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Missing metadata: licence: reason unextracted Source metadata	Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:44:03.392488+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.missing_metadata.licence.reason` Source artifact SHA-256: `ef6c68f5c9b47c2f89598ddf647f05b72e4155e8b33609ebff23936a84bbd41d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Publication status peer_reviewed Source metadata	Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:44:03.392488+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.publication_status` Source artifact SHA-256: `ef6c68f5c9b47c2f89598ddf647f05b72e4155e8b33609ebff23936a84bbd41d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Retrieved at 2026-09-15T23:29:32Z Source metadata	Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:44:03.392488+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.retrieved_at` Source artifact SHA-256: `ef6c68f5c9b47c2f89598ddf647f05b72e4155e8b33609ebff23936a84bbd41d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Scope decision included Source metadata	Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:44:03.392488+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.scope_decision` Source artifact SHA-256: `ef6c68f5c9b47c2f89598ddf647f05b72e4155e8b33609ebff23936a84bbd41d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Url https://pmc.ncbi.nlm.nih.gov/articles/PMC11964219/ Source metadata	Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:44:03.392488+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.url` Source artifact SHA-256: `ef6c68f5c9b47c2f89598ddf647f05b72e4155e8b33609ebff23936a84bbd41d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Version version of record Source metadata	Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-16T10:44:03.392488+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `ef6c68f5c9b47c2f89598ddf647f05b72e4155e8b33609ebff23936a84bbd41d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-11-02-a7f03c9e55a5 · Record review: discovered

Primary paper retained with its original identifier. Metadata inherited from the literature collection; individual result checks are separate.

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Technical metadata and extraction receipts

Stable ID: mouse-geneformer-2025

areas: cells-tissues
url: https://pmc.ncbi.nlm.nih.gov/articles/PMC11964219/
version: version of record
retrieved at: 2026-09-15T23:29:32Z
doi: 10.1371/journal.pgen.1011420
publication status: peer_reviewed
year: 2025
artifact sha256: ef6c68f5c9b47c2f89598ddf647f05b72e4155e8b33609ebff23936a84bbd41d
artifact url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11964219/fullTextXML
artifact retrieved at: 2026-09-16T10:44:03.392488+00:00
scope decision: included
missing metadata: licence: reason: unextracted

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