Model type
Single-cell transformer; this record is the paper-specific evaluated configuration.
Configuration
Human-Geneformer
Human-Geneformer is the human-pretrained reference used to evaluate the value of mouse-specific pretraining.
Sources
Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility · Materials and methods/Construction of the mouse-Geneformer/Pretraining of the mouse-Geneformer. (paragraph 1); Materials and methods/Construction of the mouse-Geneformer/Architecture. (paragraph 1)How it worksEvaluated procedure (conceptual)
Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings.
Sources
Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility · Materials and methods/Construction of the mouse-Geneformer/Architecture. (paragraph 1); Materials and methods/Construction of the mouse-Geneformer/Pretraining of the mouse-Geneformer. (paragraph 1)At a glance
Biological inputs
Expression profiles mapped to the human model’s gene representation
Sources
Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility · Materials and methods/In silico perturbation of human data using mouse-Geneformer (paragraph 1); Results/Cross-species application of mouse-Geneformer through orthologous gene name conversion/Human cell type classification using mouse-Geneformer. (paragraph 1)Outputs
Gene/cell embeddings and downstream cell-type predictions
Sources
Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility · Results/Cross-species application of mouse-Geneformer through orthologous gene name conversion/Human cell type classification using mouse-Geneformer. (paragraph 1); Discussion (paragraph 1)limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
Release 2026-09-17-d277315f7d76 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| Human-Geneformer: Human thymus cell-type classification Configuration: Human-GeneformerTask: Human thymus cell-type classificationDataset: Human thymus scRNA-seq Native human model; zero-shot setting. Independent external evaluation · Evaluation metadata: needs review | ||
| 74.48 F1 Unit: % · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedMouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility · Table 4, h/ Thymus row, Human-Geneformer Zero-shot F1 column Source checking is not independent reproduction. |
How it works
How the evaluated method works
Rank Value Encoding feeds the original Geneformer transformer encoder before adaptation to the study’s downstream tasks.
Sources
Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility · Materials and methods/Construction of the mouse-Geneformer/Architecture. (paragraph 1); Materials and methods/Construction of the mouse-Geneformer/Pretraining of the mouse-Geneformer. (paragraph 1)Underlying method and version boundaries
Geneformer ranks genes by expression scaled against its pretraining corpus, then uses a transformer encoder with a masked-gene objective. V1 and V2 have different corpora, vocabularies, sizes and context limits, so a historical paper name is not replaced with today’s default checkpoint.
Sources
huggingface.co/ctheodoris/Geneformer README.md · README.md; introduction, model description, pretrained-model and usage sections at pinned revisionWhat was evaluated
The linked evaluation record identifies Human-Geneformer: Human thymus cell-type classification. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-b3-004Strengths and limitations
Strengths and considerations
- Provides a cross-species transfer control for the mouse-specific model.
Sources
Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility · Results/Cross-species application of mouse-Geneformer through orthologous gene name conversion (paragraph 2); Materials and methods/Gene name conversion between mouse and human for cross-species application (paragraph 1)
Limitations and conditions
- Gene mapping and species differences affect transfer; this historical comparator must not be silently replaced with current Geneformer V2.
Sources
Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility · Results/Cross-species application of mouse-Geneformer through orthologous gene name conversion (paragraph 2); Results/Cross-species application of mouse-Geneformer through orthologous gene name conversion (paragraph 1)
Profile review details
Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction.
Stable record: reported-model-10d85f2a035720Specifications
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.
| Property | Description and evidence |
|---|---|
| Model type | Single-cell transformer; this record is the paper-specific evaluated configuration.Sourceshuggingface.co/ctheodoris/Geneformer README.md · README.md model description |
| Architecture / procedure | Rank Value Encoding feeds the original Geneformer transformer encoder before adaptation to the study’s downstream tasks.SourcesMouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility · Materials and methods/Construction of the mouse-Geneformer/Architecture. (paragraph 1); Materials and methods/Construction of the mouse-Geneformer/Pretraining of the mouse-Geneformer. (paragraph 1) |
| Biological inputs | Expression profiles mapped to the human model’s gene representationSourcesMouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility · Materials and methods/In silico perturbation of human data using mouse-Geneformer (paragraph 1); Results/Cross-species application of mouse-Geneformer through orthologous gene name conversion/Human cell type classification using mouse-Geneformer. (paragraph 1) |
| Outputs | Gene/cell embeddings and downstream cell-type predictionsSourcesMouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility · Results/Cross-species application of mouse-Geneformer through orthologous gene name conversion/Human cell type classification using mouse-Geneformer. (paragraph 1); Discussion (paragraph 1) |
| Parameters | An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sourcesSources (2)Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility; huggingface.co/ctheodoris/Geneformer README.md · Materials and methods/Construction of the mouse-Geneformer/Architecture.; Materials and methods/Construction of the mouse-Geneformer/Construction of mouse-Genecoupus-20M.; Materials and methods/Construction of the mouse-Geneformer/Pretraining of the mouse-Geneformer.; Materials and methods/Fine-turning of the mouse-Geneformer; Materials and methods/Cell type classification using the mouse-Geneformer and conventional methods; Materials and methods/Cell type classification using mouse-Geneformer with and without prior learning; Materials and methods/In silico perturbation experiments; Materials and methods/Gene name conversion between mouse and human for cross-species application; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision |
| Known versions / configuration | Human-Geneformer is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sourcesSourcesMouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. |
| Training data / fitting | Approximately 30 million human single-cell transcriptomes in the original comparator described by this paper.SourcesMouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility · Materials and methods/Construction of the mouse-Geneformer/Pretraining of the mouse-Geneformer. (paragraph 1); Results/Development of mouse-Geneformer (paragraph 1) |
| Context limits | A maximum input/context length for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sourcesSources (2)Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility; huggingface.co/ctheodoris/Geneformer README.md · Materials and methods/Construction of the mouse-Geneformer/Architecture.; Materials and methods/Construction of the mouse-Geneformer/Construction of mouse-Genecoupus-20M.; Materials and methods/Construction of the mouse-Geneformer/Pretraining of the mouse-Geneformer.; Materials and methods/Fine-turning of the mouse-Geneformer; Materials and methods/Cell type classification using the mouse-Geneformer and conventional methods; Materials and methods/Cell type classification using mouse-Geneformer with and without prior learning; Materials and methods/In silico perturbation experiments; Materials and methods/Gene name conversion between mouse and human for cross-species application; inspected for explicit maximum input length (dataset lengths and family-wide limits are not substituted); README.md at pinned repository revision |
| Access | Official upstream implementation and usage documentation: https://huggingface.co/ctheodoris/Geneformer/blob/1f7fbae4e469a5f4f1af8c111a529cfe1b3829f5/README.md. This pinned documentation revision is not automatically the evaluated weight revision.Sourceshuggingface.co/ctheodoris/Geneformer README.md · README.md; installation, model download and usage instructions |
| Code licence | No explicit code licence was established from the paper’s availability statement and inspected repository-root documentation. · Not reported in inspected sourcesSourceshuggingface.co/ctheodoris/Geneformer README.md · README.md and repository-root licence-file search |
| Weights licence | Apache 2.0 is declared in the official Geneformer model-card metadata; the exact historical configuration still needs its checkpoint identity.Sourceshuggingface.co/ctheodoris/Geneformer README.md · README.md front matter, license field; model-version list |
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.
22 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings. Individual claims | Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility Materials and methods/Construction of the mouse-Geneformer/Architecture. (paragraph 1); Materials and methods/Construction of the mouse-Geneformer/Pretraining of the mouse-Geneformer. (paragraph 1) Version: version of record | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Expression profiles mapped to the human model’s gene representation","Human-Geneformer","Gene/cell embeddings and downstream cell-type predictions"] Individual claims | Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility Materials and methods/Construction of the mouse-Geneformer/Architecture. (paragraph 1); Materials and methods/Construction of the mouse-Geneformer/Pretraining of the mouse-Geneformer. (paragraph 1) Version: version of record | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Evaluated procedure (conceptual) Individual claims | Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility Materials and methods/Construction of the mouse-Geneformer/Architecture. (paragraph 1); Materials and methods/Construction of the mouse-Geneformer/Pretraining of the mouse-Geneformer. (paragraph 1) Version: version of record | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Model type Single-cell transformer; this record is the paper-specific evaluated configuration. Individual claims | huggingface.co/ctheodoris/Geneformer README.md README.md model description Version: 1f7fbae4e469a5f4f1af8c111a529cfe1b3829f5 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Architecture / procedure Rank Value Encoding feeds the original Geneformer transformer encoder before adaptation to the study’s downstream tasks. Individual claims | Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility Materials and methods/Construction of the mouse-Geneformer/Architecture. (paragraph 1); Materials and methods/Construction of the mouse-Geneformer/Pretraining of the mouse-Geneformer. (paragraph 1) Version: version of record | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Weights licence Apache 2.0 is declared in the official Geneformer model-card metadata; the exact historical configuration still needs its checkpoint identity. Individual claims | huggingface.co/ctheodoris/Geneformer README.md README.md front matter, license field; model-version list Version: 1f7fbae4e469a5f4f1af8c111a529cfe1b3829f5 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Biological inputs Expression profiles mapped to the human model’s gene representation Individual claims | Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility Materials and methods/In silico perturbation of human data using mouse-Geneformer (paragraph 1); Results/Cross-species application of mouse-Geneformer through orthologous gene name conversion/Human cell type classification using mouse-Geneformer. (paragraph 1) Version: version of record | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Outputs Gene/cell embeddings and downstream cell-type predictions Individual claims | Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility Results/Cross-species application of mouse-Geneformer through orthologous gene name conversion/Human cell type classification using mouse-Geneformer. (paragraph 1); Discussion (paragraph 1) Version: version of record | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims | huggingface.co/ctheodoris/Geneformer README.md Materials and methods/Construction of the mouse-Geneformer/Architecture.; Materials and methods/Construction of the mouse-Geneformer/Construction of mouse-Genecoupus-20M.; Materials and methods/Construction of the mouse-Geneformer/Pretraining of the mouse-Geneformer.; Materials and methods/Fine-turning of the mouse-Geneformer; Materials and methods/Cell type classification using the mouse-Geneformer and conventional methods; Materials and methods/Cell type classification using mouse-Geneformer with and without prior learning; Materials and methods/In silico perturbation experiments; Materials and methods/Gene name conversion between mouse and human for cross-species application; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1f7fbae4e469a5f4f1af8c111a529cfe1b3829f5 | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims | Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility Materials and methods/Construction of the mouse-Geneformer/Architecture.; Materials and methods/Construction of the mouse-Geneformer/Construction of mouse-Genecoupus-20M.; Materials and methods/Construction of the mouse-Geneformer/Pretraining of the mouse-Geneformer.; Materials and methods/Fine-turning of the mouse-Geneformer; Materials and methods/Cell type classification using the mouse-Geneformer and conventional methods; Materials and methods/Cell type classification using mouse-Geneformer with and without prior learning; Materials and methods/In silico perturbation experiments; Materials and methods/Gene name conversion between mouse and human for cross-species application; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: version of record | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
2 source records and release history
- Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility · Original source · version of record
- huggingface.co/ctheodoris/Geneformer README.md · Original source · 1f7fbae4e469a5f4f1af8c111a529cfe1b3829f5
Technical metadata and extraction receipts
Stable ID: reported-model-10d85f2a035720
- areas
- cells-tissues
- entity level
- method
- version
- Not reported
- reported name
- Human-Geneformer
- historical missing metadata
- version: not_reported_in_legacy_extract; checkpoint revision: not_reported_in_legacy_extract; training data: not_reported_in_legacy_extract; licence: not_reported_in_legacy_extract
- 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.
- legacy kinds
- model
- entity classification
- review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: mouse-geneformer-2025; evidence-reported-base-geneformer-readme-md; source locator: Materials and methods/Construction of the mouse-Geneformer/Architecture. (paragraph 1); Materials and methods/Construction of the mouse-Geneformer/Pretraining of the mouse-Geneformer. (paragraph 1) | README.md model description | Materials and methods/Construction of the mouse-Geneformer/Pretraining of the mouse-Geneformer. (paragraph 1); Materials and methods/Construction of the mouse-Geneformer/Architecture. (paragraph 1); ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.