Model type
Study-specific predictive method; this record is the paper-specific evaluated configuration.
Pipeline
Nucleotide Transformer + NN (middle)
This fusion-breakpoint classifier uses frozen Nucleotide Transformer features with a separately trained neural-network head.
Sources
Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · Discussion (paragraph 2); Results/Classification performance (paragraph 2)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
Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1)At a glance
Biological inputs
DNA sequence around fusion breakpoints
Sources
Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · Methods/Evaluation metrics (paragraph 2); Discussion/Limitations and future directions (paragraph 3)Outputs
Fusion-breakpoint classification
Sources
Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · Methods/Evaluation metrics (paragraph 2); Methods/DNABERT2 (BERT) (paragraph 3)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 |
|---|---|---|
| Nucleotide Transformer + NN (middle): gene fusion breakpoint classification Pipeline: Nucleotide Transformer + NN (middle)Task: gene fusion breakpoint classificationDataset: gene fusion breakpoint DNA sequences middle embedding with neural-network classifier Independent external evaluation · Evaluation metadata: needs review | ||
| 0.994 ROC AUC Unit: fraction · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedBenchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · Table 2, NT / NN (middle) row, ROC AUC column Source checking is not independent reproduction. |
How it works
How the evaluated method works
DNA windows around candidate fusion breakpoints are encoded by a frozen genomic foundation model. Only the lightweight downstream classifier is trained; the middle-labelled representation is the exact configuration of this row.
Sources
Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1)What was evaluated
The linked evaluation record identifies Nucleotide Transformer + NN (middle): gene fusion breakpoint classification. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-b2-fusion-breakpoint-foundation-models-2026Strengths and limitations
Strengths and considerations
- Separates representation extraction from the training of a small task-specific classifier.
Sources
Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · Conclusion (paragraph 3); Discussion (paragraph 6)
Limitations and conditions
- A successful frozen-embedding classifier does not establish zero-shot performance or clinical validity of a fusion caller.
Sources
Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · Results/Classification performance (paragraph 3); Results/Visual assessment of embedding quality (paragraph 2)
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-1a67087ac262c5Specifications
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 | Study-specific predictive method; this record is the paper-specific evaluated configuration.SourcesBenchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1) |
| Architecture / procedure | DNA windows around candidate fusion breakpoints are encoded by a frozen genomic foundation model. Only the lightweight downstream classifier is trained; the middle-labelled representation is the exact configuration of this row.SourcesBenchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1) |
| Biological inputs | DNA sequence around fusion breakpointsSourcesBenchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · Methods/Evaluation metrics (paragraph 2); Discussion/Limitations and future directions (paragraph 3) |
| Outputs | Fusion-breakpoint classificationSourcesBenchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · Methods/Evaluation metrics (paragraph 2); Methods/DNABERT2 (BERT) (paragraph 3) |
| Parameters | 500 M-parameter Nucleotide Transformer backbone, plus a separately fitted neural classifier.SourcesBenchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · Table1; NT column, Parameters row |
| Known versions / configuration | Nucleotide Transformer + NN (middle) is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sourcesSourcesBenchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. |
| Training data / fitting | Approximately 52,000 sequences from the curated FusionAI dataset; foundation-model weights remain frozen.SourcesBenchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · Methods/Evaluation metrics (paragraph 2); Discussion/Limitations and future directions (paragraph 1) |
| Context limits | 10-kbp DNA windows in the study; model-specific embedding selection remains part of the evaluated protocol.SourcesBenchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · Results/Classification performance (paragraph 1); Results/Computational efficiency (paragraph 1) |
| Access | Official study implementation and usage documentation: https://github.com/kbi-fbmi/articles--2026fusionEmbBenchmark/blob/085a6d7d2f899b0f62d764f35d1248b2eda567da/README.md. This pinned documentation revision is not automatically the evaluated weight revision.Sourceskbi-fbmi/articles--2026fusionEmbBenchmark README.md · README.md; installation, model download and usage instructions |
| Code licence | MIT (study repository code at the cited revision; this does not establish every dependency or historical checkpoint licence).Sourceskbi-fbmi/articles--2026fusionEmbBenchmark LICENSE · LICENSE; complete licence text |
| Weights licence | The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. · Not reported in inspected sourcesSourceskbi-fbmi/articles--2026fusionEmbBenchmark README.md · README.md; checkpoint/access documentation and licence scope |
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.
19 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 | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1) Version: journal full text in PMC | 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 ["DNA sequence around fusion breakpoints","Nucleotide Transformer + NN (middle)","Fusion-breakpoint classification"] Individual claims | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1) Version: journal full text in PMC | 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 | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1) Version: journal full text in PMC | 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 Study-specific predictive method; this record is the paper-specific evaluated configuration. Individual claims | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1) Version: journal full text in PMC | 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 DNA windows around candidate fusion breakpoints are encoded by a frozen genomic foundation model. Only the lightweight downstream classifier is trained; the middle-labelled representation is the exact configuration of this row. Individual claims | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1) Version: journal full text in PMC | 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 The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. Individual claims | kbi-fbmi/articles--2026fusionEmbBenchmark README.md README.md; checkpoint/access documentation and licence scope Version: 085a6d7d2f899b0f62d764f35d1248b2eda567da | 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 |
| Biological inputs DNA sequence around fusion breakpoints Individual claims | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences Methods/Evaluation metrics (paragraph 2); Discussion/Limitations and future directions (paragraph 3) Version: journal full text in PMC | 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 Fusion-breakpoint classification Individual claims | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences Methods/Evaluation metrics (paragraph 2); Methods/DNABERT2 (BERT) (paragraph 3) Version: journal full text in PMC | 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 500 M-parameter Nucleotide Transformer backbone, plus a separately fitted neural classifier. Individual claims | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences Table1; NT column, Parameters row Version: journal full text in PMC | 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 |
| Known versions / configuration Nucleotide Transformer + NN (middle) is the comparison-table label; that label does not specify an immutable weight revision. Individual claims | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. Version: journal full text in PMC | 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
3 source records and release history
- Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · Original source · journal full text in PMC
- kbi-fbmi/articles--2026fusionEmbBenchmark README.md · Original source · 085a6d7d2f899b0f62d764f35d1248b2eda567da
- kbi-fbmi/articles--2026fusionEmbBenchmark LICENSE · Original source · 085a6d7d2f899b0f62d764f35d1248b2eda567da
Technical metadata and extraction receipts
Stable ID: reported-model-1a67087ac262c5
- areas
- dna-genomes
- entity level
- method
- version
- not stated in table
- reported name
- Nucleotide Transformer + NN (middle)
- historical missing metadata
- 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 record identifies a composed analysis workflow with separately identifiable upstream models, representations or tools and a downstream prediction/scoring procedure. Results belong to that complete composition rather than to an upstream model alone.; source ids: fusion-breakpoint-foundation-models-2026; source locator: Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1) | Discussion (paragraph 2); Results/Classification performance (paragraph 2); ambiguities: This is the paper-specific pipeline identity; unspecified component checkpoints or implementation versions are not inferred from its name.