Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences
2026 · journal full text in PMC · Peer-reviewed
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Results
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| Model or configuration | Metric | Value | Dataset | Evaluation |
|---|---|---|---|---|
| Nucleotide Transformer + NN (middle) | AUROC | 0.994 unitless | gene fusion breakpoint DNA sequences | Nucleotide Transformer + NN (middle): gene fusion breakpoint classification |
Claims
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- Nucleotide Transformer + NN (middle): description: Description Classifies gene fusion breakpoints from 10 kbp DNA windows using frozen Nucleotide Transformer embeddings, concatenating the middle embedding at the breakpoint of each sequence and training a small neural-network classifier on it. (Reviewed profile (2026-09-16): summary at Discussion (paragraph 2); Results/Classification performance (paragraph 2); architecture fact at Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1); description text also read at Methods/Embedding extraction; Abstract/Methods)
- Nucleotide Transformer + NN (middle): uses model Nucleotide Transformer: Uses model Nucleotide Transformer (Fusion breakpoint primary paper Classification performance and Discussion; frozen Nucleotide Transformer embeddings + trained NN head | Existing reviewed locator: Discussion (paragraph 2); Results/Classification performance (paragraph 2))
- Reported ROC AUC for Nucleotide Transformer + NN (middle): Printed value 0.994 (Table 2, NT / NN (middle) row, ROC AUC column)
Models, benchmarks and other records
Pipelines (1)
Tasks (1)
Datasets (1)
Evaluations (1)
Evidence
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18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Artifact retrieved at 2026-09-16T10:38:57.558209+00:00 Source metadata | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences No field-specific location recorded Version: journal full text in PMC | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Artifact SHA-256 0f4d9de77f1e39cfd2164a20653d86370767da684dc22d17e09f589761abeb5f Source metadata | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences No field-specific location recorded Version: journal full text in PMC | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13182013/fullTextXML Source metadata | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences No field-specific location recorded Version: journal full text in PMC | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Doi 10.1186/s13040-026-00553-1 Source metadata | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences No field-specific location recorded Version: journal full text in PMC | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Missing metadata: licence: reason unextracted Source metadata | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences No field-specific location recorded Version: journal full text in PMC | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Publication status peer_reviewed Source metadata | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences No field-specific location recorded Version: journal full text in PMC | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Retrieved at 2026-09-15T23:33:26Z Source metadata | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences No field-specific location recorded Version: journal full text in PMC | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Scope decision included Source metadata | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences No field-specific location recorded Version: journal full text in PMC | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Url https://pmc.ncbi.nlm.nih.gov/articles/PMC13182013/ Source metadata | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences No field-specific location recorded Version: journal full text in PMC | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Version journal full text in PMC Source metadata | Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences No field-specific location recorded Version: journal full text in PMC | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
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.
Technical metadata and extraction receipts
Stable ID: fusion-breakpoint-foundation-models-2026
- areas
- dna-genomes
- url
- https://pmc.ncbi.nlm.nih.gov/articles/PMC13182013/
- version
- journal full text in PMC
- retrieved at
- 2026-09-15T23:33:26Z
- doi
- 10.1186/s13040-026-00553-1
- publication status
- peer_reviewed
- year
- 2026
- artifact sha256
- 0f4d9de77f1e39cfd2164a20653d86370767da684dc22d17e09f589761abeb5f
- artifact url
- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13182013/fullTextXML
- artifact retrieved at
- 2026-09-16T10:38:57.558209+00:00
- scope decision
- included
- missing metadata
- licence: reason: unextracted