Source

Benchmarking DNA foundation models for genomic and genetic tasks

2025 · PMC12663285.1 · Peer-reviewed

DOI: 10.1038/s41467-025-65823-8 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
3 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
Caduceus-Ph	AUROC	0.783 unitless	Human 5mC	Caduceus-Ph: Human 5mC detection
NT-v2	AUROC	0.7377 unitless	Human 5mC	NT-v2: Human 5mC detection

Claims

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

NT-v2: family Nucleotide Transformer: Family Nucleotide Transformer (mRNABench Table 2/Appendix model inventory; GenomeOcean Table 2; respective model methods; NABench model inventory; GENEB Table 8; source-labelled configuration NT-v2 | Existing reviewed locator: Abstract (paragraph 1); Introduction (paragraph 4))
Reported AUC for Caduceus-Ph: Printed value 0.783 (Table 3, Human 5mC row, Caduceus-Ph column)
Reported AUC for NT-v2: Printed value 0.7377 (Table 3, Human 5mC row, NT-v2 column)

Models, benchmarks and other records

Configurations (2)

Tasks (1)

Human 5mC detection

Datasets (1)

Human 5mC

Evaluations (2)

Evidence

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Evidence table

Inspect claims, sources and review details

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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

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 2026-09-16T10:33:35.327Z Source metadata	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ No field-specific location recorded Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_retrieved_at` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Artifact SHA-256 5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202 Source metadata	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ No field-specific location recorded Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_sha256` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12663285/fullTextXML Source metadata	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ No field-specific location recorded Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_url` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Doi 10.1038/s41467-025-65823-8 Source metadata	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ No field-specific location recorded Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	catalogued No individual claim review recorded Audit details Field: `attributes.doi` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Missing metadata: licence: reason unextracted Source metadata	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ No field-specific location recorded Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	catalogued No individual claim review recorded Audit details Field: `attributes.missing_metadata.licence.reason` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Publication status peer_reviewed Source metadata	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ No field-specific location recorded Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	catalogued No individual claim review recorded Audit details Field: `attributes.publication_status` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Retrieved at 2026-09-15T23:25:00Z Source metadata	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ No field-specific location recorded Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	catalogued No individual claim review recorded Audit details Field: `attributes.retrieved_at` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Scope decision included Source metadata	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ No field-specific location recorded Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	catalogued No individual claim review recorded Audit details Field: `attributes.scope_decision` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Url https://pmc.ncbi.nlm.nih.gov/articles/PMC12663285/ Source metadata	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ No field-specific location recorded Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	catalogued No individual claim review recorded Audit details Field: `attributes.url` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Version PMC12663285.1 Source metadata	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ No field-specific location recorded Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	catalogued No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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

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Technical metadata and extraction receipts

Stable ID: dna-foundation-models-2025

areas: dna-genomes
url: https://pmc.ncbi.nlm.nih.gov/articles/PMC12663285/
version: PMC12663285.1
retrieved at: 2026-09-15T23:25:00Z
doi: 10.1038/s41467-025-65823-8
publication status: peer_reviewed
year: 2025
artifact sha256: 5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202
artifact url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12663285/fullTextXML
artifact retrieved at: 2026-09-16T10:33:35.327Z
scope decision: included
missing metadata: licence: reason: unextracted

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