Configuration

NT-v2

This genomic-embedding configuration is compared across classification, gene-expression, variant-effect and domain-recognition tasks.

Sources

Benchmarking DNA foundation models for genomic and genetic tasks · Abstract (paragraph 1); Introduction (paragraph 4)

1 evaluation · 1 metric row

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 DNA foundation models for genomic and genetic tasks · Results/Sequence classification: pooling methods benchmark (paragraph 2); Methods/Benchmarking methods/Sequence classification benchmark: pooling methods (paragraph 4)

At a glance

Model type

Study-specific predictive method; this record is the paper-specific evaluated configuration.

Sources

Biological inputs

DNA sequence windows, with model-specific context handling

Sources

Benchmarking DNA foundation models for genomic and genetic tasks · Discussion/Limitations (paragraph 1); Methods/Benchmarking datasets/Sequence classification datasets (paragraph 1)

Outputs

Sequence embeddings and downstream genomic predictions

Sources

Benchmarking DNA foundation models for genomic and genetic tasks · Introduction (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.

Evaluation setupMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
NT-v2: Human 5mC detection Configuration: NT-v2Task: Human 5mC detectionDataset: Human 5mC Binary epigenetic-modification classification as reported in the paper. Independent external evaluation · Evaluation metadata: needs review
0.7377 AUC Unit: unitless · Direction: unknown	Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported	source checkedBenchmarking DNA foundation models for genomic and genetic tasks · Table 3, Human 5mC row, NT-v2 column Source checking is not independent reproduction.

How it works

How the evaluated method works

Frozen sequence representations are pooled and supplied to downstream analyses. The study explicitly compares summary-token, mean and maximum pooling.

Sources

What was evaluated

The linked evaluation record identifies NT-v2: Human 5mC detection. Its dataset, split, adaptation and evidence origin remain attached to the reported results.

Sources

Benchmarking DNA foundation models for genomic and genetic tasks · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-002

Strengths and limitations

Strengths and considerations

Tests pooling choices explicitly and compares task-specific specialists.
Sources
Benchmarking DNA foundation models for genomic and genetic tasks · Methods/Benchmarking methods/Sequence classification benchmark (paragraph 3); Methods/Benchmarking methods/Sequence classification benchmark (paragraph 4)

Limitations and conditions

The paper finds task-dependent performance; a classifier on frozen features is not a label-free zero-shot prediction.
Sources
Benchmarking DNA foundation models for genomic and genetic tasks · Results/Gene expression prediction (paragraph 5); Results/Sequence classification: pooling methods benchmark (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-3af86cb274f658

Specifications

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.

Inputs, outputs and configuration
Property	Description and evidence
Model type	Study-specific predictive method; this record is the paper-specific evaluated configuration. Sources Benchmarking DNA foundation models for genomic and genetic tasks · Results/Sequence classification: pooling methods benchmark (paragraph 2); Methods/Benchmarking methods/Sequence classification benchmark: pooling methods (paragraph 4)
Architecture / procedure	Frozen sequence representations are pooled and supplied to downstream analyses. The study explicitly compares summary-token, mean and maximum pooling. Sources Benchmarking DNA foundation models for genomic and genetic tasks · Results/Sequence classification: pooling methods benchmark (paragraph 2); Methods/Benchmarking methods/Sequence classification benchmark: pooling methods (paragraph 4)
Biological inputs	DNA sequence windows, with model-specific context handling Sources Benchmarking DNA foundation models for genomic and genetic tasks · Discussion/Limitations (paragraph 1); Methods/Benchmarking datasets/Sequence classification datasets (paragraph 1)
Outputs	Sequence embeddings and downstream genomic predictions Sources Benchmarking DNA foundation models for genomic and genetic tasks · Introduction (paragraph 1); Discussion (paragraph 1)
Parameters	500 million parameters Sources Benchmarking DNA foundation models for genomic and genetic tasks · Methods/DNA foundation language models (paragraph 4); Methods/DNA foundation language models (paragraph 3)
Known versions / configuration	NT-v2-500M Sources Benchmarking DNA foundation models for genomic and genetic tasks · Methods/Model configuration selection (paragraph 1); Table Tab6 (paragraph 1)
Training data / fitting	Masked-language-model pretraining on genomes from 850 species, including the human reference genome; this study evaluates frozen representations. Sources Benchmarking DNA foundation models for genomic and genetic tasks · Methods / DNA foundation language models; Nucleotide Transformer Version2 paragraph
Context limits	12,000-nucleotide model input limit; the benchmark also specifies task-dependent shorter windows. Sources Benchmarking DNA foundation models for genomic and genetic tasks · Methods / DNA foundation language models; Nucleotide Transformer Version2 paragraph
Access	Official study implementation and usage documentation: https://github.com/ChongWuLab/dna_foundation_benchmark/blob/3f4c81ce066f3c47422a83466b085aac1a6be902/README.md. This pinned documentation revision is not automatically the evaluated weight revision. Sources ChongWuLab/dna_foundation_benchmark 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 sources Sources ChongWuLab/dna_foundation_benchmark README.md · README.md and repository-root licence-file search
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 sources Sources ChongWuLab/dna_foundation_benchmark 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

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
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 DNA foundation models for genomic and genetic tasks Original source ↗ Results/Sequence classification: pooling methods benchmark (paragraph 2); Methods/Benchmarking methods/Sequence classification benchmark: pooling methods (paragraph 4) Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram steps ["DNA sequence windows, with model-specific context handling","NT-v2","Sequence embeddings and downstream genomic predictions"] Individual claims	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ Results/Sequence classification: pooling methods benchmark (paragraph 2); Methods/Benchmarking methods/Sequence classification benchmark: pooling methods (paragraph 4) Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram title Evaluated procedure (conceptual) Individual claims	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ Results/Sequence classification: pooling methods benchmark (paragraph 2); Methods/Benchmarking methods/Sequence classification benchmark: pooling methods (paragraph 4) Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Model type Study-specific predictive method; this record is the paper-specific evaluated configuration. Individual claims	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ Results/Sequence classification: pooling methods benchmark (paragraph 2); Methods/Benchmarking methods/Sequence classification benchmark: pooling methods (paragraph 4) Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Architecture / procedure Frozen sequence representations are pooled and supplied to downstream analyses. The study explicitly compares summary-token, mean and maximum pooling. Individual claims	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ Results/Sequence classification: pooling methods benchmark (paragraph 2); Methods/Benchmarking methods/Sequence classification benchmark: pooling methods (paragraph 4) Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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	ChongWuLab/dna_foundation_benchmark README.md Original source ↗ README.md; checkpoint/access documentation and licence scope Version: 3f4c81ce066f3c47422a83466b085aac1a6be902 Retrieved: 2026-09-16T19:54:14.870570+00:00	unreported automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `e678c69a91fd0b709864d2c0b83f33e273b82e389dd07b6f380b76236631fac2` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Biological inputs DNA sequence windows, with model-specific context handling Individual claims	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ Discussion/Limitations (paragraph 1); Methods/Benchmarking datasets/Sequence classification datasets (paragraph 1) Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Outputs Sequence embeddings and downstream genomic predictions Individual claims	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ Introduction (paragraph 1); Discussion (paragraph 1) Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Parameters 500 million parameters Individual claims	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ Methods/DNA foundation language models (paragraph 4); Methods/DNA foundation language models (paragraph 3) Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Known versions / configuration NT-v2-500M Individual claims	Benchmarking DNA foundation models for genomic and genetic tasks Original source ↗ Methods/Model configuration selection (paragraph 1); Table Tab6 (paragraph 1) Version: PMC12663285.1 Retrieved: 2026-09-16T10:33:35.327Z	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.5.value` Source artifact SHA-256: `5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-09-17-d277315f7d76 · Record review: needs review

2 source records and release history

Benchmarking DNA foundation models for genomic and genetic tasks · Original source · PMC12663285.1
ChongWuLab/dna_foundation_benchmark README.md · Original source · 3f4c81ce066f3c47422a83466b085aac1a6be902

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Technical metadata and extraction receipts

Stable ID: reported-model-3af86cb274f658

areas: dna-genomes
entity level: method
version: Not reported
reported name: NT-v2
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: dna-foundation-models-2025; source locator: Results/Sequence classification: pooling methods benchmark (paragraph 2); Methods/Benchmarking methods/Sequence classification benchmark: pooling methods (paragraph 4) | Abstract (paragraph 1); Introduction (paragraph 4); 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.

Related records

model: NT-v2: Human 5mC detection

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