Source

GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies

preprint archived 2025-02-05

DOI: 10.1101/2025.01.30.635558 Original source

What this source contributed

Records in this release that cite this source. A record can cite several sources.

1 configuration
1 task
1 protocol
3 evaluations
9 results
4 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
DNABERT-2	F1	85.12 percent	GenomeOcean natural/artificial sequence test	DNABERT-2: Natural vs artificial microbial genome sequence
DNABERT-2	Precision	85.23 percent	GenomeOcean natural/artificial sequence test	DNABERT-2: Natural vs artificial microbial genome sequence
DNABERT-2	Recall	85.02 percent	GenomeOcean natural/artificial sequence test	DNABERT-2: Natural vs artificial microbial genome sequence
GenomeOcean	F1	99.03 percent	GenomeOcean natural/artificial sequence test	GenomeOcean: Natural vs artificial microbial genome sequence
GenomeOcean	Precision	99.03 percent	GenomeOcean natural/artificial sequence test	GenomeOcean: Natural vs artificial microbial genome sequence
GenomeOcean	Recall	99.03 percent	GenomeOcean natural/artificial sequence test	GenomeOcean: Natural vs artificial microbial genome sequence
Nucleotide Transformers V2	F1	83.14 percent	GenomeOcean natural/artificial sequence test	Nucleotide Transformers V2: Natural versus GenomeOcean-generated DNA classification
Nucleotide Transformers V2	Precision	83.31 percent	GenomeOcean natural/artificial sequence test	Nucleotide Transformers V2: Natural versus GenomeOcean-generated DNA classification
Nucleotide Transformers V2	Recall	82.97 percent	GenomeOcean natural/artificial sequence test	Nucleotide Transformers V2: Natural versus GenomeOcean-generated DNA classification

Claims

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

DNABERT-2 · F1 · GenomeOcean natural/artificial sequence test: attributes.metric_direction: Metric direction higher (Table 2:, row DNABERT-2, column F1; XML row2 column4)
GenomeOcean · F1 · GenomeOcean natural/artificial sequence test: attributes.metric_direction: Metric direction higher (Table 2:, row GenomeOcean, column F1; XML row4 column4)
Natural versus GenomeOcean-generated DNA classification (Natural vs artificial microbial genome sequence): links:evaluates_task:reported-task-9f9ab0090f6522: Evaluates task Natural vs artificial microbial genome sequence (Table 2:: Precision, Natural versus GenomeOcean-generated DNA classification)
Nucleotide Transformers 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 Nucleotide Transformers V2 | Existing reviewed locator: Table 2:, row Nucleotide Transformers V2, column Precision; XML row3 column2)

Models, benchmarks and other records

Evaluations (3)

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

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.

16 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 SHA-256 3cc0df52522fccda23e3958f069c916b87ee50bb5c9a992fa37e25256546e145 Source metadata	GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies Original source ↗ No field-specific location recorded Version: preprint archived 2025-02-05 Retrieved: 2026-09-17T07:56:18.823068+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_sha256` Source artifact SHA-256: `3cc0df52522fccda23e3958f069c916b87ee50bb5c9a992fa37e25256546e145` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11838515/fullTextXML Source metadata	GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies Original source ↗ No field-specific location recorded Version: preprint archived 2025-02-05 Retrieved: 2026-09-17T07:56:18.823068+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_url` Source artifact SHA-256: `3cc0df52522fccda23e3958f069c916b87ee50bb5c9a992fa37e25256546e145` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Doi 10.1101/2025.01.30.635558 Source metadata	GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies Original source ↗ No field-specific location recorded Version: preprint archived 2025-02-05 Retrieved: 2026-09-17T07:56:18.823068+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.doi` Source artifact SHA-256: `3cc0df52522fccda23e3958f069c916b87ee50bb5c9a992fa37e25256546e145` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Hash scope Exact retrieved primary paper artifact bytes. Source metadata	GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies Original source ↗ No field-specific location recorded Version: preprint archived 2025-02-05 Retrieved: 2026-09-17T07:56:18.823068+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.hash_scope` Source artifact SHA-256: `3cc0df52522fccda23e3958f069c916b87ee50bb5c9a992fa37e25256546e145` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Retrieved at 2026-09-17T07:56:18.823068+00:00 Source metadata	GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies Original source ↗ No field-specific location recorded Version: preprint archived 2025-02-05 Retrieved: 2026-09-17T07:56:18.823068+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.retrieved_at` Source artifact SHA-256: `3cc0df52522fccda23e3958f069c916b87ee50bb5c9a992fa37e25256546e145` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Review method 1 values automated-source-review Source metadata	GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies Original source ↗ No field-specific location recorded Version: preprint archived 2025-02-05 Retrieved: 2026-09-17T07:56:18.823068+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.review.method` Source artifact SHA-256: `3cc0df52522fccda23e3958f069c916b87ee50bb5c9a992fa37e25256546e145` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Review: scope Source identification and table transcription; no independent experimental reproduction. Source metadata	GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies Original source ↗ No field-specific location recorded Version: preprint archived 2025-02-05 Retrieved: 2026-09-17T07:56:18.823068+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.review.scope` Source artifact SHA-256: `3cc0df52522fccda23e3958f069c916b87ee50bb5c9a992fa37e25256546e145` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11838515/fullTextXML Source metadata	GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies Original source ↗ No field-specific location recorded Version: preprint archived 2025-02-05 Retrieved: 2026-09-17T07:56:18.823068+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.url` Source artifact SHA-256: `3cc0df52522fccda23e3958f069c916b87ee50bb5c9a992fa37e25256546e145` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Version preprint archived 2025-02-05 Source metadata	GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies Original source ↗ No field-specific location recorded Version: preprint archived 2025-02-05 Retrieved: 2026-09-17T07:56:18.823068+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `3cc0df52522fccda23e3958f069c916b87ee50bb5c9a992fa37e25256546e145` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Description Primary reference; inspect retrieval status and review scope. Source metadata	GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies Original source ↗ No field-specific location recorded Version: preprint archived 2025-02-05 Retrieved: 2026-09-17T07:56:18.823068+00:00	catalogued No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `3cc0df52522fccda23e3958f069c916b87ee50bb5c9a992fa37e25256546e145` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact

How to read the evidence

Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

Primary reference; inspect retrieval status and review scope.

Release history

No supporting source is linked yet.

Read original source

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: part2-genomeocean-2025

url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11838515/fullTextXML
doi: 10.1101/2025.01.30.635558
version: preprint archived 2025-02-05
retrieved at: 2026-09-17T07:56:18.823068+00:00
artifact sha256: 3cc0df52522fccda23e3958f069c916b87ee50bb5c9a992fa37e25256546e145
artifact url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11838515/fullTextXML
hash scope: Exact retrieved primary paper artifact bytes.
review: scope: Source identification and table transcription; no independent experimental reproduction.; method: automated-source-review

Related records

Suggest a correction