Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Protocol
Natural versus GenomeOcean-generated DNA classification (Natural vs artificial microbial genome sequence)
Natural versus GenomeOcean-generated DNA classification · Table 2:. DNABERT 2 and NTv 2 standard fine-tuning; GenomeOcean LoRA. Negatives generated by GenomeOcean itself. CAMI 2 train 18,000/validation 2,000; GTDB test 20,000; balanced natural/artificial 2 kb sequences.
Sources
GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies · Table 2:: Precision, Natural versus GenomeOcean-generated DNA classificationOverview
Key specifications have not been extracted for this record. See the linked evaluation and sources for the reported setup.
limited source coverage · Automated source review, 2026-09-17. All specifications and missing details
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
Natural versus GenomeOcean-generated DNA classification · Table 2:
Precision (percent) · Higher values are better.
Natural versus GenomeOcean-generated DNA classification (Natural vs artificial microbial genome sequence) · GenomeOcean natural/artificial sequence test
Evidence origin: Independent external evaluation, Author-reported evaluation.
GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies · Table 2:: Precision, Natural versus GenomeOcean-generated DNA classification- Self-generator recognition is not generic biological sequence quality.
- Counts are cohort sizes, not verified per-method successful-prediction coverage.
Comparison details and limitations
DNABERT 2 and NTv 2 standard fine-tuning; GenomeOcean LoRA. Negatives generated by GenomeOcean itself. CAMI 2 train 18,000/validation 2,000; GTDB test 20,000; balanced natural/artificial 2 kb sequences.
- No interval assigned unless printed in source cell.
Automated source review: 2026-09-17. Numerical source review does not establish independent reproduction.
Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.
Showing 3 of 3 matching rows.
Tested configuration
0255075100
Reported scoreMethods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Evaluation in this paper
DNABERT 2 and NTv 2 standard fine-tuning; GenomeOcean LoRA. Negatives generated by GenomeOcean itself. CAMI 2 train 18,000/validation 2,000; GTDB test 20,000; balanced natural/artificial 2 kb sequences.
Sources
GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies · Table 2:: Precision, Natural versus GenomeOcean-generated DNA classificationEvaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
No reviewed evaluations with results linked in this release.
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Protocol-valid abundance or assignment control
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Conventional reference-database method with pinned taxonomy/database
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-09-29-06401fd5b220. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Strengths and limitations
Limitations and conditions
No source-reviewed explanatory claims are recorded here yet.
Profile review details
Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.
Stable record: paper-protocol-a8c67b393443253db5Specifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | Not extracted or verified for this record. |
| Organisms | Not extracted or verified for this record. |
| Assays | Not extracted or verified for this record. |
| Splits | Not extracted or verified for this record. |
| Allowed inputs | Not extracted or verified for this record. |
| Adaptation | Not extracted or verified for this record. |
| Metrics | Not extracted or verified for this record. |
| Baselines | Not extracted or verified for this record. |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Papers and result coverage
Last literature check: 2026-09-17. Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
| Paper or primary resource | Version | Reference |
|---|---|---|
| GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies | preprint archived 2025-02-05 | Read source DOI: 10.1101/2025.01.30.635558 |
Historical gaps recorded on 2026-09-17
The catalogue now holds 9 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.
- Independent batch review before import; preserve existing observation identities.
Search and extraction details
complete comparison tables extracted pending publication review
Searches
- GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies primary paper benchmark results
Evidence locations
- Table 2:: Precision, Natural versus GenomeOcean-generated DNA classification
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.
3 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Evaluation in this paper DNABERT 2 and NTv 2 standard fine-tuning; GenomeOcean LoRA. Negatives generated by GenomeOcean itself. CAMI 2 train 18,000/validation 2,000; GTDB test 20,000; balanced natural/artificial 2 kb sequences. Individual claims | GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies Table 2:: Precision, Natural versus GenomeOcean-generated DNA classification Version: preprint archived 2025-02-05 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Introduction Natural versus GenomeOcean-generated DNA classification · Table 2:. DNABERT 2 and NTv 2 standard fine-tuning; GenomeOcean LoRA. Negatives generated by GenomeOcean itself. CAMI 2 train 18,000/validation 2,000; GTDB test 20,000; balanced natural/artificial 2 kb sequences. Individual claims | GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies Table 2:: Precision, Natural versus GenomeOcean-generated DNA classification Version: preprint archived 2025-02-05 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: evaluates task reported-task-9f9ab0090f6522 Individual claims | GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies Table 2:: Precision, Natural versus GenomeOcean-generated DNA classification Version: preprint archived 2025-02-05 | source checked automated source review · 2026-09-17 Audit detailsField: Claim: paper-claim-734285a668bd8dea20 Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
1 source records and release history
- GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies · Original source · preprint archived 2025-02-05
Technical metadata and extraction receipts
Stable ID: paper-protocol-a8c67b393443253db5
- areas
- microbes-communities
- tasks
- Natural vs artificial microbial genome sequence
- entity level
- protocol
- protocol
- DNABERT 2 and NTv 2 standard fine-tuning; GenomeOcean LoRA. Negatives generated by GenomeOcean itself. CAMI 2 train 18,000/validation 2,000; GTDB test 20,000; balanced natural/artificial 2 kb sequences.
- comparison panels
- id: part2-genomeocean-2025-T2-d2237c539e; title: Natural versus GenomeOcean-generated DNA classification · Table 2:; protocol id: paper-protocol-a8c67b393443253db5; dataset id: reported-dataset-0c3ac7efe99c37; metric: Precision; unit: percent; direction: higher; result ids: paper-result-da2786542bcec5cf7f; paper-result-fae558ea3909a73b15; paper-result-af3d9eb456d1404344; source ids: part2-genomeocean-2025; source locator: Table 2:: Precision, Natural versus GenomeOcean-generated DNA classification; context: DNABERT 2 and NTv 2 standard fine-tuning; GenomeOcean LoRA. Negatives generated by GenomeOcean itself. CAMI 2 train 18,000/validation 2,000; GTDB test 20,000; balanced natural/artificial 2 kb sequences.; caveats: Self-generator recognition is not generic biological sequence quality.; Counts are cohort sizes, not verified per-method successful-prediction coverage.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-genomeocean-2025-T2-3c62335b1d; title: Natural versus GenomeOcean-generated DNA classification · Table 2:; protocol id: paper-protocol-a8c67b393443253db5; dataset id: reported-dataset-0c3ac7efe99c37; metric: Recall; unit: percent; direction: higher; result ids: paper-result-415548dbb583463a98; paper-result-b3378778c23879d6db; paper-result-f356ae1c7c4122384a; source ids: part2-genomeocean-2025; source locator: Table 2:: Recall, Natural versus GenomeOcean-generated DNA classification; context: DNABERT 2 and NTv 2 standard fine-tuning; GenomeOcean LoRA. Negatives generated by GenomeOcean itself. CAMI 2 train 18,000/validation 2,000; GTDB test 20,000; balanced natural/artificial 2 kb sequences.; caveats: Self-generator recognition is not generic biological sequence quality.; Counts are cohort sizes, not verified per-method successful-prediction coverage.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-genomeocean-2025-T2-92317bff43; title: Natural versus GenomeOcean-generated DNA classification · Table 2:; protocol id: paper-protocol-a8c67b393443253db5; dataset id: reported-dataset-0c3ac7efe99c37; metric: F1; unit: %; direction: higher; result ids: lit-b3-028; paper-result-0209741f5d0e66b495; lit-b3-027; source ids: part2-genomeocean-2025; source locator: Table 2:: F1, Natural versus GenomeOcean-generated DNA classification; context: DNABERT 2 and NTv 2 standard fine-tuning; GenomeOcean LoRA. Negatives generated by GenomeOcean itself. CAMI 2 train 18,000/validation 2,000; GTDB test 20,000; balanced natural/artificial 2 kb sequences.; caveats: Self-generator recognition is not generic biological sequence quality.; Counts are cohort sizes, not verified per-method successful-prediction coverage.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17
- benchmark research
- review date: 2026-09-17; status: complete_comparison_tables_extracted_pending_publication_review; primary sources: part2-genomeocean-2025; inspected locators: Table 2:: Precision, Natural versus GenomeOcean-generated DNA classification; searched queries: GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies primary paper benchmark results; gaps: Independent batch review before import; preserve existing observation identities.; claim scope: Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
- legacy kinds
- benchmark
- entity classification
- review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: part2-genomeocean-2025; source locator: Table 2:: Precision, Natural versus GenomeOcean-generated DNA classification; ambiguities: None recorded
Related records
- evaluates task: Natural vs artificial microbial genome sequence
- benchmark: GenomeOcean: Natural vs artificial microbial genome sequence
- benchmark: DNABERT-2: Natural vs artificial microbial genome sequence
- subject: Natural versus GenomeOcean-generated DNA classification (Natural vs artificial microbial genome sequence): links:evaluates_task:reported-task-9f9ab0090f6522
- benchmark: Nucleotide Transformers V2: Natural versus GenomeOcean-generated DNA classification