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.
GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies · Table 2:: Precision, Natural versus GenomeOcean-generated DNA classificationAt a glance
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.
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.
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.
Published comparisons
Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies.
Natural versus GenomeOcean-generated DNA classification · Table 2:
Precision (percent) · Higher values are better for this metric.
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.
Evaluation protocol · GenomeOcean natural/artificial sequence test
- DNABERT-2 · Configuration · Independent external evaluation85.23
- Nucleotide Transformers V2 · Configuration · Author-reported evaluation83.31
- GenomeOcean · Configuration · Author-reported evaluation99.03
Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.
GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies · Table 2:: Precision, Natural versus GenomeOcean-generated DNA classificationValues, uncertainty and evidence
| Tested entity | Printed value | Uncertainty | Evidence |
|---|---|---|---|
| DNABERT-2 · Configuration | 85.23 percent | Not reported | Independent external evaluation · source checkedGenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies · Table 2:, row DNABERT-2, column Precision; XML row2 column2 |
| Nucleotide Transformers V2 · Configuration | 83.31 percent | Not reported | Author-reported evaluation · source checkedGenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies · Table 2:, row Nucleotide Transformers V2, column Precision; XML row3 column2 |
| GenomeOcean · Configuration | 99.03 percent | Not reported | Author-reported evaluation · source checkedGenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies · Table 2:, row GenomeOcean, column Precision; XML row4 column2 |
Scope and limitations
- 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.
Source transcription and grouping reviewed by automated source review on 2026-09-17. These experiments were not independently reproduced by rewire.
Tested entities and results
Release 2026-09-17-d277315f7d76 · 3 evaluations · 9 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| GenomeOcean: Natural vs artificial microbial genome sequence Configuration: GenomeOceanProtocol: Natural versus GenomeOcean-generated DNA classification (Natural vs artificial microbial genome sequence)Dataset: GenomeOcean natural/artificial sequence test 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. Author-reported evaluation · Evaluation metadata: needs review | ||
| 99.03 F1 Unit: % · Direction: higher | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedGenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies; GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies · Table 2, GenomeOcean row, F1 column Source checking is not independent reproduction. |
| 99.03% Precision Unit: percent · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedGenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies · Table 2:, row GenomeOcean, column Precision; XML row4 column2 Source checking is not independent reproduction. |
| 99.03% Recall Unit: percent · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedGenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies · Table 2:, row GenomeOcean, column Recall; XML row4 column3 Source checking is not independent reproduction. |
| DNABERT-2: Natural vs artificial microbial genome sequence Configuration: DNABERT-2Protocol: Natural versus GenomeOcean-generated DNA classification (Natural vs artificial microbial genome sequence)Dataset: GenomeOcean natural/artificial sequence test 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. Independent external evaluation · Evaluation metadata: needs review | ||
| 85.12 F1 Unit: % · Direction: higher | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedGenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies; GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies · Table 2, DNABERT-2 row, F1 column Source checking is not independent reproduction. |
| 85.02% Recall Unit: percent · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedGenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies · Table 2:, row DNABERT-2, column Recall; XML row2 column3 Source checking is not independent reproduction. |
| 85.23% Precision Unit: percent · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedGenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies · Table 2:, row DNABERT-2, column Precision; XML row2 column2 Source checking is not independent reproduction. |
| Nucleotide Transformers V2: Natural versus GenomeOcean-generated DNA classification Configuration: Nucleotide Transformers V2Protocol: Natural versus GenomeOcean-generated DNA classification (Natural vs artificial microbial genome sequence)Dataset: GenomeOcean natural/artificial sequence test 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. Author-reported evaluation · Evaluation metadata: needs review | ||
| 83.14 F1 Unit: % · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedGenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies · Table 2:, row Nucleotide Transformers V2, column F1; XML row3 column4 Source checking is not independent reproduction. |
| 82.97% Recall Unit: percent · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedGenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies · Table 2:, row Nucleotide Transformers V2, column Recall; XML row3 column3 Source checking is not independent reproduction. |
| 83.31% Precision Unit: percent · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedGenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies · Table 2:, row Nucleotide Transformers V2, column Precision; XML row3 column2 Source checking is not 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 |
What is still missing
- 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
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-a8c67b393443253db5Evidence table
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
Release 2026-09-17-d277315f7d76 · Record review: needs review
- 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