rewirebio.iobenchmarks
Dataset

RVDB C-RVDB v31.0 primary dataset, 40 sampled classes

The same primary dataset before the taxonomic refinement, with all 40 randomly sampled organism classes.

Evaluation results

3 evaluations · 12 results. Different protocols are not a single leaderboard.

Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7)
Dataset: RVDB C-RVDB v31.0 primary dataset, 40 sampled classes
0.912 Accuracy (40-class RVDB dataset)
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

blastn on the RVDB 40-class dataset (BLAST comparison)

gfm2-20261011-buzkova2026-protocol-blast-compare

Aggregation: Not reported

Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '40 classes / blastn', column 'Accuracy'
Configuration: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7)
Dataset: RVDB C-RVDB v31.0 primary dataset, 40 sampled classes
0.889 Macro F1 (40-class RVDB dataset)
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

blastn on the RVDB 40-class dataset (BLAST comparison)

gfm2-20261011-buzkova2026-protocol-blast-compare

Aggregation: Not reported

Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '40 classes / blastn', column 'F1'
Configuration: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7)
Dataset: RVDB C-RVDB v31.0 primary dataset, 40 sampled classes
0.892 Precision (40-class RVDB dataset, macro-averaged over classes)
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

blastn on the RVDB 40-class dataset (BLAST comparison)

gfm2-20261011-buzkova2026-protocol-blast-compare

Aggregation: Not reported

Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '40 classes / blastn', column 'Precision'
Configuration: BLAST 2.12.0 blastn, top hit (Bůžková et al. 2026)Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7)
Dataset: RVDB C-RVDB v31.0 primary dataset, 40 sampled classes
0.89 Recall (40-class RVDB dataset, macro-averaged over classes)
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

blastn on the RVDB 40-class dataset (BLAST comparison)

gfm2-20261011-buzkova2026-protocol-blast-compare

Aggregation: Not reported

Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '40 classes / blastn', column 'Recall'
Configuration: BLAST 2.12.0 megablast, top hit (Bůžková et al. 2026)Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7)
Dataset: RVDB C-RVDB v31.0 primary dataset, 40 sampled classes
0.849 Accuracy (40-class RVDB dataset)
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

megablast on the RVDB 40-class dataset (BLAST comparison)

gfm2-20261011-buzkova2026-protocol-blast-compare

Aggregation: Not reported

Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '40 classes / megablast', column 'Accuracy'
Configuration: BLAST 2.12.0 megablast, top hit (Bůžková et al. 2026)Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7)
Dataset: RVDB C-RVDB v31.0 primary dataset, 40 sampled classes
0.851 Macro F1 (40-class RVDB dataset)
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

megablast on the RVDB 40-class dataset (BLAST comparison)

gfm2-20261011-buzkova2026-protocol-blast-compare

Aggregation: Not reported

Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '40 classes / megablast', column 'F1'
Configuration: BLAST 2.12.0 megablast, top hit (Bůžková et al. 2026)Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7)
Dataset: RVDB C-RVDB v31.0 primary dataset, 40 sampled classes
0.906 Precision (40-class RVDB dataset, macro-averaged over classes)
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

megablast on the RVDB 40-class dataset (BLAST comparison)

gfm2-20261011-buzkova2026-protocol-blast-compare

Aggregation: Not reported

Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '40 classes / megablast', column 'Precision'
Configuration: BLAST 2.12.0 megablast, top hit (Bůžková et al. 2026)Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7)
Dataset: RVDB C-RVDB v31.0 primary dataset, 40 sampled classes
0.828 Recall (40-class RVDB dataset, macro-averaged over classes)
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

megablast on the RVDB 40-class dataset (BLAST comparison)

gfm2-20261011-buzkova2026-protocol-blast-compare

Aggregation: Not reported

Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '40 classes / megablast', column 'Recall'
Configuration: NTv3-650M, frozen embeddings, max, all tokens pooling, 1-NN (Bůžková et al. 2026)Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7)
Dataset: RVDB C-RVDB v31.0 primary dataset, 40 sampled classes
0.875 Accuracy (40-class RVDB dataset)
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

NTv3-650M (max) on the RVDB 40-class dataset (BLAST comparison)

gfm2-20261011-buzkova2026-protocol-blast-compare

Aggregation: Not reported

Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '40 classes / NTv3-650M (max)', column 'Accuracy'
Configuration: NTv3-650M, frozen embeddings, max, all tokens pooling, 1-NN (Bůžková et al. 2026)Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7)
Dataset: RVDB C-RVDB v31.0 primary dataset, 40 sampled classes
0.874 Macro F1 (40-class RVDB dataset)
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

NTv3-650M (max) on the RVDB 40-class dataset (BLAST comparison)

gfm2-20261011-buzkova2026-protocol-blast-compare

Aggregation: Not reported

Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '40 classes / NTv3-650M (max)', column 'F1'
Configuration: NTv3-650M, frozen embeddings, max, all tokens pooling, 1-NN (Bůžková et al. 2026)Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7)
Dataset: RVDB C-RVDB v31.0 primary dataset, 40 sampled classes
0.874 Precision (40-class RVDB dataset, macro-averaged over classes)
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

NTv3-650M (max) on the RVDB 40-class dataset (BLAST comparison)

gfm2-20261011-buzkova2026-protocol-blast-compare

Aggregation: Not reported

Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '40 classes / NTv3-650M (max)', column 'Precision'
Configuration: NTv3-650M, frozen embeddings, max, all tokens pooling, 1-NN (Bůžková et al. 2026)Protocol: RVDB viral classification: best frozen-embedding configuration against BLAST (Bůžková et al. 2026 Table 7)
Dataset: RVDB C-RVDB v31.0 primary dataset, 40 sampled classes
0.875 Recall (40-class RVDB dataset, macro-averaged over classes)
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

NTv3-650M (max) on the RVDB 40-class dataset (BLAST comparison)

gfm2-20261011-buzkova2026-protocol-blast-compare

Aggregation: Not reported

Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 7, row '40 classes / NTv3-650M (max)', column 'Recall'

Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.

Research readiness

0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

Release 2026-11-02-a7f03c9e55a5 · Evidence verified: Not verified

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified
  • Sample annotations are recorded: not yet verified
  • Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • A pinned run recipe exists: not yet verified
  • Compute requirements are estimated: not yet verified

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Independent validation data exist: not yet verified
  • Overlap with training data is checked: not yet verified

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Dataset and evaluation context

A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.

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.

7 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statementOriginal source and locationReview and provenance
Population
20,000 sequences; 6,000 test queries
Context-only references
Analyzing Genomic Foundation Models for Viral Sequence Identification

Original source ↗

Section 2.2; Table 1 column 'Primary dataset'

Version: bioRxiv v1, posted 2026-09-28
Retrieved: 2026-10-11T00:48:35Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.population

Source artifact SHA-256: 9a589a2088f8466502b1035228db3e594065e984e5755c25d907471225f75c19

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Source location
Section 2.2; Table 1 column 'Primary dataset'
Context-only references
Analyzing Genomic Foundation Models for Viral Sequence Identification

Original source ↗

Section 2.2; Table 1 column 'Primary dataset'

Version: bioRxiv v1, posted 2026-09-28
Retrieved: 2026-10-11T00:48:35Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.source_locator

Source artifact SHA-256: 9a589a2088f8466502b1035228db3e594065e984e5755c25d907471225f75c19

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Split
70/30 train/test, stratified by class; 350 indexed and 150 queried per class
Context-only references
Analyzing Genomic Foundation Models for Viral Sequence Identification

Original source ↗

Section 2.2; Table 1 column 'Primary dataset'

Version: bioRxiv v1, posted 2026-09-28
Retrieved: 2026-10-11T00:48:35Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.split

Source artifact SHA-256: 9a589a2088f8466502b1035228db3e594065e984e5755c25d907471225f75c19

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Total
20000
Context-only references
Analyzing Genomic Foundation Models for Viral Sequence Identification

Original source ↗

Section 2.2; Table 1 column 'Primary dataset'

Version: bioRxiv v1, posted 2026-09-28
Retrieved: 2026-10-11T00:48:35Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.total

Source artifact SHA-256: 9a589a2088f8466502b1035228db3e594065e984e5755c25d907471225f75c19

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Version
C-RVDB v31.0, 9 January 2026
Context-only references
Analyzing Genomic Foundation Models for Viral Sequence Identification

Original source ↗

Section 2.2; Table 1 column 'Primary dataset'

Version: bioRxiv v1, posted 2026-09-28
Retrieved: 2026-10-11T00:48:35Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.version

Source artifact SHA-256: 9a589a2088f8466502b1035228db3e594065e984e5755c25d907471225f75c19

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Description
The same primary dataset before the taxonomic refinement, with all 40 randomly sampled organism classes.
Context-only references
Analyzing Genomic Foundation Models for Viral Sequence Identification

Original source ↗

Section 2.2; Table 1 column 'Primary dataset'

Version: bioRxiv v1, posted 2026-09-28
Retrieved: 2026-10-11T00:48:35Z

not individually reviewed

No individual claim review recorded

Audit details

Field: description

Source artifact SHA-256: 9a589a2088f8466502b1035228db3e594065e984e5755c25d907471225f75c19

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Name
RVDB C-RVDB v31.0 primary dataset, 40 sampled classes
Context-only references
Analyzing Genomic Foundation Models for Viral Sequence Identification

Original source ↗

Section 2.2; Table 1 column 'Primary dataset'

Version: bioRxiv v1, posted 2026-09-28
Retrieved: 2026-10-11T00:48:35Z

not individually reviewed

No individual claim review recorded

Audit details

Field: name

Source artifact SHA-256: 9a589a2088f8466502b1035228db3e594065e984e5755c25d907471225f75c19

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Sources and history

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

1 source record and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: gfm2-20261011-buzkova2026-data-rvdb-40

areas
dna-genomes
contexts
research
version
C-RVDB v31.0, 9 January 2026
split
70/30 train/test, stratified by class; 350 indexed and 150 queried per class
population
20,000 sequences; 6,000 test queries
total
20000
source locator
Section 2.2; Table 1 column 'Primary dataset'
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