Benchmark

ViroBench

Evidence concern: excluded from comparisons

Table 25 prints one Macro-F1 per model for the taxonomy columns. For 143 of the 144 model-by-split taxonomy cells on the ALL-virus set, the printed value equals the mean of the five per-rank values in Table 26 rounded to two decimals. The exception is RNA-FM under the genus-disjoint split: Table 25 prints 48.67 and the mean of the Table 26 ranks (59.96, 65.35, 37.58, 58.78, 43.82) is 53.10. One of the two tables is wrong for that row, so RNA-FM ALL taxonomy G-Split should not be used in a comparison without checking the published code.ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks · Table 25, row 'RNA-FM', column 'ALL viruses / Taxonomy / G-Split'; Table 26, row 'RNA-FM'

Table 3 lists NT v3 under phage-specific pretraining coverage (P) and Table 9 lists it as non-viral (N). Table 25 groups the NTv3 rows under phage-specific coverage, which is what the configurations record. Pretraining coverage is the paper's main explanatory variable, so NT v3 rows should not be used to support a coverage-versus-performance claim.ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks · Table 3 row 'NT v3'; Table 9 row 'NT v3'; Table 25 section 'DNA Foundation Models (Phage-specific Coverage)'

Benchmark of nucleotide foundation models on viral genomics: taxonomy and host classification under genus-disjoint and temporal splits, plus genome modelling and CDS generation.

Results are recorded on the linked protocols, tasks or configurations listed below. Their settings and evaluations are kept separate.

12 protocols with results

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Results on linked records

This benchmark has no results of its own in this release. 12 linked records have results. They are not assigned to the underlying benchmark: each record keeps its own settings and evaluations, and its scores are on its own page.

ViroBench ALL viruses host classification, G-Split, Macro-F1 Protocol · part of this benchmark · 76 evaluations · 76 results
ViroBench ALL viruses host classification, T-Split, Macro-F1 Protocol · part of this benchmark · 76 evaluations · 76 results
ViroBench ALL viruses taxonomy classification, G-Split, Macro-F1 Protocol · part of this benchmark · 76 evaluations · 76 results
ViroBench ALL viruses taxonomy classification, T-Split, Macro-F1 Protocol · part of this benchmark · 76 evaluations · 76 results
ViroBench DNA viruses host classification, G-Split, Macro-F1 Protocol · part of this benchmark · 76 evaluations · 76 results
ViroBench DNA viruses host classification, T-Split, Macro-F1 Protocol · part of this benchmark · 76 evaluations · 76 results
ViroBench DNA viruses taxonomy classification, G-Split, Macro-F1 Protocol · part of this benchmark · 76 evaluations · 76 results
ViroBench DNA viruses taxonomy classification, T-Split, Macro-F1 Protocol · part of this benchmark · 76 evaluations · 76 results
ViroBench RNA viruses host classification, G-Split, Macro-F1 Protocol · part of this benchmark · 76 evaluations · 76 results
ViroBench RNA viruses host classification, T-Split, Macro-F1 Protocol · part of this benchmark · 76 evaluations · 76 results
ViroBench RNA viruses taxonomy classification, G-Split, Macro-F1 Protocol · part of this benchmark · 76 evaluations · 76 results
ViroBench RNA viruses taxonomy classification, T-Split, Macro-F1 Protocol · part of this benchmark · 76 evaluations · 76 results

Methods and evaluation design

Procedure, tasks and evaluated configurations

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 24 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

Baseline status by linked protocol

ViroBench ALL viruses host classification, G-Split, Macro-F1 · 0/2 roles measured
ViroBench ALL viruses host classification, T-Split, Macro-F1 · 0/2 roles measured
ViroBench ALL viruses taxonomy classification, G-Split, Macro-F1 · 0/2 roles measured
ViroBench ALL viruses taxonomy classification, T-Split, Macro-F1 · 0/2 roles measured
ViroBench DNA viruses host classification, G-Split, Macro-F1 · 0/2 roles measured
ViroBench DNA viruses host classification, T-Split, Macro-F1 · 0/2 roles measured
ViroBench DNA viruses taxonomy classification, G-Split, Macro-F1 · 0/2 roles measured
ViroBench DNA viruses taxonomy classification, T-Split, Macro-F1 · 0/2 roles measured
ViroBench RNA viruses host classification, G-Split, Macro-F1 · 0/2 roles measured
ViroBench RNA viruses host classification, T-Split, Macro-F1 · 0/2 roles measured
ViroBench RNA viruses taxonomy classification, G-Split, Macro-F1 · 0/2 roles measured
ViroBench RNA viruses taxonomy classification, T-Split, Macro-F1 · 0/2 roles measured

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-10-22-1b7cf027e4f6. 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 benchmark. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Strengths, limitations and unresolved questions

Evidence

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Evidence table

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
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How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release history

ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks · Original source · arXiv 2605.25388v1 (submitted 2026-05-25); 42-page PDF; KDD '26 header on every page

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Technical metadata and extraction receipts

Stable ID: lit-microbial-20261011-virobench-benchmark-virobench

areas: microbes-communities; dna-genomes
contexts: research
entity level: suite
version: arXiv 2605.25388v1
task: Viral taxonomy and host classification; viral genome modelling and CDS generation
scope note: This batch covers the classification axis only (Table 25 and two Table 4 rows): 12 protocols, ALL, DNA and RNA virus sets x taxonomy and host x genus-disjoint and temporal splits. Generation results (Tables 5, 6, 27, 28) are not extracted.
source locator: Abstract; Section 3; Table 1; Table 25

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