Evaluation

GENA-LM-bigbird-Base-t2t on ViroBench RNA viruses taxonomy classification (T-Split)

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)'

Published comparison transcribed from the pinned source; not reproduced.

Evaluation results

1 evaluation · 1 result. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: GENA-LM-bigbird-Base-t2t (ViroBench classification)	Protocol: ViroBench RNA viruses taxonomy classification, T-Split, Macro-F1 Dataset: ViroBench RNA viruses, T-Split test set	49.55 (2.87)% Macro F1 (ViroBench RNA viruses, taxonomy, T-Split) percent · higher Uncertainty: SD 2.87 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked 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)' Methods, coverage and source GENA-LM-bigbird-Base-t2t on ViroBench RNA viruses taxonomy classification (T-Split) lit-microbial-20261011-virobench-protocol-rna-taxonomy-t-split Aggregation: Not reported ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks · Table 25, row 'GENA-LM-bigbird-Base-t2t', column 'RNA viruses / Taxonomy / T-Split' (text-layer line 2585)

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

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Evaluation procedure

ViroBench RNA viruses taxonomy classification, T-Split, Macro-F1

Configuration: GENA-LM-bigbird-Base-t2t (ViroBench classification)
Protocol: ViroBench RNA viruses taxonomy classification, T-Split, Macro-F1
Dataset: ViroBench RNA viruses, T-Split test set

origin: Independent external evaluation
configuration: Primary source as retrieved 2026-10-11
protocol id: lit-microbial-20261011-virobench-protocol-rna-taxonomy-t-split
dataset version: ViroBench (arXiv 2605.25388v1)
split: T-Split test partition
population: Not reported
inputs: Viral nucleotide sequence windows of 512, 1024 or 2048 bp
adaptation: Frozen embeddings with a standardised MLP head
metric implementation: Macro-F1 x100 as printed
aggregation: Mean across hyperparameter settings (window configurations and learning rates)
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: T-Split test partition
Adaptation: Frozen embeddings with a standardised MLP head
Scoring implementation: Macro-F1 x100 as printed

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Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

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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.

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18 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Comparison: adaptation Frozen embeddings with a standardised MLP head Context-only references	ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks Original source ↗ Table 25 row 'GENA-LM-bigbird-Base-t2t', column 'RNA viruses / Taxonomy / T-Split' Version: arXiv 2605.25388v1 (submitted 2026-05-25); 42-page PDF; KDD '26 header on every page Retrieved: 2026-10-11T21:24:29Z	not individually reviewed No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `22ad7d742eeba37dd7f7f407a483776ba15fc38dedfb8c27ec05f5db231f9e42` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation Mean across hyperparameter settings (window configurations and learning rates) Context-only references	ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks Original source ↗ Table 25 row 'GENA-LM-bigbird-Base-t2t', column 'RNA viruses / Taxonomy / T-Split' Version: arXiv 2605.25388v1 (submitted 2026-05-25); 42-page PDF; KDD '26 header on every page Retrieved: 2026-10-11T21:24:29Z	not individually reviewed No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `22ad7d742eeba37dd7f7f407a483776ba15fc38dedfb8c27ec05f5db231f9e42` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks Original source ↗ Table 25 row 'GENA-LM-bigbird-Base-t2t', column 'RNA viruses / Taxonomy / T-Split' Version: arXiv 2605.25388v1 (submitted 2026-05-25); 42-page PDF; KDD '26 header on every page Retrieved: 2026-10-11T21:24:29Z	missing or unspecified No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `22ad7d742eeba37dd7f7f407a483776ba15fc38dedfb8c27ec05f5db231f9e42` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version ViroBench (arXiv 2605.25388v1) Context-only references	ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks Original source ↗ Table 25 row 'GENA-LM-bigbird-Base-t2t', column 'RNA viruses / Taxonomy / T-Split' Version: arXiv 2605.25388v1 (submitted 2026-05-25); 42-page PDF; KDD '26 header on every page Retrieved: 2026-10-11T21:24:29Z	not individually reviewed No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `22ad7d742eeba37dd7f7f407a483776ba15fc38dedfb8c27ec05f5db231f9e42` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs Viral nucleotide sequence windows of 512, 1024 or 2048 bp Context-only references	ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks Original source ↗ Table 25 row 'GENA-LM-bigbird-Base-t2t', column 'RNA viruses / Taxonomy / T-Split' Version: arXiv 2605.25388v1 (submitted 2026-05-25); 42-page PDF; KDD '26 header on every page Retrieved: 2026-10-11T21:24:29Z	not individually reviewed No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `22ad7d742eeba37dd7f7f407a483776ba15fc38dedfb8c27ec05f5db231f9e42` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: metric implementation Macro-F1 x100 as printed Context-only references	ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks Original source ↗ Table 25 row 'GENA-LM-bigbird-Base-t2t', column 'RNA viruses / Taxonomy / T-Split' Version: arXiv 2605.25388v1 (submitted 2026-05-25); 42-page PDF; KDD '26 header on every page Retrieved: 2026-10-11T21:24:29Z	not individually reviewed No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `22ad7d742eeba37dd7f7f407a483776ba15fc38dedfb8c27ec05f5db231f9e42` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: population Not reported Context-only references	ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks Original source ↗ Table 25 row 'GENA-LM-bigbird-Base-t2t', column 'RNA viruses / Taxonomy / T-Split' Version: arXiv 2605.25388v1 (submitted 2026-05-25); 42-page PDF; KDD '26 header on every page Retrieved: 2026-10-11T21:24:29Z	missing or unspecified No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.population` Source artifact SHA-256: `22ad7d742eeba37dd7f7f407a483776ba15fc38dedfb8c27ec05f5db231f9e42` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: protocol id lit-microbial-20261011-virobench-protocol-rna-taxonomy-t-split Context-only references	ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks Original source ↗ Table 25 row 'GENA-LM-bigbird-Base-t2t', column 'RNA viruses / Taxonomy / T-Split' Version: arXiv 2605.25388v1 (submitted 2026-05-25); 42-page PDF; KDD '26 header on every page Retrieved: 2026-10-11T21:24:29Z	not individually reviewed No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `22ad7d742eeba37dd7f7f407a483776ba15fc38dedfb8c27ec05f5db231f9e42` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: split T-Split test partition Context-only references	ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks Original source ↗ Table 25 row 'GENA-LM-bigbird-Base-t2t', column 'RNA viruses / Taxonomy / T-Split' Version: arXiv 2605.25388v1 (submitted 2026-05-25); 42-page PDF; KDD '26 header on every page Retrieved: 2026-10-11T21:24:29Z	not individually reviewed No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `22ad7d742eeba37dd7f7f407a483776ba15fc38dedfb8c27ec05f5db231f9e42` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Origin independent_paper Context-only references	ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks Original source ↗ Table 25 row 'GENA-LM-bigbird-Base-t2t', column 'RNA viruses / Taxonomy / T-Split' Version: arXiv 2605.25388v1 (submitted 2026-05-25); 42-page PDF; KDD '26 header on every page Retrieved: 2026-10-11T21:24:29Z	not individually reviewed No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.origin` Source artifact SHA-256: `22ad7d742eeba37dd7f7f407a483776ba15fc38dedfb8c27ec05f5db231f9e42` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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-eval-gena-lm-bigbird-base-t2t-rna-taxonomy-t-split

areas: microbes-communities; dna-genomes
contexts: research
origin: independent_paper
protocol: lit-microbial-20261011-virobench-protocol-rna-taxonomy-t-split
version: Primary source as retrieved 2026-10-11
comparison: protocol id: lit-microbial-20261011-virobench-protocol-rna-taxonomy-t-split; dataset version: ViroBench (arXiv 2605.25388v1); split: T-Split test partition; population: Not reported; inputs: Viral nucleotide sequence windows of 512, 1024 or 2048 bp; adaptation: Frozen embeddings with a standardised MLP head; metric implementation: Macro-F1 x100 as printed; aggregation: Mean across hyperparameter settings (window configurations and learning rates); budget: Not reported
source locator: Table 25 row 'GENA-LM-bigbird-Base-t2t', column 'RNA viruses / Taxonomy / T-Split'
missing metadata: comparison.budget: reason: unreported; comparison.population: reason: unreported

Related records

system: GENA-LM-bigbird-Base-t2t (ViroBench classification)
assessment: ViroBench RNA viruses taxonomy classification, T-Split, Macro-F1
data: ViroBench RNA viruses, T-Split test set
evaluation: GENA-LM-bigbird-Base-t2t RNA viruses Taxonomy T-Split

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