Configuration

NT-2.5b-ms (ViroBench classification)

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)'

NT-2.5b-ms, a configuration of Nucleotide Transformer: Frozen backbone; sequence embeddings from windows of 512, 1024 or 2048 bp fed to a standardised MLP head; pretraining coverage lineage: non-viral coverage.

12 evaluations · 12 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.

Evaluations and results

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

Sorted by Macro F1 (ViroBench ALL viruses, host, G-Split) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	Macro F1 (ViroBench ALL viruses, host, G-Split)	Macro F1 (ViroBench ALL viruses, host, T-Split)	Macro F1 (ViroBench ALL viruses, taxonomy, G-Split)	Macro F1 (ViroBench ALL viruses, taxonomy, T-Split)	Macro F1 (ViroBench DNA viruses, host, G-Split)	Macro F1 (ViroBench DNA viruses, host, T-Split)	Macro F1 (ViroBench DNA viruses, taxonomy, G-Split)	Macro F1 (ViroBench DNA viruses, taxonomy, T-Split)	Macro F1 (ViroBench RNA viruses, host, G-Split)	Macro F1 (ViroBench RNA viruses, host, T-Split)	Macro F1 (ViroBench RNA viruses, taxonomy, G-Split)	Macro F1 (ViroBench RNA viruses, taxonomy, T-Split)
NT-2.5b-ms (ViroBench classification)Evaluation	ViroBench ALL viruses host classification, G-Split, Macro-F1, ViroBench ALL viruses, G-Split test set	52.09 (14.56)%	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT-2.5b-ms (ViroBench classification)Evaluation	ViroBench ALL viruses host classification, T-Split, Macro-F1, ViroBench ALL viruses, T-Split test set	Not reported	21.18 (3.47)%	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT-2.5b-ms (ViroBench classification)Evaluation	ViroBench ALL viruses taxonomy classification, G-Split, Macro-F1, ViroBench ALL viruses, G-Split test set	Not reported	Not reported	24.10 (11.17)%	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT-2.5b-ms (ViroBench classification)Evaluation	ViroBench ALL viruses taxonomy classification, T-Split, Macro-F1, ViroBench ALL viruses, T-Split test set	Not reported	Not reported	Not reported	13.49 (6.25)%	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT-2.5b-ms (ViroBench classification)Evaluation	ViroBench DNA viruses host classification, G-Split, Macro-F1, ViroBench DNA viruses, G-Split test set	Not reported	Not reported	Not reported	Not reported	41.13 (2.31)%	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT-2.5b-ms (ViroBench classification)Evaluation	ViroBench DNA viruses host classification, T-Split, Macro-F1, ViroBench DNA viruses, T-Split test set	Not reported	Not reported	Not reported	Not reported	Not reported	40.47 (8.77)%	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT-2.5b-ms (ViroBench classification)Evaluation	ViroBench DNA viruses taxonomy classification, G-Split, Macro-F1, ViroBench DNA viruses, G-Split test set	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	31.37 (17.06)%	Not reported	Not reported	Not reported	Not reported	Not reported
NT-2.5b-ms (ViroBench classification)Evaluation	ViroBench DNA viruses taxonomy classification, T-Split, Macro-F1, ViroBench DNA viruses, T-Split test set	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	22.83 (3.81)%	Not reported	Not reported	Not reported	Not reported
NT-2.5b-ms (ViroBench classification)Evaluation	ViroBench RNA viruses host classification, G-Split, Macro-F1, ViroBench RNA viruses, G-Split test set	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	31.35 (2.16)%	Not reported	Not reported	Not reported
NT-2.5b-ms (ViroBench classification)Evaluation	ViroBench RNA viruses host classification, T-Split, Macro-F1, ViroBench RNA viruses, T-Split test set	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	3.91 (0.00)%	Not reported	Not reported
NT-2.5b-ms (ViroBench classification)Evaluation	ViroBench RNA viruses taxonomy classification, G-Split, Macro-F1, ViroBench RNA viruses, G-Split test set	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	29.09 (19.42)%	Not reported
NT-2.5b-ms (ViroBench classification)Evaluation	ViroBench RNA viruses taxonomy classification, T-Split, Macro-F1, ViroBench RNA viruses, T-Split test set	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	24.76 (8.71)%

All 12 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: NT-2.5b-ms (ViroBench classification)	Protocol: ViroBench ALL viruses host classification, G-Split, Macro-F1 Dataset: ViroBench ALL viruses, G-Split test set	52.09 (14.56)% Macro F1 (ViroBench ALL viruses, host, G-Split) percent · higher Uncertainty: SD 14.56 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 NT-2.5b-ms on ViroBench ALL viruses host classification (G-Split) lit-microbial-20261011-virobench-protocol-all-host-g-split Aggregation: Not reported ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks · Table 25, row 'NT-2.5b-ms', column 'ALL viruses / Host / G-Split' (text-layer line 2595)
Configuration: NT-2.5b-ms (ViroBench classification)	Protocol: ViroBench ALL viruses host classification, T-Split, Macro-F1 Dataset: ViroBench ALL viruses, T-Split test set	21.18 (3.47)% Macro F1 (ViroBench ALL viruses, host, T-Split) percent · higher Uncertainty: SD 3.47 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 NT-2.5b-ms on ViroBench ALL viruses host classification (T-Split) lit-microbial-20261011-virobench-protocol-all-host-t-split Aggregation: Not reported ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks · Table 25, row 'NT-2.5b-ms', column 'ALL viruses / Host / T-Split' (text-layer line 2595)
Configuration: NT-2.5b-ms (ViroBench classification)	Protocol: ViroBench ALL viruses taxonomy classification, G-Split, Macro-F1 Dataset: ViroBench ALL viruses, G-Split test set	24.10 (11.17)% Macro F1 (ViroBench ALL viruses, taxonomy, G-Split) percent · higher Uncertainty: SD 11.17 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 NT-2.5b-ms on ViroBench ALL viruses taxonomy classification (G-Split) lit-microbial-20261011-virobench-protocol-all-taxonomy-g-split Aggregation: Not reported ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks · Table 25, row 'NT-2.5b-ms', column 'ALL viruses / Taxonomy / G-Split' (text-layer line 2595)
Configuration: NT-2.5b-ms (ViroBench classification)	Protocol: ViroBench ALL viruses taxonomy classification, T-Split, Macro-F1 Dataset: ViroBench ALL viruses, T-Split test set	13.49 (6.25)% Macro F1 (ViroBench ALL viruses, taxonomy, T-Split) percent · higher Uncertainty: SD 6.25 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 NT-2.5b-ms on ViroBench ALL viruses taxonomy classification (T-Split) lit-microbial-20261011-virobench-protocol-all-taxonomy-t-split Aggregation: Not reported ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks · Table 25, row 'NT-2.5b-ms', column 'ALL viruses / Taxonomy / T-Split' (text-layer line 2595)
Configuration: NT-2.5b-ms (ViroBench classification)	Protocol: ViroBench DNA viruses host classification, G-Split, Macro-F1 Dataset: ViroBench DNA viruses, G-Split test set	41.13 (2.31)% Macro F1 (ViroBench DNA viruses, host, G-Split) percent · higher Uncertainty: SD 2.31 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 NT-2.5b-ms on ViroBench DNA viruses host classification (G-Split) lit-microbial-20261011-virobench-protocol-dna-host-g-split Aggregation: Not reported ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks · Table 25, row 'NT-2.5b-ms', column 'DNA viruses / Host / G-Split' (text-layer line 2595)
Configuration: NT-2.5b-ms (ViroBench classification)	Protocol: ViroBench DNA viruses host classification, T-Split, Macro-F1 Dataset: ViroBench DNA viruses, T-Split test set	40.47 (8.77)% Macro F1 (ViroBench DNA viruses, host, T-Split) percent · higher Uncertainty: SD 8.77 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 NT-2.5b-ms on ViroBench DNA viruses host classification (T-Split) lit-microbial-20261011-virobench-protocol-dna-host-t-split Aggregation: Not reported ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks · Table 25, row 'NT-2.5b-ms', column 'DNA viruses / Host / T-Split' (text-layer line 2595)
Configuration: NT-2.5b-ms (ViroBench classification)	Protocol: ViroBench DNA viruses taxonomy classification, G-Split, Macro-F1 Dataset: ViroBench DNA viruses, G-Split test set	31.37 (17.06)% Macro F1 (ViroBench DNA viruses, taxonomy, G-Split) percent · higher Uncertainty: SD 17.06 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 NT-2.5b-ms on ViroBench DNA viruses taxonomy classification (G-Split) lit-microbial-20261011-virobench-protocol-dna-taxonomy-g-split Aggregation: Not reported ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks · Table 25, row 'NT-2.5b-ms', column 'DNA viruses / Taxonomy / G-Split' (text-layer line 2595)
Configuration: NT-2.5b-ms (ViroBench classification)	Protocol: ViroBench DNA viruses taxonomy classification, T-Split, Macro-F1 Dataset: ViroBench DNA viruses, T-Split test set	22.83 (3.81)% Macro F1 (ViroBench DNA viruses, taxonomy, T-Split) percent · higher Uncertainty: SD 3.81 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 NT-2.5b-ms on ViroBench DNA viruses taxonomy classification (T-Split) lit-microbial-20261011-virobench-protocol-dna-taxonomy-t-split Aggregation: Not reported ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks · Table 25, row 'NT-2.5b-ms', column 'DNA viruses / Taxonomy / T-Split' (text-layer line 2595)
Configuration: NT-2.5b-ms (ViroBench classification)	Protocol: ViroBench RNA viruses host classification, G-Split, Macro-F1 Dataset: ViroBench RNA viruses, G-Split test set	31.35 (2.16)% Macro F1 (ViroBench RNA viruses, host, G-Split) percent · higher Uncertainty: SD 2.16 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 NT-2.5b-ms on ViroBench RNA viruses host classification (G-Split) lit-microbial-20261011-virobench-protocol-rna-host-g-split Aggregation: Not reported ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks · Table 25, row 'NT-2.5b-ms', column 'RNA viruses / Host / G-Split' (text-layer line 2595)
Configuration: NT-2.5b-ms (ViroBench classification)	Protocol: ViroBench RNA viruses host classification, T-Split, Macro-F1 Dataset: ViroBench RNA viruses, T-Split test set	3.91 (0.00)% Macro F1 (ViroBench RNA viruses, host, T-Split) percent · higher Uncertainty: SD 0.00 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 NT-2.5b-ms on ViroBench RNA viruses host classification (T-Split) lit-microbial-20261011-virobench-protocol-rna-host-t-split Aggregation: Not reported ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks · Table 25, row 'NT-2.5b-ms', column 'RNA viruses / Host / T-Split' (text-layer line 2595)
Configuration: NT-2.5b-ms (ViroBench classification)	Protocol: ViroBench RNA viruses taxonomy classification, G-Split, Macro-F1 Dataset: ViroBench RNA viruses, G-Split test set	29.09 (19.42)% Macro F1 (ViroBench RNA viruses, taxonomy, G-Split) percent · higher Uncertainty: SD 19.42 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 NT-2.5b-ms on ViroBench RNA viruses taxonomy classification (G-Split) lit-microbial-20261011-virobench-protocol-rna-taxonomy-g-split Aggregation: Not reported ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks · Table 25, row 'NT-2.5b-ms', column 'RNA viruses / Taxonomy / G-Split' (text-layer line 2595)
Configuration: NT-2.5b-ms (ViroBench classification)	Protocol: ViroBench RNA viruses taxonomy classification, T-Split, Macro-F1 Dataset: ViroBench RNA viruses, T-Split test set	24.76 (8.71)% Macro F1 (ViroBench RNA viruses, taxonomy, T-Split) percent · higher Uncertainty: SD 8.71 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 NT-2.5b-ms 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 'NT-2.5b-ms', column 'RNA viruses / Taxonomy / T-Split' (text-layer line 2595)

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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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Stable ID: lit-microbial-20261011-virobench-config-nt-2-5b-ms

areas: microbes-communities; dna-genomes
contexts: research
method types: foundation_model
reported name: NT-2.5b-ms
foundation model eligible: true
parameters: Frozen backbone; sequence embeddings from windows of 512, 1024 or 2048 bp fed to a standardised MLP head (Section 4.1.2; Appendix B.3); pretraining coverage lineage: non-viral coverage
source locator: Table 25 row 'NT-2.5b-ms' (section 'DNA Foundation Models (Non-viral Coverage)'); Table 9
access reuse: Not stated in the source; see the model's own release
missing metadata: version: reason: unreported; note: The printed row label is the only checkpoint identifier; Table 9 lists evaluated sub-modes
provenance note: NT-2.5b-ms as evaluated in ViroBench viral taxonomy and host classification.

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