Configuration

DNABERT-2, frozen embeddings, pooling not stated, 1-NN, long-sequence run (Bůžková et al. 2026)

DNABERT-2, frozen embeddings, pooling not stated, 1-NN, long-sequence run: 117M parameters; context 512; flex.; BPE (4,096) tokenizer; frozen weights; L2-normalised embeddings, FAISS IndexFlatIP, k = 1; overlapping 1,200-token chunks with 250-token overlap, scored per chunk.

1 evaluation · 6 results 2 open disagreements between studies involve its model

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Evaluations and results

1 evaluation · 6 results. Different protocols are not a single leaderboard.

Protocol: RVDB long-sequence viral classification, 16 classes (Bůžková et al. 2026 Table 10) · Dataset: RVDB C-RVDB v31.0 long-sequence dataset, 16 classes

Sorted by Accuracy (16-class long-sequence RVDB dataset, chunk-scored) (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	Accuracy (16-class long-sequence RVDB dataset, chunk-scored)	Balanced accuracy (16-class long-sequence RVDB dataset, chunk-scored)	Macro F1 (16-class long-sequence RVDB dataset, chunk-scored)	MCC (16-class long-sequence RVDB dataset, chunk-scored)	Precision (16-class long-sequence RVDB dataset, chunk-scored, macro-averaged over classes)	Recall (16-class long-sequence RVDB dataset, chunk-scored, macro-averaged over classes)
DNABERT-2, frozen embeddings, pooling not stated, 1-NN, long-sequence run (Bůžková et al. 2026)Evaluation	0.786	0.817	0.813	0.771	0.814	0.817

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: DNABERT-2, frozen embeddings, pooling not stated, 1-NN, long-sequence run (Bůžková et al. 2026)	Protocol: RVDB long-sequence viral classification, 16 classes (Bůžková et al. 2026 Table 10) Dataset: RVDB C-RVDB v31.0 long-sequence dataset, 16 classes	0.786 Accuracy (16-class long-sequence RVDB dataset, chunk-scored) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2ᵃ on the RVDB long-sequence dataset, 16 classes gfm2-20261011-buzkova2026-protocol-long Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 10, row 'DNABERT-2ᵃ', column 'Accuracy'
Configuration: DNABERT-2, frozen embeddings, pooling not stated, 1-NN, long-sequence run (Bůžková et al. 2026)	Protocol: RVDB long-sequence viral classification, 16 classes (Bůžková et al. 2026 Table 10) Dataset: RVDB C-RVDB v31.0 long-sequence dataset, 16 classes	0.817 Balanced accuracy (16-class long-sequence RVDB dataset, chunk-scored) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2ᵃ on the RVDB long-sequence dataset, 16 classes gfm2-20261011-buzkova2026-protocol-long Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 10, row 'DNABERT-2ᵃ', column 'Bal. Acc.'
Configuration: DNABERT-2, frozen embeddings, pooling not stated, 1-NN, long-sequence run (Bůžková et al. 2026)	Protocol: RVDB long-sequence viral classification, 16 classes (Bůžková et al. 2026 Table 10) Dataset: RVDB C-RVDB v31.0 long-sequence dataset, 16 classes	0.813 Macro F1 (16-class long-sequence RVDB dataset, chunk-scored) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2ᵃ on the RVDB long-sequence dataset, 16 classes gfm2-20261011-buzkova2026-protocol-long Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 10, row 'DNABERT-2ᵃ', column 'F1'
Configuration: DNABERT-2, frozen embeddings, pooling not stated, 1-NN, long-sequence run (Bůžková et al. 2026)	Protocol: RVDB long-sequence viral classification, 16 classes (Bůžková et al. 2026 Table 10) Dataset: RVDB C-RVDB v31.0 long-sequence dataset, 16 classes	0.771 MCC (16-class long-sequence RVDB dataset, chunk-scored) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2ᵃ on the RVDB long-sequence dataset, 16 classes gfm2-20261011-buzkova2026-protocol-long Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 10, row 'DNABERT-2ᵃ', column 'MCC'
Configuration: DNABERT-2, frozen embeddings, pooling not stated, 1-NN, long-sequence run (Bůžková et al. 2026)	Protocol: RVDB long-sequence viral classification, 16 classes (Bůžková et al. 2026 Table 10) Dataset: RVDB C-RVDB v31.0 long-sequence dataset, 16 classes	0.814 Precision (16-class long-sequence RVDB dataset, chunk-scored, 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 DNABERT-2ᵃ on the RVDB long-sequence dataset, 16 classes gfm2-20261011-buzkova2026-protocol-long Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 10, row 'DNABERT-2ᵃ', column 'Precision'
Configuration: DNABERT-2, frozen embeddings, pooling not stated, 1-NN, long-sequence run (Bůžková et al. 2026)	Protocol: RVDB long-sequence viral classification, 16 classes (Bůžková et al. 2026 Table 10) Dataset: RVDB C-RVDB v31.0 long-sequence dataset, 16 classes	0.817 Recall (16-class long-sequence RVDB dataset, chunk-scored, 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 DNABERT-2ᵃ on the RVDB long-sequence dataset, 16 classes gfm2-20261011-buzkova2026-protocol-long Aggregation: Not reported Analyzing Genomic Foundation Models for Viral Sequence Identification · Table 10, row 'DNABERT-2ᵃ', column 'Recall'

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Analyzing Genomic Foundation Models for Viral Sequence Identification · Original source · bioRxiv v1, posted 2026-09-28

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Technical metadata and extraction receipts

Stable ID: gfm2-20261011-buzkova2026-config-dnabert-2-long-pooling-unreported

areas: dna-genomes
contexts: research
method types: foundation_model
reported name: DNABERT-2
foundation model eligible: true
source locator: Table 2 row 'DNABERT-2'; Sections 2.3 and 2.5; Table 10 row 'DNABERT-2'
parameters: 117M parameters; context 512; flex.; BPE (4,096) tokenizer; frozen weights; L2-normalised embeddings, FAISS IndexFlatIP, k = 1; overlapping 1,200-token chunks with 250-token overlap, scored per chunk
missing metadata: representation: reason: unreported; note: Sections 2.5 and 3.8 and Table 10 do not say which token pooling the long-sequence run used; version: reason: unreported; note: Official Hugging Face repository named but no revision is printed (Section 2.4)
training setting: Frozen weights, no parameter update; nearest-neighbour probe over labelled reference embeddings
provenance note: DNABERT-2, frozen embeddings, pooling not stated, 1-NN, long-sequence run (Bůžková et al. 2026), as evaluated in the cited comparison.

Related records

configuration of: DNABERT-2
system: DNABERT-2ᵃ on the RVDB long-sequence dataset, 16 classes

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