Protocol

Feng G.Subterraneus 4mC sequence classification

Table 3 sequence classification; Feng et al. 2025 source-reported protocol.

Overview

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5 recorded evaluations, 5 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

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All evaluations

5 evaluations · 5 results. Different protocols are not a single leaderboard.

Protocol: Feng G.Subterraneus 4mC sequence classification · Dataset: Feng G.Subterraneus 4mC dataset

Sorted by AUROC (task: g.subterraneus 4mc) (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	AUROC (task: g.subterraneus 4mc)
NT-v2 (G.Subterraneus 4mC classification)Evaluation	0.615 (best in column)
HyenaDNA (G.Subterraneus 4mC classification)Evaluation	0.609
Caduceus-Ph (G.Subterraneus 4mC classification)Evaluation	0.608
GROVER (G.Subterraneus 4mC classification)Evaluation	0.606
DNABERT-2 (G.Subterraneus 4mC classification)Evaluation	0.58

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Caduceus-Ph (G.Subterraneus 4mC classification)	Protocol: Feng G.Subterraneus 4mC sequence classification Dataset: Feng G.Subterraneus 4mC dataset	0.608 AUROC (task: g.subterraneus 4mc) unitless · higher Uncertainty: Not reported by the source: Table 3 prints point AUCs only. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ph G.Subterraneus 4mC evaluation Table 3, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 3, row 'G.Subterraneus 4mC', column 'Caduceus-Ph'.
Configuration: DNABERT-2 (G.Subterraneus 4mC classification)	Protocol: Feng G.Subterraneus 4mC sequence classification Dataset: Feng G.Subterraneus 4mC dataset	0.58 AUROC (task: g.subterraneus 4mc) unitless · higher Uncertainty: Not reported by the source: Table 3 prints point AUCs only. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 G.Subterraneus 4mC evaluation Table 3, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 3, row 'G.Subterraneus 4mC', column 'DNABERT-2'.
Configuration: GROVER (G.Subterraneus 4mC classification)	Protocol: Feng G.Subterraneus 4mC sequence classification Dataset: Feng G.Subterraneus 4mC dataset	0.606 AUROC (task: g.subterraneus 4mc) unitless · higher Uncertainty: Not reported by the source: Table 3 prints point AUCs only. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GROVER G.Subterraneus 4mC evaluation Table 3, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 3, row 'G.Subterraneus 4mC', column 'GROVER'.
Configuration: HyenaDNA (G.Subterraneus 4mC classification)	Protocol: Feng G.Subterraneus 4mC sequence classification Dataset: Feng G.Subterraneus 4mC dataset	0.609 AUROC (task: g.subterraneus 4mc) unitless · higher Uncertainty: Not reported by the source: Table 3 prints point AUCs only. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA G.Subterraneus 4mC evaluation Table 3, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 3, row 'G.Subterraneus 4mC', column 'HyenaDNA'.
Configuration: NT-v2 (G.Subterraneus 4mC classification)	Protocol: Feng G.Subterraneus 4mC sequence classification Dataset: Feng G.Subterraneus 4mC dataset	0.615 AUROC (task: g.subterraneus 4mc) unitless · higher Uncertainty: Not reported by the source: Table 3 prints point AUCs only. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NT-v2 G.Subterraneus 4mC evaluation Table 3, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 3, row 'G.Subterraneus 4mC', column 'NT-v2'.

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

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

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Baseline coverage

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External evaluations: 5

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

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Evidence table

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Sources and history

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

2 source records and release history

Benchmarking DNA foundation models for genomic and genetic tasks · Original source · PMC12663285.1
Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 · Original source · Nature Communications 16, 10780 (2025); Supplementary Data 1-6 workbook (MOESM3, .xlsm)

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Technical metadata and extraction receipts

Stable ID: feng-dna-fm-20261014-protocol-t3-g-subterraneus-4mc

areas: dna-genomes
contexts: research
scope note: Frozen last-layer mean token embeddings from each pretrained model, scored by a supervised random forest classifier fitted for this exact task (not label-free prediction). Original predefined split retained where clearly defined; otherwise a random 70:30 train/test split. DNABERT-2/NT-v2 benchmark datasets are re-split 70:30 keeping class proportions. Random forest hyperparameters tuned by fivefold cross-validation. No whole-chromosome holdout (Methods, 'Sequence classification benchmark').
task: G.Subterraneus 4mC sequence classification (AUC)
version: Table 3
metric: auroc
metric direction: higher
comparison limit: Within-row comparison only: rows differ in source dataset, species, sequence length and split.

Related records

subject: reported_finding: feng-dna-fm-20261014-protocol-t3-g-subterraneus-4mc
assessment: Caduceus-Ph G.Subterraneus 4mC evaluation
assessment: DNABERT-2 G.Subterraneus 4mC evaluation
assessment: GROVER G.Subterraneus 4mC evaluation
assessment: HyenaDNA G.Subterraneus 4mC evaluation
assessment: NT-v2 G.Subterraneus 4mC evaluation

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