Caduceus-Ph G.Subterraneus 4mC sequence-classification evaluation; Feng et al. 2025. Transcribed, not reproduced.
1 evaluation · 1 result. Different protocols are not a single leaderboard.
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| 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 checkedMethods, coverage and sourceCaduceus-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'. |
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Table 3, frozen embeddings + task-specific random forest classifier
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16 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Comparison: adaptation Frozen pretrained representation plus a supervised random-forest classifier head fitted for this exact task Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: aggregation Not reported Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: budget Not reported Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: dataset version Not reported Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: inputs DNA sequence windows for G.Subterraneus 4mC classification Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: metric implementation Not reported Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: population N4-methylcytosine (4mC) site detection benchmark, G. subterraneus set of six species datasets; 41 bp sequences centred on potential 4mC sites (Methods, 'Sequence classification datasets', 4mC site detection in multiple species; Supplementary Note 1 (Supplementary Information pages 1-2)); sequence length median 41 bp (range 41-41 bp) per Supplementary Data 6. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: protocol id feng-dna-fm-20261014-protocol-t3-g-subterraneus-4mc Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: split 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'). Supplementary Data 6: 63567 training and 27243 test sequences. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Origin independent_paper Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Version: PMC12663285.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
Stable ID: feng-dna-fm-20261014-eval-t3-g-subterraneus-4mc-caduceus-ph