DNABERT-2 benchmark mouse transcription factor binding site prediction set (Supplementary Note 1 (Supplementary Information pages 1-2), datasets adopted from DNABERT-2); as used in Feng et al. 2025 Table 2.
5 evaluations · 5 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Caduceus-Ph (Mouse TFBS 3 classification) | Protocol: Feng Mouse TFBS 3 sequence classification Dataset: Feng Mouse TFBS 3 dataset | 0.935 AUROC (task: mouse tfbs 3) unitless · higher Uncertainty: Not reported by the source: Table 2 prints point AUCs only. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCaduceus-Ph Mouse TFBS 3 evaluation Table 2, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 2, row 'Mouse TFBS 3', column 'Caduceus-Ph'. |
| Configuration: DNABERT-2 (Mouse TFBS 3 classification) | Protocol: Feng Mouse TFBS 3 sequence classification Dataset: Feng Mouse TFBS 3 dataset | 0.931 AUROC (task: mouse tfbs 3) unitless · higher Uncertainty: Not reported by the source: Table 2 prints point AUCs only. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 Mouse TFBS 3 evaluation Table 2, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 2, row 'Mouse TFBS 3', column 'DNABERT-2'. |
| Configuration: GROVER (Mouse TFBS 3 classification) | Protocol: Feng Mouse TFBS 3 sequence classification Dataset: Feng Mouse TFBS 3 dataset | 0.933 AUROC (task: mouse tfbs 3) unitless · higher Uncertainty: Not reported by the source: Table 2 prints point AUCs only. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGROVER Mouse TFBS 3 evaluation Table 2, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 2, row 'Mouse TFBS 3', column 'GROVER'. |
| Configuration: HyenaDNA (Mouse TFBS 3 classification) | Protocol: Feng Mouse TFBS 3 sequence classification Dataset: Feng Mouse TFBS 3 dataset | 0.894 AUROC (task: mouse tfbs 3) unitless · higher Uncertainty: Not reported by the source: Table 2 prints point AUCs only. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA Mouse TFBS 3 evaluation Table 2, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 2, row 'Mouse TFBS 3', column 'HyenaDNA'. |
| Configuration: NT-v2 (Mouse TFBS 3 classification) | Protocol: Feng Mouse TFBS 3 sequence classification Dataset: Feng Mouse TFBS 3 dataset | 0.927 AUROC (task: mouse tfbs 3) unitless · higher Uncertainty: Not reported by the source: Table 2 prints point AUCs only. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceTable 2, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 2, row 'Mouse TFBS 3', column 'NT-v2'. |
Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
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Release 2026-11-02-a7f03c9e55a5 · Evidence verified: Not verified
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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
33 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Negatives 1638 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Supplementary Data 6, row 'Mouse TFBS 3'; Supplementary Note 1 (Supplementary Information pages 1-2) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12663285.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Negatives 1638 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 Supplementary Data 6, row 'Mouse TFBS 3'; Supplementary Note 1 (Supplementary Information pages 1-2) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications 16, 10780 (2025); Supplementary Data 1-6 workbook (MOESM3, .xlsm) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Negatives 1638 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Information Supplementary Data 6, row 'Mouse TFBS 3'; Supplementary Note 1 (Supplementary Information pages 1-2) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications 16, 10780 (2025); Supplementary Information PDF (MOESM1, 11 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Population DNABERT-2 benchmark mouse transcription factor binding site prediction set (Supplementary Note 1 (Supplementary Information pages 1-2), datasets adopted from DNABERT-2); sequence length median 101 bp (range 101-101 bp) per Supplementary Data 6. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Supplementary Data 6, row 'Mouse TFBS 3'; Supplementary Note 1 (Supplementary Information pages 1-2) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12663285.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Population DNABERT-2 benchmark mouse transcription factor binding site prediction set (Supplementary Note 1 (Supplementary Information pages 1-2), datasets adopted from DNABERT-2); sequence length median 101 bp (range 101-101 bp) per Supplementary Data 6. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 Supplementary Data 6, row 'Mouse TFBS 3'; Supplementary Note 1 (Supplementary Information pages 1-2) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications 16, 10780 (2025); Supplementary Data 1-6 workbook (MOESM3, .xlsm) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Population DNABERT-2 benchmark mouse transcription factor binding site prediction set (Supplementary Note 1 (Supplementary Information pages 1-2), datasets adopted from DNABERT-2); sequence length median 101 bp (range 101-101 bp) per Supplementary Data 6. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Information Supplementary Data 6, row 'Mouse TFBS 3'; Supplementary Note 1 (Supplementary Information pages 1-2) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications 16, 10780 (2025); Supplementary Information PDF (MOESM1, 11 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Positives 1638 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Supplementary Data 6, row 'Mouse TFBS 3'; Supplementary Note 1 (Supplementary Information pages 1-2) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12663285.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Positives 1638 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 Supplementary Data 6, row 'Mouse TFBS 3'; Supplementary Note 1 (Supplementary Information pages 1-2) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications 16, 10780 (2025); Supplementary Data 1-6 workbook (MOESM3, .xlsm) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Positives 1638 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Information Supplementary Data 6, row 'Mouse TFBS 3'; Supplementary Note 1 (Supplementary Information pages 1-2) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications 16, 10780 (2025); Supplementary Information PDF (MOESM1, 11 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Scope note Supplementary Note 2 (Supplementary Information pages 3-4) marks this dataset as not fully relying on experimental evidence or gold-standard sources. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Supplementary Data 6, row 'Mouse TFBS 3'; Supplementary Note 1 (Supplementary Information pages 1-2) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12663285.1 | not individually reviewed No individual claim review recorded 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-dataset-t2-mouse-tfbs-3