DNABERT-2 (GUE) human transcription factor binding site prediction set (Supplementary Note 1); as used in Feng et al. 2025 Table 1.
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 (Human TFBS 5 classification) | Protocol: Feng Human TFBS 5 sequence classification Dataset: Feng Human TFBS 5 dataset | 0.929 AUROC (task: human tfbs 5) unitless · higher Uncertainty: Not reported by the source: Table 1 prints point AUCs only. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCaduceus-Ph Human TFBS 5 evaluation Table 1, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 1, row 'Human TFBS 5', column 'Caduceus-Ph'. Printed in bold (caption: higher than at least two other AUCs, p < 0.01, one-sided DeLong). |
| Configuration: DNABERT-2 (Human TFBS 5 classification) | Protocol: Feng Human TFBS 5 sequence classification Dataset: Feng Human TFBS 5 dataset | 0.92 AUROC (task: human tfbs 5) unitless · higher Uncertainty: Not reported by the source: Table 1 prints point AUCs only. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 Human TFBS 5 evaluation Table 1, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 1, row 'Human TFBS 5', column 'DNABERT-2'. |
| Configuration: GROVER (Human TFBS 5 classification) | Protocol: Feng Human TFBS 5 sequence classification Dataset: Feng Human TFBS 5 dataset | 0.931 AUROC (task: human tfbs 5) unitless · higher Uncertainty: Not reported by the source: Table 1 prints point AUCs only. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGROVER Human TFBS 5 evaluation Table 1, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 1, row 'Human TFBS 5', column 'GROVER'. Printed in bold (caption: higher than at least two other AUCs, p < 0.01, one-sided DeLong). |
| Configuration: HyenaDNA (Human TFBS 5 classification) | Protocol: Feng Human TFBS 5 sequence classification Dataset: Feng Human TFBS 5 dataset | 0.916 AUROC (task: human tfbs 5) unitless · higher Uncertainty: Not reported by the source: Table 1 prints point AUCs only. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenaDNA Human TFBS 5 evaluation Table 1, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 1, row 'Human TFBS 5', column 'HyenaDNA'. |
| Configuration: NT-v2 (Human TFBS 5 classification) | Protocol: Feng Human TFBS 5 sequence classification Dataset: Feng Human TFBS 5 dataset | 0.915 AUROC (task: human tfbs 5) unitless · higher Uncertainty: Not reported by the source: Table 1 prints point AUCs only. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceTable 1, frozen embeddings + task-specific random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks · Table 1, row 'Human TFBS 5', column 'NT-v2'. |
Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.
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.
30 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Negatives 10500 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Supplementary Data 6, row 'Human TFBS 5'; Supplementary Note 1 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 10500 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 Supplementary Data 6, row 'Human TFBS 5'; Supplementary Note 1 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 10500 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Information Supplementary Data 6, row 'Human TFBS 5'; Supplementary Note 1 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 (GUE) human transcription factor binding site prediction set (Supplementary Note 1); 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 'Human TFBS 5'; Supplementary Note 1 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 (GUE) human transcription factor binding site prediction set (Supplementary Note 1); 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 'Human TFBS 5'; Supplementary Note 1 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 (GUE) human transcription factor binding site prediction set (Supplementary Note 1); 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 'Human TFBS 5'; Supplementary Note 1 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 10500 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Supplementary Data 6, row 'Human TFBS 5'; Supplementary Note 1 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 10500 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 Supplementary Data 6, row 'Human TFBS 5'; Supplementary Note 1 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 10500 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Information Supplementary Data 6, row 'Human TFBS 5'; Supplementary Note 1 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 |
| Source location Supplementary Data 6, row 'Human TFBS 5'; Supplementary Note 1 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Supplementary Data 6, row 'Human TFBS 5'; Supplementary Note 1 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-20261013-dataset-t1-human-tfbs-5