Genomic Benchmarks human_enhancers_ensembl (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 (Enhancer Ensembl classification) | Protocol: Feng Enhancer Ensembl sequence classification Dataset: Feng Enhancer Ensembl dataset | 0.943 AUROC (task: enhancer ensembl) 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 Enhancer Ensembl 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 'Enhancer Ensembl', column 'Caduceus-Ph'. Printed in bold (caption: higher than at least two other AUCs, p < 0.01, one-sided DeLong). |
| Configuration: DNABERT-2 (Enhancer Ensembl classification) | Protocol: Feng Enhancer Ensembl sequence classification Dataset: Feng Enhancer Ensembl dataset | 0.937 AUROC (task: enhancer ensembl) 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 Enhancer Ensembl 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 'Enhancer Ensembl', column 'DNABERT-2'. |
| Configuration: GROVER (Enhancer Ensembl classification) | Protocol: Feng Enhancer Ensembl sequence classification Dataset: Feng Enhancer Ensembl dataset | 0.938 AUROC (task: enhancer ensembl) 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 Enhancer Ensembl 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 'Enhancer Ensembl', column 'GROVER'. |
| Configuration: HyenaDNA (Enhancer Ensembl classification) | Protocol: Feng Enhancer Ensembl sequence classification Dataset: Feng Enhancer Ensembl dataset | 0.936 AUROC (task: enhancer ensembl) 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 Enhancer Ensembl 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 'Enhancer Ensembl', column 'HyenaDNA'. |
| Configuration: NT-v2 (Enhancer Ensembl classification) | Protocol: Feng Enhancer Ensembl sequence classification Dataset: Feng Enhancer Ensembl dataset | 0.939 AUROC (task: enhancer ensembl) 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 sourceNT-v2 Enhancer Ensembl 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 'Enhancer Ensembl', column 'NT-v2'. Printed in bold (caption: higher than at least two other AUCs, p < 0.01, one-sided DeLong). |
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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A pinned recipe describes the inputs, environment and resource requirements.
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Separate data and exposure records support an independent test.
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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
24 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Population Genomic Benchmarks human_enhancers_ensembl (Supplementary Note 1); sequence length median 200 bp (range 200-200 bp) per Supplementary Data 6. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Supplementary Data 6, row 'Enhancer Ensembl'; 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 Genomic Benchmarks human_enhancers_ensembl (Supplementary Note 1); sequence length median 200 bp (range 200-200 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 'Enhancer Ensembl'; 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 Genomic Benchmarks human_enhancers_ensembl (Supplementary Note 1); sequence length median 200 bp (range 200-200 bp) per Supplementary Data 6. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Information Supplementary Data 6, row 'Enhancer Ensembl'; 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 |
| Scope note Supplementary Data 6 prints a multi-class label distribution (7684/3842/3842) and the same sizes as the Enhancer dataset, although Table 1 reports a binary AUC. The printed sizes are kept as printed. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Supplementary Data 6, row 'Enhancer Ensembl'; 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. |
| Scope note Supplementary Data 6 prints a multi-class label distribution (7684/3842/3842) and the same sizes as the Enhancer dataset, although Table 1 reports a binary AUC. The printed sizes are kept as printed. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 Supplementary Data 6, row 'Enhancer Ensembl'; 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 |
| Scope note Supplementary Data 6 prints a multi-class label distribution (7684/3842/3842) and the same sizes as the Enhancer dataset, although Table 1 reports a binary AUC. The printed sizes are kept as printed. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Information Supplementary Data 6, row 'Enhancer Ensembl'; 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 'Enhancer Ensembl'; Supplementary Note 1 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Supplementary Data 6, row 'Enhancer Ensembl'; 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. |
| Source location Supplementary Data 6, row 'Enhancer Ensembl'; Supplementary Note 1 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 Supplementary Data 6, row 'Enhancer Ensembl'; 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 |
| Source location Supplementary Data 6, row 'Enhancer Ensembl'; Supplementary Note 1 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Information Supplementary Data 6, row 'Enhancer Ensembl'; 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 |
| Species Homo sapiens Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Supplementary Data 6, row 'Enhancer Ensembl'; 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-enhancer-ensembl