tables_not_extracted: evidence-expansion-dna-foundation-models-2025-5d8ca9bc
Tables not extracted of Benchmarking DNA foundation models for genomic and genetic tasks
Not extracted as results: Table 2 rows other than the two Arabidopsis promoter rows (bacterial promoters, human vs worm, mouse TFBS); Table 3 except the Human 5mC Caduceus-Ph and NT-v2 cells (human 6mA, yeast histone marks, 4mC in six species); Supplementary Tables 1-4 (pooling counts, multi-class accuracy, random forest vs XGBoost, short vs long input); Supplementary Data 3 (top genes), 4 (per-chromosome-group AUCs behind Tables 5 and 6) and 5 (HyenaDNA re-pretraining); Supplementary Tables 5-8 (hyperparameter grids, embedding dimensions) and Supplementary Fig. 1 (classifier comparison); Figures 2-4 including runtime. These are outside the human diagnostic and regulatory use cases or repeat main-table values at another aggregation.
Descriptive fact transcribed from the pinned source.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Claimed field tables_not_extracted Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Tables 2-3; Supplementary Tables 1-8 and Supplementary Fig. 1; Supplementary Data 3-5; Figures 2-4 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. |
| Claimed field tables_not_extracted Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 Tables 2-3; Supplementary Tables 1-8 and Supplementary Fig. 1; Supplementary Data 3-5; Figures 2-4 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 |
| Claimed field tables_not_extracted Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Information Tables 2-3; Supplementary Tables 1-8 and Supplementary Fig. 1; Supplementary Data 3-5; Figures 2-4 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 Tables 2-3; Supplementary Tables 1-8 and Supplementary Fig. 1; Supplementary Data 3-5; Figures 2-4 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Tables 2-3; Supplementary Tables 1-8 and Supplementary Fig. 1; Supplementary Data 3-5; Figures 2-4 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 Tables 2-3; Supplementary Tables 1-8 and Supplementary Fig. 1; Supplementary Data 3-5; Figures 2-4 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 Tables 2-3; Supplementary Tables 1-8 and Supplementary Fig. 1; Supplementary Data 3-5; Figures 2-4 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 Tables 2-3; Supplementary Tables 1-8 and Supplementary Fig. 1; Supplementary Data 3-5; Figures 2-4 Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Information Tables 2-3; Supplementary Tables 1-8 and Supplementary Fig. 1; Supplementary Data 3-5; Figures 2-4 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 |
| Claimed value Not extracted as results: Table 2 rows other than the two Arabidopsis promoter rows (bacterial promoters, human vs worm, mouse TFBS); Table 3 except the Human 5mC Caduceus-Ph and NT-v2 cells (human 6mA, yeast histone marks, 4mC in six species); Supplementary Tables 1-4 (pooling counts, multi-class accuracy, random forest vs XGBoost, short vs long input); Supplementary Data 3 (top genes), 4 (per-chromosome-group AUCs behind Tables 5 and 6) and 5 (HyenaDNA re-pretraining); Supplementary Tables 5-8 (hyperparameter grids, embedding dimensions) and Supplementary Fig. 1 (classifier comparison); Figures 2-4 including runtime. These are outside the human diagnostic and regulatory use cases or repeat main-table values at another aggregation. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Tables 2-3; Supplementary Tables 1-8 and Supplementary Fig. 1; Supplementary Data 3-5; Figures 2-4 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. |
| Claimed value Not extracted as results: Table 2 rows other than the two Arabidopsis promoter rows (bacterial promoters, human vs worm, mouse TFBS); Table 3 except the Human 5mC Caduceus-Ph and NT-v2 cells (human 6mA, yeast histone marks, 4mC in six species); Supplementary Tables 1-4 (pooling counts, multi-class accuracy, random forest vs XGBoost, short vs long input); Supplementary Data 3 (top genes), 4 (per-chromosome-group AUCs behind Tables 5 and 6) and 5 (HyenaDNA re-pretraining); Supplementary Tables 5-8 (hyperparameter grids, embedding dimensions) and Supplementary Fig. 1 (classifier comparison); Figures 2-4 including runtime. These are outside the human diagnostic and regulatory use cases or repeat main-table values at another aggregation. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 Tables 2-3; Supplementary Tables 1-8 and Supplementary Fig. 1; Supplementary Data 3-5; Figures 2-4 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 |
| Claimed value Not extracted as results: Table 2 rows other than the two Arabidopsis promoter rows (bacterial promoters, human vs worm, mouse TFBS); Table 3 except the Human 5mC Caduceus-Ph and NT-v2 cells (human 6mA, yeast histone marks, 4mC in six species); Supplementary Tables 1-4 (pooling counts, multi-class accuracy, random forest vs XGBoost, short vs long input); Supplementary Data 3 (top genes), 4 (per-chromosome-group AUCs behind Tables 5 and 6) and 5 (HyenaDNA re-pretraining); Supplementary Tables 5-8 (hyperparameter grids, embedding dimensions) and Supplementary Fig. 1 (classifier comparison); Figures 2-4 including runtime. These are outside the human diagnostic and regulatory use cases or repeat main-table values at another aggregation. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Information Tables 2-3; Supplementary Tables 1-8 and Supplementary Fig. 1; Supplementary Data 3-5; Figures 2-4 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 |
| Description Descriptive fact transcribed from the pinned source. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Tables 2-3; Supplementary Tables 1-8 and Supplementary Fig. 1; Supplementary Data 3-5; Figures 2-4 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. |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: superseded
3 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 Information · Original source · Nature Communications 16, 10780 (2025); Supplementary Information PDF (MOESM1, 11 pages)
- 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)
Superseded by tables_not_extracted: evidence-expansion-dna-foundation-models-2025-5d8ca9bc
Download this release (gzip)Technical metadata and extraction receipts
Stable ID: feng-dna-fm-20261013-claim-not-extracted
- field
- tables_not_extracted
- value
- Not extracted as results: Table 2 rows other than the two Arabidopsis promoter rows (bacterial promoters, human vs worm, mouse TFBS); Table 3 except the Human 5mC Caduceus-Ph and NT-v2 cells (human 6mA, yeast histone marks, 4mC in six species); Supplementary Tables 1-4 (pooling counts, multi-class accuracy, random forest vs XGBoost, short vs long input); Supplementary Data 3 (top genes), 4 (per-chromosome-group AUCs behind Tables 5 and 6) and 5 (HyenaDNA re-pretraining); Supplementary Tables 5-8 (hyperparameter grids, embedding dimensions) and Supplementary Fig. 1 (classifier comparison); Figures 2-4 including runtime. These are outside the human diagnostic and regulatory use cases or repeat main-table values at another aggregation.
- source locator
- Tables 2-3; Supplementary Tables 1-8 and Supplementary Fig. 1; Supplementary Data 3-5; Figures 2-4
- review
- method: source-hash-verification; ai-assisted-source-review; rendered-source-visual-check; method note: Checked against the article XML tables and figures, all 11 pages of the Supplementary Information PDF and the six workbook sheets.; reviewer: claude; reviewer note: Independent Claude (Opus 5.5) review agent, separate from the extraction agent feng-19 that built this batch. Automated review only; no human review claimed. Transcription, not reproduction.; reviewed at: 2026-10-13T14:40:00Z; artifact sha256: 5d8ca9bcf88cc1b38ad667906a2e4699b1aefa6d31c6f49259784930353f3202; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12663285/fullTextXML; note: Hand transcription by the extraction agent, written out by extract/extract_feng.py. Independent review: wording matches the cited text; nothing added that the source does not say.