Per-test-group AUCs behind the Table 6 three-group mean stored on amp-feng-20261007-eval-qtl-ipaqtl-alphagenome-output-tracks; Feng et al. 2025 Supplementary Data 4. Transcribed, not reproduced. Supplementary Data 4 legend: 'There are notable differences between different test sets for paQTL and ipaQTL.'
1 evaluation · 3 results. Different protocols are not a single leaderboard.
Protocol: Feng ipaQTL discrimination · Dataset: Feng ipaQTL discrimination long-window dataset
Sorted by AUROC (task: ipaqtl; outer test group 1 only (chromosomes 3, 6, 9, 12, 16, 18, 19, 21), not averaged) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | AUROC (task: ipaqtl; outer test group 1 only (chromosomes 3, 6, 9, 12, 16, 18, 19, 21), not averaged) | AUROC (task: ipaqtl; outer test group 2 only (chromosomes 2, 5, 11, 14, 17, 20, 22, X), not averaged) | AUROC (task: ipaqtl; outer test group 3 only (chromosomes 1, 4, 7, 8, 10, 13, 15), not averaged) |
|---|---|---|---|
| AlphaGenome, output tracks* (ipaQTL discrimination)Evaluation | 0.863 | 0.853 | 0.878 |
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AlphaGenome, output tracks* (ipaQTL discrimination) | Protocol: Feng ipaQTL discrimination Dataset: Feng ipaQTL discrimination long-window dataset | 0.863 AUROC (task: ipaqtl; outer test group 1 only (chromosomes 3, 6, 9, 12, 16, 18, 19, 21), not averaged) unitless · higher Uncertainty: Not reported by the source: Supplementary Data 4 prints one AUC per test group, with no interval. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaGenome, output tracks ipaQTL per-test-group evaluation Table 6 set-up, AUC reported separately for each outer chromosome test group (Supplementary Data 4); frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 · Supplementary Data 4 (workbook sheet 'Data 4'), block 'ipaQTL', row 'AlphaGenome, output tracks', column 'Test Group 1 AUC' (cell B66). Test group 1 is chromosomes 3, 6, 9, 12, 16, 18, 19, 21 (Methods, 'Variant effect quantification benchmark'). |
| Configuration: AlphaGenome, output tracks* (ipaQTL discrimination) | Protocol: Feng ipaQTL discrimination Dataset: Feng ipaQTL discrimination long-window dataset | 0.853 AUROC (task: ipaqtl; outer test group 2 only (chromosomes 2, 5, 11, 14, 17, 20, 22, X), not averaged) unitless · higher Uncertainty: Not reported by the source: Supplementary Data 4 prints one AUC per test group, with no interval. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaGenome, output tracks ipaQTL per-test-group evaluation Table 6 set-up, AUC reported separately for each outer chromosome test group (Supplementary Data 4); frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 · Supplementary Data 4 (workbook sheet 'Data 4'), block 'ipaQTL', row 'AlphaGenome, output tracks', column 'Test Group 2 AUC' (cell C66). Test group 2 is chromosomes 2, 5, 11, 14, 17, 20, 22, X (Methods, 'Variant effect quantification benchmark'). |
| Configuration: AlphaGenome, output tracks* (ipaQTL discrimination) | Protocol: Feng ipaQTL discrimination Dataset: Feng ipaQTL discrimination long-window dataset | 0.878 AUROC (task: ipaqtl; outer test group 3 only (chromosomes 1, 4, 7, 8, 10, 13, 15), not averaged) unitless · higher Uncertainty: Not reported by the source: Supplementary Data 4 prints one AUC per test group, with no interval. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaGenome, output tracks ipaQTL per-test-group evaluation Table 6 set-up, AUC reported separately for each outer chromosome test group (Supplementary Data 4); frozen embeddings + random forest classifier Aggregation: Not reported Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 · Supplementary Data 4 (workbook sheet 'Data 4'), block 'ipaQTL', row 'AlphaGenome, output tracks', column 'Test Group 3 AUC' (cell D66). Test group 3 is chromosomes 1, 4, 7, 8, 10, 13, 15 (Methods, 'Variant effect quantification benchmark'). |
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Table 6 set-up, AUC reported separately for each outer chromosome test group (Supplementary Data 4); frozen embeddings + random forest classifier
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32 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 QTL task Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded 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 independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: adaptation Frozen pretrained representation plus a supervised random-forest classifier head fitted for this exact QTL task Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 No field-specific location recorded 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 independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: aggregation Per outer chromosome test group: one AUC for each of the three held-out groups, not averaged (Supplementary Data 4); the group is named in each result's metric qualifier Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded 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 independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: aggregation Per outer chromosome test group: one AUC for each of the three held-out groups, not averaged (Supplementary Data 4); the group is named in each result's metric qualifier Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 No field-specific location recorded 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 independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: budget Not reported Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. 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: Supplementary Data 1-6 No field-specific location recorded 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) | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: dataset version Not reported Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. 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: Supplementary Data 1-6 No field-specific location recorded 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) | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: inputs Alternate-minus-reference embedding representation around each ipaQTL variant (long window) Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks No field-specific location recorded 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 independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: inputs Alternate-minus-reference embedding representation around each ipaQTL variant (long window) Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks: Supplementary Data 1-6 No field-specific location recorded 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 independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
Stable ID: feng-dna-fm-20261014-eval-sd4-qtl-ipaqtl-alphagenome-output-tracks