Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Pipeline
ENCODE-rE2G extended logistic regression plus AlphaGenome K562 RNA-seq input × gradient feature
ENCODE-rE2G extended logistic regression plus AlphaGenome K562 RNA-seq input × gradient feature. This is the configuration evaluated in the Nature paper, not an identification of the current hosted API revision.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspectedUnderlying model: AlphaGenome. Results on this page belong to this pipeline and its evaluated settings.
At a glance
Key specifications have not been extracted for this record. See the linked evaluation and sources for the reported setup.
limited source coverage · Automated source review, 2026-09-17. All specifications and missing details
Evaluations and results
Release 2026-09-17-d277315f7d76 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| ENCODE-rE2G extended logistic regression plus AlphaGenome K562 RNA-seq input × gradient feature: Supervised enhancer–gene linking Pipeline: ENCODE-rE2G extended logistic regression plus AlphaGenome K562 RNA-seq input × gradient featureProtocol: Supervised enhancer–gene linking (AlphaGenome paper)Dataset subset: Supervised enhancer–gene linking: evaluated data subset Add the K562 RNA-seq input×gradient score to ENCODE-rE2G extended, rerun its full logistic-regression training pipeline and evaluate out-of-fold predictions. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.78 auprc Unit: dimensionless · Direction: higher Aggregation: auPRC over labelled element–gene pairs, with separate distance-to-TSS strata in the paper. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!M18 Source checking is not independent reproduction. |
How it works
Evaluated configuration
ENCODE-rE2G extended logistic-regression pipeline augmented by the AlphaGenome K562 RNA-seq input×gradient feature; Table4 row18 matches Extended Data Fig.7b, not the separate multimodal variant-feature pipeline in Fig.7c. Add the K562 RNA-seq input×gradient score to ENCODE-rE2G extended, rerun its full logistic-regression training pipeline and evaluate out-of-fold predictions.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspectedStrengths and limitations
Limitations and conditions
- The publication result does not establish equivalence to another checkpoint or hosted service.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected
Profile review details
Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction.
Stable record: alphagenome-2026-model-d5baef97883591faSpecifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Evaluated system | ENCODE-rE2G extended logistic regression plus AlphaGenome K562 RNA-seq input × gradient featureSources (3)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected |
| Checkpoint artifact | Not established for these paper scores; no released checkpoint is inferred. · Needs further source reviewSources (3)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected |
| Evaluation scope | Supervised downstream pipelineSources (3)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected |
| Components | Not extracted or verified for this record. |
| Inputs | Not extracted or verified for this record. |
| Outputs | Not extracted or verified for this record. |
| Adaptation | Not extracted or verified for this record. |
| Implementation | Not extracted or verified for this record. |
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.
21 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Evaluated system ENCODE-rE2G extended logistic regression plus AlphaGenome K562 RNA-seq input × gradient feature Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Evaluated system ENCODE-rE2G extended logistic regression plus AlphaGenome K562 RNA-seq input × gradient feature Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Evaluated system ENCODE-rE2G extended logistic regression plus AlphaGenome K562 RNA-seq input × gradient feature Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| Checkpoint artifact Not established for these paper scores; no released checkpoint is inferred. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | unextracted automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Checkpoint artifact Not established for these paper scores; no released checkpoint is inferred. Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | unextracted automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Checkpoint artifact Not established for these paper scores; no released checkpoint is inferred. Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 | unextracted automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| Evaluation scope Supervised downstream pipeline Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Evaluation scope Supervised downstream pipeline Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Evaluation scope Supervised downstream pipeline Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| Limitation The publication result does not establish equivalence to another checkpoint or hosted service. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
3 source records and release history
- AlphaGenome Nature 2026 supplementary comparison tables · Original source · Nature version of record, 28 January 2026
- AlphaGenome Nature 2026 supplementary methods · Original source · Supplement to Nature version of record, 28 January 2026; content hash pinned
- alphagenome: Journal full-text XML · Original source · Retrieved page snapshot; no immutable publisher revision supplied
Technical metadata and extraction receipts
Stable ID: alphagenome-2026-model-d5baef97883591fa
- areas
- dna-genomes
- entity level
- method
- configuration type
- pipeline
- version
- ENCODE-rE2G extended logistic regression plus AlphaGenome K562 RNA-seq input × gradient feature
- legacy kinds
- model
- entity classification
- review date: 2026-09-17; rationale: This record identifies a composed analysis workflow with separately identifiable upstream models, representations or tools and a downstream prediction/scoring procedure. Results belong to that complete composition rather than to an upstream model alone.; source ids: source-alphagenome-nature2026-tables; source-alphagenome-nature2026-supplementary-methods; evidence-official-56e5abfb5f12f1cd3b20; source locator: 'Suppl Table 4 Variant performan'!A18:P18; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking; Main paper Extended Data Fig. 7b, curve legend and panel title; original Fig14_ESM.jpg visually inspected; ambiguities: None recorded