Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Pipeline
ENCODE e2g extended: ENCODE-rE2G extended logistic regression (paper Table 4)
ENCODE e2g extended: ENCODE-rE2G extended logistic regression (paper Table 4). A comparator reported by the AlphaGenome authors; protocol pages specify the dataset and adaptation.
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 inspectedAt 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 e2g extended: ENCODE-rE2G extended logistic regression (paper Table 4): Supervised enhancer–gene linking Pipeline: ENCODE e2g extended: ENCODE-rE2G extended logistic regression (paper Table 4)Protocol: 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 | ||
| 0.76 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'!L18 Source checking is not independent reproduction. |
How it works
How this comparator was evaluated
The source table identifies ENCODE e2g extended. 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
- A table label does not establish identity with any other catalogue configuration bearing the same name.
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-comparator-5b70f2a000382e2dSpecifications
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 |
|---|---|
| Reported method | ENCODE e2g extendedSources (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 |
| Exact checkpoint | Not established by the summary table; inspect the protocol and original implementation. · 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 |
| 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.
15 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported method ENCODE e2g extended 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 |
| Reported method ENCODE e2g extended 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 |
| Reported method ENCODE e2g extended 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 |
| Exact checkpoint Not established by the summary table; inspect the protocol and original implementation. 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 |
| Exact checkpoint Not established by the summary table; inspect the protocol and original implementation. 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 |
| Exact checkpoint Not established by the summary table; inspect the protocol and original implementation. 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 |
| Limitation A table label does not establish identity with any other catalogue configuration bearing the same name. 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 |
| Limitation A table label does not establish identity with any other catalogue configuration bearing the same name. 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 |
| Limitation A table label does not establish identity with any other catalogue configuration bearing the same name. 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 |
| How this comparator was evaluated The source table identifies ENCODE e2g extended. 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. 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-comparator-5b70f2a000382e2d
- areas
- dna-genomes
- entity level
- method
- configuration type
- pipeline
- version
- ENCODE e2g extended: ENCODE-rE2G extended logistic regression (paper Table 4)
- 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