Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Configuration
Pangolin (paper Table 4)
Pangolin (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'!A3:P3; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.30–31, ClinVar VariantsAt 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 · 5 evaluations · 5 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| Pangolin (paper Table 4): Deep intronic and synonymous variants splicing-based classification Configuration: Pangolin (paper Table 4)Protocol: Deep intronic and synonymous variants splicing-based classification (AlphaGenome paper)Dataset subset: Deep intronic and synonymous variants splicing-based classification: evaluated data subset Score each variant from its predicted splicing changes and compare with the selected ClinVar pathogenicity labels. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.640893 auprc_max_abs_track_aggregation Unit: dimensionless · Direction: higher Aggregation: auPRC in the category, retaining its own class prevalence and sampling scheme. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L3 Source checking is not independent reproduction. |
| Pangolin (paper Table 4): Splicing-QTL causality Configuration: Pangolin (paper Table 4)Protocol: Splicing-QTL causality (AlphaGenome paper)Dataset subset: Splicing-QTL causality: evaluated data subset Compare predicted splicing effects for causal sQTLs and matched negatives; keep the wide and proximal splice-distance analyses distinct. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.731911 tissue_weighted_mean_auprc Unit: dimensionless · Direction: higher Aggregation: auPRC per tissue, averaged with variant-count weights. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L5 Source checking is not independent reproduction. |
| Pangolin (paper Table 4): Author MFASS splice-disruption prediction Configuration: Pangolin (paper Table 4)Protocol: Author MFASS splice-disruption prediction (AlphaGenome paper)Dataset subset: Author MFASS splice-disruption prediction: evaluated data subset Use the MFASS-specific donor/acceptor and junction scoring procedure, sum splicing components, then average across tissues. Compare with the source’s exon-inclusion disruption label. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.541972 all_tissues_auprc Unit: dimensionless · Direction: higher Aggregation: auPRC for the splice-disrupting label defined by the MFASS exon-inclusion threshold. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L8 Source checking is not independent reproduction. |
| Pangolin (paper Table 4): Zero-shot GTEx splicing-outlier prediction Configuration: Pangolin (paper Table 4)Protocol: Zero-shot GTEx splicing-outlier prediction (AlphaGenome paper)Dataset subset: Zero-shot GTEx splicing-outlier prediction: evaluated data subset Evaluate the sequence-derived scores directly on the held-out variants. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.139737 auprc Unit: dimensionless · Direction: higher Aggregation: Pooled auPRC across GTEx tissues after assigning positive variants their observed tissues and negatives tissues sampled to match the positive tissue distribution. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L6 Source checking is not independent reproduction. |
| Pangolin (paper Table 4): Splice-site-region variants splicing-based classification Configuration: Pangolin (paper Table 4)Protocol: Splice-site-region variants splicing-based classification (AlphaGenome paper)Dataset subset: Splice-site-region variants splicing-based classification: evaluated data subset Score each variant from its predicted splicing changes and compare with the selected ClinVar pathogenicity labels. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.553822 auprc_max_abs_track_aggregation Unit: dimensionless · Direction: higher Aggregation: auPRC in the category, retaining its own class prevalence and sampling scheme. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L4 Source checking is not independent reproduction. |
How it works
How this comparator was evaluated
The source table identifies Pangolin. Score each variant from its predicted splicing changes and compare with the selected ClinVar pathogenicity labels.
Sources (3)
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A3:P3; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.30–31, ClinVar VariantsStrengths 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'!A3:P3; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.30–31, ClinVar Variants
Profile review details
Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction.
Stable record: alphagenome-2026-comparator-a547052f2798e278Specifications
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 | PangolinSources (3)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A3:P3; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.30–31, ClinVar Variants |
| 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'!A3:P3; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.30–31, ClinVar Variants |
| Model type | Not extracted or verified for this record. |
| Inputs | Not extracted or verified for this record. |
| Outputs | Not extracted or verified for this record. |
| Parameters | Not extracted or verified for this record. |
| Training data | Not extracted or verified for this record. |
| Context limits | Not extracted or verified for this record. |
| Access | Not extracted or verified for this record. |
| Code licence | Not extracted or verified for this record. |
| Weights licence | 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 Pangolin Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A3:P3; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.30–31, ClinVar Variants 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 Pangolin Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A3:P3; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.30–31, ClinVar Variants 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 Pangolin Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A3:P3; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.30–31, ClinVar Variants 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'!A3:P3; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.30–31, ClinVar Variants 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'!A3:P3; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.30–31, ClinVar Variants 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'!A3:P3; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.30–31, ClinVar Variants 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'!A3:P3; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.30–31, ClinVar Variants 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'!A3:P3; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.30–31, ClinVar Variants 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'!A3:P3; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.30–31, ClinVar Variants 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 Pangolin. Score each variant from its predicted splicing changes and compare with the selected ClinVar pathogenicity labels. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A3:P3; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.30–31, ClinVar Variants 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-a547052f2798e278
- areas
- dna-genomes
- entity level
- method
- configuration type
- reported_configuration
- version
- Pangolin (paper Table 4)
- legacy kinds
- model
- entity classification
- review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: source-alphagenome-nature2026-tables; source-alphagenome-nature2026-supplementary-methods; evidence-official-56e5abfb5f12f1cd3b20; source locator: 'Suppl Table 4 Variant performan'!A3:P3; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.30–31, ClinVar Variants; ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.
Related records
- model: Pangolin (paper Table 4): Zero-shot GTEx splicing-outlier prediction
- model: Pangolin (paper Table 4): Deep intronic and synonymous variants splicing-based classification
- model: Pangolin (paper Table 4): Splicing-QTL causality
- model: Pangolin (paper Table 4): Author MFASS splice-disruption prediction
- model: Pangolin (paper Table 4): Splice-site-region variants splicing-based classification