Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
benchmark · protocol
Author MFASS splice-disruption prediction (AlphaGenome paper)
Can sequence-derived splicing changes predict experimentally measured exon disruption in MFASS?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8At a glance
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 |
|---|---|
| Dataset and biological context | MFASS reporter-assay SNVs processed using the MMSplice-paper MFASS notebook; mislabelled strands removed. The paper’s cleaned-dataset totals are not a reported test-subset count.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8 |
| Split | Zero-shot scorer development uses validation chromosomes 1,2,4,5,7,8,10,11,13,14,15,17,20,22,X; final test chromosomes are 3,6,9,12,16,18,19,21. This partitions variant evaluation labels; the distilled model’s teachers were trained on all reference-genome folds.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8 |
| Allowed inputs and adaptation | REF/ALT sequence, the assayed exon’s donor/acceptor identity and paper-specific splicing-head scores.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8 |
| Metrics as reported | all_tissues_auprcAlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8 |
| Aggregation | auPRC for the splice-disrupting label defined by the MFASS exon-inclusion threshold.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8 |
| Uncertainty | Not reported for these summary-table scores. · Not reported in inspected sourcesAlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8 |
| Entity type | protocol |
| Organisms | Not extracted or verified for this record. |
| Assays | Not extracted or verified for this record. |
| Baselines | Not extracted or verified for this record. |
How it works
Conceptual summary of the cited procedure; model-specific conditions are given below.
Read the diagram as text
- Clean author MFASS labels
- Apply author chromosome partition
- Compute exon-specific composite score
- Average tissues and evaluate auPRC
What is tested
Can sequence-derived splicing changes predict experimentally measured exon disruption in MFASS?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8Procedure
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.
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8Tested models and results
Release 2026-09-17-a757f4af4277 · 2 evaluations · 2 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| AlphaGenome distilled all-fold student: Author MFASS splice-disruption prediction Model: AlphaGenome distilled all-fold student · Benchmark: Author MFASS splice-disruption prediction (AlphaGenome paper) · Dataset: 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 | ||
| 0.51 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'!M8 Source checking is not independent reproduction. |
| Pangolin (paper Table 4): Author MFASS splice-disruption prediction Model: Pangolin (paper Table 4) · Benchmark: Author MFASS splice-disruption prediction (AlphaGenome paper) · Dataset: 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. |
Strengths and limitations
Limitations and conditions
- This is the author’s MFASS analysis, not rewire MFASS v2. The methods first prescribe logits, then describe probability/usage differences; do not silently reconstruct an exact scorer implementation from this wording. Do not assign cleaned full-dataset counts to its held-out test subset.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8
- This is an author-reported protocol, not a rewire rerun. Different datasets, processing and adaptations cannot support an unrestricted leaderboard.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8
Profile review details
Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction.
Stable record: alphagenome-2026-t4-protocol-7Evidence table
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.
42 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8 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 |
| Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8 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 |
| Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8 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 |
| Diagram steps ["Clean author MFASS labels","Apply author chromosome partition","Compute exon-specific composite score","Average tissues and evaluate auPRC"] Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8 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 |
| Diagram steps ["Clean author MFASS labels","Apply author chromosome partition","Compute exon-specific composite score","Average tissues and evaluate auPRC"] Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8 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 |
| Diagram steps ["Clean author MFASS labels","Apply author chromosome partition","Compute exon-specific composite score","Average tissues and evaluate auPRC"] Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8 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 |
| Diagram title Author MFASS splice-disruption prediction: evaluation procedure Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8 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 |
| Diagram title Author MFASS splice-disruption prediction: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8 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 |
| Diagram title Author MFASS splice-disruption prediction: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8 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 |
| Dataset and biological context MFASS reporter-assay SNVs processed using the MMSplice-paper MFASS notebook; mislabelled strands removed. The paper’s cleaned-dataset totals are not a reported test-subset count. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS; methods: pp.31–32, MFASS; paper: Fig.3i; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 7; sheet rows 8 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-a757f4af4277 · Record review: needs review
- 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-t4-protocol-7
- areas
- dna-genomes
- entity level
- protocol
- version
- Nature version of record, 28 January 2026
- source evaluation index
- 7
- source table
- 4
- reference levels
- metric: all_tissues_auprc; printed value: 0.02; numeric value: 0.02; source locator: Suppl Table 4 Variant performan!J8; note: Source reference quantity for relative-performance calculation, not a measured baseline run.