benchmark · protocol

Human splice-site classification: annotation-derived (AlphaGenome paper)

Can the model identify donor and acceptor splice sites on each DNA strand?

AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5

3 evaluations · 3 metric rows

At 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.

Data, procedure and scoring
Property	Description and evidence
Dataset and biological context	GENCODE v46 GTF-annotated splice sites; the two label sources are separate evaluations.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5
Split	Fold-1 ensemble evaluated on held-out intervals from chromosomes 1,3,5,7,9 to overlap the peer models’ test data.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5
Allowed inputs and adaptation	Reference DNA sequence and predicted donor+/acceptor+/donor−/acceptor− probabilities; SpliceAI and DeltaSplice are comparison models.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5
Metrics as reported	auPRCAlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5
Aggregation	Compute auPRC separately for four strand/site classes and average the four values.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5
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 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5
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

Human splice-site classification: annotation-derived: evaluation procedure

Conceptual summary of the cited procedure; model-specific conditions are given below.

Read the diagram as text

Held-out sequence
Predict four splice-site classes
Match RNA-derived or GTF labels
Average class-specific auPRC

What is tested

Can the model identify donor and acceptor splice sites on each DNA strand?

Procedure

Compare probabilities with the selected binary splice-site labels at genomic positions.

Tested models and results

Release 2026-09-17-a757f4af4277 · 3 evaluations · 3 metric rows. Different protocols are not a single leaderboard.

Evaluated configurationMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
AlphaGenome ensemble of four fold-1 models: Human splice-site classification: annotation-derived Model: AlphaGenome ensemble of four fold-1 models · Benchmark: Human splice-site classification: annotation-derived (AlphaGenome paper) · Dataset: Human splice-site classification: annotation-derived: evaluated data subset Compare probabilities with the selected binary splice-site labels at genomic positions. Author-reported evaluation · Evaluation metadata: needs review
0.82 auPRC Unit: dimensionless · Direction: higher Aggregation: Compute auPRC separately for four strand/site classes and average the four values.	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K4; 'Suppl Table 3 Track performance'!K5 Source checking is not independent reproduction.
DeltaSplice (paper Table 3): Human splice-site classification: annotation-derived Model: DeltaSplice (paper Table 3) · Benchmark: Human splice-site classification: annotation-derived (AlphaGenome paper) · Dataset: Human splice-site classification: annotation-derived: evaluated data subset Compare probabilities with the selected binary splice-site labels at genomic positions. Author-reported evaluation · Evaluation metadata: needs review
0.850 auPRC Unit: dimensionless · Direction: higher Aggregation: Compute auPRC separately for four strand/site classes and average the four values.	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J5 Source checking is not independent reproduction.
SpliceAI (paper Table 3): Human splice-site classification: annotation-derived Model: SpliceAI (paper Table 3) · Benchmark: Human splice-site classification: annotation-derived (AlphaGenome paper) · Dataset: Human splice-site classification: annotation-derived: evaluated data subset Compare probabilities with the selected binary splice-site labels at genomic positions. Author-reported evaluation · Evaluation metadata: needs review
0.815 auPRC Unit: dimensionless · Direction: higher Aggregation: Compute auPRC separately for four strand/site classes and average the four values.	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J4 Source checking is not independent reproduction.

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

RNA-derived labels represent observed sites; GTF labels represent annotation. These are not interchangeable populations. Pangolin is excluded because its outputs do not separate donors from acceptors.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5
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 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5

Profile review details

Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction.

Stable record: alphagenome-2026-t3-protocol-2

Evidence 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

Claims, original sources and review scope · Release 2026-09-17-a757f4af4277
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 Original source ↗ 'Suppl Table 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5 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 Retrieved: 2026-09-17T06:37:01.778972+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 Retrieved: 2026-09-17T06:31:06.887921+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
Diagram steps ["Held-out sequence","Predict four splice-site classes","Match RNA-derived or GTF labels","Average class-specific auPRC"] Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps ["Held-out sequence","Predict four splice-site classes","Match RNA-derived or GTF labels","Average class-specific auPRC"] Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5 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 Retrieved: 2026-09-17T06:37:01.778972+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
Diagram steps ["Held-out sequence","Predict four splice-site classes","Match RNA-derived or GTF labels","Average class-specific auPRC"] Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 Retrieved: 2026-09-17T06:31:06.887921+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
Diagram title Human splice-site classification: annotation-derived: evaluation procedure Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title Human splice-site classification: annotation-derived: evaluation procedure Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5 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 Retrieved: 2026-09-17T06:37:01.778972+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0` Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf Inspected artifact
Diagram title Human splice-site classification: annotation-derived: evaluation procedure Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 Retrieved: 2026-09-17T06:31:06.887921+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact
Dataset and biological context GENCODE v46 GTF-annotated splice sites; the two label sources are separate evaluations. Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A4:N4; 'Suppl Table 3 Track performance'!A5:N5; Supplementary Methods p.22, Splice Site Classification; methods: p.22, Splice Site Classification; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 2; sheet rows 4, 5 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:53:03.009088+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `d159b791fc6cb7b679c151727b7b05a6e5b6388b08a89b675014983d85b6df36` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

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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

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Technical metadata and extraction receipts

Stable ID: alphagenome-2026-t3-protocol-2

areas: dna-genomes
entity level: protocol
version: Nature version of record, 28 January 2026
source evaluation index: 2
source table: 3
reference levels: metric: auPRC; printed value: 0; numeric value: 0; source locator: Suppl Table 3 Track performance!H4; note: Source reference quantity for relative-performance calculation, not a measured baseline run.; metric: auPRC; printed value: 0; numeric value: 0; source locator: Suppl Table 3 Track performance!H5; note: Source reference quantity for relative-performance calculation, not a measured baseline run.

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