benchmark · protocol

Human splice-junction classification and count prediction (AlphaGenome paper)

Can sequence identify observed donor–acceptor junctions and predict their quantitative support?

AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9

2 evaluations · 4 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	Filtered RNA-seq junctions on fold-1 held-out intervals; observed splice sites define candidate pairings.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9
Split	Held-out intervals of fold-1 evaluated with a model ensemble trained on fold-1 training data.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9
Allowed inputs and adaptation	Predicted junction counts; Splam comparison scores each pair using the smaller donor/acceptor probability.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9
Metrics as reported	auPRC; pearsonrAlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9
Aggregation	Classification: auPRC per tissue averaged across tissues. Quantitative endpoint: Pearson correlation of log-transformed counts; do not pool these two metric rows.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9
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'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9
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-junction classification and count prediction: evaluation procedure

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

Read the diagram as text

Construct candidate junction pairs
Predict junction support
Separate classification and nonzero-count endpoints
Compute tissue metrics

What is tested

Can sequence identify observed donor–acceptor junctions and predict their quantitative support?

Procedure

For classification, contrast read-supported junctions with unobserved donor–acceptor pairs. For count prediction, correlate log(1+x)-transformed predicted and observed counts only on nonzero observed junctions.

Tested models and results

Release 2026-09-17-a757f4af4277 · 2 evaluations · 4 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
Splam (paper Table 3): Human splice-junction classification and count prediction Model: Splam (paper Table 3) · Benchmark: Human splice-junction classification and count prediction (AlphaGenome paper) · Dataset: Human splice-junction classification and count prediction: evaluated data subset For classification, contrast read-supported junctions with unobserved donor–acceptor pairs. For count prediction, correlate log(1+x)-transformed predicted and observed counts only on nonzero observed junctions. Author-reported evaluation · Evaluation metadata: needs review
0.136 pearsonr Unit: correlation · Direction: higher Aggregation: Classification: auPRC per tissue averaged across tissues. Quantitative endpoint: Pearson correlation of log-transformed counts; do not pool these two metric rows.	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J8 Source checking is not independent reproduction.
0.507 auPRC Unit: dimensionless · Direction: higher Aggregation: Classification: auPRC per tissue averaged across tissues. Quantitative endpoint: Pearson correlation of log-transformed counts; do not pool these two metric rows.	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J9 Source checking is not independent reproduction.
AlphaGenome fold-1 ensemble, splice-junction head: Human splice-junction classification and count prediction Model: AlphaGenome fold-1 ensemble, splice-junction head · Benchmark: Human splice-junction classification and count prediction (AlphaGenome paper) · Dataset: Human splice-junction classification and count prediction: evaluated data subset For classification, contrast read-supported junctions with unobserved donor–acceptor pairs. For count prediction, correlate log(1+x)-transformed predicted and observed counts only on nonzero observed junctions. Author-reported evaluation · Evaluation metadata: needs review
0.82 pearsonr Unit: correlation · Direction: higher Aggregation: Classification: auPRC per tissue averaged across tissues. Quantitative endpoint: Pearson correlation of log-transformed counts; do not pool these two metric rows.	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K8 Source checking is not independent reproduction.
0.82 auPRC Unit: dimensionless · Direction: higher Aggregation: Classification: auPRC per tissue averaged across tissues. Quantitative endpoint: Pearson correlation of log-transformed counts; do not pool these two metric rows.	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K9 Source checking is not independent reproduction.

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

The PSI3/PSI5 analyses on chromosome2 are a separate analysis, not the Table3 auPRC/count endpoints. Unobserved junctions are assay-derived negative labels, not proof of biological impossibility.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9
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'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9

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-4

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'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9 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'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9 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'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9 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 ["Construct candidate junction pairs","Predict junction support","Separate classification and nonzero-count endpoints","Compute tissue metrics"] Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9 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 ["Construct candidate junction pairs","Predict junction support","Separate classification and nonzero-count endpoints","Compute tissue metrics"] Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 3 Track performance'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9 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 ["Construct candidate junction pairs","Predict junction support","Separate classification and nonzero-count endpoints","Compute tissue metrics"] Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 3 Track performance'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9 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-junction classification and count prediction: evaluation procedure Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9 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-junction classification and count prediction: evaluation procedure Individual claims	AlphaGenome Nature 2026 supplementary methods Original source ↗ 'Suppl Table 3 Track performance'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9 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-junction classification and count prediction: evaluation procedure Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 3 Track performance'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9 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 Filtered RNA-seq junctions on fold-1 held-out intervals; observed splice sites define candidate pairings. Individual claims	alphagenome: Journal full-text XML Original source ↗ 'Suppl Table 3 Track performance'!A8:N8; 'Suppl Table 3 Track performance'!A9:N9; Supplementary Methods p.23, Splice Junction Prediction; methods: p.23, Splice Junction Prediction; paper: Extended Data Fig.2b; tables: Suppl Table 3 Track performance; evaluation index 4; sheet rows 8, 9 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-4

areas: dna-genomes
entity level: protocol
version: Nature version of record, 28 January 2026
source evaluation index: 4
source table: 3
reference levels: metric: pearsonr; printed value: 0; numeric value: 0; source locator: Suppl Table 3 Track performance!H8; note: Source reference quantity for relative-performance calculation, not a measured baseline run.; metric: auPRC; printed value: 0.324; numeric value: 0.32400000000000001; source locator: Suppl Table 3 Track performance!H9; note: Source reference quantity for relative-performance calculation, not a measured baseline run.

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