Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
benchmark · protocol
TF ChIP-seq track prediction at 128 bp (AlphaGenome paper)
Can reference sequence predict held-out TF ChIP-seq signal on Enformer’s target definition?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39At 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 | Enformer/Basenji2 target tracks at 128-bp resolution, with matched Enformer training sequence intervals.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39 |
| Split | Exclude test intervals whose full AlphaGenome input overlaps Enformer training intervals.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39 |
| Allowed inputs and adaptation | Full AlphaGenome reference-DNA context with the Enformer-specific head; table separately compares human-fine-tuned and not-fine-tuned Enformer models.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39 |
| Metrics as reported | pearsonrAlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39 |
| Aggregation | Pearson correlation summarized over the relevant modality tracks.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39 |
| 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'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39 |
| 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
- Matched Enformer split
- Exclude overlapping test contexts
- Predict 128-bp target tracks
- Compare each Enformer variant
What is tested
Can reference sequence predict held-out TF ChIP-seq signal on Enformer’s target definition?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39Procedure
Compare signals in aligned Enformer target bins with the dedicated head and the corresponding Enformer version.
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39Tested models and results
Release 2026-09-17-a757f4af4277 · 3 evaluations · 3 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| AlphaGenome Enformer-split model with 128 bp Enformer head: TF ChIP-seq track prediction at 128 bp Model: AlphaGenome Enformer-split model with 128 bp Enformer head · Benchmark: TF ChIP-seq track prediction at 128 bp (AlphaGenome paper) · Dataset: TF ChIP-seq track prediction at 128 bp: evaluated data subset Compare signals in aligned Enformer target bins with the dedicated head and the corresponding Enformer version. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.58 pearsonr Unit: correlation · Direction: higher Aggregation: Pearson correlation summarized over the relevant modality tracks. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K38; 'Suppl Table 3 Track performance'!K39 Source checking is not independent reproduction. |
| Enformer (human not fine-tuned) (paper Table 3): TF ChIP-seq track prediction at 128 bp Model: Enformer (human not fine-tuned) (paper Table 3) · Benchmark: TF ChIP-seq track prediction at 128 bp (AlphaGenome paper) · Dataset: TF ChIP-seq track prediction at 128 bp: evaluated data subset Compare signals in aligned Enformer target bins with the dedicated head and the corresponding Enformer version. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.541 pearsonr Unit: correlation · Direction: higher Aggregation: Pearson correlation summarized over the relevant modality tracks. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J39 Source checking is not independent reproduction. |
| Enformer (human fine-tuned) (paper Table 3): TF ChIP-seq track prediction at 128 bp Model: Enformer (human fine-tuned) (paper Table 3) · Benchmark: TF ChIP-seq track prediction at 128 bp (AlphaGenome paper) · Dataset: TF ChIP-seq track prediction at 128 bp: evaluated data subset Compare signals in aligned Enformer target bins with the dedicated head and the corresponding Enformer version. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.572 pearsonr Unit: correlation · Direction: higher Aggregation: Pearson correlation summarized over the relevant modality tracks. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J38 Source checking is not independent reproduction. |
Strengths and limitations
Limitations and conditions
- Matched targets do not imply identical input context. Enformer fine-tuning variants remain separate comparator rows, not separate independent AlphaGenome experiments.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39
- 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'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39
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-22Evidence 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 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39 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 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39 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 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39 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 ["Matched Enformer split","Exclude overlapping test contexts","Predict 128-bp target tracks","Compare each Enformer variant"] Individual claims | alphagenome: Journal full-text XML 'Suppl Table 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39 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 ["Matched Enformer split","Exclude overlapping test contexts","Predict 128-bp target tracks","Compare each Enformer variant"] Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39 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 ["Matched Enformer split","Exclude overlapping test contexts","Predict 128-bp target tracks","Compare each Enformer variant"] Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39 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 TF ChIP-seq track prediction at 128 bp: evaluation procedure Individual claims | alphagenome: Journal full-text XML 'Suppl Table 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39 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 TF ChIP-seq track prediction at 128 bp: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39 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 TF ChIP-seq track prediction at 128 bp: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39 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 Enformer/Basenji2 target tracks at 128-bp resolution, with matched Enformer training sequence intervals. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 3 Track performance'!A38:N38; 'Suppl Table 3 Track performance'!A39:N39; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions; methods: p.24, Benchmarking Against Enformer Track Predictions; methods: p.21, Correlation for Continuous Tracks; paper: Extended Data Fig.3a,b; tables: Suppl Table 3 Track performance; evaluation index 22; sheet rows 38, 39 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-t3-protocol-22
- areas
- dna-genomes
- entity level
- protocol
- version
- Nature version of record, 28 January 2026
- source evaluation index
- 22
- source table
- 3
- reference levels
- metric: pearsonr; printed value: 0; numeric value: 0; source locator: Suppl Table 3 Track performance!H38; note: Source reference quantity for relative-performance calculation, not a measured baseline run.; metric: pearsonr; printed value: 0; numeric value: 0; source locator: Suppl Table 3 Track performance!H39; note: Source reference quantity for relative-performance calculation, not a measured baseline run.
Related records
- benchmark: AlphaGenome Enformer-split model with 128 bp Enformer head: TF ChIP-seq track prediction at 128 bp
- benchmark: Enformer (human not fine-tuned) (paper Table 3): TF ChIP-seq track prediction at 128 bp
- benchmark: Enformer (human fine-tuned) (paper Table 3): TF ChIP-seq track prediction at 128 bp
- benchmark: TF ChIP-seq track prediction at 128 bp: evaluated data subset