Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
benchmark · protocol
Cell-type difference in chromatin contact-map prediction (AlphaGenome paper)
Can reference sequence predict the difference in contact organization between H1-hESC and HFF cells?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41At 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 | H1-hESC and HFFc6 Micro-C datasets matching Orca’s evaluation.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41 |
| Split | Intersection of Orca test chromosomes9/10 with AlphaGenome/Borzoi fold-0 held-out intervals.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41 |
| Allowed inputs and adaptation | Reference DNA; contact maps resized from AlphaGenome native bins to Orca’s 4-kb grid using bilinear interpolation.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41 |
| Metrics as reported | Cell-type difference @4kb pearsonrAlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41 |
| Aggregation | Mean Pearson correlation across held-out interval evaluations; the difference-map endpoint is distinct from individual-cell-type accuracy.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41 |
| 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'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41 |
| 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
- Shared held-out chromosome intervals
- Resize predictions to Orca grid
- Subtract matched cell-type maps
- Compute interval Pearson correlations
What is tested
Can reference sequence predict the difference in contact organization between H1-hESC and HFF cells?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41Procedure
Reimplement the Orca H1-hESC minus HFF difference evaluation on the same held-out windows.
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41Tested 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 fold-0 contact-map model, bilinearly resized to Orca 4 kb bins: Cell-type difference in chromatin contact-map prediction Model: AlphaGenome fold-0 contact-map model, bilinearly resized to Orca 4 kb bins · Benchmark: Cell-type difference in chromatin contact-map prediction (AlphaGenome paper) · Dataset: Cell-type difference in chromatin contact-map prediction: evaluated data subset Reimplement the Orca H1-hESC minus HFF difference evaluation on the same held-out windows. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.42 Cell-type difference
@4kb pearsonr Unit: correlation · Direction: higher Aggregation: Mean Pearson correlation across held-out interval evaluations; the difference-map endpoint is distinct from individual-cell-type accuracy. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K41 Source checking is not independent reproduction. |
| Orca (paper Table 3): Cell-type difference in chromatin contact-map prediction Model: Orca (paper Table 3) · Benchmark: Cell-type difference in chromatin contact-map prediction (AlphaGenome paper) · Dataset: Cell-type difference in chromatin contact-map prediction: evaluated data subset Reimplement the Orca H1-hESC minus HFF difference evaluation on the same held-out windows. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.294 Cell-type difference
@4kb pearsonr Unit: correlation · Direction: higher Aggregation: Mean Pearson correlation across held-out interval evaluations; the difference-map endpoint is distinct from individual-cell-type accuracy. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J41 Source checking is not independent reproduction. |
Strengths and limitations
Limitations and conditions
- Resampling changes the grid and is part of this protocol. Do not treat native AlphaGenome resolution or the cell-difference endpoint as interchangeable with the tabulated 4-kb per-cell evaluation.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41
- 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'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41
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-24Evidence 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'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41 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'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41 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'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41 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 ["Shared held-out chromosome intervals","Resize predictions to Orca grid","Subtract matched cell-type maps","Compute interval Pearson correlations"] Individual claims | alphagenome: Journal full-text XML 'Suppl Table 3 Track performance'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41 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 ["Shared held-out chromosome intervals","Resize predictions to Orca grid","Subtract matched cell-type maps","Compute interval Pearson correlations"] Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 3 Track performance'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41 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 ["Shared held-out chromosome intervals","Resize predictions to Orca grid","Subtract matched cell-type maps","Compute interval Pearson correlations"] Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 3 Track performance'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41 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 Cell-type difference in chromatin contact-map prediction: evaluation procedure Individual claims | alphagenome: Journal full-text XML 'Suppl Table 3 Track performance'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41 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 Cell-type difference in chromatin contact-map prediction: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 3 Track performance'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41 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 Cell-type difference in chromatin contact-map prediction: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 3 Track performance'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41 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 H1-hESC and HFFc6 Micro-C datasets matching Orca’s evaluation. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 3 Track performance'!A41:N41; Supplementary Methods pp.23–24, Contact Maps Performance; methods: pp.23–24, Contact Maps Performance; paper: Extended Data Fig.4; tables: Suppl Table 3 Track performance; evaluation index 24; sheet rows 41 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-24
- areas
- dna-genomes
- entity level
- protocol
- version
- Nature version of record, 28 January 2026
- source evaluation index
- 24
- source table
- 3
- reference levels
- metric: Cell-type difference @4kb pearsonr; printed value: 0; numeric value: 0; source locator: Suppl Table 3 Track performance!H41; note: Source reference quantity for relative-performance calculation, not a measured baseline run.
Related records
- benchmark: AlphaGenome fold-0 contact-map model, bilinearly resized to Orca 4 kb bins: Cell-type difference in chromatin contact-map prediction
- benchmark: Orca (paper Table 3): Cell-type difference in chromatin contact-map prediction
- benchmark: Cell-type difference in chromatin contact-map prediction: evaluated data subset