AlphaGenome Nature 2026 supplementary methods
Supplement to Nature version of record, 28 January 2026; content hash pinned
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- AlphaGenome absolute multimodal scores → RandomForestClassifier: uses model: Uses model AlphaGenome ('Suppl Table 4 Variant performan'!A14:P14; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality)
- AlphaGenome Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head: family: Family AlphaGenome ('Suppl Table 3 Track performance'!A12:N12; Supplementary Methods p.24, Benchmarking Against Borzoi Track Predictions)
- AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head: family: Family AlphaGenome ('Suppl Table 3 Track performance'!A10:N10; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions)
- AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head: family: Family AlphaGenome ('Suppl Table 3 Track performance'!A21:N21; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions)
- AlphaGenome distilled all-fold student: family: Family AlphaGenome ('Suppl Table 4 Variant performan'!A35:P35; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs)
- AlphaGenome distilled all-fold student: family: Family AlphaGenome ('Suppl Table 4 Variant performan'!A27:P27; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs)
- AlphaGenome distilled all-fold student: family: Family AlphaGenome ('Suppl Table 4 Variant performan'!A33:P33; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs)
- AlphaGenome distilled all-fold student: family: Family AlphaGenome ('Suppl Table 4 Variant performan'!A2:P2; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.30–31, ClinVar Variants)
- AlphaGenome distilled all-fold student: family: Family AlphaGenome ('Suppl Table 4 Variant performan'!A31:P31; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs)
- AlphaGenome distilled all-fold student: family: Family AlphaGenome ('Suppl Table 4 Variant performan'!A37:P37; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs)
- AlphaGenome distilled all-fold student: family: Family AlphaGenome ('Suppl Table 4 Variant performan'!A13:P13; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.33, zero-shot and supervised eQTL causality)
- AlphaGenome distilled all-fold student: family: Family AlphaGenome ('Suppl Table 4 Variant performan'!A19:P19; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs)
- AlphaGenome distilled all-fold student: family: Family AlphaGenome ('Suppl Table 4 Variant performan'!A21:P21; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs)
- AlphaGenome distilled all-fold student: family: Family AlphaGenome ('Suppl Table 4 Variant performan'!A29:P29; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs)
- AlphaGenome distilled all-fold student: family: Family AlphaGenome ('Suppl Table 4 Variant performan'!A17:P17; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.39, Enhancer-gene linking)
- AlphaGenome distilled all-fold student: family: Family AlphaGenome ('Suppl Table 4 Variant performan'!A8:P8; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.31–32, MFASS)
- AlphaGenome distilled all-fold student: family: Family AlphaGenome ('Suppl Table 4 Variant performan'!A25:P25; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs)
- AlphaGenome distilled all-fold student: family: Family AlphaGenome ('Suppl Table 4 Variant performan'!A23:P23; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.36–37, Chromatin accessibility variants & bQTLs)
- AlphaGenome distilled all-fold student: family: Family AlphaGenome ('Suppl Table 4 Variant performan'!A9:P9; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.36, Polyadenylation variants)
- AlphaGenome distilled cell-type-matched DNase scorer, Borzoi-matched locus subset: family: Family AlphaGenome ('Suppl Table 4 Variant performan'!A11:P11; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption)
- AlphaGenome distilled cell-type-matched DNase scorer, ChromBPNet-matched locus subset: family: Family AlphaGenome ('Suppl Table 4 Variant performan'!A10:P10; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption)
- AlphaGenome distilled multimodal DNase, RNA-seq and histone ChIP-seq features → per-locus LassoCV: uses model: Uses model AlphaGenome ('Suppl Table 4 Variant performan'!A12:P12; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.40, Benchmarking on CAGI5 MPRA; Table10 cell-type matching; ExtendedDataFig8 caption)
- AlphaGenome Enformer-split model with 128 bp Enformer head: family: Family AlphaGenome ('Suppl Table 3 Track performance'!A19:N19; Supplementary Methods p.24, Benchmarking Against Enformer Track Predictions)
- AlphaGenome ensemble of four fold-1 models: family: Family AlphaGenome ('Suppl Table 3 Track performance'!A2:N2; Supplementary Methods p.22, Splice Site Classification)
- AlphaGenome fold-0 contact-map model, bilinearly resized to Orca 4 kb bins: family: Family AlphaGenome ('Suppl Table 3 Track performance'!A40:N40; Supplementary Methods pp.23–24, Contact Maps Performance)
Models, benchmarks and other records
Configurations (39)
- AlphaGenome Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head
- AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head
- AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head
- AlphaGenome distilled all-fold student
- AlphaGenome distilled all-fold student
- AlphaGenome distilled all-fold student
- AlphaGenome distilled all-fold student
- AlphaGenome distilled all-fold student
- AlphaGenome distilled all-fold student
- AlphaGenome distilled all-fold student
- AlphaGenome distilled all-fold student
- AlphaGenome distilled all-fold student
- AlphaGenome distilled all-fold student
- AlphaGenome distilled all-fold student
- AlphaGenome distilled all-fold student
- AlphaGenome distilled all-fold student
- AlphaGenome distilled all-fold student
- AlphaGenome distilled all-fold student
- AlphaGenome distilled cell-type-matched DNase scorer, Borzoi-matched locus subset
- AlphaGenome distilled cell-type-matched DNase scorer, ChromBPNet-matched locus subset
- AlphaGenome Enformer-split model with 128 bp Enformer head
- AlphaGenome ensemble of four fold-1 models
- AlphaGenome fold-0 contact-map model, bilinearly resized to Orca 4 kb bins
- AlphaGenome fold-0 track model on comparator-matched test peaks
- AlphaGenome fold-1 ensemble, splice-junction head
Pipelines (8)
- AbSplice: retrained AbSplice (paper Table 4)
- AlphaGenome absolute multimodal scores → RandomForestClassifier
- AlphaGenome distilled multimodal DNase, RNA-seq and histone ChIP-seq features → per-locus LassoCV
- AlphaGenome variant scores plus expressed-splice-site feature → Explainable Boosting Classifier
- borzoi-ensemble: multimodal features + LASSO (paper Table 4)
- borzoi-ensemble: variant scores + random forest (paper Table 4)
- ENCODE e2g extended: ENCODE-rE2G extended logistic regression (paper Table 4)
- ENCODE-rE2G extended logistic regression plus AlphaGenome K562 RNA-seq input × gradient feature
Protocols (51)
- African-ancestry LCL caQTL classification (AlphaGenome paper)
- African-ancestry LCL caQTL effect-size prediction (AlphaGenome paper)
- Alternative polyadenylation coverage ratios (AlphaGenome paper)
- ATAC prediction on held-out peaks (AlphaGenome paper)
- ATAC track prediction at 32 bp (AlphaGenome paper)
- ATAC track prediction at 128 bp (AlphaGenome paper)
- Author MFASS splice-disruption prediction (AlphaGenome paper)
- Base-resolution RNA-seq prediction (AlphaGenome paper)
- CAGE track prediction at 32 bp (AlphaGenome paper)
- CAGE track prediction at 128 bp (AlphaGenome paper)
- Cell-type difference in chromatin contact-map prediction (AlphaGenome paper)
- chromatin contact-map prediction (AlphaGenome paper)
- Coronary smooth-muscle caQTL effect-size prediction (AlphaGenome paper)
- Deep intronic and synonymous variants splicing-based classification (AlphaGenome paper)
- DNase prediction on held-out peaks (AlphaGenome paper)
- DNase track prediction at 32 bp (AlphaGenome paper)
- DNase track prediction at 128 bp (AlphaGenome paper)
- eQTL effect direction (AlphaGenome paper)
- eQTL effect-size ranking (AlphaGenome paper)
- European-ancestry LCL caQTL classification (AlphaGenome paper)
- European-ancestry LCL caQTL effect-size prediction (AlphaGenome paper)
- histone ChIP-seq track prediction at 32 bp (AlphaGenome paper)
- histone ChIP-seq track prediction at 128 bp (AlphaGenome paper)
- Human splice-junction classification and count prediction (AlphaGenome paper)
- Human splice-site classification: annotation-derived (AlphaGenome paper)
Dataset subsets (51)
- African-ancestry LCL caQTL classification: evaluated data subset
- African-ancestry LCL caQTL effect-size prediction: evaluated data subset
- Alternative polyadenylation coverage ratios: evaluated data subset
- ATAC prediction on held-out peaks: evaluated data subset
- ATAC track prediction at 32 bp: evaluated data subset
- ATAC track prediction at 128 bp: evaluated data subset
- Author MFASS splice-disruption prediction: evaluated data subset
- Base-resolution RNA-seq prediction: evaluated data subset
- CAGE track prediction at 32 bp: evaluated data subset
- CAGE track prediction at 128 bp: evaluated data subset
- Cell-type difference in chromatin contact-map prediction: evaluated data subset
- chromatin contact-map prediction: evaluated data subset
- Coronary smooth-muscle caQTL effect-size prediction: evaluated data subset
- Deep intronic and synonymous variants splicing-based classification: evaluated data subset
- DNase prediction on held-out peaks: evaluated data subset
- DNase track prediction at 32 bp: evaluated data subset
- DNase track prediction at 128 bp: evaluated data subset
- eQTL effect direction: evaluated data subset
- eQTL effect-size ranking: evaluated data subset
- European-ancestry LCL caQTL classification: evaluated data subset
- European-ancestry LCL caQTL effect-size prediction: evaluated data subset
- histone ChIP-seq track prediction at 32 bp: evaluated data subset
- histone ChIP-seq track prediction at 128 bp: evaluated data subset
- Human splice-junction classification and count prediction: evaluated data subset
- Human splice-site classification: annotation-derived: evaluated data subset
Evaluations (120)
- AbSplice: retrained AbSplice (paper Table 4): Supervised GTEx splicing-outlier prediction
- AlphaGenome absolute multimodal scores → RandomForestClassifier: Supervised distance-balanced eQTL causality
- AlphaGenome Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head: ATAC track prediction at 32 bp
- AlphaGenome Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head: CAGE track prediction at 32 bp
- AlphaGenome Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head: DNase track prediction at 32 bp
- AlphaGenome Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head: histone ChIP-seq track prediction at 32 bp
- AlphaGenome Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head: RNA-seq track prediction at 32 bp
- AlphaGenome Borzoi-fold-1 model fine-tuned with 32 bp Borzoi-matching head: TF ChIP-seq track prediction at 32 bp
- AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head: Alternative polyadenylation coverage ratios
- AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head: Base-resolution RNA-seq prediction
- AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head: RNA expression correlation across genes
- AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head: RNA expression correlation across tracks
- AlphaGenome distilled all-fold student: African-ancestry LCL caQTL classification
- AlphaGenome distilled all-fold student: African-ancestry LCL caQTL effect-size prediction
- AlphaGenome distilled all-fold student: Author MFASS splice-disruption prediction
- AlphaGenome distilled all-fold student: Coronary smooth-muscle caQTL effect-size prediction
- AlphaGenome distilled all-fold student: Deep intronic and synonymous variants splicing-based classification
- AlphaGenome distilled all-fold student: eQTL effect direction
- AlphaGenome distilled all-fold student: eQTL effect-size ranking
- AlphaGenome distilled all-fold student: European-ancestry LCL caQTL classification
- AlphaGenome distilled all-fold student: European-ancestry LCL caQTL effect-size prediction
- AlphaGenome distilled all-fold student: Microglia caQTL effect-size prediction
- AlphaGenome distilled all-fold student: Missense variants splicing-based classification
- AlphaGenome distilled all-fold student: Polyadenylation-QTL causality
- AlphaGenome distilled all-fold student: SPI1 binding QTL classification
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| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Artifact format original_pdf Source metadata | AlphaGenome Nature 2026 supplementary methods No field-specific location recorded Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Artifact SHA-256 86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0 Source metadata | AlphaGenome Nature 2026 supplementary methods No field-specific location recorded Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Artifact url https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM1_ESM.pdf Source metadata | AlphaGenome Nature 2026 supplementary methods No field-specific location recorded Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Hash scope SHA-256 of exact publisher PDF bytes Source metadata | AlphaGenome Nature 2026 supplementary methods No field-specific location recorded Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Retrieved at 2026-09-17T06:37:01.778972+00:00 Source metadata | AlphaGenome Nature 2026 supplementary methods No field-specific location recorded Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
Review method1 values
| AlphaGenome Nature 2026 supplementary methods No field-specific location recorded Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Url https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM1_ESM.pdf Source metadata | AlphaGenome Nature 2026 supplementary methods No field-specific location recorded Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Version Supplement to Nature version of record, 28 January 2026; content hash pinned Source metadata | AlphaGenome Nature 2026 supplementary methods No field-specific location recorded Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Description Publisher supplementary methods, figures and notes. Original bytes independently fetched for evaluation-table extraction. Source metadata | AlphaGenome Nature 2026 supplementary methods No field-specific location recorded Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Search facets None recorded Source metadata | AlphaGenome Nature 2026 supplementary methods No field-specific location recorded Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
Publisher supplementary methods, figures and notes. Original bytes independently fetched for evaluation-table extraction.
Technical metadata and extraction receipts
Stable ID: source-alphagenome-nature2026-supplementary-methods
- url
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM1_ESM.pdf
- artifact url
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM1_ESM.pdf
- version
- Supplement to Nature version of record, 28 January 2026; content hash pinned
- retrieved at
- 2026-09-17T06:37:01.778972+00:00
- artifact sha256
- 86b2e6a07543e3c201e2e157a3e9c6eb5235ff13eb8a5224f6fcb6fe1808d4c0
- artifact format
- original_pdf
- hash scope
- SHA-256 of exact publisher PDF bytes
- review
- method: automated-source-review