alphagenome: Journal full-text XML

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Records in this release that cite this source. A record can cite several sources.

• 1 model
• 39 configurations
• 8 pipelines
• 51 protocols
• 51 dataset subsets
• 120 evaluations
• 130 results
• 35 evidence claims

Results

Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.

Claims

Statements this source supports, each with where in the source it was checked.

• 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

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.