Configuration

AlphaGenome (Either Module) (Alavi 2026)

ALPHAGENOME (EITHER MODULE) as configured in Alavi 2026.

Overview

AlphaGenome: AlphaGenome predicts regulatory activity and variant effects from long DNA sequences, with outputs for expression, splicing, chromatin and contact maps.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

3 evaluations · 14 results. Different protocols are not a single leaderboard.

Sorted by Accuracy (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	Accuracy	False positive rate (type I error: false positives as a share of the benign set)	Precision	Proportion (type II error: false negatives as a share of the splicing set (false-negative rate))	Recall	Specificity	Proportion (share of 306 further OPA1 pathogenic substitutions called splice-altering)	Proportion (share of 69 OPA1 VUS substitutions called splice-altering)
AlphaGenome (Either Module) (Alavi 2026)Evaluation	Splice-defect classification of OPA1 variants with thresholds tuned on the same sets (Alavi Table III, evaluation sets), OPA1 LOVD evaluation sets (49 splicing, 79 benign)	88.3% (best in column)	4 (5.1%) (best in column)	90.5% (best in column)	11 (22.4%) (best in column)	38 (77.6%) (best in column)	75 (94.9%) (best in column)	Not reported	Not reported
AlphaGenome (Either Module) (Alavi 2026)Evaluation	Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV), Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	71.6%	21 (19.6%)	67.2%	33 (43.4%)	43 (56.6%)	86 (80.4%)	Not reported	Not reported
AlphaGenome (Either Module) (Alavi 2026)Evaluation	Share of further OPA1 pathogenic substitutions and VUS called splice-altering (Alavi Table III, extended corpus), OPA1 extended LOVD corpus (306 pathogenic substitutions, 69 VUS)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	66 (21.6%)	7 (10.1%)

All 14 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AlphaGenome (Either Module) (Alavi 2026)	Protocol: Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV) Dataset: Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	71.6% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome (Either Module) on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes) rna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table IV, row 'ALPHAGENOME (EITHER MODULE)', column 'Accuracy' (PDF page 9 of 11)
Configuration: AlphaGenome (Either Module) (Alavi 2026)	Protocol: Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV) Dataset: Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	67.2% Precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome (Either Module) on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes) rna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table IV, row 'ALPHAGENOME (EITHER MODULE)', column 'PPV' (PDF page 9 of 11)
Configuration: AlphaGenome (Either Module) (Alavi 2026)	Protocol: Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV) Dataset: Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	43 (56.6%) Recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome (Either Module) on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes) rna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table IV, row 'ALPHAGENOME (EITHER MODULE)', column 'Sensitivity' (PDF page 9 of 11)
Configuration: AlphaGenome (Either Module) (Alavi 2026)	Protocol: Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV) Dataset: Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	86 (80.4%) Specificity percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome (Either Module) on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes) rna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table IV, row 'ALPHAGENOME (EITHER MODULE)', column 'Specificity' (PDF page 9 of 11)
Configuration: AlphaGenome (Either Module) (Alavi 2026)	Protocol: Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV) Dataset: Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	21 (19.6%) False positive rate (type I error: false positives as a share of the benign set) percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome (Either Module) on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes) rna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table IV, row 'ALPHAGENOME (EITHER MODULE)', column 'Type I error' (PDF page 9 of 11)
Configuration: AlphaGenome (Either Module) (Alavi 2026)	Protocol: Spliceogenic versus benign classification on an independent 65-gene set with OPA1-derived thresholds (Alavi Table IV) Dataset: Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes)	33 (43.4%) Proportion (type II error: false negatives as a share of the splicing set (false-negative rate)) percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome (Either Module) on Multi-gene spliceogenic test set (76 spliceogenic, 107 benign, 65 genes) rna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table IV, row 'ALPHAGENOME (EITHER MODULE)', column 'Type II error' (PDF page 9 of 11)
Configuration: AlphaGenome (Either Module) (Alavi 2026)	Protocol: Splice-defect classification of OPA1 variants with thresholds tuned on the same sets (Alavi Table III, evaluation sets) Dataset: OPA1 LOVD evaluation sets (49 splicing, 79 benign)	88.3% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome (Either Module) on OPA1 LOVD evaluation sets (49 splicing, 79 benign) rna-splicing-20261011-alavi2026-protocol-opa1-evaluation Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table III, row 'ALPHAGENOME (EITHER MODULE)', column 'Accuracy' (PDF page 6 of 11)
Configuration: AlphaGenome (Either Module) (Alavi 2026)	Protocol: Splice-defect classification of OPA1 variants with thresholds tuned on the same sets (Alavi Table III, evaluation sets) Dataset: OPA1 LOVD evaluation sets (49 splicing, 79 benign)	90.5% Precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome (Either Module) on OPA1 LOVD evaluation sets (49 splicing, 79 benign) rna-splicing-20261011-alavi2026-protocol-opa1-evaluation Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table III, row 'ALPHAGENOME (EITHER MODULE)', column 'PPV' (PDF page 6 of 11)
Configuration: AlphaGenome (Either Module) (Alavi 2026)	Protocol: Splice-defect classification of OPA1 variants with thresholds tuned on the same sets (Alavi Table III, evaluation sets) Dataset: OPA1 LOVD evaluation sets (49 splicing, 79 benign)	38 (77.6%) Recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome (Either Module) on OPA1 LOVD evaluation sets (49 splicing, 79 benign) rna-splicing-20261011-alavi2026-protocol-opa1-evaluation Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table III, row 'ALPHAGENOME (EITHER MODULE)', column 'Sensitivity' (PDF page 6 of 11)
Configuration: AlphaGenome (Either Module) (Alavi 2026)	Protocol: Splice-defect classification of OPA1 variants with thresholds tuned on the same sets (Alavi Table III, evaluation sets) Dataset: OPA1 LOVD evaluation sets (49 splicing, 79 benign)	75 (94.9%) Specificity percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome (Either Module) on OPA1 LOVD evaluation sets (49 splicing, 79 benign) rna-splicing-20261011-alavi2026-protocol-opa1-evaluation Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table III, row 'ALPHAGENOME (EITHER MODULE)', column 'Specificity' (PDF page 6 of 11)
Configuration: AlphaGenome (Either Module) (Alavi 2026)	Protocol: Splice-defect classification of OPA1 variants with thresholds tuned on the same sets (Alavi Table III, evaluation sets) Dataset: OPA1 LOVD evaluation sets (49 splicing, 79 benign)	4 (5.1%) False positive rate (type I error: false positives as a share of the benign set) percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome (Either Module) on OPA1 LOVD evaluation sets (49 splicing, 79 benign) rna-splicing-20261011-alavi2026-protocol-opa1-evaluation Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table III, row 'ALPHAGENOME (EITHER MODULE)', column 'Type I error' (PDF page 6 of 11)
Configuration: AlphaGenome (Either Module) (Alavi 2026)	Protocol: Splice-defect classification of OPA1 variants with thresholds tuned on the same sets (Alavi Table III, evaluation sets) Dataset: OPA1 LOVD evaluation sets (49 splicing, 79 benign)	11 (22.4%) Proportion (type II error: false negatives as a share of the splicing set (false-negative rate)) percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome (Either Module) on OPA1 LOVD evaluation sets (49 splicing, 79 benign) rna-splicing-20261011-alavi2026-protocol-opa1-evaluation Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table III, row 'ALPHAGENOME (EITHER MODULE)', column 'Type II error' (PDF page 6 of 11)
Configuration: AlphaGenome (Either Module) (Alavi 2026)	Protocol: Share of further OPA1 pathogenic substitutions and VUS called splice-altering (Alavi Table III, extended corpus) Dataset: OPA1 extended LOVD corpus (306 pathogenic substitutions, 69 VUS)	66 (21.6%) Proportion (share of 306 further OPA1 pathogenic substitutions called splice-altering) percent · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome (Either Module) on OPA1 extended LOVD corpus (306 pathogenic substitutions, 69 VUS) rna-splicing-20261011-alavi2026-protocol-opa1-extended-positive-calls Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table III, row 'ALPHAGENOME (EITHER MODULE)', column 'Positive mutations' (PDF page 6 of 11)
Configuration: AlphaGenome (Either Module) (Alavi 2026)	Protocol: Share of further OPA1 pathogenic substitutions and VUS called splice-altering (Alavi Table III, extended corpus) Dataset: OPA1 extended LOVD corpus (306 pathogenic substitutions, 69 VUS)	7 (10.1%) Proportion (share of 69 OPA1 VUS substitutions called splice-altering) percent · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome (Either Module) on OPA1 extended LOVD corpus (306 pathogenic substitutions, 69 VUS) rna-splicing-20261011-alavi2026-protocol-opa1-extended-positive-calls Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Table III, row 'ALPHAGENOME (EITHER MODULE)', column 'Positive VUS' (PDF page 6 of 11)

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Original source · bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages)

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Technical metadata and extraction receipts

Stable ID: rna-splicing-20261011-alavi2026-config-alphagenome-either-module

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: ALPHAGENOME (EITHER MODULE)
foundation model eligible: false
version: Google Cloud API (research access), version not printed
parameters: Positive if either the splice-site module (>= 0.14) or the splice-junction module (>= 0.43) is positive
access reuse: Google DeepMind Research Access program API
source locator: Methods C to H; Table III and IV row label

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