| 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 checkedMethods, coverage and sourceAlphaGenome (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) |
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| 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 checkedMethods, coverage and sourceAlphaGenome (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) |
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| 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 checkedMethods, coverage and sourceAlphaGenome (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) |
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| 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 checkedMethods, coverage and sourceAlphaGenome (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) |
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| 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 checkedMethods, coverage and sourceAlphaGenome (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) |
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| 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 checkedMethods, coverage and sourceAlphaGenome (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) |
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| Configuration: AlphaGenome Junction Scorer (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) | 68.9% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaGenome Junction Scorer 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 JUNCTION SCORER', column 'Accuracy' (PDF page 9 of 11) |
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| Configuration: AlphaGenome Junction Scorer (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) | 68.6% Precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaGenome Junction Scorer 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 JUNCTION SCORER', column 'PPV' (PDF page 9 of 11) |
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| Configuration: AlphaGenome Junction Scorer (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) | 35 (46.1%) Recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaGenome Junction Scorer 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 JUNCTION SCORER', column 'Sensitivity' (PDF page 9 of 11) |
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| Configuration: AlphaGenome Junction Scorer (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) | 91 (85.0%) Specificity percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaGenome Junction Scorer 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 JUNCTION SCORER', column 'Specificity' (PDF page 9 of 11) |
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| Configuration: AlphaGenome Junction Scorer (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) | 16 (15.0%) 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 checkedMethods, coverage and sourceAlphaGenome Junction Scorer 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 JUNCTION SCORER', column 'Type I error' (PDF page 9 of 11) |
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| Configuration: AlphaGenome Junction Scorer (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) | 41 (53.9%) 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 checkedMethods, coverage and sourceAlphaGenome Junction Scorer 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 JUNCTION SCORER', column 'Type II error' (PDF page 9 of 11) |
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| Configuration: AlphaGenome Splice Scorer (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% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaGenome Splice Scorer 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 SPLICE SCORER', column 'Accuracy' (PDF page 9 of 11) |
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| Configuration: AlphaGenome Splice Scorer (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) | 67.4% Precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaGenome Splice Scorer 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 SPLICE SCORER', column 'PPV' (PDF page 9 of 11) |
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| Configuration: AlphaGenome Splice Scorer (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) | 31 (40.8%) Recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaGenome Splice Scorer 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 SPLICE SCORER', column 'Sensitivity' (PDF page 9 of 11) |
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| Configuration: AlphaGenome Splice Scorer (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) | 92 (86.0%) Specificity percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaGenome Splice Scorer 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 SPLICE SCORER', column 'Specificity' (PDF page 9 of 11) |
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| Configuration: AlphaGenome Splice Scorer (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) | 15 (13.9%) 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 checkedMethods, coverage and sourceAlphaGenome Splice Scorer 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 SPLICE SCORER', column 'Type I error' (PDF page 9 of 11) |
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| Configuration: AlphaGenome Splice Scorer (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) | 45 (59.2%) 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 checkedMethods, coverage and sourceAlphaGenome Splice Scorer 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 SPLICE SCORER', column 'Type II error' (PDF page 9 of 11) |
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| Configuration: Borzoi (128-bp) (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) | 80.9% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBorzoi (128-bp) 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 'BORZOI (128-BP)', column 'Accuracy' (PDF page 9 of 11) |
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| Configuration: Borzoi (128-bp) (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) | 87.5% Precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBorzoi (128-bp) 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 'BORZOI (128-BP)', column 'PPV' (PDF page 9 of 11) |
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| Configuration: Borzoi (128-bp) (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) | 49 (64.5%) Recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBorzoi (128-bp) 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 'BORZOI (128-BP)', column 'Sensitivity' (PDF page 9 of 11) |
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| Configuration: Borzoi (128-bp) (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) | 100 (93.5%) Specificity percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBorzoi (128-bp) 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 'BORZOI (128-BP)', column 'Specificity' (PDF page 9 of 11) |
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| Configuration: Borzoi (128-bp) (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) | 7 (6.5%) 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 checkedMethods, coverage and sourceBorzoi (128-bp) 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 'BORZOI (128-BP)', column 'Type I error' (PDF page 9 of 11) |
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| Configuration: Borzoi (128-bp) (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) | 27 (35.5%) 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 checkedMethods, coverage and sourceBorzoi (128-bp) 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 'BORZOI (128-BP)', column 'Type II error' (PDF page 9 of 11) |
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| Configuration: Borzoi (32-bp) (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) | 86.9% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBorzoi (32-bp) 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 'BORZOI (32-BP)', column 'Accuracy' (PDF page 9 of 11) |
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