| Configuration: Evo2 40B (without human identifier) (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) | 85.2% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEvo2 40B (without human identifier) 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 'EVO2 40B (W/O HU. IDENT.)', column 'Accuracy' (PDF page 9 of 11) |
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| Configuration: Evo2 40B (without human identifier) (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% Precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEvo2 40B (without human identifier) 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 'EVO2 40B (W/O HU. IDENT.)', column 'PPV' (PDF page 9 of 11) |
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| Configuration: Evo2 40B (without human identifier) (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 sourceEvo2 40B (without human identifier) 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 'EVO2 40B (W/O HU. IDENT.)', column 'Sensitivity' (PDF page 9 of 11) |
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| Configuration: Evo2 40B (without human identifier) (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) | 107 (100%) Specificity percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEvo2 40B (without human identifier) 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 'EVO2 40B (W/O HU. IDENT.)', column 'Specificity' (PDF page 9 of 11) |
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| Configuration: Evo2 40B (without human identifier) (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) | 0 (0.0 %) 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 sourceEvo2 40B (without human identifier) 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 'EVO2 40B (W/O HU. IDENT.)', column 'Type I error' (PDF page 9 of 11) |
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| Configuration: Evo2 40B (without human identifier) (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 sourceEvo2 40B (without human identifier) 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 'EVO2 40B (W/O HU. IDENT.)', column 'Type II error' (PDF page 9 of 11) |
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| Configuration: Evo2 40B (without human identifier) (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) | 93% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEvo2 40B (without human identifier) 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 'EVO2 40B (W/O HU. IDENT.)', column 'Accuracy' (PDF page 6 of 11) |
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| Configuration: Evo2 40B (without human identifier) (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) | 88.5% Precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEvo2 40B (without human identifier) 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 'EVO2 40B (W/O HU. IDENT.)', column 'PPV' (PDF page 6 of 11) |
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| Configuration: Evo2 40B (without human identifier) (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) | 46 (93.9%) Recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEvo2 40B (without human identifier) 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 'EVO2 40B (W/O HU. IDENT.)', column 'Sensitivity' (PDF page 6 of 11) |
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| Configuration: Evo2 40B (without human identifier) (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) | 73 (92.4%) Specificity percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEvo2 40B (without human identifier) 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 'EVO2 40B (W/O HU. IDENT.)', column 'Specificity' (PDF page 6 of 11) |
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| Configuration: Evo2 40B (without human identifier) (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) | 6 (7.6%) 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 sourceEvo2 40B (without human identifier) 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 'EVO2 40B (W/O HU. IDENT.)', column 'Type I error' (PDF page 6 of 11) |
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| Configuration: Evo2 40B (without human identifier) (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) | 3 (6.1%) 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 sourceEvo2 40B (without human identifier) 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 'EVO2 40B (W/O HU. IDENT.)', column 'Type II error' (PDF page 6 of 11) |
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| Configuration: Evo2 40B (without human identifier) (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) | 280 (91.5%) 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 checkedMethods, coverage and sourceEvo2 40B (without human identifier) 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 'EVO2 40B (W/O HU. IDENT.)', column 'Positive mutations' (PDF page 6 of 11) |
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| Configuration: Evo2 40B (without human identifier) (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) | 46 (66.7%) 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 checkedMethods, coverage and sourceEvo2 40B (without human identifier) 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 'EVO2 40B (W/O HU. IDENT.)', column 'Positive VUS' (PDF page 6 of 11) |
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