Published comparison transcribed from the pinned source; not reproduced.
1 evaluation · 6 results. Different protocols are not a single leaderboard.
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)
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 | 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 |
|---|---|---|---|---|---|---|
| SpliceAI (Alavi 2026)Evaluation | 95.3% | 3 (3.8%) | 93.9% | 3 (6.1%) | 46 (93.9%) | 76 (96.2%) |
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: SpliceAI (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) | 95.3% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSpliceAI 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 'SPLICEAI', column 'Accuracy' (PDF page 6 of 11) |
| Configuration: SpliceAI (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) | 93.9% Precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSpliceAI 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 'SPLICEAI', column 'PPV' (PDF page 6 of 11) |
| Configuration: SpliceAI (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 sourceSpliceAI 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 'SPLICEAI', column 'Sensitivity' (PDF page 6 of 11) |
| Configuration: SpliceAI (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) | 76 (96.2%) Specificity percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSpliceAI 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 'SPLICEAI', column 'Specificity' (PDF page 6 of 11) |
| Configuration: SpliceAI (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 (3.8%) 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 sourceSpliceAI 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 'SPLICEAI', column 'Type I error' (PDF page 6 of 11) |
| Configuration: SpliceAI (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 sourceSpliceAI 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 'SPLICEAI', column 'Type II error' (PDF page 6 of 11) |
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18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Comparison: adaptation zero-shot scores with thresholds grid-searched on the OPA1 evaluation sets Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Table III row 'SPLICEAI' Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. |
| Comparison: aggregation Whole set Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Table III row 'SPLICEAI' Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. |
| Comparison: budget Not reported Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Table III row 'SPLICEAI' Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. |
| Comparison: dataset version As assembled by Alavi 2026 Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Table III row 'SPLICEAI' Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. |
| Comparison: inputs Single-nucleotide variant with genomic sequence context (GRCh38) Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Table III row 'SPLICEAI' Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. |
| Comparison: metric implementation Equations 1 to 5 (type I error, type II error, accuracy, specificity, sensitivity); PPV Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Table III row 'SPLICEAI' Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. |
| Comparison: population 49 OPA1 single-nucleotide substitutions annotated 'consequence: splicing defect' and 79 benign or likely benign substitutions from LOVD (retrieved 2026-04-15), GRCh38, NM_015560.2 Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Table III row 'SPLICEAI' Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. |
| Comparison: protocol id rna-splicing-20261011-alavi2026-protocol-opa1-evaluation Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Table III row 'SPLICEAI' Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. |
| Comparison: split No split Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Table III row 'SPLICEAI' Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. |
| Origin independent_paper Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Table III row 'SPLICEAI' Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: rna-splicing-20261011-alavi2026-eval-opa1-evaluation-spliceai