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 |
|---|---|---|---|---|---|---|
| AlphaGenome Composite (Alavi 2026 v2)Evaluation | 95.3% | 1 (1.3%) | 97.8% | 5 (10.2%) | 44 (89.8%) | 78 (98.7%) |
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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, version 2) Table III row 'ALPHAGENOME COMPOSITE' Version: bioRxiv preprint version 2, posted 2026-10-31; full-text PDF (12 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, downloaded in a browser on 2026-11-01 (bioRxiv refused the scripted request). bioRxiv stamps the PDF when serving it (ModDate D:20261101144527 in this copy), so later retrievals differ. |
| Comparison: aggregation Whole set Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) Table III row 'ALPHAGENOME COMPOSITE' Version: bioRxiv preprint version 2, posted 2026-10-31; full-text PDF (12 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, downloaded in a browser on 2026-11-01 (bioRxiv refused the scripted request). bioRxiv stamps the PDF when serving it (ModDate D:20261101144527 in this copy), so later retrievals differ. |
| Comparison: budget Not reported Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) Table III row 'ALPHAGENOME COMPOSITE' Version: bioRxiv preprint version 2, posted 2026-10-31; full-text PDF (12 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, downloaded in a browser on 2026-11-01 (bioRxiv refused the scripted request). bioRxiv stamps the PDF when serving it (ModDate D:20261101144527 in this copy), so later retrievals differ. |
| Comparison: dataset version As assembled by Alavi 2026 Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) Table III row 'ALPHAGENOME COMPOSITE' Version: bioRxiv preprint version 2, posted 2026-10-31; full-text PDF (12 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, downloaded in a browser on 2026-11-01 (bioRxiv refused the scripted request). bioRxiv stamps the PDF when serving it (ModDate D:20261101144527 in this copy), so later retrievals differ. |
| Comparison: inputs Single-nucleotide variant with genomic sequence context (GRCh38) Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) Table III row 'ALPHAGENOME COMPOSITE' Version: bioRxiv preprint version 2, posted 2026-10-31; full-text PDF (12 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, downloaded in a browser on 2026-11-01 (bioRxiv refused the scripted request). bioRxiv stamps the PDF when serving it (ModDate D:20261101144527 in this copy), so later retrievals differ. |
| 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, version 2) Table III row 'ALPHAGENOME COMPOSITE' Version: bioRxiv preprint version 2, posted 2026-10-31; full-text PDF (12 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, downloaded in a browser on 2026-11-01 (bioRxiv refused the scripted request). bioRxiv stamps the PDF when serving it (ModDate D:20261101144527 in this copy), so later retrievals differ. |
| 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, version 2) Table III row 'ALPHAGENOME COMPOSITE' Version: bioRxiv preprint version 2, posted 2026-10-31; full-text PDF (12 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, downloaded in a browser on 2026-11-01 (bioRxiv refused the scripted request). bioRxiv stamps the PDF when serving it (ModDate D:20261101144527 in this copy), so later retrievals differ. |
| Comparison: protocol id rna-splicing-20261011-alavi2026-protocol-opa1-evaluation Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) Table III row 'ALPHAGENOME COMPOSITE' Version: bioRxiv preprint version 2, posted 2026-10-31; full-text PDF (12 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, downloaded in a browser on 2026-11-01 (bioRxiv refused the scripted request). bioRxiv stamps the PDF when serving it (ModDate D:20261101144527 in this copy), so later retrievals differ. |
| Comparison: split No split Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) Table III row 'ALPHAGENOME COMPOSITE' Version: bioRxiv preprint version 2, posted 2026-10-31; full-text PDF (12 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, downloaded in a browser on 2026-11-01 (bioRxiv refused the scripted request). bioRxiv stamps the PDF when serving it (ModDate D:20261101144527 in this copy), so later retrievals differ. |
| Origin independent_paper Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) Table III row 'ALPHAGENOME COMPOSITE' Version: bioRxiv preprint version 2, posted 2026-10-31; full-text PDF (12 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, downloaded in a browser on 2026-11-01 (bioRxiv refused the scripted request). bioRxiv stamps the PDF when serving it (ModDate D:20261101144527 in this copy), so later retrievals differ. |
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
Stable ID: rna-splicing-20261101-alavi2026-v2-eval-opa1-evaluation-alphagenome-composite