Published comparison transcribed from the pinned source; not reproduced.
1 evaluation · 6 results. Different protocols are not a single leaderboard.
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)
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 Splice-Site Usage (Alavi 2026 v2)Evaluation | 68.3% | 0 (0.0 %) | 100% | 58 (76.3%) | 18 (23.7%) | 107 (100%) |
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AlphaGenome Splice-Site Usage (Alavi 2026 v2) | 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) | 68.3% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcerna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) · Table IV, row 'ALPHAGENOME SPLICE-SITE USAGE', column 'Accuracy' (PDF page 9 of 12) |
| Configuration: AlphaGenome Splice-Site Usage (Alavi 2026 v2) | 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 sourcerna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) · Table IV, row 'ALPHAGENOME SPLICE-SITE USAGE', column 'PPV' (PDF page 9 of 12) |
| Configuration: AlphaGenome Splice-Site Usage (Alavi 2026 v2) | 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) | 18 (23.7%) Recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcerna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) · Table IV, row 'ALPHAGENOME SPLICE-SITE USAGE', column 'Sensitivity' (PDF page 9 of 12) |
| Configuration: AlphaGenome Splice-Site Usage (Alavi 2026 v2) | 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 sourcerna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) · Table IV, row 'ALPHAGENOME SPLICE-SITE USAGE', column 'Specificity' (PDF page 9 of 12) |
| Configuration: AlphaGenome Splice-Site Usage (Alavi 2026 v2) | 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 sourcerna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) · Table IV, row 'ALPHAGENOME SPLICE-SITE USAGE', column 'Type I error' (PDF page 9 of 12) |
| Configuration: AlphaGenome Splice-Site Usage (Alavi 2026 v2) | 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) | 58 (76.3%) 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 sourcerna-splicing-20261011-alavi2026-protocol-multigene Aggregation: Not reported Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) · Table IV, row 'ALPHAGENOME SPLICE-SITE USAGE', column 'Type II error' (PDF page 9 of 12) |
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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 IV row 'ALPHAGENOME SPLICE-SITE USAGE' 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 IV row 'ALPHAGENOME SPLICE-SITE USAGE' 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 IV row 'ALPHAGENOME SPLICE-SITE USAGE' 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 IV row 'ALPHAGENOME SPLICE-SITE USAGE' 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 IV row 'ALPHAGENOME SPLICE-SITE USAGE' 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 IV row 'ALPHAGENOME SPLICE-SITE USAGE' 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 76 functionally validated spliceogenic substitutions across 64 gene symbols: 26 at canonical ±1,2 positions, 35 at near-splice intronic positions (+3 to +7, -3 to -7 and -13) and 15 exonic substitutions, from Bournazos et al. 2022 (RNA diagnostics in clinically accessible specimens) and Dawes et al. 2023 (SpliceVault), with 107 high-confidence ClinVar benign intronic substitutions at ±3 to ±10 from 46 of those genes Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) Table IV row 'ALPHAGENOME SPLICE-SITE USAGE' 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-multigene Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) Table IV row 'ALPHAGENOME SPLICE-SITE USAGE' 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 IV row 'ALPHAGENOME SPLICE-SITE USAGE' 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 IV row 'ALPHAGENOME SPLICE-SITE USAGE' 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-multigene-alphagenome-splice-site-usage