Result

Proportion (type II error: false negatives as a share of the splicing set (false-negative rate)) of AlphaGenome Splice-Junctions (Alavi 2026 v2) on OPA1 LOVD evaluation sets (49 splicing, 79 benign)

2 (4.1%) Proportion (type II error: false negatives as a share of the splicing set (false-negative rate))

Methods

Tested configuration: AlphaGenome Splice-Junctions (Alavi 2026 v2)
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)
Procedure: Splice-defect classification of OPA1 variants with thresholds tuned on the same sets (Alavi Table III, evaluation sets)
Evaluation: AlphaGenome Splice-Junctions on OPA1 LOVD evaluation sets (49 splicing, 79 benign) (Alavi 2026 v2)
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Independent external evaluation · source checkedProbing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) · Table III, row 'ALPHAGENOME SPLICE-JUNCTIONS', column 'Type II error' (PDF page 6 of 12)

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.

Reproduction

Split: No split
Adaptation: zero-shot scores with thresholds grid-searched on the OPA1 evaluation sets
Scoring implementation: Equations 1 to 5 (type I error, type II error, accuracy, specificity, sensitivity); PPV

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

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Evidence table

Inspect claims, sources and review details

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1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Reported result 2 (4.1%) Individual claims	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) Original source ↗ Table III, row 'ALPHAGENOME SPLICE-JUNCTIONS', column 'Type II error' (PDF page 6 of 12) Version: bioRxiv preprint version 2, posted 2026-10-31; full-text PDF (12 pages) Retrieved: 2026-11-01T14:45:27Z	source checked ["deterministic-table-parse","source-hash-verification","automated-source-review","ai-assisted-source-review"] · 2026-11-01 independent paper Audit details Matched by two parses of the pinned PDF: pdftotext -layout in build.py and pdftotext -raw in check_cells.py (cell-check.tsv, 56 of 56). Count, percentage, accuracy and PPV arithmetic checked for every row. Verdict in docs/reviews/2026-11-01-alavi-v2-rerun.md. Replaces version 1 result rna-splicing-20261011-alavi2026-result-opa1-evaluation-alphagenome-junction-scorer-type-ii-error, which stays disputed and is not linked because the release drops records that link to disputed ones. Field: `attributes.printed_value` Source artifact SHA-256: `07bd32fffc1b31c222d43b0b18c213928e3fe111cc71c02fe2f95e64e6f7a798` 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. Inspected artifact Extraction artifact SHA-256: `07bd32fffc1b31c222d43b0b18c213928e3fe111cc71c02fe2f95e64e6f7a798` Extraction artifact

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Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

1 source record and release history

Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026, version 2) · Original source · bioRxiv preprint version 2, posted 2026-10-31; full-text PDF (12 pages)

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Technical metadata and extraction receipts

Stable ID: rna-splicing-20261101-alavi2026-v2-result-opa1-evaluation-alphagenome-splice-junctions-type-ii-error

metric: proportion
metric direction: lower
unit: percent
printed value: 2 (4.1%)
source locator: Table III, row 'ALPHAGENOME SPLICE-JUNCTIONS', column 'Type II error' (PDF page 6 of 12)
review: method: deterministic-table-parse; source-hash-verification; automated-source-review; ai-assisted-source-review; method note: pdftotext -layout (poppler 26.08.0) on the pinned PDF; value rows found by token pattern, 13 rows per table and row-label fragments asserted; printed cell text kept exactly; bracketed percentages checked against counts, and accuracy and PPV checked against the row's counts; the 126 non-AlphaGenome cells asserted equal to the stored version 1 results.; reviewer: claude; reviewer note: Claude agent for issue #213; no human review claimed. Extractor and reviewer were the same agent in the same session.; date: 2026-11-01; artifact sha256: 07bd32fffc1b31c222d43b0b18c213928e3fe111cc71c02fe2f95e64e6f7a798; retrieval url: https://www.biorxiv.org/content/10.64898/2026.10.02.756289v2.full.pdf; note: Matched by two parses of the pinned PDF: pdftotext -layout in build.py and pdftotext -raw in check_cells.py (cell-check.tsv, 56 of 56). Count, percentage, accuracy and PPV arithmetic checked for every row. Verdict in docs/reviews/2026-11-01-alavi-v2-rerun.md. Replaces version 1 result rna-splicing-20261011-alavi2026-result-opa1-evaluation-alphagenome-junction-scorer-type-ii-error, which stays disputed and is not linked because the release drops records that link to disputed ones.
numeric value: 4.1
missing metadata: uncertainty: reason: unreported
metric qualifier: type II error: false negatives as a share of the splicing set (false-negative rate)
unit detail: Cell prints the count of false negatives with the percentage of the splicing set in brackets; numeric_value is the percentage

Related records

evaluation: AlphaGenome Splice-Junctions on OPA1 LOVD evaluation sets (49 splicing, 79 benign) (Alavi 2026 v2)

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