SpliceAI2 tissue-specific training-strategy and variant-effect checks
Ablation results of Tissue-specific junction usage differences across GTEx tissue pairs, held-out chromosomes (SpliceAI2 paper, Pearson)
Extended Data Fig. 4a prints Pearson r 0.37 (one-hot, from scratch), 0.38 (147 RBP, from scratch), 0.43 (one-hot, fine-tune) and 0.44 (147 RBP, fine-tune). Extended Data Fig. 4c prints Pearson r 0.5393 for ridge regression on measured reference usage alone and 0.5395 with SpliceAI2 tissue predictions added; the authors state there was no additional benefit from tissue-specific predictions for tissue-specific variant effects.
Extended Data Fig. 4a prints Pearson r 0.37 (one-hot, from scratch), 0.38 (147 RBP, from scratch), 0.43 (one-hot, fine-tune) and 0.44 (147 RBP, fine-tune). Extended Data Fig. 4c prints Pearson r 0.5393 for ridge regression on measured reference usage alone and 0.5395 with SpliceAI2 tissue predictions added; the authors state there was no additional benefit from tissue-specific predictions for tissue-specific variant effects.
Evidence
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Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
6 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Claimed field ablation_results Context-only references | A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Extended Data Fig. 4a and 4c (page 55); Main 'Modeling tissue-specific splicing' paragraph 5 Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. |
| Source location Extended Data Fig. 4a and 4c (page 55); Main 'Modeling tissue-specific splicing' paragraph 5 Context-only references | A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Extended Data Fig. 4a and 4c (page 55); Main 'Modeling tissue-specific splicing' paragraph 5 Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. |
| Claimed value Extended Data Fig. 4a prints Pearson r 0.37 (one-hot, from scratch), 0.38 (147 RBP, from scratch), 0.43 (one-hot, fine-tune) and 0.44 (147 RBP, fine-tune). Extended Data Fig. 4c prints Pearson r 0.5393 for ridge regression on measured reference usage alone and 0.5395 with SpliceAI2 tissue predictions added; the authors state there was no additional benefit from tissue-specific predictions for tissue-specific variant effects. Context-only references | A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Extended Data Fig. 4a and 4c (page 55); Main 'Modeling tissue-specific splicing' paragraph 5 Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. |
| Description Extended Data Fig. 4a prints Pearson r 0.37 (one-hot, from scratch), 0.38 (147 RBP, from scratch), 0.43 (one-hot, fine-tune) and 0.44 (147 RBP, fine-tune). Extended Data Fig. 4c prints Pearson r 0.5393 for ridge regression on measured reference usage alone and 0.5395 with SpliceAI2 tissue predictions added; the authors state there was no additional benefit from tissue-specific predictions for tissue-specific variant effects. Context-only references | A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Extended Data Fig. 4a and 4c (page 55); Main 'Modeling tissue-specific splicing' paragraph 5 Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. |
| Relationship: subject rna-splicing-20261013-spliceai2-protocol-gtex-tissue-specific Context-only references | A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Extended Data Fig. 4a and 4c (page 55); Main 'Modeling tissue-specific splicing' paragraph 5 Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. |
| Name SpliceAI2 tissue-specific training-strategy and variant-effect checks Context-only references | A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Extended Data Fig. 4a and 4c (page 55); Main 'Modeling tissue-specific splicing' paragraph 5 Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) · Original source · bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages)
Technical metadata and extraction receipts
Stable ID: rna-splicing-20261013-spliceai2-claim-tissue-ablations
- field
- ablation_results
- value
- Extended Data Fig. 4a prints Pearson r 0.37 (one-hot, from scratch), 0.38 (147 RBP, from scratch), 0.43 (one-hot, fine-tune) and 0.44 (147 RBP, fine-tune). Extended Data Fig. 4c prints Pearson r 0.5393 for ridge regression on measured reference usage alone and 0.5395 with SpliceAI2 tissue predictions added; the authors state there was no additional benefit from tissue-specific predictions for tissue-specific variant effects.
- source locator
- Extended Data Fig. 4a and 4c (page 55); Main 'Modeling tissue-specific splicing' paragraph 5
- review
- method: pdf-text-parse; independent-cell-check; reviewer: claude; reviewer note: Claude (Opus 5.5) research agent, independent reviewer; did not extract this batch; no human review claimed; date: 2026-10-13; artifact sha256: f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b; retrieval url: https://www.biorxiv.org/content/10.64898/2026.10.08.757673v1.full.pdf; method note: Sentence located in the reviewer's own pdftotext output of the pinned PDF; printed value and its context re-read.; note: Checked against the pinned source by the independent reviewer; verdict and correction list in docs/reviews/use-cases/spliceai2-2026-10-13.md and this batch's review.json. Developer-reported value, not reproduced. Extraction method: Bar labels present in the pinned text layer of page 55 (asserted); bar order read from the render.