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Evaluation

SpliceAI2 SF3B1 fine-tune on uveal melanoma junction usage differences

Developer-reported comparison transcribed from the pinned source; not reproduced.

Evaluation results

1 evaluation · 1 result. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: SpliceAI2 fine-tuned on SF3B1-mutant and wild-type uveal melanoma (Jaganathan et al. 2026)Protocol: SF3B1-associated junction usage differences in uveal melanoma, held-out genes (SpliceAI2 paper, Pearson)
Dataset: TCGA uveal melanoma RNA-seq, SF3B1-mutant and wild-type (as used by Jaganathan et al. 2026)
0.49 Pearson (junctions with competing acceptor 10 to 30 nt, weak polypyrimidine tract and A-rich branch point; held-out genes)
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

SpliceAI2 SF3B1 fine-tune on uveal melanoma junction usage differences

rna-splicing-20261013-spliceai2-protocol-uvm-sf3b1

Aggregation: Not reported

A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) · Main 'Modeling tissue-specific splicing' paragraph 4 '(Pearson r = 0.49; Fig. 2d)'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

Research readiness

0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

Evidence incomplete

Replay metrics

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Missing or unresolved evidence

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  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified
  • Sample annotations are recorded: not yet verified
  • Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • A pinned run recipe exists: not yet verified
  • Compute requirements are estimated: not yet verified

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Independent validation data exist: not yet verified
  • Overlap with training data is checked: not yet verified

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Evaluation procedure

SF3B1-associated junction usage differences in uveal melanoma, held-out genes (SpliceAI2 paper, Pearson)

Configuration
SpliceAI2 fine-tuned on SF3B1-mutant and wild-type uveal melanoma (Jaganathan et al. 2026)
Protocol
SF3B1-associated junction usage differences in uveal melanoma, held-out genes (SpliceAI2 paper, Pearson)
Dataset
TCGA uveal melanoma RNA-seq, SF3B1-mutant and wild-type (as used by Jaganathan et al. 2026)
origin
Author-reported evaluation
configuration
bioRxiv v1, retrieved 2026-10-13
protocol id
rna-splicing-20261013-spliceai2-protocol-uvm-sf3b1
adaptation
Fine-tuned on 18 mutant and 62 wild-type tumours
budget
Not reported
dataset version
TCGA-UVM via Genomic Data Commons
split
Held-out genes
population
Junctions with all three SF3B1-associated features (Fig. 2d, rightmost bar labelled 697)
inputs
Sequence plus SF3B1-mutant and wild-type 147-RBP signatures
metric implementation
Pearson on mutant-minus-wild-type usage differences
aggregation
Pooled over junctions

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split
Held-out genes
Adaptation
Fine-tuned on 18 mutant and 62 wild-type tumours
Scoring implementation
Pearson on mutant-minus-wild-type usage differences

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

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

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.

18 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statementOriginal source and locationReview and provenance
Comparison: adaptation
Fine-tuned on 18 mutant and 62 wild-type tumours
Context-only references
A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026)

Original source ↗

Main 'Modeling tissue-specific splicing' paragraph 4; Fig. 2d

Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages)
Retrieved: 2026-10-13T12:40:34Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b

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.

Inspected artifact

Comparison: aggregation
Pooled over junctions
Context-only references
A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026)

Original source ↗

Main 'Modeling tissue-specific splicing' paragraph 4; Fig. 2d

Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages)
Retrieved: 2026-10-13T12:40:34Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b

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.

Inspected artifact

Comparison: budget
Not reported
Context-only references
A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026)

Original source ↗

Main 'Modeling tissue-specific splicing' paragraph 4; Fig. 2d

Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages)
Retrieved: 2026-10-13T12:40:34Z

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.budget

Source artifact SHA-256: f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b

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.

Inspected artifact

Comparison: dataset version
TCGA-UVM via Genomic Data Commons
Context-only references
A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026)

Original source ↗

Main 'Modeling tissue-specific splicing' paragraph 4; Fig. 2d

Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages)
Retrieved: 2026-10-13T12:40:34Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.dataset_version

Source artifact SHA-256: f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b

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.

Inspected artifact

Comparison: inputs
Sequence plus SF3B1-mutant and wild-type 147-RBP signatures
Context-only references
A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026)

Original source ↗

Main 'Modeling tissue-specific splicing' paragraph 4; Fig. 2d

Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages)
Retrieved: 2026-10-13T12:40:34Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.inputs

Source artifact SHA-256: f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b

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.

Inspected artifact

Comparison: metric implementation
Pearson on mutant-minus-wild-type usage differences
Context-only references
A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026)

Original source ↗

Main 'Modeling tissue-specific splicing' paragraph 4; Fig. 2d

Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages)
Retrieved: 2026-10-13T12:40:34Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.metric_implementation

Source artifact SHA-256: f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b

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.

Inspected artifact

Comparison: population
Junctions with all three SF3B1-associated features (Fig. 2d, rightmost bar labelled 697)
Context-only references
A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026)

Original source ↗

Main 'Modeling tissue-specific splicing' paragraph 4; Fig. 2d

Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages)
Retrieved: 2026-10-13T12:40:34Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.population

Source artifact SHA-256: f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b

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.

Inspected artifact

Comparison: protocol id
rna-splicing-20261013-spliceai2-protocol-uvm-sf3b1
Context-only references
A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026)

Original source ↗

Main 'Modeling tissue-specific splicing' paragraph 4; Fig. 2d

Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages)
Retrieved: 2026-10-13T12:40:34Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.protocol_id

Source artifact SHA-256: f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b

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.

Inspected artifact

Comparison: split
Held-out genes
Context-only references
A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026)

Original source ↗

Main 'Modeling tissue-specific splicing' paragraph 4; Fig. 2d

Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages)
Retrieved: 2026-10-13T12:40:34Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.split

Source artifact SHA-256: f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b

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.

Inspected artifact

Origin
author_reported
Context-only references
A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026)

Original source ↗

Main 'Modeling tissue-specific splicing' paragraph 4; Fig. 2d

Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages)
Retrieved: 2026-10-13T12:40:34Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.origin

Source artifact SHA-256: f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b

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.

Inspected artifact

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: rna-splicing-20261013-spliceai2-eval-uvm-sf3b1-spliceai2-sf3b1-uvm

areas
dna-genomes
contexts
research
origin
author_reported
protocol
rna-splicing-20261013-spliceai2-protocol-uvm-sf3b1
version
bioRxiv v1, retrieved 2026-10-13
comparison
protocol id: rna-splicing-20261013-spliceai2-protocol-uvm-sf3b1; adaptation: Fine-tuned on 18 mutant and 62 wild-type tumours; budget: Not reported; dataset version: TCGA-UVM via Genomic Data Commons; split: Held-out genes; population: Junctions with all three SF3B1-associated features (Fig. 2d, rightmost bar labelled 697); inputs: Sequence plus SF3B1-mutant and wild-type 147-RBP signatures; metric implementation: Pearson on mutant-minus-wild-type usage differences; aggregation: Pooled over junctions
source locator
Main 'Modeling tissue-specific splicing' paragraph 4; Fig. 2d
missing metadata
comparison.budget: reason: inapplicable; note: Pretrained scoring; no search or training budget
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