rewirebio.iobenchmarks
Evaluation

Pangolin on UK Biobank carrier protein levels (Pearson, SpliceAI2 paper)

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

Evaluation results

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

Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: Pangolin, per-position score at the effect position, masking off (Jaganathan et al. 2026)Protocol: Carrier plasma protein levels for rare splice-region variants, UK Biobank (SpliceAI2 paper, Pearson)
Dataset: UK Biobank rare splice-region variants with carrier plasma protein levels (Jaganathan et al. 2026)
-0.475 Pearson (with mean carrier plasma protein z-score; more negative is better)
unitless · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

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

Pangolin on UK Biobank carrier protein levels (Pearson, SpliceAI2 paper)

rna-splicing-20261013-spliceai2-protocol-ukb-proteomics

Aggregation: Not reported

A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) · Fig. 3f (page 15), bar label for 'Pangolin'

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

Exact outcomes, predictions, identifiers and evaluator are connected.

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

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

Carrier plasma protein levels for rare splice-region variants, UK Biobank (SpliceAI2 paper, Pearson)

Configuration
Pangolin, per-position score at the effect position, masking off (Jaganathan et al. 2026)
Protocol
Carrier plasma protein levels for rare splice-region variants, UK Biobank (SpliceAI2 paper, Pearson)
Dataset
UK Biobank rare splice-region variants with carrier plasma protein levels (Jaganathan et al. 2026)
origin
Author-reported evaluation
configuration
bioRxiv v1, retrieved 2026-10-13
protocol id
rna-splicing-20261013-spliceai2-protocol-ukb-proteomics
adaptation
Not reported
budget
Not reported
dataset version
UK Biobank WGS and Olink plasma proteomics (application 33751)
split
None
population
6,149 rare splice-region variants in 1,656 genes
inputs
Model delta at the nearest canonical splice site (GENCODE v39), loss positive and gain negative
metric implementation
Pearson correlation with mean carrier protein z-score
aggregation
Pooled over variants

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

Reproduction

Split
None
Adaptation
Not reported
Scoring implementation
Pearson correlation with mean carrier protein z-score

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

Original source ↗

Fig. 3f, bar 'Pangolin'

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

Original source ↗

Fig. 3f, bar 'Pangolin'

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 ↗

Fig. 3f, bar 'Pangolin'

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
UK Biobank WGS and Olink plasma proteomics (application 33751)
Context-only references
A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026)

Original source ↗

Fig. 3f, bar 'Pangolin'

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
Model delta at the nearest canonical splice site (GENCODE v39), loss positive and gain negative
Context-only references
A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026)

Original source ↗

Fig. 3f, bar 'Pangolin'

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 correlation with mean carrier protein z-score
Context-only references
A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026)

Original source ↗

Fig. 3f, bar 'Pangolin'

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
6,149 rare splice-region variants in 1,656 genes
Context-only references
A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026)

Original source ↗

Fig. 3f, bar 'Pangolin'

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

Original source ↗

Fig. 3f, bar 'Pangolin'

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
None
Context-only references
A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026)

Original source ↗

Fig. 3f, bar 'Pangolin'

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 ↗

Fig. 3f, bar 'Pangolin'

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-ukb-proteomics-pangolin-position-resolved

areas
dna-genomes
contexts
research
origin
author_reported
protocol
rna-splicing-20261013-spliceai2-protocol-ukb-proteomics
version
bioRxiv v1, retrieved 2026-10-13
comparison
protocol id: rna-splicing-20261013-spliceai2-protocol-ukb-proteomics; adaptation: Not reported; budget: Not reported; dataset version: UK Biobank WGS and Olink plasma proteomics (application 33751); split: None; population: 6,149 rare splice-region variants in 1,656 genes; inputs: Model delta at the nearest canonical splice site (GENCODE v39), loss positive and gain negative; metric implementation: Pearson correlation with mean carrier protein z-score; aggregation: Pooled over variants
source locator
Fig. 3f, bar 'Pangolin'
missing metadata
comparison.adaptation: reason: inapplicable; note: Pretrained weights; no adaptation to the benchmark; comparison.budget: reason: inapplicable; note: Pretrained scoring; no search or training budget
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