rewirebio.iobenchmarks
Evaluation

RNA-MSM zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, median)

Published comparison transcribed from the pinned source; not reproduced.

Evaluation results

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Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: RNA-MSM (zero-shot, Wang et al. 2026)Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (median over structures)
Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)
0.679 F1 (attention; median over structures)
unitless · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

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

RNA-MSM zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, median)

lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-median

Aggregation: Not reported

Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 5, row 'RNA-MSM', column 'F1 score' (Median)

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

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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

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Verified: Not verified

Evidence incomplete

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  • 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
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Verified: Not verified

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Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

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  • File checksums match the recorded files: not yet verified
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Verified: Not verified

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Evaluation procedure

Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (median over structures)

Configuration
RNA-MSM (zero-shot, Wang et al. 2026)
Protocol
Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (median over structures)
Dataset
TS-Hard test set (15 PDB structures) (Wang et al. 2026)
origin
Author-reported evaluation
configuration
Primary source as retrieved 2026-10-11
protocol id
lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-median
dataset version
Wang et al. 2026
split
Test (TS-Hard)
population
Not reported
inputs
attention
adaptation
Zero-shot: symmetrised, APC-corrected attention map from one head-layer and threshold chosen on VL1 by F1
metric implementation
F1 score
aggregation
Median
budget
Not reported

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

Reproduction

Split
Test (TS-Hard)
Adaptation
Zero-shot: symmetrised, APC-corrected attention map from one head-layer and threshold chosen on VL1 by F1
Scoring implementation
F1 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

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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.

36 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
Zero-shot: symmetrised, APC-corrected attention map from one head-layer and threshold chosen on VL1 by F1
Context-only references
Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning

Original source ↗

Supplementary Table 5, row 'RNA-MSM'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML
Retrieved: 2026-10-11T21:27:04Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: 835b64d52ae892cad113e798b2976c398dc9ed12178f675e0eabd2169f533808

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: adaptation
Zero-shot: symmetrised, APC-corrected attention map from one head-layer and threshold chosen on VL1 by F1
Context-only references
Zero-shot benchmarking of RNA language models: Supplementary Information

Original source ↗

Supplementary Table 5, row 'RNA-MSM'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: bbag098_supplymentary_information_20260209.docx from the Europe PMC supplementary files archive for PMC12963973
Retrieved: 2026-10-11T21:27:04Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: c8fc78c3d8538c9431fc0448a4068a7643dfb7d74558877fd40b36feba71e214

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: aggregation
Median
Context-only references
Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning

Original source ↗

Supplementary Table 5, row 'RNA-MSM'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML
Retrieved: 2026-10-11T21:27:04Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: 835b64d52ae892cad113e798b2976c398dc9ed12178f675e0eabd2169f533808

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: aggregation
Median
Context-only references
Zero-shot benchmarking of RNA language models: Supplementary Information

Original source ↗

Supplementary Table 5, row 'RNA-MSM'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: bbag098_supplymentary_information_20260209.docx from the Europe PMC supplementary files archive for PMC12963973
Retrieved: 2026-10-11T21:27:04Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: c8fc78c3d8538c9431fc0448a4068a7643dfb7d74558877fd40b36feba71e214

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: budget
Not reported
Context-only references
Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning

Original source ↗

Supplementary Table 5, row 'RNA-MSM'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML
Retrieved: 2026-10-11T21:27:04Z

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.budget

Source artifact SHA-256: 835b64d52ae892cad113e798b2976c398dc9ed12178f675e0eabd2169f533808

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: budget
Not reported
Context-only references
Zero-shot benchmarking of RNA language models: Supplementary Information

Original source ↗

Supplementary Table 5, row 'RNA-MSM'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: bbag098_supplymentary_information_20260209.docx from the Europe PMC supplementary files archive for PMC12963973
Retrieved: 2026-10-11T21:27:04Z

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.budget

Source artifact SHA-256: c8fc78c3d8538c9431fc0448a4068a7643dfb7d74558877fd40b36feba71e214

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: dataset version
Wang et al. 2026
Context-only references
Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning

Original source ↗

Supplementary Table 5, row 'RNA-MSM'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML
Retrieved: 2026-10-11T21:27:04Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.dataset_version

Source artifact SHA-256: 835b64d52ae892cad113e798b2976c398dc9ed12178f675e0eabd2169f533808

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: dataset version
Wang et al. 2026
Context-only references
Zero-shot benchmarking of RNA language models: Supplementary Information

Original source ↗

Supplementary Table 5, row 'RNA-MSM'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: bbag098_supplymentary_information_20260209.docx from the Europe PMC supplementary files archive for PMC12963973
Retrieved: 2026-10-11T21:27:04Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.dataset_version

Source artifact SHA-256: c8fc78c3d8538c9431fc0448a4068a7643dfb7d74558877fd40b36feba71e214

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: inputs
attention
Context-only references
Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning

Original source ↗

Supplementary Table 5, row 'RNA-MSM'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML
Retrieved: 2026-10-11T21:27:04Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.inputs

Source artifact SHA-256: 835b64d52ae892cad113e798b2976c398dc9ed12178f675e0eabd2169f533808

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: inputs
attention
Context-only references
Zero-shot benchmarking of RNA language models: Supplementary Information

Original source ↗

Supplementary Table 5, row 'RNA-MSM'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: bbag098_supplymentary_information_20260209.docx from the Europe PMC supplementary files archive for PMC12963973
Retrieved: 2026-10-11T21:27:04Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.inputs

Source artifact SHA-256: c8fc78c3d8538c9431fc0448a4068a7643dfb7d74558877fd40b36feba71e214

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

How to read the evidence

Sources and history

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

2 source records and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: lit-rna-20261011-rnalm-zeroshot-eval-rna-msm-default-t5-f1-score-median

areas
rna-transcriptomes
contexts
research
origin
author_reported
protocol
lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-median
version
Primary source as retrieved 2026-10-11
comparison
protocol id: lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-median; dataset version: Wang et al. 2026; split: Test (TS-Hard); population: Not reported; inputs: attention; adaptation: Zero-shot: symmetrised, APC-corrected attention map from one head-layer and threshold chosen on VL1 by F1; metric implementation: F1 score; aggregation: Median; budget: Not reported
source locator
Supplementary Table 5, row 'RNA-MSM'
missing metadata
comparison.budget: reason: unreported; comparison.population: reason: unreported
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