MCC (attention; mean over structures) of 3UTRBERT (K5) (zero-shot, Wang et al. 2026) on TS-Hard test set (15 PDB structures) (Wang et al. 2026)
0.003±0.019 MCC (attention; mean over structures)
Methods
- Tested configuration
- 3UTRBERT (K5) (zero-shot, Wang et al. 2026)
- Protocol
- Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, MCC (mean over structures)
- Dataset
- TS-Hard test set (15 PDB structures) (Wang et al. 2026)
- Procedure
- Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, MCC (mean over structures)
- Evaluation
- 3UTRBERT (K5) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, MCC, mean)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- SD 0.019
- Evidence
- Independent external evaluation · source checkedZero-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 '3UTRBERT (K5)', column 'MCC' (Mean ± Std)
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
- Test (TS-Hard)
- Adaptation
- Zero-shot: symmetrised, APC-corrected attention map from one head-layer and threshold chosen on VL1 by F1
- Scoring implementation
- MCC
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.
2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 0.003±0.019 Individual claims | Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning Supplementary Table 5, row '3UTRBERT (K5)', column 'MCC' (Mean ± Std) 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 | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-12 independent paper Audit detailsExtraction: Parsed the table cells (w:tc runs) of word/document.xml in the pinned supplementary .docx with extract/extract_rnalm_zeroshot.py; row label and column header taken from the same table. Supplementary Table 5 body row 11. Independent review 2026-10-12: value, locator, metric, unit, direction and linked configuration and protocol checked. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
| Reported result 0.003±0.019 Individual claims | Zero-shot benchmarking of RNA language models: Supplementary Information Supplementary Table 5, row '3UTRBERT (K5)', column 'MCC' (Mean ± Std) 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 | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-12 independent paper Audit detailsExtraction: Parsed the table cells (w:tc runs) of word/document.xml in the pinned supplementary .docx with extract/extract_rnalm_zeroshot.py; row label and column header taken from the same table. Supplementary Table 5 body row 11. Independent review 2026-10-12: value, locator, metric, unit, direction and linked configuration and protocol checked. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- Zero-shot benchmarking of RNA language models: Supplementary Information · Original source · bbag098_supplymentary_information_20260209.docx from the Europe PMC supplementary files archive for PMC12963973
- Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Original source · Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML
Technical metadata and extraction receipts
Stable ID: lit-rna-20261011-rnalm-zeroshot-result-3utrbert-k5-t5-mcc-mean
- metric
- matthews-correlation-coefficient
- metric direction
- higher
- unit
- unitless
- printed value
- 0.003±0.019
- source locator
- Supplementary Table 5, row '3UTRBERT (K5)', column 'MCC' (Mean ± Std)
- review
- method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Re-fetched the Europe PMC supplementary archive; the .docx inside matched its SHA-256. An independent w:tc parse of Supplementary Tables 4-11 matched all 1190 printed values, numeric values, standard deviations and locators; 48 cells were also checked by hand against a textutil rendering.; reviewer: claude; reviewer note: Claude review agent reviewer-ro-1, independent of the extractor lit-rna-otheromics; no human review claimed; date: 2026-10-12; artifact sha256: c8fc78c3d8538c9431fc0448a4068a7643dfb7d74558877fd40b36feba71e214; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12963973/supplementaryFiles; note: Extraction: Parsed the table cells (w:tc runs) of word/document.xml in the pinned supplementary .docx with extract/extract_rnalm_zeroshot.py; row label and column header taken from the same table. Supplementary Table 5 body row 11. Independent review 2026-10-12: value, locator, metric, unit, direction and linked configuration and protocol checked.
- numeric value
- 0.003
- metric qualifier
- attention; mean over structures
- uncertainty
- type: standard_deviation; value: 0.019; center: 0.003; printed: 0.003±0.019; scope: across structures