Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning
Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML · Peer-reviewed
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Results
Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.
Models, benchmarks and other records
Benchmarks (1)
Protocols (36)
- Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), CLS embedding, 1 − OR (mean over repeated random samplings of sequence pairs)
- Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), CLS embedding, AUC (mean over repeated random samplings of sequence pairs)
- Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), CLS embedding, F1 (mean over repeated random samplings of sequence pairs)
- Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), CLS embedding, MCC (mean over repeated random samplings of sequence pairs)
- Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, 1 − OR (mean over repeated random samplings of sequence pairs)
- Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, AUC (mean over repeated random samplings of sequence pairs)
- Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, F1 (mean over repeated random samplings of sequence pairs)
- Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, MCC (mean over repeated random samplings of sequence pairs)
- Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, AUC (mean over assays)
- Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, AUC (median over assays)
- Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, MCC (mean over assays)
- Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, MCC (median over assays)
- Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, SR (mean over assays)
- Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, SR (median over assays)
- Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), WT-LLR, AUC (mean over assays)
- Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), WT-LLR, AUC (median over assays)
- Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), WT-LLR, MCC (mean over assays)
- Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), WT-LLR, MCC (median over assays)
- Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), WT-LLR, SR (mean over assays)
- Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), WT-LLR, SR (median over assays)
- Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, 1 − OR (mean over repeated random samplings of sequence pairs)
- Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, AUC (mean over repeated random samplings of sequence pairs)
- Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, F1 (mean over repeated random samplings of sequence pairs)
- Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, MCC (mean over repeated random samplings of sequence pairs)
- Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), FFT embedding, 1 − OR (mean over repeated random samplings of sequence pairs)
Datasets (5)
Evaluations (1,190)
- 3UTRBERT (K3) zero-shot family classification on RfamSample (561 Rfam families) (CLS embedding, 1 − OR, sampled-mean)
- 3UTRBERT (K3) zero-shot family classification on RfamSample (561 Rfam families) (CLS embedding, AUC, sampled-mean)
- 3UTRBERT (K3) zero-shot family classification on RfamSample (561 Rfam families) (CLS embedding, F1, sampled-mean)
- 3UTRBERT (K3) zero-shot family classification on RfamSample (561 Rfam families) (CLS embedding, MCC, sampled-mean)
- 3UTRBERT (K3) zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, 1 − OR, sampled-mean)
- 3UTRBERT (K3) zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, AUC, sampled-mean)
- 3UTRBERT (K3) zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, F1, sampled-mean)
- 3UTRBERT (K3) zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, MCC, sampled-mean)
- 3UTRBERT (K3) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, AUC, mean)
- 3UTRBERT (K3) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, AUC, median)
- 3UTRBERT (K3) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, MCC, mean)
- 3UTRBERT (K3) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, MCC, median)
- 3UTRBERT (K3) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, SR, mean)
- 3UTRBERT (K3) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, SR, median)
- 3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, 1 − OR, sampled-mean)
- 3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, AUC, sampled-mean)
- 3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, F1, sampled-mean)
- 3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, MCC, sampled-mean)
- 3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, 1 − OR, sampled-mean)
- 3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, AUC, sampled-mean)
- 3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, F1, sampled-mean)
- 3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, MCC, sampled-mean)
- 3UTRBERT (K3) zero-shot secondary structure on TS test set (70 PDB structures) (attention, F1 score, mean)
- 3UTRBERT (K3) zero-shot secondary structure on TS test set (70 PDB structures) (attention, F1 score, median)
- 3UTRBERT (K3) zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean)
Evidence
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Evidence table
Inspect claims, sources and review details
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18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.artifact_sha256 835b64d52ae892cad113e798b2976c398dc9ed12178f675e0eabd2169f533808 Source metadata | Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning No field-specific location recorded Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12963973/fullTextXML Source metadata | Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning No field-specific location recorded Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Doi 10.1093/bib/bbag098 Source metadata | Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning No field-specific location recorded Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Licence CC-BY-4.0 Source metadata | Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning No field-specific location recorded Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Limitations1 values
| Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning No field-specific location recorded Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Media type application/xml Source metadata | Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning No field-specific location recorded Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Publication status peer_reviewed Source metadata | Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning No field-specific location recorded Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Retrieved at 2026-10-11T21:27:04Z Source metadata | Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning No field-specific location recorded Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Url https://doi.org/10.1093/bib/bbag098 Source metadata | Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning No field-specific location recorded Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Version Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML Source metadata | Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning No field-specific location recorded Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Primary source retrieved and hashed for the 2026-10-11 RNA and other-omics literature pass.
Technical metadata and extraction receipts
Stable ID: lit-rna-20261011-rnalm-zeroshot-source-wang2026
- areas
- rna-transcriptomes
- contexts
- research
- url
- https://doi.org/10.1093/bib/bbag098
- artifact url
- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12963973/fullTextXML
- version
- Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML
- retrieved at
- 2026-10-11T21:27:04Z
- artifact sha256
- 835b64d52ae892cad113e798b2976c398dc9ed12178f675e0eabd2169f533808
- doi
- 10.1093/bib/bbag098
- publication status
- peer_reviewed
- licence
- CC-BY-4.0
- media type
- application/xml
- limitations
- All benchmark numbers are in the supplementary Word file; the main text shows them as figures only.