Dataset

ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)

ArchiveII without long group II introns, made non-redundant at 80% identity with MMseqs2; homology defined at the RNA type level.

Evaluation results

292 evaluations · 292 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: 3UTRBERT (K3) (zero-shot, Wang et al. 2026)	Protocol: 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) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.307±0.005 One minus overlap ratio (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.005 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, 1 − OR, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t7-1-or-sampled-mean 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 7, row '3UTRBERT (K3)', column '1 − OR'
Configuration: 3UTRBERT (K3) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), FFT embedding, AUC (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.623±0.002 AUROC (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.002 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, AUC, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t7-auc-sampled-mean 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 7, row '3UTRBERT (K3)', column 'AUC'
Configuration: 3UTRBERT (K3) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), FFT embedding, F1 (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.667±0.000 F1 (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.000 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, F1, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t7-f1-sampled-mean 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 7, row '3UTRBERT (K3)', column 'F1'
Configuration: 3UTRBERT (K3) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), FFT embedding, MCC (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.015±0.003 MCC (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.003 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, MCC, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t7-mcc-sampled-mean 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 7, row '3UTRBERT (K3)', column 'MCC'
Configuration: 3UTRBERT (K3) (zero-shot, Wang et al. 2026)	Protocol: 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) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.291±0.003 One minus overlap ratio (CLS embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.003 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, 1 − OR, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t9-1-or-sampled-mean 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 9, row '3UTRBERT (K3)', column '1 − OR'
Configuration: 3UTRBERT (K3) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, AUC (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.621±0.001 AUROC (CLS embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.001 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, AUC, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t9-auc-sampled-mean 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 9, row '3UTRBERT (K3)', column 'AUC'
Configuration: 3UTRBERT (K3) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, F1 (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.667±0.000 F1 (CLS embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.000 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, F1, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t9-f1-sampled-mean 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 9, row '3UTRBERT (K3)', column 'F1'
Configuration: 3UTRBERT (K3) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, MCC (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.025±0.003 MCC (CLS embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.003 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, MCC, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t9-mcc-sampled-mean 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 9, row '3UTRBERT (K3)', column 'MCC'
Configuration: 3UTRBERT (K4) (zero-shot, Wang et al. 2026)	Protocol: 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) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.371±0.002 One minus overlap ratio (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.002 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K4) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, 1 − OR, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t7-1-or-sampled-mean 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 7, row '3UTRBERT (K4)', column '1 − OR'
Configuration: 3UTRBERT (K4) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), FFT embedding, AUC (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.647±0.001 AUROC (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.001 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K4) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, AUC, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t7-auc-sampled-mean 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 7, row '3UTRBERT (K4)', column 'AUC'
Configuration: 3UTRBERT (K4) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), FFT embedding, F1 (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.667±0.000 F1 (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.000 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K4) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, F1, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t7-f1-sampled-mean 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 7, row '3UTRBERT (K4)', column 'F1'
Configuration: 3UTRBERT (K4) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), FFT embedding, MCC (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.032±0.001 MCC (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.001 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K4) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, MCC, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t7-mcc-sampled-mean 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 7, row '3UTRBERT (K4)', column 'MCC'
Configuration: 3UTRBERT (K4) (zero-shot, Wang et al. 2026)	Protocol: 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) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.326±0.003 One minus overlap ratio (CLS embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.003 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K4) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, 1 − OR, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t9-1-or-sampled-mean 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 9, row '3UTRBERT (K4)', column '1 − OR'
Configuration: 3UTRBERT (K4) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, AUC (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.640±0.001 AUROC (CLS embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.001 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K4) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, AUC, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t9-auc-sampled-mean 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 9, row '3UTRBERT (K4)', column 'AUC'
Configuration: 3UTRBERT (K4) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, F1 (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.667±0.000 F1 (CLS embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.000 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K4) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, F1, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t9-f1-sampled-mean 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 9, row '3UTRBERT (K4)', column 'F1'
Configuration: 3UTRBERT (K4) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, MCC (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.003±0.003 MCC (CLS embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.003 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K4) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, MCC, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t9-mcc-sampled-mean 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 9, row '3UTRBERT (K4)', column 'MCC'
Configuration: 3UTRBERT (K5) (zero-shot, Wang et al. 2026)	Protocol: 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) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.243±0.002 One minus overlap ratio (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.002 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K5) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, 1 − OR, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t7-1-or-sampled-mean 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 7, row '3UTRBERT (K5)', column '1 − OR'
Configuration: 3UTRBERT (K5) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), FFT embedding, AUC (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.469±0.001 AUROC (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.001 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K5) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, AUC, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t7-auc-sampled-mean 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 7, row '3UTRBERT (K5)', column 'AUC'
Configuration: 3UTRBERT (K5) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), FFT embedding, F1 (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.657±0.000 F1 (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.000 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K5) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, F1, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t7-f1-sampled-mean 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 7, row '3UTRBERT (K5)', column 'F1'
Configuration: 3UTRBERT (K5) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), FFT embedding, MCC (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.073±0.001 MCC (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.001 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K5) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, MCC, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t7-mcc-sampled-mean 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 7, row '3UTRBERT (K5)', column 'MCC'
Configuration: 3UTRBERT (K5) (zero-shot, Wang et al. 2026)	Protocol: 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) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.353±0.002 One minus overlap ratio (CLS embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.002 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K5) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, 1 − OR, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t9-1-or-sampled-mean 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 9, row '3UTRBERT (K5)', column '1 − OR'
Configuration: 3UTRBERT (K5) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, AUC (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.638±0.000 AUROC (CLS embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.000 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K5) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, AUC, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t9-auc-sampled-mean 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 9, row '3UTRBERT (K5)', column 'AUC'
Configuration: 3UTRBERT (K5) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, F1 (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.667±0.000 F1 (CLS embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.000 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K5) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, F1, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t9-f1-sampled-mean 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 9, row '3UTRBERT (K5)', column 'F1'
Configuration: 3UTRBERT (K5) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, MCC (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.007±0.004 MCC (CLS embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.004 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K5) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, MCC, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t9-mcc-sampled-mean 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 9, row '3UTRBERT (K5)', column 'MCC'
Configuration: 3UTRBERT (K6) (zero-shot, Wang et al. 2026)	Protocol: 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) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.266±0.003 One minus overlap ratio (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.003 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K6) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, 1 − OR, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t7-1-or-sampled-mean 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 7, row '3UTRBERT (K6)', column '1 − OR'

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Source location Main text Methods 'Datasets'; Supplementary Table 2 for ArchiveII Context-only references	Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning Original source ↗ Main text Methods 'Datasets'; Supplementary Table 2 for ArchiveII 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 Audit details Field: `attributes.source_locator` Source artifact SHA-256: `835b64d52ae892cad113e798b2976c398dc9ed12178f675e0eabd2169f533808` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Split Whole dataset (zero-shot) Context-only references	Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning Original source ↗ Main text Methods 'Datasets'; Supplementary Table 2 for ArchiveII 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 Audit details Field: `attributes.split` Source artifact SHA-256: `835b64d52ae892cad113e798b2976c398dc9ed12178f675e0eabd2169f533808` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Version As constructed by Wang et al. 2026 (Zenodo record 18218776) Context-only references	Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning Original source ↗ Main text Methods 'Datasets'; Supplementary Table 2 for ArchiveII 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 Audit details Field: `attributes.version` Source artifact SHA-256: `835b64d52ae892cad113e798b2976c398dc9ed12178f675e0eabd2169f533808` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description ArchiveII without long group II introns, made non-redundant at 80% identity with MMseqs2; homology defined at the RNA type level. Context-only references	Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning Original source ↗ Main text Methods 'Datasets'; Supplementary Table 2 for ArchiveII 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 Audit details Field: `description` Source artifact SHA-256: `835b64d52ae892cad113e798b2976c398dc9ed12178f675e0eabd2169f533808` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Name ArchiveII-Nr (1273 RNAs) (Wang et al. 2026) Context-only references	Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning Original source ↗ Main text Methods 'Datasets'; Supplementary Table 2 for ArchiveII 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 Audit details Field: `name` Source artifact SHA-256: `835b64d52ae892cad113e798b2976c398dc9ed12178f675e0eabd2169f533808` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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

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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

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Stable ID: lit-rna-20261011-rnalm-zeroshot-data-archiveii-nr

areas: rna-transcriptomes
contexts: research
version: As constructed by Wang et al. 2026 (Zenodo record 18218776)
split: Whole dataset (zero-shot)
source locator: Main text Methods 'Datasets'; Supplementary Table 2 for ArchiveII

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