Configuration

NT (zero-shot, Wang et al. 2026)

NT evaluated zero-shot by Wang et al. 2026.

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

22 evaluations · 22 results. Different protocols are not a single leaderboard.

Sorted by AUROC (CLS embedding; mean over random samplings of sequence pairs) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	AUROC (CLS embedding; mean over random samplings of sequence pairs)	AUROC (FFT embedding; mean over random samplings of sequence pairs)	F1 (CLS embedding; mean over random samplings of sequence pairs)	F1 (FFT embedding; mean over random samplings of sequence pairs)	MCC (CLS embedding; mean over random samplings of sequence pairs)	MCC (FFT embedding; mean over random samplings of sequence pairs)	One minus overlap ratio (CLS embedding; mean over random samplings of sequence pairs)	One minus overlap ratio (FFT embedding; mean over random samplings of sequence pairs)	Absolute spearman correlation (PLL-D; mean over assays)	Absolute spearman correlation (PLL-D; median over assays)	AUROC (PLL-D; mean over assays)	AUROC (PLL-D; median over assays)	MCC (PLL-D; mean over assays)	MCC (PLL-D; median over assays)
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), CLS embedding, AUC (mean over repeated random samplings of sequence pairs), RfamSample (561 Rfam families) (Wang et al. 2026)	0.806±0.001 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, AUC (mean over repeated random samplings of sequence pairs), ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.686±0.001	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, AUC (mean over assays), RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.557±0.056	Not reported	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, AUC (median over assays), RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.547	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, MCC (mean over assays), RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.082±0.076	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, MCC (median over assays), RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.075
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, SR (mean over assays), RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.111±0.109	Not reported	Not reported	Not reported	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, SR (median over assays), RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.085	Not reported	Not reported	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, 1 − OR (mean over repeated random samplings of sequence pairs), RfamSample (561 Rfam families) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.575±0.001 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, AUC (mean over repeated random samplings of sequence pairs), RfamSample (561 Rfam families) (Wang et al. 2026)	Not reported	0.772±0.001 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, F1 (mean over repeated random samplings of sequence pairs), RfamSample (561 Rfam families) (Wang et al. 2026)	Not reported	Not reported	Not reported	0.709±0.001 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, MCC (mean over repeated random samplings of sequence pairs), RfamSample (561 Rfam families) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	0.352±0.001 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	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), ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.346±0.002	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), FFT embedding, AUC (mean over repeated random samplings of sequence pairs), ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	Not reported	0.656±0.001	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), FFT embedding, F1 (mean over repeated random samplings of sequence pairs), ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	Not reported	Not reported	Not reported	0.672±0.001	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), FFT embedding, MCC (mean over repeated random samplings of sequence pairs), ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	0.113±0.003	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), CLS embedding, 1 − OR (mean over repeated random samplings of sequence pairs), RfamSample (561 Rfam families) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.629±0.000 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), CLS embedding, F1 (mean over repeated random samplings of sequence pairs), RfamSample (561 Rfam families) (Wang et al. 2026)	Not reported	Not reported	0.733±0.001 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), CLS embedding, MCC (mean over repeated random samplings of sequence pairs), RfamSample (561 Rfam families) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	0.422±0.002 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	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), ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.413±0.002	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, F1 (mean over repeated random samplings of sequence pairs), ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	Not reported	Not reported	0.682±0.000	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
NT (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, MCC (mean over repeated random samplings of sequence pairs), ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	0.214±0.001	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported

All 22 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: NT (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, AUC (mean over assays) Dataset: RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	0.557±0.056 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.056 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NT zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, AUC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t11-auc-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 11, row 'NT', column 'AUC' (Mean ± Std)
Configuration: NT (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, AUC (median over assays) Dataset: RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	0.547 AUROC (PLL-D; median over assays) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NT zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, AUC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t11-auc-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 11, row 'NT', column 'AUC' (Median)
Configuration: NT (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, MCC (mean over assays) Dataset: RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	0.082±0.076 MCC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.076 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NT zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t11-mcc-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 11, row 'NT', column 'MCC' (Mean ± Std)
Configuration: NT (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, MCC (median over assays) Dataset: RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	0.075 MCC (PLL-D; median over assays) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NT zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t11-mcc-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 11, row 'NT', column 'MCC' (Median)
Configuration: NT (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, SR (mean over assays) Dataset: RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	0.111±0.109 Absolute spearman correlation (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.109 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NT zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, SR, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t11-sr-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 11, row 'NT', column 'SR' (Mean ± Std)
Configuration: NT (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, SR (median over assays) Dataset: RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	0.085 Absolute spearman correlation (PLL-D; median over assays) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NT zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, SR, median) lit-rna-20261011-rnalm-zeroshot-protocol-t11-sr-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 11, row 'NT', column 'SR' (Median)
Configuration: NT (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, 1 − OR (mean over repeated random samplings of sequence pairs) Dataset: RfamSample (561 Rfam families) (Wang et al. 2026)	0.575±0.001 One minus overlap ratio (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 NT zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, 1 − OR, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t6-1-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 6, row 'NT', column '1 − OR'
Configuration: NT (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, AUC (mean over repeated random samplings of sequence pairs) Dataset: RfamSample (561 Rfam families) (Wang et al. 2026)	0.772±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 NT zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, AUC, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t6-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 6, row 'NT', column 'AUC'
Configuration: NT (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, F1 (mean over repeated random samplings of sequence pairs) Dataset: RfamSample (561 Rfam families) (Wang et al. 2026)	0.709±0.001 F1 (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 NT zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, F1, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t6-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 6, row 'NT', column 'F1'
Configuration: NT (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, MCC (mean over repeated random samplings of sequence pairs) Dataset: RfamSample (561 Rfam families) (Wang et al. 2026)	0.352±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 NT zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, MCC, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t6-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 6, row 'NT', column 'MCC'
Configuration: NT (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)	0.346±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 NT 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 'NT', column '1 − OR'
Configuration: NT (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)	0.656±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 NT 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 'NT', column 'AUC'
Configuration: NT (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)	0.672±0.001 F1 (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 NT 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 'NT', column 'F1'
Configuration: NT (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)	0.113±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 NT 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 'NT', column 'MCC'
Configuration: NT (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), CLS embedding, 1 − OR (mean over repeated random samplings of sequence pairs) Dataset: RfamSample (561 Rfam families) (Wang et al. 2026)	0.629±0.000 One minus overlap ratio (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 NT zero-shot family classification on RfamSample (561 Rfam families) (CLS embedding, 1 − OR, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t8-1-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 8, row 'NT', column '1 − OR'
Configuration: NT (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), CLS embedding, AUC (mean over repeated random samplings of sequence pairs) Dataset: RfamSample (561 Rfam families) (Wang et al. 2026)	0.806±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 NT zero-shot family classification on RfamSample (561 Rfam families) (CLS embedding, AUC, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t8-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 8, row 'NT', column 'AUC'
Configuration: NT (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), CLS embedding, F1 (mean over repeated random samplings of sequence pairs) Dataset: RfamSample (561 Rfam families) (Wang et al. 2026)	0.733±0.001 F1 (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 NT zero-shot family classification on RfamSample (561 Rfam families) (CLS embedding, F1, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t8-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 8, row 'NT', column 'F1'
Configuration: NT (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), CLS embedding, MCC (mean over repeated random samplings of sequence pairs) Dataset: RfamSample (561 Rfam families) (Wang et al. 2026)	0.422±0.002 MCC (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 NT zero-shot family classification on RfamSample (561 Rfam families) (CLS embedding, MCC, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t8-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 8, row 'NT', column 'MCC'
Configuration: NT (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)	0.413±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 NT 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 'NT', column '1 − OR'
Configuration: NT (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)	0.686±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 NT 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 'NT', column 'AUC'
Configuration: NT (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)	0.682±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 NT 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 'NT', column 'F1'
Configuration: NT (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)	0.214±0.001 MCC (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 NT 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 'NT', column 'MCC'

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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

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Stable ID: lit-rna-20261011-rnalm-zeroshot-config-nt-wang2026

areas: rna-transcriptomes
contexts: research
method types: foundation_model
reported name: NT
foundation model eligible: true
parameters: Pretrained weights used without fine-tuning (zero-shot); attention maps, embeddings or token logits read out as described in the Methods
access reuse: Public download location listed in Supplementary Table 1
source locator: Supplementary Table 1 row 'NT'
checkpoint: https://github.com/instadeepai/nucleotide-transformer (downloaded 2024/8/26; version column 'v2-250m-multi-species'; variant label in results tables 'none')
version: v2-250m-multi-species

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