Protocol

Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, AUC (mean over assays)

Zero-shot: pseudo-log-likelihood difference from token logits; AUC reported as mean over assays (Supplementary Table 11).

35 evaluations · 35 results

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.

35 recorded evaluations, 35 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

35 evaluations · 35 results. Different protocols are not a single leaderboard.

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)

Sorted by AUROC (PLL-D; mean over assays) (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	AUROC (PLL-D; mean over assays)
EVO1.5 (8k_base) (zero-shot, Wang et al. 2026)Evaluation	0.588±0.056 (best in column)
AIDO.RNA (1.6B) (zero-shot, Wang et al. 2026)Evaluation	0.585±0.067
AIDO.RNA (650M) (zero-shot, Wang et al. 2026)Evaluation	0.584±0.070
RiNALMo (mega) (zero-shot, Wang et al. 2026)Evaluation	0.584±0.073
RiNALMo (giga) (zero-shot, Wang et al. 2026)Evaluation	0.581±0.075
Uni-RNA (L12) (zero-shot, Wang et al. 2026)Evaluation	0.577±0.065
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	0.575±0.072
DGRNA (zero-shot, Wang et al. 2026)Evaluation	0.572±0.054
Uni-RNA (L8) (zero-shot, Wang et al. 2026)Evaluation	0.571±0.052
RNA-FM (zero-shot, Wang et al. 2026)Evaluation	0.569±0.057
RiNALMo (micro) (zero-shot, Wang et al. 2026)Evaluation	0.565±0.064
GenerRNA (zero-shot, Wang et al. 2026)Evaluation	0.564±0.059
LAMAR (4k) (zero-shot, Wang et al. 2026)Evaluation	0.562±0.054
LucaOne (D17.6M) (zero-shot, Wang et al. 2026)Evaluation	0.559±0.055
RFamLlama (Large) (zero-shot, Wang et al. 2026)Evaluation	0.559±0.042
PlantRNA-FM (zero-shot, Wang et al. 2026)Evaluation	0.558±0.051
RFamLlama (Base) (zero-shot, Wang et al. 2026)Evaluation	0.558±0.046
LAMAR (2k) (zero-shot, Wang et al. 2026)Evaluation	0.557±0.046
NT (zero-shot, Wang et al. 2026)Evaluation	0.557±0.056
EVO1 (8k_base) (zero-shot, Wang et al. 2026)Evaluation	0.556±0.048
LucaOne (G36.8M) (zero-shot, Wang et al. 2026)Evaluation	0.551±0.042
RNAErnie (zero-shot, Wang et al. 2026)Evaluation	0.551±0.045
UTR_LM (zero-shot, Wang et al. 2026)Evaluation	0.551±0.049
3UTRBERT (K4) (zero-shot, Wang et al. 2026)Evaluation	0.550±0.037
MP-RNA (zero-shot, Wang et al. 2026)Evaluation	0.550±0.043
SpliceBERT (zero-shot, Wang et al. 2026)Evaluation	0.550±0.044
RNABERT (zero-shot, Wang et al. 2026)Evaluation	0.544±0.041
DNABERT-2 (zero-shot, Wang et al. 2026)Evaluation	0.543±0.031
3UTRBERT (K5) (zero-shot, Wang et al. 2026)Evaluation	0.542±0.035
3UTRBERT (K6) (zero-shot, Wang et al. 2026)Evaluation	0.541±0.034
LucaOne (D36.0M) (zero-shot, Wang et al. 2026)Evaluation	0.541±0.035
DNABERT (k=6) (zero-shot, Wang et al. 2026)Evaluation	0.540±0.035
ProtRNA (zero-shot, Wang et al. 2026)Evaluation	0.539±0.026
3UTRBERT (K3) (zero-shot, Wang et al. 2026)Evaluation	0.535±0.037
DNABERT (k=3) (zero-shot, Wang et al. 2026)Evaluation	0.535±0.025

All 35 result rows with coverage, uncertainty and sources

Filter evaluations

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: 3UTRBERT (K3) (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)	0.535±0.037 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.037 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K3) 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 '3UTRBERT (K3)', column 'AUC' (Mean ± Std)
Configuration: 3UTRBERT (K4) (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)	0.550±0.037 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.037 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K4) 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 '3UTRBERT (K4)', column 'AUC' (Mean ± Std)
Configuration: 3UTRBERT (K5) (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)	0.542±0.035 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.035 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K5) 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 '3UTRBERT (K5)', column 'AUC' (Mean ± Std)
Configuration: 3UTRBERT (K6) (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)	0.541±0.034 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.034 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K6) 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 '3UTRBERT (K6)', column 'AUC' (Mean ± Std)
Configuration: AIDO.RNA (1.6B) (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)	0.585±0.067 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.067 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AIDO.RNA (1.6B) 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 'AIDO.RNA (1.6B)', column 'AUC' (Mean ± Std)
Configuration: AIDO.RNA (650M) (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)	0.584±0.070 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.070 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AIDO.RNA (650M) 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 'AIDO.RNA (650M)', column 'AUC' (Mean ± Std)
Configuration: DGRNA (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)	0.572±0.054 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.054 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DGRNA 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 'DGRNA', column 'AUC' (Mean ± Std)
Configuration: DNABERT-2 (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)	0.543±0.031 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.031 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT-2 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 'DNABERT-2', column 'AUC' (Mean ± Std)
Configuration: DNABERT (k=3) (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)	0.535±0.025 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.025 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT (k=3) 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 'DNABERT (k=3)', column 'AUC' (Mean ± Std)
Configuration: DNABERT (k=6) (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)	0.540±0.035 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.035 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT (k=6) 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 'DNABERT (k=6)', column 'AUC' (Mean ± Std)
Configuration: EVO1.5 (8k_base) (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)	0.588±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 EVO1.5 (8k_base) 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 'EVO1.5 (8k_base)', column 'AUC' (Mean ± Std)
Configuration: EVO1 (8k_base) (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)	0.556±0.048 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.048 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source EVO1 (8k_base) 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 'EVO1 (8k_base)', column 'AUC' (Mean ± Std)
Configuration: GenerRNA (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)	0.564±0.059 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.059 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GenerRNA 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 'GenerRNA', column 'AUC' (Mean ± Std)
Configuration: LAMAR (2k) (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±0.046 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.046 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LAMAR (2k) 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 'LAMAR (2k)', column 'AUC' (Mean ± Std)
Configuration: LAMAR (4k) (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)	0.562±0.054 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.054 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LAMAR (4k) 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 'LAMAR (4k)', column 'AUC' (Mean ± Std)
Configuration: LucaOne (D17.6M) (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)	0.559±0.055 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.055 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LucaOne (D17.6M) 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 'LucaOne (D17.6M)', column 'AUC' (Mean ± Std)
Configuration: LucaOne (D36.0M) (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)	0.541±0.035 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.035 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LucaOne (D36.0M) 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 'LucaOne (D36.0M)', column 'AUC' (Mean ± Std)
Configuration: LucaOne (G36.8M) (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)	0.551±0.042 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.042 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LucaOne (G36.8M) 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 'LucaOne (G36.8M)', column 'AUC' (Mean ± Std)
Configuration: MP-RNA (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)	0.550±0.043 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.043 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MP-RNA 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 'MP-RNA', 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 (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: PlantRNA-FM (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)	0.558±0.051 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.051 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PlantRNA-FM 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 'PlantRNA-FM', column 'AUC' (Mean ± Std)
Configuration: ProtRNA (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)	0.539±0.026 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.026 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ProtRNA 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 'ProtRNA', column 'AUC' (Mean ± Std)
Configuration: RFamLlama (Base) (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)	0.558±0.046 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.046 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RFamLlama (Base) 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 'RFamLlama (Base)', column 'AUC' (Mean ± Std)
Configuration: RFamLlama (Large) (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)	0.559±0.042 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.042 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RFamLlama (Large) 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 'RFamLlama (Large)', column 'AUC' (Mean ± Std)
Configuration: RiNALMo (giga) (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)	0.581±0.075 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.075 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RiNALMo (giga) 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 'RiNALMo (giga)', column 'AUC' (Mean ± Std)

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

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Explore all linked results

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

External evaluations: 35

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Protocol-valid seeded random ranking; no fitting on assay labels

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Established label-free reference with explicitly permitted sequence/MSA inputs

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Strengths, limitations and unresolved questions

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.

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance

No evidence rows match these filters. Choose another scope or clear the search.

How to read the evidence

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

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: lit-rna-20261011-rnalm-zeroshot-protocol-t11-auc-mean

areas: rna-transcriptomes
contexts: research
protocol: Zero-shot: pseudo-log-likelihood difference from token logits. Metric AUC, mean over assays.
version: Wang et al. 2026
metric: auroc
metric direction: higher
unit: unitless
metric qualifier: PLL-D; mean over assays
source locator: Supplementary Table 11 caption and column 'AUC'; main text Methods
limitations: Zero-shot only; no fine-tuning or task head.; Binarisation for MCC, F1 and AUC in the fitness task is not described in the main text or supplement.

Related records

Suggest a correction