Protocol

Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures)

Zero-shot: symmetrised, APC-corrected attention map from one head-layer and threshold chosen on VL1 by F1; F1 score reported as mean over structures (Supplementary Table 5).

32 evaluations · 32 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.

32 recorded evaluations, 32 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

32 evaluations · 32 results. Different protocols are not a single leaderboard.

Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) · Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)

Sorted by F1 (attention; mean over structures) (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	F1 (attention; mean over structures)
RNA-MSM (zero-shot, Wang et al. 2026)Evaluation	0.645±0.136 (best in column)
MP-RNA (zero-shot, Wang et al. 2026)Evaluation	0.545±0.217
AIDO.RNA (1.6B) (zero-shot, Wang et al. 2026)Evaluation	0.512±0.262
RNA-km (zero-shot, Wang et al. 2026)Evaluation	0.444±0.206
RiNALMo (giga) (zero-shot, Wang et al. 2026)Evaluation	0.365±0.214
AIDO.RNA (650M) (zero-shot, Wang et al. 2026)Evaluation	0.331±0.217
ERNIE-RNA (zero-shot, Wang et al. 2026)Evaluation	0.291±0.185
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	0.284±0.163
ProtRNA (zero-shot, Wang et al. 2026)Evaluation	0.280±0.189
RiNALMo (mega) (zero-shot, Wang et al. 2026)Evaluation	0.265±0.204
Uni-RNA (L8) (zero-shot, Wang et al. 2026)Evaluation	0.262±0.143
LucaOne (G36.8M) (zero-shot, Wang et al. 2026)Evaluation	0.246±0.227
RNAErnie (zero-shot, Wang et al. 2026)Evaluation	0.240±0.152
Uni-RNA (L12) (zero-shot, Wang et al. 2026)Evaluation	0.225±0.152
RNA-FM (zero-shot, Wang et al. 2026)Evaluation	0.224±0.228
RiNALMo (micro) (zero-shot, Wang et al. 2026)Evaluation	0.190±0.121
LucaOne (D36.0M) (zero-shot, Wang et al. 2026)Evaluation	0.187±0.162
LucaOne (D17.6M) (zero-shot, Wang et al. 2026)Evaluation	0.185±0.157
PlantRNA-FM (zero-shot, Wang et al. 2026)Evaluation	0.109±0.096
RFamLlama (Large) (zero-shot, Wang et al. 2026)Evaluation	0.047±0.040
LAMAR (2k) (zero-shot, Wang et al. 2026)Evaluation	0.035±0.020
SpliceBERT (zero-shot, Wang et al. 2026)Evaluation	0.030±0.023
LAMAR (4k) (zero-shot, Wang et al. 2026)Evaluation	0.020±0.035
3UTRBERT (K6) (zero-shot, Wang et al. 2026)Evaluation	0.019±0.010
RFamLlama (Base) (zero-shot, Wang et al. 2026)Evaluation	0.019±0.015
UTR_LM (zero-shot, Wang et al. 2026)Evaluation	0.016±0.018
3UTRBERT (K4) (zero-shot, Wang et al. 2026)Evaluation	0.015±0.025
3UTRBERT (K3) (zero-shot, Wang et al. 2026)Evaluation	0.014±0.015
3UTRBERT (K5) (zero-shot, Wang et al. 2026)Evaluation	0.014±0.019
RNABERT (zero-shot, Wang et al. 2026)Evaluation	0.014±0.026
DNABERT (k=6) (zero-shot, Wang et al. 2026)Evaluation	0.011±0.011
DNABERT (k=3) (zero-shot, Wang et al. 2026)Evaluation	0.003±0.007

All 32 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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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 secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.014±0.015 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.015 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K3) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row '3UTRBERT (K3)', column 'F1 score' (Mean ± Std)
Configuration: 3UTRBERT (K4) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.015±0.025 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.025 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K4) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row '3UTRBERT (K4)', column 'F1 score' (Mean ± Std)
Configuration: 3UTRBERT (K5) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.014±0.019 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.019 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K5) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row '3UTRBERT (K5)', column 'F1 score' (Mean ± Std)
Configuration: 3UTRBERT (K6) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.019±0.010 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.010 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K6) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row '3UTRBERT (K6)', column 'F1 score' (Mean ± Std)
Configuration: AIDO.RNA (1.6B) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.512±0.262 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.262 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AIDO.RNA (1.6B) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'AIDO.RNA (1.6B)', column 'F1 score' (Mean ± Std)
Configuration: AIDO.RNA (650M) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.331±0.217 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.217 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AIDO.RNA (650M) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'AIDO.RNA (650M)', column 'F1 score' (Mean ± Std)
Configuration: DNABERT (k=3) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.003±0.007 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.007 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT (k=3) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'DNABERT (k=3)', column 'F1 score' (Mean ± Std)
Configuration: DNABERT (k=6) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.011±0.011 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.011 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT (k=6) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'DNABERT (k=6)', column 'F1 score' (Mean ± Std)
Configuration: ERNIE-RNA (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.291±0.185 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.185 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ERNIE-RNA zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'ERNIE-RNA', column 'F1 score' (Mean ± Std)
Configuration: LAMAR (2k) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.035±0.020 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.020 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LAMAR (2k) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'LAMAR (2k)', column 'F1 score' (Mean ± Std)
Configuration: LAMAR (4k) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.020±0.035 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.035 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LAMAR (4k) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'LAMAR (4k)', column 'F1 score' (Mean ± Std)
Configuration: LucaOne (D17.6M) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.185±0.157 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.157 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LucaOne (D17.6M) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'LucaOne (D17.6M)', column 'F1 score' (Mean ± Std)
Configuration: LucaOne (D36.0M) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.187±0.162 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.162 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LucaOne (D36.0M) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'LucaOne (D36.0M)', column 'F1 score' (Mean ± Std)
Configuration: LucaOne (G36.8M) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.246±0.227 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.227 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LucaOne (G36.8M) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'LucaOne (G36.8M)', column 'F1 score' (Mean ± Std)
Configuration: MP-RNA (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.545±0.217 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.217 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MP-RNA zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'MP-RNA', column 'F1 score' (Mean ± Std)
Configuration: PlantRNA-FM (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.109±0.096 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.096 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PlantRNA-FM zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'PlantRNA-FM', column 'F1 score' (Mean ± Std)
Configuration: ProtRNA (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.280±0.189 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.189 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ProtRNA zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'ProtRNA', column 'F1 score' (Mean ± Std)
Configuration: RFamLlama (Base) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.019±0.015 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.015 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RFamLlama (Base) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'RFamLlama (Base)', column 'F1 score' (Mean ± Std)
Configuration: RFamLlama (Large) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.047±0.040 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.040 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RFamLlama (Large) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'RFamLlama (Large)', column 'F1 score' (Mean ± Std)
Configuration: RiNALMo (giga) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.365±0.214 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.214 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RiNALMo (giga) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'RiNALMo (giga)', column 'F1 score' (Mean ± Std)
Configuration: RiNALMo (mega) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.265±0.204 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.204 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RiNALMo (mega) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'RiNALMo (mega)', column 'F1 score' (Mean ± Std)
Configuration: RiNALMo (micro) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.190±0.121 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.121 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RiNALMo (micro) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'RiNALMo (micro)', column 'F1 score' (Mean ± Std)
Configuration: RNA-FM (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.224±0.228 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.228 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RNA-FM zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'RNA-FM', column 'F1 score' (Mean ± Std)
Configuration: RNA-km (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.444±0.206 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.206 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RNA-km zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'RNA-km', column 'F1 score' (Mean ± Std)
Configuration: RNA-MSM (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.645±0.136 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.136 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-MSM zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 5, row 'RNA-MSM', column 'F1 score' (Mean ± Std)

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External evaluations: 31

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

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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
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-protocol-t5-f1-score-mean

areas: rna-transcriptomes
contexts: research
protocol: Zero-shot: symmetrised, APC-corrected attention map from one head-layer and threshold chosen on VL1 by F1. Metric F1 score, mean over structures.
version: Wang et al. 2026
metric: f1-score
metric direction: higher
unit: unitless
metric qualifier: attention; mean over structures
source locator: Supplementary Table 5 caption and column 'F1 score'; main text Methods
limitations: Zero-shot only; no fine-tuning or task head.; Base pairs come from 3D structures; one head-layer and threshold per model chosen on VL1.

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