Protocol

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

Zero-shot: symmetrised, APC-corrected attention map from one head-layer and threshold chosen on VL1 by F1; MCC 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, MCC (mean over structures) · Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)

Sorted by MCC (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	MCC (attention; mean over structures)
RNA-MSM (zero-shot, Wang et al. 2026)Evaluation	0.654±0.138 (best in column)
MP-RNA (zero-shot, Wang et al. 2026)Evaluation	0.547±0.215
AIDO.RNA (1.6B) (zero-shot, Wang et al. 2026)Evaluation	0.520±0.263
RNA-km (zero-shot, Wang et al. 2026)Evaluation	0.453±0.201
RiNALMo (giga) (zero-shot, Wang et al. 2026)Evaluation	0.375±0.222
AIDO.RNA (650M) (zero-shot, Wang et al. 2026)Evaluation	0.365±0.227
ERNIE-RNA (zero-shot, Wang et al. 2026)Evaluation	0.341±0.176
ProtRNA (zero-shot, Wang et al. 2026)Evaluation	0.301±0.195
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	0.286±0.162
RiNALMo (mega) (zero-shot, Wang et al. 2026)Evaluation	0.265±0.210
Uni-RNA (L8) (zero-shot, Wang et al. 2026)Evaluation	0.264±0.148
LucaOne (G36.8M) (zero-shot, Wang et al. 2026)Evaluation	0.261±0.230
RNAErnie (zero-shot, Wang et al. 2026)Evaluation	0.243±0.152
RNA-FM (zero-shot, Wang et al. 2026)Evaluation	0.231±0.228
Uni-RNA (L12) (zero-shot, Wang et al. 2026)Evaluation	0.221±0.153
RiNALMo (micro) (zero-shot, Wang et al. 2026)Evaluation	0.204±0.135
LucaOne (D36.0M) (zero-shot, Wang et al. 2026)Evaluation	0.196±0.173
LucaOne (D17.6M) (zero-shot, Wang et al. 2026)Evaluation	0.189±0.159
PlantRNA-FM (zero-shot, Wang et al. 2026)Evaluation	0.104±0.094
RFamLlama (Large) (zero-shot, Wang et al. 2026)Evaluation	0.039±0.041
LAMAR (2k) (zero-shot, Wang et al. 2026)Evaluation	0.032±0.025
SpliceBERT (zero-shot, Wang et al. 2026)Evaluation	0.020±0.026
LAMAR (4k) (zero-shot, Wang et al. 2026)Evaluation	0.014±0.029
RFamLlama (Base) (zero-shot, Wang et al. 2026)Evaluation	0.009±0.021
3UTRBERT (K6) (zero-shot, Wang et al. 2026)Evaluation	0.007±0.025
RNABERT (zero-shot, Wang et al. 2026)Evaluation	0.007±0.023
UTR_LM (zero-shot, Wang et al. 2026)Evaluation	0.006±0.018
3UTRBERT (K4) (zero-shot, Wang et al. 2026)Evaluation	0.003±0.026
3UTRBERT (K5) (zero-shot, Wang et al. 2026)Evaluation	0.003±0.019
3UTRBERT (K3) (zero-shot, Wang et al. 2026)Evaluation	0.000±0.014
DNABERT (k=6) (zero-shot, Wang et al. 2026)Evaluation	-0.002±0.018
DNABERT (k=3) (zero-shot, Wang et al. 2026)Evaluation	-0.010±0.010

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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.000±0.014 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.014 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row '3UTRBERT (K3)', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.003±0.026 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.026 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row '3UTRBERT (K4)', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.003±0.019 MCC (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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row '3UTRBERT (K5)', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.007±0.025 MCC (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 (K6) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row '3UTRBERT (K6)', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.520±0.263 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.263 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'AIDO.RNA (1.6B)', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.365±0.227 MCC (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 AIDO.RNA (650M) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'AIDO.RNA (650M)', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	-0.010±0.010 MCC (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 DNABERT (k=3) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'DNABERT (k=3)', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	-0.002±0.018 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.018 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'DNABERT (k=6)', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.341±0.176 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.176 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'ERNIE-RNA', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.032±0.025 MCC (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 LAMAR (2k) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'LAMAR (2k)', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.014±0.029 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.029 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'LAMAR (4k)', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.189±0.159 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.159 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'LucaOne (D17.6M)', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.196±0.173 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.173 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'LucaOne (D36.0M)', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.261±0.230 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.230 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'LucaOne (G36.8M)', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.547±0.215 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.215 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'MP-RNA', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.104±0.094 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.094 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'PlantRNA-FM', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.301±0.195 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.195 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'ProtRNA', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.009±0.021 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.021 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'RFamLlama (Base)', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.039±0.041 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.041 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'RFamLlama (Large)', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.375±0.222 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.222 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'RiNALMo (giga)', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.265±0.210 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.210 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'RiNALMo (mega)', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.204±0.135 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.135 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'RiNALMo (micro)', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.231±0.228 MCC (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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'RNA-FM', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.453±0.201 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.201 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'RNA-km', column 'MCC' (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, MCC (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.654±0.138 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.138 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, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'RNA-MSM', column 'MCC' (Mean ± Std)

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
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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-mcc-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 MCC, mean over structures.
version: Wang et al. 2026
metric: matthews-correlation-coefficient
metric direction: higher
unit: unitless
metric qualifier: attention; mean over structures
source locator: Supplementary Table 5 caption and column 'MCC'; 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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