Protocol

Wang et al. 2026 zero-shot secondary structure, TS test set (70 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 4).

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.

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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 test set (70 PDB structures), attention, MCC (mean over structures) · Dataset: TS test set (70 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	0.588±0.217 (best in column)
AIDO.RNA (1.6B) (zero-shot, Wang et al. 2026)Evaluation	0.518±0.258
MP-RNA (zero-shot, Wang et al. 2026)Evaluation	0.510±0.200
RNA-km (zero-shot, Wang et al. 2026)Evaluation	0.501±0.233
AIDO.RNA (650M) (zero-shot, Wang et al. 2026)Evaluation	0.427±0.235
RiNALMo (giga) (zero-shot, Wang et al. 2026)Evaluation	0.423±0.257
ERNIE-RNA (zero-shot, Wang et al. 2026)Evaluation	0.351±0.230
ProtRNA (zero-shot, Wang et al. 2026)Evaluation	0.351±0.237
RiNALMo (mega) (zero-shot, Wang et al. 2026)Evaluation	0.342±0.225
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	0.311±0.200
RNAErnie (zero-shot, Wang et al. 2026)Evaluation	0.290±0.221
RiNALMo (micro) (zero-shot, Wang et al. 2026)Evaluation	0.275±0.184
RNA-FM (zero-shot, Wang et al. 2026)Evaluation	0.273±0.239
LucaOne (G36.8M) (zero-shot, Wang et al. 2026)Evaluation	0.268±0.238
Uni-RNA (L12) (zero-shot, Wang et al. 2026)Evaluation	0.258±0.203
Uni-RNA (L8) (zero-shot, Wang et al. 2026)Evaluation	0.258±0.202
LucaOne (D17.6M) (zero-shot, Wang et al. 2026)Evaluation	0.228±0.196
LucaOne (D36.0M) (zero-shot, Wang et al. 2026)Evaluation	0.214±0.203
PlantRNA-FM (zero-shot, Wang et al. 2026)Evaluation	0.155±0.137
RFamLlama (Large) (zero-shot, Wang et al. 2026)Evaluation	0.042±0.058
SpliceBERT (zero-shot, Wang et al. 2026)Evaluation	0.033±0.045
RFamLlama (Base) (zero-shot, Wang et al. 2026)Evaluation	0.031±0.045
LAMAR (2k) (zero-shot, Wang et al. 2026)Evaluation	0.029±0.027
LAMAR (4k) (zero-shot, Wang et al. 2026)Evaluation	0.025±0.039
UTR_LM (zero-shot, Wang et al. 2026)Evaluation	0.016±0.037
RNABERT (zero-shot, Wang et al. 2026)Evaluation	0.010±0.029
3UTRBERT (K5) (zero-shot, Wang et al. 2026)Evaluation	0.007±0.040
3UTRBERT (K3) (zero-shot, Wang et al. 2026)Evaluation	0.004±0.030
3UTRBERT (K6) (zero-shot, Wang et al. 2026)Evaluation	0.003±0.032
3UTRBERT (K4) (zero-shot, Wang et al. 2026)Evaluation	0.001±0.026
DNABERT (k=6) (zero-shot, Wang et al. 2026)Evaluation	0.001±0.024
DNABERT (k=3) (zero-shot, Wang et al. 2026)Evaluation	-0.008±0.025

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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.004±0.030 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.030 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K3) zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.001±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 test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.007±0.040 MCC (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 3UTRBERT (K5) zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.003±0.032 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.032 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 3UTRBERT (K6) zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.518±0.258 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.258 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 test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.427±0.235 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.235 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 test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	-0.008±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 DNABERT (k=3) zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.001±0.024 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.024 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 test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.351±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 ERNIE-RNA zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.029±0.027 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.027 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LAMAR (2k) zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.025±0.039 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.039 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LAMAR (4k) zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.228±0.196 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.196 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 test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.214±0.203 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.203 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 test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.268±0.238 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.238 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 test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.510±0.200 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.200 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MP-RNA zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.155±0.137 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.137 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PlantRNA-FM zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.351±0.237 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.237 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ProtRNA zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.031±0.045 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.045 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RFamLlama (Base) zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.042±0.058 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.058 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RFamLlama (Large) zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.423±0.257 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.257 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RiNALMo (giga) zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.342±0.225 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.225 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RiNALMo (mega) zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.275±0.184 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.184 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RiNALMo (micro) zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.273±0.239 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.239 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RNA-FM zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.501±0.233 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.233 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RNA-km zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, 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 test set (70 PDB structures), attention, MCC (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.588±0.217 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.217 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-MSM zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-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 4, row 'RNA-MSM', column 'MCC' (Mean ± Std)

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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-t4-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 4 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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