Protocol

Wang et al. 2026 zero-shot secondary structure, TS test set (70 PDB structures), attention, MCC (median over structures)

Zero-shot: symmetrised, APC-corrected attention map from one head-layer and threshold chosen on VL1 by F1; MCC reported as median over structures (Supplementary Table 4).

32 evaluations · 32 results

Overview

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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

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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 (median over structures) · Dataset: TS test set (70 PDB structures) (Wang et al. 2026)

Sorted by MCC (attention; median 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; median over structures)
RNA-MSM (zero-shot, Wang et al. 2026)Evaluation	0.634 (best in column)
AIDO.RNA (1.6B) (zero-shot, Wang et al. 2026)Evaluation	0.595
MP-RNA (zero-shot, Wang et al. 2026)Evaluation	0.515
RNA-km (zero-shot, Wang et al. 2026)Evaluation	0.489
AIDO.RNA (650M) (zero-shot, Wang et al. 2026)Evaluation	0.469
RiNALMo (giga) (zero-shot, Wang et al. 2026)Evaluation	0.416
ERNIE-RNA (zero-shot, Wang et al. 2026)Evaluation	0.356
ProtRNA (zero-shot, Wang et al. 2026)Evaluation	0.323
RiNALMo (mega) (zero-shot, Wang et al. 2026)Evaluation	0.317
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	0.308
RiNALMo (micro) (zero-shot, Wang et al. 2026)Evaluation	0.268
Uni-RNA (L12) (zero-shot, Wang et al. 2026)Evaluation	0.244
RNAErnie (zero-shot, Wang et al. 2026)Evaluation	0.236
LucaOne (G36.8M) (zero-shot, Wang et al. 2026)Evaluation	0.228
Uni-RNA (L8) (zero-shot, Wang et al. 2026)Evaluation	0.219
RNA-FM (zero-shot, Wang et al. 2026)Evaluation	0.186
LucaOne (D17.6M) (zero-shot, Wang et al. 2026)Evaluation	0.182
LucaOne (D36.0M) (zero-shot, Wang et al. 2026)Evaluation	0.135
PlantRNA-FM (zero-shot, Wang et al. 2026)Evaluation	0.116
RFamLlama (Large) (zero-shot, Wang et al. 2026)Evaluation	0.036
LAMAR (2k) (zero-shot, Wang et al. 2026)Evaluation	0.031
RFamLlama (Base) (zero-shot, Wang et al. 2026)Evaluation	0.029
SpliceBERT (zero-shot, Wang et al. 2026)Evaluation	0.022
3UTRBERT (K6) (zero-shot, Wang et al. 2026)Evaluation	0.008
UTR_LM (zero-shot, Wang et al. 2026)Evaluation	0.006
DNABERT (k=6) (zero-shot, Wang et al. 2026)Evaluation	0.003
LAMAR (4k) (zero-shot, Wang et al. 2026)Evaluation	0
RNABERT (zero-shot, Wang et al. 2026)Evaluation	-0.001
3UTRBERT (K3) (zero-shot, Wang et al. 2026)Evaluation	-0.002
3UTRBERT (K5) (zero-shot, Wang et al. 2026)Evaluation	-0.002
3UTRBERT (K4) (zero-shot, Wang et al. 2026)Evaluation	-0.005
DNABERT (k=3) (zero-shot, Wang et al. 2026)Evaluation	-0.006

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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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	-0.002 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row '3UTRBERT (K3)', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	-0.005 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row '3UTRBERT (K4)', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	-0.002 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row '3UTRBERT (K5)', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.008 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row '3UTRBERT (K6)', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.595 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'AIDO.RNA (1.6B)', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.469 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'AIDO.RNA (650M)', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	-0.006 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'DNABERT (k=3)', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.003 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'DNABERT (k=6)', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.356 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'ERNIE-RNA', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.031 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'LAMAR (2k)', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'LAMAR (4k)', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.182 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'LucaOne (D17.6M)', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.135 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'LucaOne (D36.0M)', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.228 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'LucaOne (G36.8M)', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.515 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'MP-RNA', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.116 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'PlantRNA-FM', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.323 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'ProtRNA', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.029 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'RFamLlama (Base)', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.036 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'RFamLlama (Large)', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.416 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'RiNALMo (giga)', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.317 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'RiNALMo (mega)', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.268 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'RiNALMo (micro)', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.186 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'RNA-FM', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.489 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'RNA-km', column 'MCC' (Median)
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 (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.634 MCC (attention; median over structures) unitless · higher Uncertainty: Not reported by the source 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, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'RNA-MSM', column 'MCC' (Median)

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Stable ID: lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-median

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, median over structures.
version: Wang et al. 2026
metric: matthews-correlation-coefficient
metric direction: higher
unit: unitless
metric qualifier: attention; median 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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