Protocol

Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 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 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 (median over structures) · Dataset: TS-Hard test set (15 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	0.69 (best in column)
AIDO.RNA (1.6B) (zero-shot, Wang et al. 2026)Evaluation	0.618
MP-RNA (zero-shot, Wang et al. 2026)Evaluation	0.516
AIDO.RNA (650M) (zero-shot, Wang et al. 2026)Evaluation	0.412
RNA-km (zero-shot, Wang et al. 2026)Evaluation	0.41
ERNIE-RNA (zero-shot, Wang et al. 2026)Evaluation	0.369
RiNALMo (giga) (zero-shot, Wang et al. 2026)Evaluation	0.347
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	0.323
ProtRNA (zero-shot, Wang et al. 2026)Evaluation	0.295
RNAErnie (zero-shot, Wang et al. 2026)Evaluation	0.237
Uni-RNA (L8) (zero-shot, Wang et al. 2026)Evaluation	0.217
Uni-RNA (L12) (zero-shot, Wang et al. 2026)Evaluation	0.199
RiNALMo (mega) (zero-shot, Wang et al. 2026)Evaluation	0.198
RiNALMo (micro) (zero-shot, Wang et al. 2026)Evaluation	0.188
LucaOne (G36.8M) (zero-shot, Wang et al. 2026)Evaluation	0.185
RNA-FM (zero-shot, Wang et al. 2026)Evaluation	0.164
LucaOne (D17.6M) (zero-shot, Wang et al. 2026)Evaluation	0.127
LucaOne (D36.0M) (zero-shot, Wang et al. 2026)Evaluation	0.11
PlantRNA-FM (zero-shot, Wang et al. 2026)Evaluation	0.082
RFamLlama (Large) (zero-shot, Wang et al. 2026)Evaluation	0.042
LAMAR (2k) (zero-shot, Wang et al. 2026)Evaluation	0.033
SpliceBERT (zero-shot, Wang et al. 2026)Evaluation	0.025
RFamLlama (Base) (zero-shot, Wang et al. 2026)Evaluation	0.015
3UTRBERT (K6) (zero-shot, Wang et al. 2026)Evaluation	0.009
DNABERT (k=6) (zero-shot, Wang et al. 2026)Evaluation	0.003
LAMAR (4k) (zero-shot, Wang et al. 2026)Evaluation	0
UTR_LM (zero-shot, Wang et al. 2026)Evaluation	0
3UTRBERT (K3) (zero-shot, Wang et al. 2026)Evaluation	-0.001
3UTRBERT (K5) (zero-shot, Wang et al. 2026)Evaluation	-0.001
RNABERT (zero-shot, Wang et al. 2026)Evaluation	-0.001
3UTRBERT (K4) (zero-shot, Wang et al. 2026)Evaluation	-0.005
DNABERT (k=3) (zero-shot, Wang et al. 2026)Evaluation	-0.005

All 32 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: 3UTRBERT (K3) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	-0.001 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	-0.001 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.009 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.618 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.412 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 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 DNABERT (k=3) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.369 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.033 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.127 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.11 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.185 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.516 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.082 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'PlantRNA-FM', column 'MCC' (Median)
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 (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.295 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'ProtRNA', column 'MCC' (Median)
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 (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.015 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.042 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.347 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.198 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.188 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.164 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.41 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, 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-Hard test set (15 PDB structures), attention, MCC (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.69 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-Hard test set (15 PDB structures) (attention, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 5, row 'RNA-MSM', column 'MCC' (Median)

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

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Explore all linked results

Baseline coverage

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

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

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

Author-reported evaluations: 1
External evaluations: 31

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

Null control

Proposed control: requires review

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

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

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

Conventional reference

Proposed control: requires review

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

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

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

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

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

Run instructions

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

Strengths, limitations and unresolved questions

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

0 evidence rows matching the loaded filters

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

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

How to read the evidence

Sources and history

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

2 source records and release history

Zero-shot benchmarking of RNA language models: Supplementary Information · Original source · bbag098_supplymentary_information_20260209.docx from the Europe PMC supplementary files archive for PMC12963973
Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Original source · Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: lit-rna-20261011-rnalm-zeroshot-protocol-t5-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 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.

Related records

Suggest a correction