RNA-MSM (zero-shot, Wang et al. 2026); https://github.com/yikunpku/RNA-MSM (downloaded 2024/10/8; version column '-'; variant label in results tables 'none')

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Evaluations and results

8 evaluations · 8 results. Different protocols are not a single leaderboard.

Sorted by F1 (attention; mean over structures) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	F1 (attention; mean over structures)	F1 (attention; median over structures)	MCC (attention; mean over structures)	MCC (attention; median over structures)
RNA-MSM (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures), TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.645±0.136 (best in column)	Not reported	Not reported	Not reported
RNA-MSM (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot secondary structure, TS test set (70 PDB structures), attention, F1 score (mean over structures), TS test set (70 PDB structures) (Wang et al. 2026)	0.582±0.217	Not reported	Not reported	Not reported
RNA-MSM (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot secondary structure, TS test set (70 PDB structures), attention, F1 score (median over structures), TS test set (70 PDB structures) (Wang et al. 2026)	Not reported	0.631	Not reported	Not reported
RNA-MSM (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot secondary structure, TS test set (70 PDB structures), attention, MCC (mean over structures), TS test set (70 PDB structures) (Wang et al. 2026)	Not reported	Not reported	0.588±0.217	Not reported
RNA-MSM (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot secondary structure, TS test set (70 PDB structures), attention, MCC (median over structures), TS test set (70 PDB structures) (Wang et al. 2026)	Not reported	Not reported	Not reported	0.634
RNA-MSM (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (median over structures), TS-Hard test set (15 PDB structures) (Wang et al. 2026)	Not reported	0.679 (best in column)	Not reported	Not reported
RNA-MSM (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, MCC (mean over structures), TS-Hard test set (15 PDB structures) (Wang et al. 2026)	Not reported	Not reported	0.654±0.138 (best in column)	Not reported
RNA-MSM (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, MCC (median over structures), TS-Hard test set (15 PDB structures) (Wang et al. 2026)	Not reported	Not reported	Not reported	0.69 (best in column)

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Tested configuration	Protocol and dataset	Finding	Evidence and details
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, F1 score (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.582±0.217 F1 (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, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-f1-score-mean Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'RNA-MSM', column 'F1 score' (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, F1 score (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.631 F1 (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, F1 score, median) lit-rna-20261011-rnalm-zeroshot-protocol-t4-f1-score-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 'F1 score' (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 (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)
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)
Configuration: RNA-MSM (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.645±0.136 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.136 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-MSM zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-mean Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 5, row 'RNA-MSM', column 'F1 score' (Mean ± Std)
Configuration: RNA-MSM (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS-Hard test set (15 PDB structures), attention, F1 score (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.679 F1 (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, F1 score, median) lit-rna-20261011-rnalm-zeroshot-protocol-t5-f1-score-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 'F1 score' (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 (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)
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)

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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

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Technical metadata and extraction receipts

Stable ID: lit-rna-20261011-rnalm-zeroshot-config-rna-msm-wang2026

areas: rna-transcriptomes
contexts: research
method types: foundation_model
reported name: RNA-MSM
foundation model eligible: true
parameters: Pretrained weights used without fine-tuning (zero-shot); attention maps, embeddings or token logits read out as described in the Methods
access reuse: Public download location listed in Supplementary Table 1
source locator: Supplementary Table 1 row 'RNA-MSM'
checkpoint: https://github.com/yikunpku/RNA-MSM (downloaded 2024/10/8; version column '-'; variant label in results tables 'none')
missing metadata: version: reason: unreported; note: No version column entry for this checkpoint in Supplementary Table 1

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