Configuration

Uni-RNA (L16) (zero-shot, Wang et al. 2026)

Uni-RNA (L16) evaluated zero-shot by Wang et al. 2026.

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.

Evaluations and results

36 evaluations · 36 results. Different protocols are not a single leaderboard.

Sorted by AUROC (CLS embedding; mean over random samplings of sequence pairs) (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	AUROC (CLS embedding; mean over random samplings of sequence pairs)	AUROC (FFT embedding; mean over random samplings of sequence pairs)	F1 (attention; mean over structures)	F1 (attention; median over structures)	F1 (CLS embedding; mean over random samplings of sequence pairs)	F1 (FFT embedding; mean over random samplings of sequence pairs)	MCC (attention; mean over structures)	MCC (attention; median over structures)	MCC (CLS embedding; mean over random samplings of sequence pairs)	MCC (FFT embedding; mean over random samplings of sequence pairs)	One minus overlap ratio (CLS embedding; mean over random samplings of sequence pairs)	One minus overlap ratio (FFT embedding; mean over random samplings of sequence pairs)	Absolute spearman correlation (PLL-D; mean over assays)	Absolute spearman correlation (PLL-D; median over assays)	Absolute spearman correlation (WT-LLR; mean over assays)	Absolute spearman correlation (WT-LLR; median over assays)	AUROC (PLL-D; mean over assays)	AUROC (PLL-D; median over assays)	AUROC (WT-LLR; mean over assays)	AUROC (WT-LLR; median over assays)	MCC (PLL-D; mean over assays)	MCC (PLL-D; median over assays)	MCC (WT-LLR; mean over assays)	MCC (WT-LLR; median over assays)
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), CLS embedding, AUC (mean over repeated random samplings of sequence pairs), RfamSample (561 Rfam families) (Wang et al. 2026)	0.849±0.001 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, AUC (mean over repeated random samplings of sequence pairs), ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.803±0.001	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), WT-LLR, AUC (mean over assays), RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.584±0.080	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), WT-LLR, AUC (median over assays), RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.554	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), WT-LLR, MCC (mean over assays), RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.140±0.113	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), WT-LLR, MCC (median over assays), RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.1
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), WT-LLR, SR (mean over assays), RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.173±0.164	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), WT-LLR, SR (median over assays), RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.111	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, AUC (mean over assays), RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.575±0.072	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, AUC (median over assays), RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.543	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, MCC (mean over assays), RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.107±0.105	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, MCC (median over assays), RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.063	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, SR (mean over assays), RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.145±0.142	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, SR (median over assays), RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.087	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (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)	Not reported	Not reported	0.307±0.197 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (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	Not reported	Not reported	0.307 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (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	Not reported	Not reported	Not reported	Not reported	0.311±0.200 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (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	Not reported	Not reported	Not reported	Not reported	0.308	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (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)	Not reported	Not reported	0.284±0.163	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (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	Not reported	Not reported	0.286	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (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	Not reported	Not reported	Not reported	Not reported	0.286±0.162	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (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	Not reported	Not reported	Not reported	Not reported	0.323 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, 1 − OR (mean over repeated random samplings of sequence pairs), RfamSample (561 Rfam families) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.683±0.002 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, AUC (mean over repeated random samplings of sequence pairs), RfamSample (561 Rfam families) (Wang et al. 2026)	Not reported	0.828±0.001 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, F1 (mean over repeated random samplings of sequence pairs), RfamSample (561 Rfam families) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	0.759±0.001 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, MCC (mean over repeated random samplings of sequence pairs), RfamSample (561 Rfam families) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.480±0.003 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), FFT embedding, 1 − OR (mean over repeated random samplings of sequence pairs), ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.623±0.002	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), FFT embedding, AUC (mean over repeated random samplings of sequence pairs), ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	Not reported	0.798±0.001	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), FFT embedding, F1 (mean over repeated random samplings of sequence pairs), ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	0.750±0.001	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), FFT embedding, MCC (mean over repeated random samplings of sequence pairs), ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.440±0.002	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), CLS embedding, 1 − OR (mean over repeated random samplings of sequence pairs), RfamSample (561 Rfam families) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.709±0.002 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), CLS embedding, F1 (mean over repeated random samplings of sequence pairs), RfamSample (561 Rfam families) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	0.776±0.001 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), CLS embedding, MCC (mean over repeated random samplings of sequence pairs), RfamSample (561 Rfam families) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.528±0.002 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, 1 − OR (mean over repeated random samplings of sequence pairs), ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.636±0.001	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, F1 (mean over repeated random samplings of sequence pairs), ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	0.748±0.001	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Uni-RNA (L16) (zero-shot, Wang et al. 2026)Evaluation	Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), CLS embedding, MCC (mean over repeated random samplings of sequence pairs), ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.455±0.007	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported

All 36 result rows with coverage, uncertainty and sources

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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: Uni-RNA (L16) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), WT-LLR, AUC (mean over assays) Dataset: RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	0.584±0.080 AUROC (WT-LLR; mean over assays) unitless · higher Uncertainty: SD 0.080 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (WT-LLR, AUC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t10-auc-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 10, row 'Uni-RNA (L16)', column 'AUC' (Mean ± Std)
Configuration: Uni-RNA (L16) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), WT-LLR, AUC (median over assays) Dataset: RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	0.554 AUROC (WT-LLR; median over assays) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (WT-LLR, AUC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t10-auc-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 10, row 'Uni-RNA (L16)', column 'AUC' (Median)
Configuration: Uni-RNA (L16) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), WT-LLR, MCC (mean over assays) Dataset: RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	0.140±0.113 MCC (WT-LLR; mean over assays) unitless · higher Uncertainty: SD 0.113 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (WT-LLR, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t10-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 10, row 'Uni-RNA (L16)', column 'MCC' (Mean ± Std)
Configuration: Uni-RNA (L16) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), WT-LLR, MCC (median over assays) Dataset: RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	0.1 MCC (WT-LLR; median over assays) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (WT-LLR, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t10-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 10, row 'Uni-RNA (L16)', column 'MCC' (Median)
Configuration: Uni-RNA (L16) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), WT-LLR, SR (mean over assays) Dataset: RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	0.173±0.164 Absolute spearman correlation (WT-LLR; mean over assays) unitless · higher Uncertainty: SD 0.164 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (WT-LLR, SR, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t10-sr-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 10, row 'Uni-RNA (L16)', column 'SR' (Mean ± Std)
Configuration: Uni-RNA (L16) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), WT-LLR, SR (median over assays) Dataset: RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	0.111 Absolute spearman correlation (WT-LLR; median over assays) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (WT-LLR, SR, median) lit-rna-20261011-rnalm-zeroshot-protocol-t10-sr-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 10, row 'Uni-RNA (L16)', column 'SR' (Median)
Configuration: Uni-RNA (L16) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, AUC (mean over assays) Dataset: RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	0.575±0.072 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.072 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, AUC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t11-auc-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 11, row 'Uni-RNA (L16)', column 'AUC' (Mean ± Std)
Configuration: Uni-RNA (L16) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, AUC (median over assays) Dataset: RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	0.543 AUROC (PLL-D; median over assays) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, AUC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t11-auc-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 11, row 'Uni-RNA (L16)', column 'AUC' (Median)
Configuration: Uni-RNA (L16) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, MCC (mean over assays) Dataset: RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	0.107±0.105 MCC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.105 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t11-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 11, row 'Uni-RNA (L16)', column 'MCC' (Mean ± Std)
Configuration: Uni-RNA (L16) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, MCC (median over assays) Dataset: RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	0.063 MCC (PLL-D; median over assays) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, MCC, median) lit-rna-20261011-rnalm-zeroshot-protocol-t11-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 11, row 'Uni-RNA (L16)', column 'MCC' (Median)
Configuration: Uni-RNA (L16) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, SR (mean over assays) Dataset: RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	0.145±0.142 Absolute spearman correlation (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.142 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, SR, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t11-sr-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 11, row 'Uni-RNA (L16)', column 'SR' (Mean ± Std)
Configuration: Uni-RNA (L16) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, SR (median over assays) Dataset: RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	0.087 Absolute spearman correlation (PLL-D; median over assays) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, SR, median) lit-rna-20261011-rnalm-zeroshot-protocol-t11-sr-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 11, row 'Uni-RNA (L16)', column 'SR' (Median)
Configuration: Uni-RNA (L16) (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)	0.307±0.197 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.197 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) 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 'Uni-RNA (L16)', column 'F1 score' (Mean ± Std)
Configuration: Uni-RNA (L16) (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)	0.307 F1 (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 Uni-RNA (L16) 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 'Uni-RNA (L16)', column 'F1 score' (Median)
Configuration: Uni-RNA (L16) (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)	0.311±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 Uni-RNA (L16) 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 'Uni-RNA (L16)', column 'MCC' (Mean ± Std)
Configuration: Uni-RNA (L16) (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)	0.308 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 Uni-RNA (L16) 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 'Uni-RNA (L16)', column 'MCC' (Median)
Configuration: Uni-RNA (L16) (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)	0.284±0.163 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.163 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) 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 'Uni-RNA (L16)', column 'F1 score' (Mean ± Std)
Configuration: Uni-RNA (L16) (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)	0.286 F1 (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 Uni-RNA (L16) 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 'Uni-RNA (L16)', column 'F1 score' (Median)
Configuration: Uni-RNA (L16) (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)	0.286±0.162 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.162 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) 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 'Uni-RNA (L16)', column 'MCC' (Mean ± Std)
Configuration: Uni-RNA (L16) (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)	0.323 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 Uni-RNA (L16) 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 'Uni-RNA (L16)', column 'MCC' (Median)
Configuration: Uni-RNA (L16) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, 1 − OR (mean over repeated random samplings of sequence pairs) Dataset: RfamSample (561 Rfam families) (Wang et al. 2026)	0.683±0.002 One minus overlap ratio (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.002 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, 1 − OR, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t6-1-or-sampled-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 6, row 'Uni-RNA (L16)', column '1 − OR'
Configuration: Uni-RNA (L16) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, AUC (mean over repeated random samplings of sequence pairs) Dataset: RfamSample (561 Rfam families) (Wang et al. 2026)	0.828±0.001 AUROC (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.001 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, AUC, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t6-auc-sampled-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 6, row 'Uni-RNA (L16)', column 'AUC'
Configuration: Uni-RNA (L16) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, F1 (mean over repeated random samplings of sequence pairs) Dataset: RfamSample (561 Rfam families) (Wang et al. 2026)	0.759±0.001 F1 (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.001 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, F1, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t6-f1-sampled-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 6, row 'Uni-RNA (L16)', column 'F1'
Configuration: Uni-RNA (L16) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot family classification, RfamSample (561 Rfam families), FFT embedding, MCC (mean over repeated random samplings of sequence pairs) Dataset: RfamSample (561 Rfam families) (Wang et al. 2026)	0.480±0.003 MCC (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.003 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, MCC, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t6-mcc-sampled-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 6, row 'Uni-RNA (L16)', column 'MCC'
Configuration: Uni-RNA (L16) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot RNA type classification, ArchiveII-Nr (1273 RNAs), FFT embedding, 1 − OR (mean over repeated random samplings of sequence pairs) Dataset: ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)	0.623±0.002 One minus overlap ratio (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.002 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Uni-RNA (L16) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, 1 − OR, sampled-mean) lit-rna-20261011-rnalm-zeroshot-protocol-t7-1-or-sampled-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 7, row 'Uni-RNA (L16)', column '1 − OR'

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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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Stable ID: lit-rna-20261011-rnalm-zeroshot-config-uni-rna-l16-wang2026

areas: rna-transcriptomes
contexts: research
method types: foundation_model
reported name: Uni-RNA (L16)
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 'Uni-RNA'
checkpoint: https://github.com/ComDec/unirna_tf (downloaded 2025/12/17; version column 'unirna_L12 (L12)/unirna_L16 (L16)/unirna_L8 (L8)'; variant label in results tables 'L16')
version: L16

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