Configuration

LAMAR (2k) (zero-shot, Wang et al. 2026)

LAMAR (2k) 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)
LAMAR (2k) (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)	0.848±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
LAMAR (2k) (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)	0.749±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
LAMAR (2k) (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	0.547±0.039	Not reported	Not reported	Not reported	Not reported	Not reported
LAMAR (2k) (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	0.529	Not reported	Not reported	Not reported	Not reported
LAMAR (2k) (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	0.072±0.059	Not reported
LAMAR (2k) (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	0.062
LAMAR (2k) (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	0.093±0.078	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
LAMAR (2k) (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	0.063	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
LAMAR (2k) (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	0.557±0.046	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
LAMAR (2k) (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	0.552	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
LAMAR (2k) (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	0.079±0.065	Not reported	Not reported	Not reported
LAMAR (2k) (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	0.062	Not reported	Not reported
LAMAR (2k) (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	0.108±0.082	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
LAMAR (2k) (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	0.104	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
LAMAR (2k) (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	0.037±0.021 (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
LAMAR (2k) (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	0.037 (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
LAMAR (2k) (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	0.029±0.027	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
LAMAR (2k) (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	0.031	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
LAMAR (2k) (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	0.035±0.020	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
LAMAR (2k) (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	0.035	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
LAMAR (2k) (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	0.032±0.025 (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
LAMAR (2k) (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	0.033 (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
LAMAR (2k) (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	0.691±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
LAMAR (2k) (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	0.842±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
LAMAR (2k) (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	0.769±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
LAMAR (2k) (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	0.510±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
LAMAR (2k) (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	0.542±0.000	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
LAMAR (2k) (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	0.754±0.000	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
LAMAR (2k) (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	0.724±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
LAMAR (2k) (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	0.358±0.005	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
LAMAR (2k) (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	0.711±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
LAMAR (2k) (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
LAMAR (2k) (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	0.527±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
LAMAR (2k) (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	0.532±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
LAMAR (2k) (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	0.722±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
LAMAR (2k) (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	0.366±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

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: LAMAR (2k) (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)	0.547±0.039 AUROC (WT-LLR; mean over assays) unitless · higher Uncertainty: SD 0.039 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LAMAR (2k) 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 'LAMAR (2k)', column 'AUC' (Mean ± Std)
Configuration: LAMAR (2k) (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)	0.529 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 LAMAR (2k) 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 'LAMAR (2k)', column 'AUC' (Median)
Configuration: LAMAR (2k) (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)	0.072±0.059 MCC (WT-LLR; mean over assays) unitless · higher Uncertainty: SD 0.059 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LAMAR (2k) 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 'LAMAR (2k)', column 'MCC' (Mean ± Std)
Configuration: LAMAR (2k) (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)	0.062 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 LAMAR (2k) 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 'LAMAR (2k)', column 'MCC' (Median)
Configuration: LAMAR (2k) (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)	0.093±0.078 Absolute spearman correlation (WT-LLR; mean over assays) unitless · higher Uncertainty: SD 0.078 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LAMAR (2k) 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 'LAMAR (2k)', column 'SR' (Mean ± Std)
Configuration: LAMAR (2k) (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)	0.063 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 LAMAR (2k) 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 'LAMAR (2k)', column 'SR' (Median)
Configuration: LAMAR (2k) (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)	0.557±0.046 AUROC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.046 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LAMAR (2k) 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 'LAMAR (2k)', column 'AUC' (Mean ± Std)
Configuration: LAMAR (2k) (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)	0.552 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 LAMAR (2k) 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 'LAMAR (2k)', column 'AUC' (Median)
Configuration: LAMAR (2k) (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)	0.079±0.065 MCC (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.065 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LAMAR (2k) 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 'LAMAR (2k)', column 'MCC' (Mean ± Std)
Configuration: LAMAR (2k) (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)	0.062 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 LAMAR (2k) 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 'LAMAR (2k)', column 'MCC' (Median)
Configuration: LAMAR (2k) (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)	0.108±0.082 Absolute spearman correlation (PLL-D; mean over assays) unitless · higher Uncertainty: SD 0.082 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LAMAR (2k) 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 'LAMAR (2k)', column 'SR' (Mean ± Std)
Configuration: LAMAR (2k) (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)	0.104 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 LAMAR (2k) 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 'LAMAR (2k)', column 'SR' (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, F1 score (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.037±0.021 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.021 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, 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 'LAMAR (2k)', column 'F1 score' (Mean ± Std)
Configuration: LAMAR (2k) (zero-shot, Wang et al. 2026)	Protocol: Wang et al. 2026 zero-shot secondary structure, TS test set (70 PDB structures), attention, F1 score (median over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.037 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 LAMAR (2k) 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 'LAMAR (2k)', column 'F1 score' (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 (mean over structures) Dataset: TS test set (70 PDB structures) (Wang et al. 2026)	0.029±0.027 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.027 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LAMAR (2k) zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean) lit-rna-20261011-rnalm-zeroshot-protocol-t4-mcc-mean Aggregation: Not reported Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning · Supplementary Table 4, row 'LAMAR (2k)', column 'MCC' (Mean ± Std)
Configuration: LAMAR (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 (2k) (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)	0.035±0.020 F1 (attention; mean over structures) unitless · higher Uncertainty: SD 0.020 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, 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 'LAMAR (2k)', column 'F1 score' (Mean ± Std)
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, F1 score (median over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.035 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 LAMAR (2k) 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 'LAMAR (2k)', column 'F1 score' (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 (mean over structures) Dataset: TS-Hard test set (15 PDB structures) (Wang et al. 2026)	0.032±0.025 MCC (attention; mean over structures) unitless · higher Uncertainty: SD 0.025 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LAMAR (2k) 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 'LAMAR (2k)', column 'MCC' (Mean ± Std)
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 (2k) (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)	0.691±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 LAMAR (2k) 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 'LAMAR (2k)', column '1 − OR'
Configuration: LAMAR (2k) (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)	0.842±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 LAMAR (2k) 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 'LAMAR (2k)', column 'AUC'
Configuration: LAMAR (2k) (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)	0.769±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 LAMAR (2k) 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 'LAMAR (2k)', column 'F1'
Configuration: LAMAR (2k) (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)	0.510±0.002 MCC (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 LAMAR (2k) 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 'LAMAR (2k)', column 'MCC'
Configuration: LAMAR (2k) (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)	0.542±0.000 One minus overlap ratio (FFT embedding; mean over random samplings of sequence pairs) unitless · higher Uncertainty: SD 0.000 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source LAMAR (2k) 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 'LAMAR (2k)', 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-lamar-2k-wang2026

areas: rna-transcriptomes
contexts: research
method types: foundation_model
reported name: LAMAR (2k)
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 'LAMAR'
checkpoint: https://huggingface.co/zhw-e8/LAMAR/tree/main (downloaded 2025/6/23; version column 'mammalian80D_2048len1mer1sw_80M (2k)/mammalian80D_4096len1mer1sw_80M (4k)'; variant label in results tables '2k')
version: 2k

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