Table 1 Performance comparison on CDS downstream tasks using Spearman’s correlation

	Model	mRFP expression	Fungal expression	E. coli proteins	mRNA stability	Tc-riboswitch	SARS-CoV-2 vaccine degradation
Nucleotide-based	TextCNN	0.62	0.53	0.39	0.01	0.41	0.55
	RNABERT	0.40	0.41	0.39	0.16	0.47	0.64
	RNA-FM	0.80	0.59	0.43	0.34	0.58	0.74
	UTRLM	0.68	0.48	0.19	0.23	0.19	0.78
	RNAErnie	0.79	0.42	0.19	0.16	0.34	0.81
	ERNIE-RNA	0.50	0.31	0.30	0.44	0.39	0.87
kmer-based	3UTRBERT	0.85	0.69	0.47	0.50	0.30	0.84
Codon-based	TF-IDF	0.57	0.68	0.44	0.54	0.49	0.69
	TextCNN	0.78	0.76	0.36	0.26	0.43	0.80
	Codon2vec	0.77	0.61	0.43	0.33	0.56	0.70
	mRNAFM	0.88	0.78	0.49	0.48	0.26	0.85
	CaLM	0.86	0.75	0.58	0.44	0.37	0.84
	CodonBERT	0.88	0.89	0.57	0.35	0.48	0.78
Combined	mRNABERT	0.89	0.89	0.58	0.56	0.58	0.89

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