Algorithm 1 Generating synonymous codon mask

$$\begin{array}{cc}\hfill & \mathrm{Require}:\text{Input codon sequence:}\text{input}\_\text{codons}\in {\mathbb{R}}^{(B,\text{seqlen},4)}\hfill \\ \hfill & \mathrm{Require}:\text{Synonymous codon mapping:}\text{synonymous}\_\text{codons}\_\text{dict}\hfill \\ \hfill & \mathrm{Require}:\text{Nucleotide index mapping:}\text{nucleotide}\_\text{index}=\{A:0,T:1,C:2,G:3\}\hfill \\ \hfill & \mathrm{Ensure}:\text{Output mask:}M\in {\mathbb{R}}^{(B,\text{seqlen},4)}\hfill \\ \hfill & 1:\text{Initialize mask:}M\leftarrow 0\hfill \\ \hfill & 2:\mathbf{for}\text{each batch index}b\mathbf{do}\hfill \\ \hfill & 3:\mathbf{for}\text{each nucleotide position}p\text{in}[1,\text{seqlen}∕3]\mathbf{do}\hfill \\ \hfill & 4:\text{codon}\_\text{start}\leftarrow p\times 3\hfill \\ \hfill & 5:\text{codon}\leftarrow \text{input}\_\text{codons}[b,\text{codon}\_\text{start}:\text{codon}\_\text{start}+3]\hfill \\ \hfill & 6:\text{aa}\leftarrow \text{codon}\_\text{to}\_\text{amino}\_\text{acid}(\text{codon})\hfill \\ \hfill & 7:\text{synonymous}\_\text{codons}\leftarrow \text{synonymous}\_\text{codons}\_\text{dict}[\text{aa}]\hfill \\ \hfill & 8:\mathbf{for}\text{each synonymous codon syn}\_\text{codon}\mathbf{do}\hfill \\ \hfill & 9:\mathbf{for}\text{each nucleotide position}{p}^{\prime }\text{in}[0,1,2]\mathbf{do}\hfill \\ \hfill & 10:\text{nucleotide}\leftarrow \text{syn}\_\text{codon}[p^{\prime }]\hfill \\ \hfill & 11:M[b,\text{codon}\_\text{start}+p^{\prime },\text{nucleotide}\_\text{index}[\text{nucleotide}]]\leftarrow 1\hfill \\ \hfill & 12:\mathbf{end}\mathbf{for}\hfill \\ \hfill & 13:\mathbf{end}\mathbf{for}\hfill \\ \hfill & 14:\mathbf{end}\mathbf{for}\hfill \\ \hfill & 15:\mathbf{end}\mathbf{for}\hfill \\ \hfill & 16:\mathbf{return}M\hfill \end{array}$$