## 2 Materials and Methods
### Methods
\begin{table}
\begin{tabular}{c c} \hline \hline
**Layer** & **Parameters** \\ \hline Input & - \\ \hline Gaussian Noise & Standard deviation = 0.2 \\ \hline Conv1D & Kernels = 128 \\ Kernel size = 7 \\ \hline Group Normalization & Groups = 2 \\ \hline Max pooling & Window size = 2 \\ \hline Dropout & Dropout rate = 0.2 \\ \hline Conv1D & Kernels = 256 \\ Kernel size = 6 \\ \hline Group Normalization & Groups = 2 \\ \hline Max pooling & Window size = 2 \\ \hline Dropout & Dropout rate = 0.15 \\ \hline Conv1D & Kernels = 256 \\ Kernel size = 5 \\ \hline Group Normalization & Groups = 2 \\ \hline Max pooling & Window size = 2 \\ \hline Dropout & Dropout rate = 0.04 \\ \hline Flatten & - \\ \hline Dense & Nodes = 16 \\ \hline Output & Nodes = 1 \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Detailed architecture of the proposed model for both stages. Figure 1: Illustration of the proposed model architecture. To demonstrate our model's performance, we used another highly regarded encoding technique denoted 'nucleotide chemical properties (NCP) and nucleotide density (ND)'. This encoding technique accounts for the fact that the four nucleic acids, adenine (A), cytosine (C), guanine (G), and thymine (T), have diverse chemical properties [29]. In addition, the technique allows adenine and cytosine to be sorted as amino groups, while guanine and thymine are classified as keto groups based on their chemical functionality. Cytosine and guanine form strong hydrogen bonds, whereas adenine and thymine can form weak hydrogen bonds. Adenine and guanine are purines, whereas cytosine and thymine are pyrimidines. Consequently, nucleic acids can be divided into three different classes, as shown in Table 2.  
To define these properties, we used the trinity of the ring structures, hydrogen bond strength, and functional group classifications. In addition, the values of 0 and 1 were assigned to the trinity for classification purposes. For the first element ring, a structure with a value of 1 indicates a purine, and a value of 0 indicates a pyrimidine. For the second element of the trinity, the values 0 and 1 indicate the strength of the hydrogen bonds; 1 classifies a strong hydrogen bond, and 0 classifies a weak hydrogen bond. The third and last element of our trinity indicates whether the nucleotide is an amino or keto, where 1 signifies an amino, and 0 characterizes a keto. To incorporate these properties, three coordinates (\(x,y,z\)) were utilized to illustrate the chemical properties of the four nucleotides. If the ring structure, hydrogen bond, and chemical functionality are represented by the coordinates \(x,y,\) and \(z\), then a particular nucleotide can be encoded by (\(x_{i},y_{i},z_{i}\)) [30]:  
\[x_{i}=\left\{ \begin{array}{l}1\;if\;s_{i}\in\{A,\;G\}\\ 0\;if\;s_{i}\in\{C,\;T\}\end{array} \right. \tag{3}\]  
\[y_{i}=\left\{ \begin{array}{l}1\;if\;s_{i}\in\{A,\;T\}\\ 0\;if\;s_{i}\in\{C,\;G\}\end{array} \right. \tag{4}\]  
\[z_{i}=\left\{ \begin{array}{l}1\;if\;s_{i}\in\{A,\;C\}\\ 0\;if\;s_{i}\in\{G,\;T\}\end{array} \right. \tag{5}\]  
where nucleotide density (ND) provides information about the nucleotide's frequency as well as the nucleotide's location. The nucleotide density \(d_{i}\) of a specific nucleotide \(n_{j}\) at a certain position in a given sequence \(i\) can be defined as follows:  
\[d_{i}=\frac{1}{|N_{i}|}\underset{j=1}{\sum}f\big{(}n_{j}\big{)},\;f\big{(}n_ {j}\big{)}=\left\{ \begin{array}{l}1\;if\;n_{j}=q\\ 0\;otherwise\end{array} \right. \tag{6}\]  
where \(d_{i}\) indicates the nucleotide density of each position \(i\) in a given DNA sequence. \(|\,N_{i}|\) characterizes the length of the subsequence from the very first position to position \(i\) of the sequence. The \(n_{j}\) states the base in position \(j\) of a given DNA sequence and \(q\in\{A,\;C,\;G,\;T\}\). The combination of the nucleotide density and nucleotide chemical properties yields a matrix with 41 rows and 4 columns, which are used to epitomize each DNA sequence. The first three elements represent the nucleotide chemical properties, and