Fig. 2

Architecture overview of the proposed model, AptaTrans. A The AptaTrans architecture consists of four parts: tokenization, transformer-based encoders, convolution blocks, and a fully connected layer. In (A), an interaction matrix is generated by computing the dot products of the pairs between the RNA and amino acid token embedding vectors from the encoders. B Shows a transformer-based encoder that includes an embedding layer, a positional encoder, a vanilla transformer encoder, C convolution layers, and D a single convolution layer that includes batch normalization and an activation function