all atoms within the molecule or bimolecule are encoded using embedding layer according to their elements, while the first element in eq (1) represents the embedding layer of CLS atom. n max refers to the maximum number of atoms in a molecule or bimolecule within the database. We employ PAD token to ensure a fixed input size when the number of atoms is less than n max . The initial pair representation is denoted as the molecular or bimolecular distance kernel matrix P 0 , where