The bond prediction module comprises a two-layer GRU 45 followed by a two-layer fully connected layer. The initial state vector of the GRU is a concatenation of the graph hidden state vector h g and the 64-dimensional embedded representation of the predicted atoms Emb(y a ), and is converted to 256 dimensions in a single fully connected layer. The output of the GRU is transformed to y b by the fully connected layer with the hidden layer having 64 dimensions and ReLu function as the activation function. The dimension of outputs is four, including the label indicating no bond. The probability of a bond is obtained by applying a Softmax function.