A neural network apparatus for generating a new chemical structure may receive a structure input of a chemical structure; generate, based on the structure input, a negative attention vector that indicates a respective probability of presence of each of a plurality of blacklists in the structure input; generate a structure expression by encoding the structure input; generate a final reverse blacklist vector that does not include the plurality of blacklists, based on the negative attention vector and the structure expression; and generate the new chemical structure by decoding the final reverse blacklist vector.