Initial hierarchical embeddings that include an initial molecular graph embedding, an initial subgraph embedding, and an initial atomic embedding, are generated. An initial molecular graph includes initial nodes and initial edges, the initial nodes represent initial atoms, the initial edges represent chemical bonds connecting the initial atoms, and each initial subgraph represents a regional molecular structure of the initial molecular graph. Noises are removed from the initial hierarchical embeddings to obtain generated hierarchical embeddings, the noises are predicted based on a machine learning model that includes learned relationships among molecular graphs, subgraphs, and atoms. The generated hierarchical embeddings are decoded into molecular structure information of a generated molecule, and the molecular structure information includes atom types of used atoms in the generated molecule and chemical bond types of inter-atomic chemical bonds connecting the used atoms in the generated molecule. Apparatus and non-transitory computer-readable storage medium counterpart embodiments are also contemplated.