Molecular Graph Generation by Decomposition and Reassembling

Designing molecular structures with desired chemical properties is an essential task in drug discovery and materials design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial explosion of the candidate space of molecules. Here we propose a novel decomposition-and-reassembling-based approach, which does not include any optimization in hidden space, and our generation process is highly interpretable. Our method is a two-step procedure: In the first decomposition step, we apply frequent subgraph mining to a molecular database to collect a smaller size of subgraphs as building blocks of molecules. In the second reassembling step, we search desirable building blocks guided via reinforcement learning and combine them to generate new molecules. Our experiments show that our method not only can find better molecules in terms of two standard criteria, the penalized log P and druglikeness, but also can generate drug molecules showing the valid intermediate molecules.