An Interpretability-augmented Genetic Expert for Deep Molecular Optimization

Pierre Wüthrich, Jun Jin Choong, Shinya Yuki

Keywords: graph neural network, generative model, molecular optimization

TL;DR: We proposed an interpretability-augmented genetic expert for deep molecular optimization

Abstract: The recently proposed genetic expert guided learning (GEGL) framework has demonstrated impressive performances on several de novo molecular design tasks. Despite the displayed state-of-the art results, the proposed system relies on an expert-designed Genetic expert. Although hand-crafted experts allow to navigate the chemical space efficiently, designing such experts requires a significant amount of effort and might contain inherent biases which can potentially slow down convergence or even lead to sub-optimal solutions. In this research, we propose a novel genetic expert named InFrag which is free of design rules and can generate new molecules by combining promising molecular fragments. Fragments are obtained by using an additional graph convolutional neural network which computes attributions for each atom for a given molecule. Molecular substructures which contribute positively to the task score are kept and combined to propose novel molecules. We experimentally demonstrate that, within the GEGL framework, our proposed attribution-based genetic expert is either competitive or outperforms the original expert-designed genetic expert on goal-directed optimization tasks. When limiting the number of optimization rounds to one and three rounds, a performance increase of approximately $ 43\%$ and $20\%$ respectively is observed compared to the baseline genetic expert.