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Workshop: Machine Learning in Structural Biology Workshop

ChemSpacE: Interpretable and Interactive Chemical Space Exploration

Yuanqi Du · Xian Liu · Nilay Shah · Shengchao Liu · Jieyu Zhang · Bolei Zhou


Discovering meaningful molecules in the vast combinatorial chemical space has been a long-standing challenge in many fields from materials science to drug discovery. Recent advances in machine learning, especially generative models, have made remarkable progress and demonstrate considerable promise for automated molecule design. Nevertheless, most molecule generative models remain black-box systems, whose utility is limited by a lack of interpretability and human participation in the generation process. In this work we propose \textbf{Chem}ical \textbf{Spac}e \textbf{E}xplorer (ChemSpacE), a simple yet effective method for exploring the chemical space with pre-trained deep generative models. It enables users to interact with existing generative models and inform the molecule generation process. We demonstrate the efficacy of ChemSpacE on the molecule optimization task and the molecule manipulation task in single property and multi-property settings. On the molecule optimization task, the performance of ChemSpacE is on par with previous black-box optimization methods yet is considerably faster and more sample efficient. Furthermore, the interface from ChemSpacE facilitates human-in-the-loop chemical space exploration and interactive molecule design.

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