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Barking up the right tree: an approach to search over molecule synthesis DAGs
John Bradshaw · Brooks Paige · Matt Kusner · Marwin Segler · José Miguel Hernández-Lobato

Wed Dec 09 08:00 AM -- 08:10 AM (PST) @ Orals & Spotlights: COVID/Applications/Composition
in Orals & Spotlights Track 15: COVID/Applications/Composition »

When designing new molecules with particular properties, it is not only important what to make but crucially how to make it. These instructions form a synthesis directed acyclic graph (DAG), describing how a large vocabulary of simple building blocks can be recursively combined through chemical reactions to create more complicated molecules of interest. In contrast, many current deep generative models for molecules ignore synthesizability. We therefore propose a deep generative model that better represents the real world process, by directly outputting molecule synthesis DAGs. We argue that this provides sensible inductive biases, ensuring that our model searches over the same chemical space that chemists would also have access to, as well as interoperability. We show that our approach is able to model chemical space well, producing a wide range of diverse molecules, and allows for unconstrained optimization of an inherently constrained problem: maximize certain chemical properties such that discovered molecules are synthesizable.

Author Information

John Bradshaw (University of Cambridge/MPI for Intelligent Systems)
Brooks Paige (University College London)
Matt Kusner (University College London)
Marwin Segler (BenevolentAI)
Jose Miguel Hernández-Lobato (University of Cambridge)

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