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Optimizing molecules for desired properties is a fundamental yet challenging task in chemistry, material science, and drug discovery. This paper develops a novel algorithm for optimizing molecular properties via an Expectation- Maximization (EM) like explainable evolutionary process. The algorithm is designed to mimic human experts in the process of searching for desirable molecules and alternate between two stages: the first stage on explainable local search which identifies rationales, i.e., critical subgraph patterns accounting for desired molecular properties, and the second stage on molecule completion which explores the larger space of molecules containing good rationales. We test our approach against various baselines on a real-world multi-property optimization task where each method is given the same number of queries to the property oracle. We show that our evolution-by-explanation algorithm is 79% better than the best baseline in terms of a generic metric combining aspects such as success rate, novelty, and diversity. Human expert evaluation on optimized molecules shows that 60% of top molecules obtained from our methods are deemed successful.
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Multi-Objective Molecule Generation using Interpretable Substructures
Drug discovery aims to find novel compounds with specified chemical property profiles. In terms of generative modeling, the goal is to learn to sample molecules in the intersection of multiple property constraints. This task becomes increasingly challenging when there are many property constraints. We propose to offset this complexity by composing molecules from a vocabulary of substructures that we call molecular rationales. These rationales are identified from molecules as substructures that are likely responsible for each property of interest. We then learn to expand rationales into a full molecule using graph generative models. Our final generative model composes molecules as mixtures of multiple rationale completions, and this mixture is fine-tuned to preserve the properties of interest. We evaluate our model on various drug design tasks and demonstrate significant improvements over state-of-the-art baselines in terms of accuracy, diversity, and novelty of generated compounds.
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- Award ID(s):
- 1918839
- PAR ID:
- 10219628
- Date Published:
- Journal Name:
- Proceedings of the 37th International Conference on Machine Learning
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Accepted Manuscript1.0
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