Abstract
Molecular design using data-driven generative models has emerged as a promising technology, impacting various fields such as drug discovery and the development of functional materials. However, this approach is often susceptible to optimization failure due to reward hacking, where prediction models fail to accurately predict properties for designed molecules that considerably deviate from the training data. While methods for estimating prediction reliability, such as the applicability domain (AD), have been proposed for mitigating reward hacking, multi-objective optimization makes it challenging. The difficulty arises from the need to determine in advance whether the multiple ADs with some reliability levels overlap in chemical space, and to appropriately adjust the reliability levels for each property prediction. Herein, we propose a reliable design framework to perform multi-objective optimization using generative models while preventing reward hacking. To demonstrate the effectiveness of the proposed framework, we designed candidates for anticancer drugs as a typical example of multi-objective optimization. We successfully designed molecules with high predicted values and reliabilities, including an approved drug. In addition, the reliability levels can be automatically adjusted according to the property prioritization specified by the user without any detailed settings. Our approach presents a solution to the essential problem of designing molecules using data-driven generative models.
Supplementary materials
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Supporting Information
Description
Scaling function to standardize reliability levels; Examples of designed molecules with high reward values; Designed molecules identical to known molecules that are active against EGFR; Examples of molecules designed without reliability consideration; Examples of molecules reproduced as a result of molecular design when similar molecules across the three datasets are removed; Example of molecules with high reward values designed when similar molecules across the three datasets are removed; Process of molecular design with the adjusted reliability levels when the number of properties to optimize was 13; The values of adjusted reliability levels when 13 properties to be optimized; Scaling functions for properties; Correlation plots of the predicted properties for test data in each fold and corresponding experimental values.
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