CELLS: Cost-Effective Evolution in Latent Space for Goal-Directed Molecular Generation

• URL: http://arxiv.org/abs/2112.00905v1
• Date: Tue, 30 Nov 2021 11:02:18 GMT
• Title: CELLS: Cost-Effective Evolution in Latent Space for Goal-Directed Molecular Generation
• Authors: Zhiyuan Chen, Xiaomin Fang, Fan Wang, Xiaotian Fan, Hua Wu, Haifeng Wang
• Abstract summary: We propose a cost-effective evolution strategy in latent space, which optimize the molecular latent representation vectors. We adopt a pre-trained molecular generative model to map the latent and observation spaces. We conduct extensive experiments on multiple optimization tasks comparing the proposed framework to several advanced techniques.
• Score: 23.618366377098614
• License: http://creativecommons.org/licenses/by-nc-sa/4.0/
• Abstract: Efficiently discovering molecules that meet various property requirements can significantly benefit the drug discovery industry. Since it is infeasible to search over the entire chemical space, recent works adopt generative models for goal-directed molecular generation. They tend to utilize the iterative processes, optimizing the parameters of the molecular generative models at each iteration to produce promising molecules for further validation. Assessments are exploited to evaluate the generated molecules at each iteration, providing direction for model optimization. However, most previous works require a massive number of expensive and time-consuming assessments, e.g., wet experiments and molecular dynamic simulations, leading to the lack of practicability. To reduce the assessments in the iterative process, we propose a cost-effective evolution strategy in latent space, which optimizes the molecular latent representation vectors instead. We adopt a pre-trained molecular generative model to map the latent and observation spaces, taking advantage of the large-scale unlabeled molecules to learn chemical knowledge. To further reduce the number of expensive assessments, we introduce a pre-screener as the proxy to the assessments. We conduct extensive experiments on multiple optimization tasks comparing the proposed framework to several advanced techniques, showing that the proposed framework achieves better performance with fewer assessments.

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