Multi-Objective Molecular Design Through Learning Latent Pareto Set

Molecular design inherently involves the optimization of multiple conflicting objectives, such as enhancing bio-activity and ensuring synthesizability. Evaluating these objectives often requires resource-intensive computations or physical experiments. Current molecular design methodologies typically approximate the Pareto set using a limited number of molecules. In this paper, we present an innovative approach, called Multi-Objective Molecular Design through Learning Latent Pareto Set (MLPS). MLPS initially utilizes an encoder-decoder model to seamlessly transform the discrete chemical space into a continuous latent space. We then employ local Bayesian optimization models to efficiently search for local optimal solutions (i.e., molecules) within predefined trust regions. Using surrogate objective values derived from these local models, we train a global Pareto set learning model to understand the mapping between direction vectors (called “preferences”) in the objective space and the entire Pareto set in the continuous latent space. Both the global Pareto set learning model and local Bayesian optimization models collaborate to discover high-quality solutions and adapt the trust regions dynamically. Our work is an effective endeavor towards learning the Pareto set for multi-objective molecular design, providing decision-makers with the capability to fine-tune their preferences and thoroughly explore the Pareto set. Experimental results demonstrate that MLPS achieves state-of-the-art performance across various multi-objective scenarios, encompassing diverse objective types and varying numbers of objectives. The effectiveness of MLPS was further validated through real-world challenges in discovering antifungal peptides with low toxicity and high activity.