Paddy: an evolutionary optimization algorithm for chemical systems and spaces

Abstract

Optimization of chemical systems and processes have been enhanced and enabled by the development of new algorithms and analytical approaches. While several methods systematically investigate how underlying variables correlate with a given outcome, there is often a substantial number of experiments needed to accurately model such relationships. As chemical systems increase in complexity, algorithms are needed to propose experiments that efficiently optimize the underlying objective, while effectively sampling parameter space to avoid convergence on local minima. We have developed the Paddy software package based on the Paddy field algorithm, a biologically inspired evolutionary optimization algorithm that propagates parameters without direct inference of the underlying objective function. We benchmarked Paddy against several optimization approaches: the Tree of Parzen Estimator through the Hyperopt software library, Bayesian optimization with a Gaussian process via Meta's Ax framework, and two population-based methods from EvoTorch—an evolutionary algorithm with Gaussian mutation, and a genetic algorithm using both a Gaussian mutation and single-point crossover—all representing diverse approaches to optimization. Paddy's performance is benchmarked for mathematical and chemical optimization tasks including global optimization of a two-dimensional bimodal distribution, interpolation of an irregular sinusoidal function, hyperparameter optimization of an artificial neural network tasked with classification of solvent for reaction components, targeted molecule generation by optimizing input vectors for a decoder network, and sampling discrete experimental space for optimal experimental planning. Paddy demonstrates robust versatility by maintaining strong performance across all optimization benchmarks, compared to other algorithms with varying performance. Additionally, Paddy avoids early convergence with its ability to bypass local optima in search of global solutions. We anticipate that the facile, versatile, robust and open-source nature of Paddy will serve as a toolkit in chemical problem-solving tasks towards automated experimentation with high priority for exploratory sampling and innate resistance to early convergence to identify optimal solutions.