Paddy: Evolutionary Optimization Algorithm for Chemical Systems and Spaces

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Paddy: Evolutionary Optimization Algorithm for Chemical Systems and Spaces


Armen Beck, Jonathan Fine, Gaurav Chopra


Optimization of chemical systems and processes have been enhanced and enabled by the guidance of algorithms and analytical approaches. While many methods will systematically investigate how underlying variables govern a given outcome, there is often a substantial number of experiments needed to accurately model these relations. As chemical systems increase in complexity, inexhaustive processes must propose experiments that efficiently optimize the underlying objective, while ideally avoiding convergence on unsatisfactory local minima. We have developed the Paddy software package around the Paddy Field Algorithm, a biologically inspired evolutionary optimization algorithm that propagates parameters without direct inference of the underlying objective function. Benchmarked against the Tree of Parzen Estimator, a Bayesian algorithm implemented in the Hyperopt software Library, Paddy displays efficient optimization with lower runtime, and avoidance of early convergence. Herein we report these findings for the cases of: 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, and targeted molecule generation via optimization of input vectors for a decoder network. We anticipate that the facile nature of Paddy will serve to aid in automated experimentation, where minimization of investigative trials and or diversity of suitable solutions is of high priority.

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