Speciated evolution of oscillatory mass-action chemical reaction networks

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Abstract
Evolutionary algorithms, a class of optimization techniques inspired by biological evolution, have emerged as powerful tools for the optimization of complex systems, including the evolution of mass-action chemical reaction networks. This work explores the application of evolutionary algorithms in this domain, presenting a novel approach inspired by neural network evolution methodologies. A key feature of the algorithm is speciation, which separates candidate reaction networks into groups based on their similarity, which maintains diversity and protects innovations. Crossover has also been shown to be an effective means of improving evolutionary success in other domains. However, crossover of mass-action networks is tested and found to be detrimental to the evolutionary process. This work goes beyond theoretical exploration by offering a practical contribution in the form of a user-friendly software module. This module encapsulates the newly devised algorithm, enabling researchers and practitioners to readily apply the speciation-based approach in their own investigations of mass-action chemical reaction networks. Author summary Evolutionary algorithms are an optimization technique inspired by biological evolution. They can be used to solve complex multi-dimensional problems for which analytic solutions are infeasible. We developed a novel evolutionary algorithm for use with mass-action chemical reaction networks. This algorithm implements two features of biological evolution, speciation and crossover, in an effort to generate chemical reaction networks with specific behaviors. Here, this novel algorithm is demonstrated by generating chemical reaction networks whose chemical species oscillate in time. This algorithm is encapsulated in a julia package and is publicly available as ReactionNetworkEvolution.jl.

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