ISRES+: an improved evolutionary strategy for function minimization to estimate the free parameters of systems biology models

• Published in: Bioinformatics (Oxford, England) England), 2023-07, Vol.39 (7)
• Main Authors: Bandodkar, Prasad, Shaikh, Razeen, Reeves, Gregory T
• Format: Article
• Language: English
• Subjects: Algorithms; Humans; Models, Biological; Original Paper; Systems Biology - methods
• ISSN: 1367-4811; 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btad403

Abstract Motivation Mathematical models in systems biology help generate hypotheses, guide experimental design, and infer the dynamics of gene regulatory networks. These models are characterized by phenomenological or mechanistic parameters, which are typically hard to measure. Therefore, efficient parameter estimation is central to model development. Global optimization techniques, such as evolutionary algorithms (EAs), are applied to estimate model parameters by inverse modeling, i.e. calibrating models by minimizing a function that evaluates a measure of the error between model predictions and experimental data. EAs estimate model parameters “fittest individuals” by generating a large population of individuals using strategies like recombination and mutation over multiple “generations.” Typically, only a few individuals from each generation are used to create new individuals in the next generation. Improved Evolutionary Strategy by Stochastic Ranking (ISRES), proposed by Runnarson and Yao, is one such EA that is widely used in systems biology to estimate parameters. ISRES uses information at most from a pair of individuals in any generation to create a new population to minimize the error. In this article, we propose an efficient evolutionary strategy, ISRES+, which builds on ISRES by combining information from all individuals across the population and across all generations to develop a better understanding of the fitness landscape. Results ISRES+ uses the additional information generated by the algorithm during evolution to approximate the local neighborhood around the best-fit individual using linear least squares fits in one and two dimensions, enabling efficient parameter estimation. ISRES+ outperforms ISRES and results in fitter individuals with a tighter distribution over multiple runs, such that a typical run of ISRES+ estimates parameters with a higher goodness-of-fit compared with ISRES. Availability and implementation Algorithm and implementation: Github—https://github.com/gtreeves/isres-plus-bandodkar-2022.