Optimization of Agent-Based Models Through Coarse-Graining

A Case Study in Microbial Ecology

Authors

  • Sherli Koshy-Chenthittayil Center for Quantitative Medicine, University of Connecticut Health Center (koshychenthittayil@uchc.edu) Author
  • Pedro Mendes bCenter for Quantitative Medicine and Center for Cell Analysis and Modeling, University of Connecticut Health Center (pmendes@uchc.edu) Author
  • Reinhard Laubenbacher Department of Medicine, University of Florida (reinhard.laubenbacher@medicine.ufl.edu) Author

DOI:

https://doi.org/10.30707/LiB8.1.1647878866.083342

Keywords:

Optimization, Agent-based models, Pareto frontier, Microbial biofilms

Abstract

Optimization and control are important objectives across biology and biomedicine, and mathematical models are a key enabling technology. This paper reports a computational study of model-based multi-objective optimization in the setting of microbial ecology, using agent-based models. This modeling framework is well-suited to the field, but is not amenable to standard control-theoretic approaches. Furthermore, due to computational complexity, simulation-based optimization approaches are often challenging to implement. This paper presents the results of an approach that combines control-dependent model reduction with Pareto optimization, applied to two models of multi-species bacterial biofilms. It shows that this approach can be successful for models whose computational complexity prevents effective simulation-based optimization.

Downloads

Published

2021-09-24

Issue

Section

Research

How to Cite

Optimization of Agent-Based Models Through Coarse-Graining: A Case Study in Microbial Ecology. (2021). Letters in Biomathematics, 8(1), 167-178. https://doi.org/10.30707/LiB8.1.1647878866.083342

Most read articles by the same author(s)