Optimization of Agent-Based Models Through Coarse-Graining: A Case Study in Microbial Ecology.

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 coarse-graining 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.