Genetic Algorithms for model refinement and rule discovery in a high-dimensional agent-based model of inflammation

Abstract

Introduction Agent-based modeling frequently used modeling method for multi-scale mechanistic modeling. However, the same properties that make agent-based models (ABMs) well suited to representing biological systems also present significant challenges with respect to their construction and calibration, particularly with respect to the selection of potential mechanistic rules and the large number of free parameters often present in these models. We have proposed that various machine learning approaches (such as genetic algorithms (GAs)) can be used to more effectively and efficiently deal with rule selection and parameter space characterization; the current work applies GAs to the challenge of calibrating a complex ABM to a specific data set, while preserving biological heterogeneity. Methods This project uses a GA to augment the rule-set for a previously validated ABM of acute systemic inflammation, the Innate Immune Response ABM (IIRABM) to clinical time series data of systemic cytokine levels from a population of burn patients. The genome for the GA is a vector generated from the IIRABM’s Model Rule Matrix (MRM), which is a matrix representation of not only the constants/parameters associated with the IIRABM’s cytokine interaction rules, but also the existence of rules themselves. Capturing heterogeneity is accomplished by a fitness function that incorporates the sample value range (“error bars”) of the clinical data. Results The GA-enabled parameter space exploration resulted in a set of putative MRM rules and associated parameterizations which closely match the cytokine time course data used to design the fitness function. The number of non-zero elements in the MRM increases significantly as the model parameterizations evolve towards a fitness function minimum, transitioning from a sparse to a dense matrix. This results in a model structure that more closely resembles (at a superficial level) the structure of data generated by a standard differential gene expression experimental study. Conclusion We present an HPC-enabled evolutionary computing approach to calibrate a complex ABM to clinical data while preserving biological heterogeneity. The integration of machine learning, HPC, and multi-scale mechanistic modeling provides a pathway forward to effectively represent the heterogeneity of clinical populations and their data. Author Summary In this work, we utilize genetic algorithms (GA) to operate on the internal rule set of a computational of the human immune response to injury, the Innate Immune Response Agent-Based Model (IIRABM), such that it is iteratively refined to generate cytokine time series that closely match what is seen in a clinical cohort of burn patients. At the termination of the GA, there exists an ensemble of candidate model rule-sets/parameterizations which are validated by the experimental data;