Forecasting and Predicting Stochastic Agent-Based Model Data with Biologically-Informed Neural Networks

• Published in: Bulletin of mathematical biology 2024-11, Vol.86 (11), p.130, Article 130
• Main Author: Nardini, John T.
• Format: Article
• Language: English
• Subjects: Agent-based models; Animals; Biological activity; Biological models (mathematics); Cell Biology; Cell migration; Cell Movement - physiology; Computer Simulation; Dictyostelium - physiology; Forecasting; Humans; Ill posed problems; Life Sciences; Mathematical and Computational Biology; Mathematical Concepts; Mathematics; Mathematics and Statistics; Models, Biological; Multivariate analysis; Neural networks; Neural Networks, Computer; Original Article; Parameter estimation; Partial differential equations; Predictions; Spatial data; Stochastic Processes; Stochasticity; Systems Analysis; Tumorigenesis; Wound healing
• ISSN: 0092-8240; 1522-9602; 1522-9602
• DOI: 10.1007/s11538-024-01357-2

Collective migration is an important component of many biological processes, including wound healing, tumorigenesis, and embryo development. Spatial agent-based models (ABMs) are often used to model collective migration, but it is challenging to thoroughly predict these models’ behavior throughout parameter space due to their random and computationally intensive nature. Modelers often coarse-grain ABM rules into mean-field differential equation (DE) models. While these DE models are fast to simulate, they suffer from poor (or even ill-posed) ABM predictions in some regions of parameter space. In this work, we describe how biologically-informed neural networks (BINNs) can be trained to learn interpretable BINN-guided DE models capable of accurately predicting ABM behavior. In particular, we show that BINN-guided partial DE (PDE) simulations can (1) forecast future spatial ABM data not seen during model training, and (2) predict ABM data at previously-unexplored parameter values. This latter task is achieved by combining BINN-guided PDE simulations with multivariate interpolation. We demonstrate our approach using three case study ABMs of collective migration that imitate cell biology experiments and find that BINN-guided PDEs accurately forecast and predict ABM data with a one-compartment PDE when the mean-field PDE is ill-posed or requires two compartments. This work suggests that BINN-guided PDEs allow modelers to efficiently explore parameter space, which may enable data-driven tasks for ABMs, such as estimating parameters from experimental data. All code and data from our study is available at https://github.com/johnnardini/Forecasting_predicting_ABMs .