论文标题

从基于随机代理的模型模拟中学习微分方程模型

Learning differential equation models from stochastic agent-based model simulations

论文作者

Nardini, John T., Baker, Ruth E., Simpson, Matthew J., Flores, Kevin B.

论文摘要

基于代理的模型提供了一个灵活的框架,该框架经常用于建模许多生物系统,包括细胞迁移,分子动力学,生态学和流行病学。由于其固有的随机性和繁重的计算要求,对模型动力学的分析可能具有挑战性。对基于代理的模型分析的常见方法包括对模型的大量蒙特卡洛模拟或粗粒微分方程模型的推导,以预测基于代理模型的预期或平均输出。但是,这两种方法都有局限性,但是,由于基于复杂的代理模型的广泛计算可能是不可行的,而且粗粒的微分方程模型可能无法准确描述某些参数制度中的模型动力学。我们建议来自方程学习领域的方法为基于代理的模型分析提供了一种有希望的,新颖和统一的方法。方程学习是来自数据科学的最新研究领域,旨在直接从数据中推断微分方程模型。我们使用本教程来回顾如何使用方程学习中的方法来从基于代理的模型模拟中学习微分方程模型。我们证明了该框架易于使用,几乎需要模型模拟,并且准确地预测了粗粒差分方程模型无法做到的参数区域中的模型动力学。我们通过几个案例研究强调了这些优势,这些案例研究涉及两个基于代理的模型,这些模型广泛适用于生物学现象:一种通常用于探索细胞生物学实验和易感感染的感染性疾病传播模型的出生死亡移民模型。

Agent-based models provide a flexible framework that is frequently used for modelling many biological systems, including cell migration, molecular dynamics, ecology, and epidemiology. Analysis of the model dynamics can be challenging due to their inherent stochasticity and heavy computational requirements. Common approaches to the analysis of agent-based models include extensive Monte Carlo simulation of the model or the derivation of coarse-grained differential equation models to predict the expected or averaged output from the agent-based model. Both of these approaches have limitations, however, as extensive computation of complex agent-based models may be infeasible, and coarse-grained differential equation models can fail to accurately describe model dynamics in certain parameter regimes. We propose that methods from the equation learning field provide a promising, novel, and unifying approach for agent-based model analysis. Equation learning is a recent field of research from data science that aims to infer differential equation models directly from data. We use this tutorial to review how methods from equation learning can be used to learn differential equation models from agent-based model simulations. We demonstrate that this framework is easy to use, requires few model simulations, and accurately predicts model dynamics in parameter regions where coarse-grained differential equation models fail to do so. We highlight these advantages through several case studies involving two agent-based models that are broadly applicable to biological phenomena: a birth-death-migration model commonly used to explore cell biology experiments and a susceptible-infected-recovered model of infectious disease spread.

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