Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems.
Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems.
复制标题
基于多尺度代理模型的有效数值实施的策略来描述生物系统。
DOI：
10.1007/s12195-014-0363-6
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发表时间：
2015-03
影响因子：
2.8
通讯作者：
Linderman JJ
中科院分区：
文献类型：
--
作者：
Cilfone NA;Kirschner DE;Linderman JJ
生物相关的过程在多个时空尺度上运作。对于模拟这种生物复杂性的计算建模方法，个体尺度模型必须以允许跨尺度动态交换信息的方式联系起来。一种强大的方法是将离散建模方法——基于智能体的模型（ABMs）与连续体模型相结合，形成混合模型。混合多尺度ABMs已被用于模拟生物系统的紧急反应。本文综述了混合多尺度ABMs的两个方面：连接单个尺度模型和有效求解生成的模型。我们讨论了与连接单个尺度模型相关的计算选择，同时保持模型的可追溯性。我们演示了现有的数值方法在混合多尺度ABMs环境中的实现。通过一个描述结核分枝杆菌感染的例子模型，我们展示了各种数值方法组合的相对计算速度。有效连接和解决混合多尺度ABMs是模型可移植性、模块化及其在系统层面理解生物现象的关键。
Biologically related processes operate across multiple spatiotemporal scales. For computational modeling methodologies to mimic this biological complexity, individual scale models must be linked in ways that allow for dynamic exchange of information across scales. A powerful methodology is to combine a discrete modeling approach, agent-based models (ABMs), with continuum models to form hybrid models. Hybrid multi-scale ABMs have been used to simulate emergent responses of biological systems. Here, we review two aspects of hybrid multi-scale ABMs: linking individual scale models and efficiently solving the resulting model. We discuss the computational choices associated with aspects of linking individual scale models while simultaneously maintaining model tractability. We demonstrate implementations of existing numerical methods in the context of hybrid multi-scale ABMs. Using an example model describing Mycobacterium tuberculosis infection, we show relative computational speeds of various combinations of numerical methods. Efficient linking and solution of hybrid multi-scale ABMs is key to model portability, modularity, and their use in understanding biological phenomena at a systems level.