杰克斯运动模型:神经常规微分方程启发了运动模型的参数化
Paul van Lent1, Olga Bunkova1, Bálint Magyar1
1Intelligent Systems, Delft University of Technology, Delft, Zuid-Holland, Netherlands.
PLoS computational biology
|July 7, 2025
概括
我们开发了jaxkineticmodel,一个JAX/Diffrax框架,用于大规模代谢运动模型的高效参数化. 这种工具加速了模型培训,并使混合模型成为可能,推进了系统生物学研究.
科学领域:
- 系统生物学 系统生物学
- 计算生物学 计算生物学
- 生物物理学的生物物理.
背景情况:
- 用常规微分方程 (ODE) 描述的代谢运动模型对于理解生物系统至关重要.
- 参数化大规模的ODE模型带来了重大的计算挑战.
- 神经常规微分方程 (NODE) 为时间序列数据建模提供了有前途的方法.
研究的目的:
- 为系统生物学标记语言 (SBML) 模型引入一个新的模拟和培训框架 - - jaxkineticmodel.
- 为了利用JAX/Diffrax加速运动模型参数化并实现混合建模.
- 为大型代谢动力学模型提供一个强大的平台,以有效地适应这些模型.
主要方法:
- 使用JAX/Diffrax.实现一个模拟和培训框架.
- 利用JAX的自动区分和即时编译来提高性能.
- 开发混合动力模型与神经网络的混合能力.
主要成果:
- 在不同参数初始化不同的SBML模型中演示了动力模型的强有力的训练.
- 成功地将框架应用于复杂的糖解模型.
- 展示了动力模型与神经网络的混合化,用于未知的反应机制.
结论:
- 杰克斯运动模型框架有效地适应大型代谢运动模型.
- 它为推进系统生物学研究和建模提供了一个强大的平台.
- 该框架有助于整合机械和数据驱动的建模方法.
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