arXiv:2512.10309q-bio.MNcs.LG2025-12被引 2

用神经网络加速复杂化学反应模拟,提升罕见事件捕捉能力。

Tracking large chemical reaction networks and rare events by neural networks

  • 结合自然梯度与变分原理,优化神经网络求解速度
  • 在MAPK通路等大网络上实现5至22倍提速,精度更高
  • 适用于高维与稀有事件场景,适合生物动力学研究者

化学反应网络广泛用于建模化学动力学、系统生物学和流行病学中的随机过程。由于状态空间随系统规模呈指数增长,求解其控制方程——化学主方程——面临巨大挑战。自回归神经网络虽提供灵活框架,但高维系统及稀有事件下效率受限。本文通过采用自然梯度下降和时变变分原理,实现5至22倍加速,并引入增强采样策略捕捉稀有事件。在复杂的丝裂原活化蛋白激酶(MAPK)级联网络等挑战性系统中,相比先前神经网络方法,计算成本更低、精度更高,这是此前方法处理过的最大生物网络。进一步将该方法扩展至二维格点上的反应-扩散系统(如Schlögl模型),超越了仅限一维的近期张量网络方法。本方法为一般化学反应网络的高效建模提供了新路径。

原文摘要 · Abstract (English)

Chemical reaction networks are widely used to model stochastic dynamics in chemical kinetics, systems biology and epidemiology. Solving the chemical master equation that governs these systems poses a significant challenge due to the large state space exponentially growing with system sizes. The development of autoregressive neural networks offers a flexible framework for this problem; however, its efficiency is limited especially for high-dimensional systems and in scenarios with rare events. Here, we push the frontier of neural-network approach by exploiting faster optimizations such as natural gradient descent and time-dependent variational principle, achieving a 5- to 22-fold speedup, and by leveraging enhanced-sampling strategies to capture rare events. We demonstrate reduced computational cost and higher accuracy over the previous neural-network method in challenging reaction networks, including the mitogen-activated protein kinase (MAPK) cascade network, the hitherto largest biological network handled by the previous approaches of solving the chemical master equation. We further apply the approach to spatially extended reaction-diffusion systems, the Schlögl model with rare events, on two-dimensional lattices, beyond the recent tensor-network approach that handles one-dimensional lattices. The present approach thus enables efficient modeling of chemical reaction networks in general.

化学动力学神经网络稀有事件生物建模

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