arXiv:2505.20327q-bio.QMcs.AI2025-05

比较两种方法在钙信号建模中的表现,发现正则化最小二乘法更优。

Data-driven multi-agent modelling of calcium interactions in cell culture: PINN vs Regularized Least-squares

  • 用正则化最小二乘法和物理信息神经网络对比钙信号动力学建模。
  • 正则化方法参数估计准确,数据拟合效果好;神经网络表现不佳。
  • 适合对生物系统建模感兴趣的科研人员参考。

数据驱动的生物系统动力学发现可更好地观测与表征过程,如细胞培养中的钙信号传导。近年来,稀疏非线性动力学识别(SINDy)等技术突破了传统方法的局限,后者需依赖预先设定的候选项库,而现实中难以获取。受交通密度估计与控制理论启发,本文提出一种钙输送在细胞群体中动态特性的表征与性能分析方法。研究对比了约束正则化最小二乘法(CRLSM)与物理信息神经网络(PINN)在求解常微分方程(ODE)主控方程中的系统辨识与参数发现能力。结果显示,CRLSM在使用学习到的参数时,能实现较优的参数估计与良好数据拟合;而尽管初始假设,当前配置下的PINN未能达到CRLSM的性能,且无法提供合理的参数估计。然而,仅测试了有限的PINN架构,未来通过超参数调优及不确定性量化有望显著提升其表现。

原文摘要 · Abstract (English)

Data-driven discovery of dynamics in biological systems allows for better observation and characterization of processes, such as calcium signaling in cell culture. Recent advancements in techniques allow the exploration of previously unattainable insights of dynamical systems, such as the Sparse Identification of Non-Linear Dynamics (SINDy), overcoming the limitations of more classic methodologies. The latter requires some prior knowledge of an effective library of candidate terms, which is not realistic for a real case study. Using inspiration from fields like traffic density estimation and control theory, we propose a methodology for characterization and performance analysis of calcium delivery in a family of cells. In this work, we compare the performance of the Constrained Regularized Least-Squares Method (CRLSM) and Physics-Informed Neural Networks (PINN) for system identification and parameter discovery for governing ordinary differential equations (ODEs). The CRLSM achieves a fairly good parameter estimate and a good data fit when using the learned parameters in the Consensus problem. On the other hand, despite the initial hypothesis, PINNs fail to match the CRLSM performance and, under the current configuration, do not provide fair parameter estimation. However, we have only studied a limited number of PINN architectures, and it is expected that additional hyperparameter tuning, as well as uncertainty quantification, could significantly improve the performance in future works.

生物建模神经网络参数估计

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