arXiv:2509.07013cs.LGq-bio.PE2025-09

用深度学习加速传染病模型参数校准,10秒完成传统方法需数小时的任务。

Generalized Machine Learning for Fast Calibration of Agent-Based Epidemic Models

  • 构建双向LSTM模型,直接从疫情数据反推参数,跳过反复模拟。
  • 在5000种情景下测试,精度远超传统方法,计算提速超10倍。
  • 开源工具包支持实时疫情建模,适合公共卫生应急决策者使用。

基于代理的模型(ABMs)广泛用于研究传染病动态,但其校准通常计算量大,限制了在时间敏感的公共卫生场景中的应用。本文提出DeepIMC(深度逆映射校准)框架,通过机器学习直接学习从疫情时间序列到流行病学参数的逆映射。DeepIMC在基于代理模型(如SIR模型)生成的合成疫情轨迹上训练双向长短期记忆网络(BiLSTM),实现推理时无需重复模拟的快速参数估计。我们通过包含5000个异构疫情情景的仿真研究评估DeepIMC,并与无似然马尔可夫链蒙特卡洛方法(ABC)进行对比。结果表明,DeepIMC显著提升参数恢复精度,生成锐利且校准良好的预测区间,计算时间减少一个数量级以上。尽管结构可识别性约束限制了所有参数的同时精确恢复,但校准后的模型能可靠再现疫情轨迹,并利用估计参数实现准确的前向预测。DeepIMC已集成于开源R包epiworldRCalibrate中,便于实时疫情建模与政策分析应用。总体而言,DeepIMC为基于代理的流行病模型提供了可扩展、操作高效的替代校准方案。

原文摘要 · Abstract (English)

Agent-based models (ABMs) are widely used to study infectious disease dynamics, but their calibration is often computationally intensive, limiting their applicability in time-sensitive public health settings. We propose DeepIMC (Deep Inverse Mapping Calibration), a machine learning-based calibration framework that directly learns the inverse mapping from epidemic time series to epidemiological parameters. DeepIMC trains a bidirectional Long Short-Term Memory (BiLSTM) neural network on synthetic epidemic trajectories generated from agent-based models such as the Susceptible-Infected-Recovered (SIR) model, enabling rapid parameter estimation without repeated simulation at inference time. We evaluate DeepIMC through an extensive simulation study comprising 5,000 heterogeneous epidemic scenarios and benchmark its performance against Approximate Bayesian Computation (ABC) using likelihood-free Markov Chain Monte Carlo. The results show that DeepIMC substantially improves parameter recovery accuracy, produces sharp and well-calibrated predictive intervals, and reduces computational time by more than an order of magnitude relative to ABC. Although structural parameter identifiability constraints limit the precise recovery of all model parameters simultaneously, the calibrated models reliably reproduce epidemic trajectories and support accurate forward prediction with their estimated parameters. DeepIMC is implemented in the open-source R package epiworldRCalibrate, facilitating practical adoption for real-time epidemic modeling and policy analysis. Overall, our findings demonstrate that DeepIMC provides a scalable, operationally effective alternative to traditional simulation-based calibration methods for agent-based epidemic models.

传染病建模深度学习参数校准实时预测

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