arXiv:2606.27286cs.AI2026-06

用神经网络加速传染病模型参数估计,比传统方法快近300倍。

Simulation-based inference for rapid Bayesian parameter estimation in epidemiological models: a comparison with MCMC

论文配图:Simulation-based inference for rapid Bayesian parameter estimation in epidemiological models: a comparison with MCMC
图 1 · 摘自论文原文
  • 用神经后验估计替代马尔可夫链蒙特卡洛进行参数推断
  • 31天推断仅需60秒,201天重建也只需157秒
  • 适合需要快速响应的疫情实时分析场景

机制性传染病模型广泛用于疾病预测和公共卫生决策。传统贝叶斯校准多采用马尔可夫链蒙特卡洛(MCMC),但在高维非线性系统和频繁近实时分析中计算成本高昂。本文研究基于模拟的推断(SBI)方法,采用神经后验估计,对德国2020年新冠肺炎重症监护床位占用数据驱动的SECIR模型进行贝叶斯校准。在多个疫情阶段对比了SBI与MCMC,涵盖31天推断窗口及包含多个传播变化点的201天重构难题。通过Wasserstein距离、Kullback-Leibler散度和后验预测检验评估后验一致性。31天窗口下,SBI与MCMC后验分布高度一致,并准确再现实际ICU轨迹;201天设置中,虽不确定性增加,但主要后验结构仍被保留。SBI结合CPU与GPU资源,显著降低计算时间:31天问题仅需60-70秒(单块GPU),而MCMC需约1000秒;201天问题平均仅需157秒,远低于MCMC超过19,000秒的耗时。结果表明,SBI为机制性传染病模型提供了一种快速高效的贝叶斯校准框架,支持重复近实时推断与快速疫情分析。

原文摘要 · Abstract (English)

Mechanistic epidemiological models are widely used to support infectious disease forecasting and public-health decision making. Bayesian calibration of such models is commonly performed using Markov chain Monte Carlo (MCMC), which can become computationally expensive for high-dimensional nonlinear systems and repeated near-real-time analyses. Here, we investigate simulation-based inference (SBI) using neural posterior estimation as a scalable alternative for Bayesian calibration of a mechanistic SECIR epidemiological model using COVID-19 intensive care unit (ICU) occupancy data from Germany during 2020. We compared SBI and MCMC across multiple epidemic phases using both 31-day inference windows and a substantially more challenging 201-day reconstruction problem involving multiple transmission change points. Posterior agreement was evaluated quantitatively using Wasserstein distances and Kullback-Leibler divergences together with posterior predictive checks. Across the 31-day windows, SBI recovered posterior distributions in strong agreement with MCMC while accurately reproducing observed ICU trajectories. In the 201-day setting, SBI preserved the dominant posterior structure despite increased uncertainty. SBI, by combining CPU and GPU resources, substantially reduced computational runtime compared with MCMC, which was restricted to running on CPUs. Whereas MCMC required approximately 1000 seconds for the 31-day inference problems, SBI achieved comparable posterior and predictive performance in approximately 60-70 seconds on a single GPU. For the 201-day inference problem, SBI required an average of 157 seconds, while the MCMC runs took over 19,000 seconds. Our results demonstrate that SBI provides a rapid and computationally efficient framework for Bayesian calibration of mechanistic epidemiological models, supporting repeated near-real-time inference and rapid outbreak analysis.

贝叶斯推断疫情建模加速计算

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