用于分区流行病学模型的物理信息神经网络方法。

IF 3.8 2区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS PLoS Computational Biology Pub Date : 2024-09-05 DOI:10.1371/journal.pcbi.1012387
Caterina Millevoi, Damiano Pasetto, Massimiliano Ferronato
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引用次数: 0

摘要

分区模型为分析疫情爆发期间的相关传播过程、制作短期预测或传播方案以及评估疫苗接种活动的影响提供了简单而有效的工具。然而,对其进行校准并不简单,因为许多因素都会导致传播动态的快速变化。例如,个人意识可能会发生变化、非药物干预措施的实施以及新变种的出现。因此,传播率等模型参数注定会随时间而变化,从而使其评估更具挑战性。在此,我们建议使用物理信息神经网络(PINNs)来跟踪模型参数和状态变量的时间变化。PINNs 能够同时考虑数据信息(通常是不确定的)和系统的支配方程,因此最近在许多工程应用中备受关注。PINNs 识别未知模型参数的能力使其特别适用于解决难以解决的逆问题,例如在流行病学模型应用中出现的问题。在此,我们开发了一种简化拆分的 PINNs 实现方法,以 SIR 模型方程和传染病数据为基础,估计流行病状态变量和传播率的时间变化。其主要思路是先对流行病学数据进行分拆训练,然后再对系统方程的残差进行训练。我们将所提出的方法应用于五个合成测试案例和两个真实场景,这两个场景再现了意大利 COVID-19 大流行的头几个月。结果表明,PINNs 的拆分实施在准确性(高达一个数量级)和计算时间(加快 20%)方面优于联合方法。最后,我们说明了所提出的 PINN 方法也可用于对流行病的动态进行短期预测。
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A Physics-Informed Neural Network approach for compartmental epidemiological models.

Compartmental models provide simple and efficient tools to analyze the relevant transmission processes during an outbreak, to produce short-term forecasts or transmission scenarios, and to assess the impact of vaccination campaigns. However, their calibration is not straightforward, since many factors contribute to the rapid change of the transmission dynamics. For example, there might be changes in the individual awareness, the imposition of non-pharmacological interventions and the emergence of new variants. As a consequence, model parameters such as the transmission rate are doomed to vary in time, making their assessment more challenging. Here, we propose to use Physics-Informed Neural Networks (PINNs) to track the temporal changes in the model parameters and the state variables. PINNs recently gained attention in many engineering applications thanks to their ability to consider both the information from data (typically uncertain) and the governing equations of the system. The ability of PINNs to identify unknown model parameters makes them particularly suitable to solve ill-posed inverse problems, such as those arising in the application of epidemiological models. Here, we develop a reduced-split approach for the implementation of PINNs to estimate the temporal changes in the state variables and transmission rate of an epidemic based on the SIR model equation and infectious data. The main idea is to split the training first on the epidemiological data, and then on the residual of the system equations. The proposed method is applied to five synthetic test cases and two real scenarios reproducing the first months of the Italian COVID-19 pandemic. Our results show that the split implementation of PINNs outperforms the joint approach in terms of accuracy (up to one order of magnitude) and computational times (speed up of 20%). Finally, we illustrate that the proposed PINN-method can also be adopted to produced short-term forecasts of the dynamics of an epidemic.

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来源期刊
PLoS Computational Biology
PLoS Computational Biology BIOCHEMICAL RESEARCH METHODS-MATHEMATICAL & COMPUTATIONAL BIOLOGY
CiteScore
7.10
自引率
4.70%
发文量
820
审稿时长
2.5 months
期刊介绍: PLOS Computational Biology features works of exceptional significance that further our understanding of living systems at all scales—from molecules and cells, to patient populations and ecosystems—through the application of computational methods. Readers include life and computational scientists, who can take the important findings presented here to the next level of discovery. Research articles must be declared as belonging to a relevant section. More information about the sections can be found in the submission guidelines. Research articles should model aspects of biological systems, demonstrate both methodological and scientific novelty, and provide profound new biological insights. Generally, reliability and significance of biological discovery through computation should be validated and enriched by experimental studies. Inclusion of experimental validation is not required for publication, but should be referenced where possible. Inclusion of experimental validation of a modest biological discovery through computation does not render a manuscript suitable for PLOS Computational Biology. Research articles specifically designated as Methods papers should describe outstanding methods of exceptional importance that have been shown, or have the promise to provide new biological insights. The method must already be widely adopted, or have the promise of wide adoption by a broad community of users. Enhancements to existing published methods will only be considered if those enhancements bring exceptional new capabilities.
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