论文标题
使用隔室模型对非药物干预措施的推理,预测和优化:Pyross库
Inference, prediction and optimization of non-pharmaceutical interventions using compartment models: the PyRoss library
论文作者
论文摘要
Pyross是一个开源Python库,为NPI在年龄和接触结构的流行病学隔室模型中提供了一个集成平台,用于推理,预测和优化。该报告概述了Pyross库的基本原理和功能,其中各种插图和示例着重于混杂的,年龄结构化的人群。 Pyross库支持随机配方的任意结构化模型(作为主方程)或确定性(作为ODES),并允许中途从一个到另一个过渡。通过支持其他隔间分区,Pyross可以模仿时间 - 感染模型,并允许对住院或隔离等医疗阶段进行建模和预测。 Pyross库可以使用贝叶斯参数推断与流行病学数据合适,以便可以通过其证据权衡竞争模型。 Pyross通过卷积由流行病学数据,模型选择,参数和内在随机性引起的不确定性来完全贝叶斯对理想化NPI的影响。包括针对用户定义的成本功能优化时间相关的NPI方案的算法。 Pyross目前针对混合良好人群的年龄结构化隔间框架将在以后的报告中进行扩展,包括按位置,职业,旅行网络的使用以及与评估疾病扩散和NPI的影响有关的隔室。我们认为,通过允许任意粒度的社会数据与贝叶斯参数的估计相比,与其他详细流行性建模的方法相比,这种隔间模型可以与贝叶斯参数估计相结合。我们邀请其他人使用Pyross图书馆进行研究,以解决当今的Covid-19危机,并计划未来的大流行。
PyRoss is an open-source Python library that offers an integrated platform for inference, prediction and optimisation of NPIs in age- and contact-structured epidemiological compartment models. This report outlines the rationale and functionality of the PyRoss library, with various illustrations and examples focusing on well-mixed, age-structured populations. The PyRoss library supports arbitrary structured models formulated stochastically (as master equations) or deterministically (as ODEs) and allows mid-run transitioning from one to the other. By supporting additional compartmental subdivision ad libitum, PyRoss can emulate time-since-infection models and allows medical stages such as hospitalization or quarantine to be modelled and forecast. The PyRoss library enables fitting to epidemiological data, as available, using Bayesian parameter inference, so that competing models can be weighed by their evidence. PyRoss allows fully Bayesian forecasts of the impact of idealized NPIs by convolving uncertainties arising from epidemiological data, model choice, parameters, and intrinsic stochasticity. Algorithms to optimize time-dependent NPI scenarios against user-defined cost functions are included. PyRoss's current age-structured compartment framework for well-mixed populations will in future reports be extended to include compartments structured by location, occupation, use of travel networks and other attributes relevant to assessing disease spread and the impact of NPIs. We argue that such compartment models, by allowing social data of arbitrary granularity to be combined with Bayesian parameter estimation for poorly-known disease variables, could enable more powerful and robust prediction than other approaches to detailed epidemic modelling. We invite others to use the PyRoss library for research to address today's COVID-19 crisis, and to plan for future pandemics.