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TransCode:Uncovering COVID-19 transmission patterns via deep learning

Infectious Diseases of Poverty 2023年第1期12卷 82-101页

作者： Jinfu Ren Mutong Liu Yang Liu Jiming Liu Department of Computer Science Hong Kong Baptist UniversityHong Kong SARChina

Background The heterogeneity of COVID-19 spread dynamics is determined by complex spatiotemporal transmission patterns at a fine scale,especially in densely populated regions.In this study,we aim to discover such fine-scale transmission patterns via deep learning.Methods We introduce the notion of TransCode to characterize fine-scale spatiotemporal transmission patterns of COVID-19 caused by metapopulation mobility and contact behaviors.First,in Hong Kong,China,we construct the mobility trajectories of confirmed cases using their visiting records.Then we estimate the transmissibility of individual cases in different locations based on their temporal infectiousness distribution.Integrating the spatial and temporal information,we represent the TransCode via spatiotemporal transmission networks.Further,we propose a deep transfer learning model to adapt the TransCode of Hong Kong,China to achieve fine-scale transmission characterization and risk prediction in six densely populated metropolises:New York City,San Francisco,Toronto,London,Berlin,and Tokyo,where fine-scale data are limited.All the data used in this study are publicly available.Results The TransCode of Hong Kong,China derived from the spatial transmission information and temporal infectiousness distribution of individual cases reveals the transmission patterns(e.g.,the imported and exported transmission intensities)at the district and constituency levels during different COVID-19 outbreaks waves.By adapting the TransCode of Hong Kong,China to other data-limited densely populated metropolises,the proposed method outperforms other representative methods by more than 10%in terms of the prediction accuracy of the disease dynamics(i.e.,the trend of case numbers),and the fine-scale spatiotemporal transmission patterns in these metropolises could also be well captured due to some shared intrinsically common patterns of human mobility and contact behaviors at the metapopulation level.Conclusions The fine-scale transmission patterns due to the metapopulation level

关键词： COVID-19 densely populated regions Spatiotemporal transmission dynamics and heterogeneity Meta-population Human mobility and contact behaviors TransCode Deep transfer learning

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Optimal resource allocation with spatiotemporal transmission discovery for efective disease control

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Infectious Diseases of Poverty 2022年第2期11卷 102-103页

作者： Jinfu Ren Mutong Liu Yang Liu Jiming Liu Department of Computer Science Hong Kong Baptist UniversityKowloonHong Kong Special Administrative RegionPeople’s Republic of China

Background:The new waves of COVID-19 outbreaks caused by the SARS-CoV-2 Omicron variant are developing rapidly and getting out of control around the world,especially in highly populated regions.The healthcare capacity(especially the testing resources,vaccination coverage,and hospital capacity)is becoming extremely insufcient as the demand will far exceed the supply.To address this time-critical issue,we need to answer a key question:How can we efectively infer the daily transmission risks in diferent districts using machine learning methods and thus lay out the corresponding resource prioritization strategies,so as to alleviate the impact of the Omicron outbreaks?Methods:We propose a computational method for future risk mapping and optimal resource allocation based on the quantitative characterization of spatiotemporal transmission patterns of the Omicron variant.We collect the publicly available data from the ofcial website of the Hong Kong Special Administrative Region(HKSAR)Government and the study period in this paper is from December 27,2021 to July 17,2022(including a period for future prediction).First,we construct the spatiotemporal transmission intensity matrices across diferent districts based on infection case records.With the constructed cross-district transmission matrices,we forecast the future risks of various locations daily by means of the Gaussian process.Finally,we develop a transmission-guided resource prioritization strategy that enables efective control of Omicron outbreaks under limited capacity.Results:We conduct a comprehensive investigation of risk mapping and resource allocation in Hong Kong,China.The maps of the district-level transmission risks clearly demonstrate the irregular and spatiotemporal varying patterns of the risks,making it difcult for the public health authority to foresee the outbreaks and plan the responses accordingly.With the guidance of the inferred transmission risks,the developed prioritization strategy enables the optimal testing resource allocation for integrativ

关键词： COVID-19 Omicron outbreak densely populated regions Spatiotemporal transmission risk Optimal resource allocation Integrative case management Efective disease control

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