COVID-19 Community Temporal Visualizer: a new methodology for the network-based analysis and visualization of COVID-19 data

Understanding the evolution of the spread of the COVID-19 pandemic requires the analysis of several data at the spatial and temporal levels. Here, we present a new network-based methodology to analyze COVID-19 data measures containing spatial and temporal features and its application on a real dataset. The goal of the methodology is to analyze sets of homogeneous datasets (i.e. COVID-19 data taken in different periods and in several regions) using a statistical test to find similar/dissimilar datasets, mapping such similarity information on a graph and then using a community detection algorithm to visualize and analyze the spatio-temporal evolution of data. We evaluated diverse Italian COVID-19 data made publicly available by the Italian Protezione Civile Department at https://github.com/pcm-dpc/COVID-19/. Furthermore, we considered the climate data related to two periods and we integrated them with COVID-19 data measures to detect new communities related to climate changes. In conclusion, the application of the proposed methodology provides a network-based representation of the COVID-19 measures by highlighting the different behaviour of regions with respect to pandemics data released by Protezione Civile and climate data. The methodology and its implementation as R function are publicly available at https://github.com/mmilano87/analyzeC19D .

[1]  Mostafa A. Elhosseini,et al.  Association between weather data and COVID-19 pandemic predicting mortality rate: Machine learning approaches , 2020, Chaos, Solitons & Fractals.

[2]  M. Newman,et al.  Finding community structure in networks using the eigenvectors of matrices. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[3]  Steve Gregory,et al.  Finding overlapping communities in networks by label propagation , 2009, ArXiv.

[4]  Matthieu Latapy,et al.  Computing Communities in Large Networks Using Random Walks , 2004, J. Graph Algorithms Appl..

[5]  Shunjie Chen,et al.  Statistical and network analysis of 1212 COVID-19 patients in Henan, China , 2020, International Journal of Infectious Diseases.

[6]  Gábor Csárdi,et al.  The igraph software package for complex network research , 2006 .

[7]  Wojciech Samek,et al.  Explainable AI: Interpreting, Explaining and Visualizing Deep Learning , 2019, Explainable AI.

[8]  Zunyou Wu,et al.  Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72 314 Cases From the Chinese Center for Disease Control and Prevention. , 2020, JAMA.

[9]  Tijana Milenkovic,et al.  MAGNA++: Maximizing Accuracy in Global Network Alignment via both node and edge conservation , 2015, Bioinform..

[10]  Stijn van Dongen,et al.  Graph Clustering Via a Discrete Uncoupling Process , 2008, SIAM J. Matrix Anal. Appl..

[11]  M. Sobsey,et al.  Effects of Air Temperature and Relative Humidity on Coronavirus Survival on Surfaces , 2010, Applied and Environmental Microbiology.

[12]  E. Miccadei,et al.  Preliminary Analysis of Relationships between COVID19 and Climate, Morphology, and Urbanization in the Lombardy Region (Northern Italy) , 2020, International journal of environmental research and public health.

[13]  Á. Briz‐Redón,et al.  The effect of climate on the spread of the COVID-19 pandemic: A review of findings, and statistical and modelling techniques , 2020 .

[14]  Muhammad Farhan Bashir,et al.  Correlation between climate indicators and COVID-19 pandemic in New York, USA , 2020, Science of The Total Environment.

[15]  D. Legates,et al.  Observed and Potential Impacts of the COVID-19 Pandemic on the Environment , 2020, International journal of environmental research and public health.

[16]  Martin Rosvall,et al.  An information-theoretic framework for resolving community structure in complex networks , 2007, Proceedings of the National Academy of Sciences.

[17]  A. Kumar Modeling geographical spread of COVID-19 in India using network-based approach , 2020, medRxiv.

[18]  R. Duval,et al.  Human Coronaviruses: Insights into Environmental Resistance and Its Influence on the Development of New Antiseptic Strategies , 2012, Viruses.

[19]  Wojciech Samek,et al.  Explainable ai – preface , 2019 .

[20]  Zechao Li,et al.  Tracking the evolution of overlapping communities in dynamic social networks , 2018, Knowl. Based Syst..

[21]  Marco Roccetti,et al.  Is a COVID-19 Second Wave Possible in Emilia-Romagna (Italy)? Forecasting a Future Outbreak with Particulate Pollution and Machine Learning , 2020, Comput..

[22]  Liang Zhao,et al.  Evaluating and Comparing the IGraph Community Detection Algorithms , 2014, 2014 Brazilian Conference on Intelligent Systems.

[23]  Zhao Yang,et al.  A Comparative Analysis of Community Detection Algorithms on Artificial Networks , 2016, Scientific Reports.

[24]  J. Reichardt,et al.  Statistical mechanics of community detection. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[25]  C. Troise,et al.  The Evolution of Covid-19 in Italy after the Spring of 2020: An Unpredicted Summer Respite Followed by a Second Wave , 2020, International journal of environmental research and public health.

[26]  Mario Cannataro,et al.  L-HetNetAligner: A novel algorithm for Local Alignment of Heterogeneous Biological Networks , 2020, Scientific Reports.

[27]  Marianna Milano Tools for Semantic Analysis Based on Semantic Similarity , 2019, Encyclopedia of Bioinformatics and Computational Biology.

[28]  E. Gehan A GENERALIZED WILCOXON TEST FOR COMPARING ARBITRARILY SINGLY-CENSORED SAMPLES. , 1965, Biometrika.

[29]  Why COVID-19 models should incorporate the network of social interactions , 2020 .

[30]  L. Luo,et al.  Temperature significant change COVID-19 Transmission in 429 cities , 2020, medRxiv.

[31]  Climate effect on COVID-19 spread rate: an online surveillance tool , 2020, medRxiv.

[32]  L. Freeman Centrality in social networks conceptual clarification , 1978 .

[33]  M. Mildner,et al.  Re-epithelialization and immune cell behaviour in an ex vivo human skin model , 2020, Scientific Reports.

[34]  M. Zoran,et al.  Assessing the relationship between ground levels of ozone (O3) and nitrogen dioxide (NO2) with coronavirus (COVID-19) in Milan, Italy , 2020, Science of The Total Environment.

[35]  Helena A Herrmann,et al.  Using network science to propose strategies for effectively dealing with pandemics: The COVID-19 example , 2020, medRxiv.

[36]  Y. Hu,et al.  Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China , 2020, The Lancet.

[37]  G. Zehender,et al.  Early phylogenetic estimate of the effective reproduction number of SARS‐CoV‐2 , 2020, Journal of medical virology.

[38]  M. Newman,et al.  Finding community structure in very large networks. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[39]  Srinivasan Parthasarathy,et al.  An event-based framework for characterizing the evolutionary behavior of interaction graphs , 2007, KDD '07.

[40]  Srinivasan Parthasarathy,et al.  An event-based framework for characterizing the evolutionary behavior of interaction graphs , 2009, ACM Trans. Knowl. Discov. Data.

[41]  A. Barabasi,et al.  Quantifying social group evolution , 2007, Nature.

[42]  Martin Rosvall,et al.  Maps of random walks on complex networks reveal community structure , 2007, Proceedings of the National Academy of Sciences.

[43]  Bin Wu,et al.  Dynamic Community Detection Algorithm Based on Incremental Identification , 2015, 2015 IEEE International Conference on Data Mining Workshop (ICDMW).

[44]  Mario Cannataro,et al.  Explainable Sentiment Analysis with Applications in Medicine , 2018, 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

[45]  M E J Newman,et al.  Community structure in social and biological networks , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[46]  M. Cannataro,et al.  COVID-WAREHOUSE: A Data Warehouse of Italian COVID-19, Pollution, and Climate Data , 2020, International journal of environmental research and public health.

[47]  Santo Fortunato,et al.  Community detection in networks: A user guide , 2016, ArXiv.

[48]  Almas Mirzakhmetov,et al.  A Network-Based Stochastic Epidemic Simulator: Controlling COVID-19 With Region-Specific Policies , 2020, IEEE Journal of Biomedical and Health Informatics.

[49]  O. Reich,et al.  Modeling COVID-19 on a network: super-spreaders, testing and containment , 2020, medRxiv.

[50]  Santo Fortunato,et al.  Finding Statistically Significant Communities in Networks , 2010, PloS one.

[51]  Yongjian Zhu,et al.  Association between ambient temperature and COVID-19 infection in 122 cities from China , 2020, Science of The Total Environment.

[52]  Mario Cannataro,et al.  Challenges and Opportunities for Visualization and Analysis of Graph-Modeled Medical Data , 2017 .

[53]  M. V. Van Kerkhove,et al.  A case-crossover analysis of the impact of weather on primary cases of Middle East respiratory syndrome , 2019, BMC Infectious Diseases.

[54]  A. Rinaldo,et al.  Spread and dynamics of the COVID-19 epidemic in Italy: Effects of emergency containment measures , 2020, Proceedings of the National Academy of Sciences.

[55]  Y. Zhao,et al.  Effects of temperature variation and humidity on the mortality of COVID-19 in Wuhan , 2020, medRxiv.

[56]  Marco Roccetti,et al.  Particulate Matter and COVID-19 Disease Diffusion in Emilia-Romagna (Italy). Already a Cold Case? , 2020, Comput..

[57]  Jean-Loup Guillaume,et al.  Fast unfolding of communities in large networks , 2008, 0803.0476.

[58]  Ramadhan Tosepu,et al.  Correlation between weather and Covid-19 pandemic in Jakarta, Indonesia , 2020, Science of The Total Environment.

[59]  H. A. Varol,et al.  A Network-Based Stochastic Epidemic Simulator: Controlling COVID-19 With Region-Specific Policies , 2020, IEEE Journal of Biomedical and Health Informatics.

[60]  Réka Albert,et al.  Near linear time algorithm to detect community structures in large-scale networks. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[61]  Deepayan Chakrabarti,et al.  Evolutionary clustering , 2006, KDD '06.

[62]  Przemyslaw Kazienko,et al.  Predicting Group Evolution in the Social Network , 2012, SocInfo.