CSE 8803 EPI, Fall 2020

Data Science for Epidemiology

Data Science for Epidemiology

- Tina Rosenberg. Stopping Pandemics Before they Start, New York Times, June 2017.
- Ed Young. The next plauge is coming: Is America ready?, The Atlantic, July/Aug 2018.
- H. Hethcote. Sections 1-2.4. The mathematics of infectious diseases, SIAM Review, 2000.
- Ina Holmdahl and Caroline Buckee. Wrong but Useful — What Covid-19 Epidemiologic Models Can and Cannot Tell Us, The New England Journal of Medicine, July 2020.
- Simon Frost, Epidemiological Models Interactive Example (try it out!): SIR in Python using scipy, Accessed Aug 2020.
- Another Interactive COVID-19 SEIR model (try it out!): Modeling COVID-19 Spread vs Healthcare Capacity, Accessed Aug 2020.
- (Details about Bernoulli's model) M. Glomski and E. Ohanian. Eradicating a Disease: Lessons from Mathematical Epidemiology. College Mathematics Journal. 2012.
- Chapter 21 from Easley and Kleinberg: Epidemics.
- Stephen Eubank, Hasan Guclu, V.S. Anil Kumar, Madhav Marathe, Aravind Srinivasan, Zoltan Toroczkai and Nan Wang. Modeling disease outbreaks in realistic urban social networks. Nature. 2004.
- D. Balcan, V. Colizza, B. Goncalves, H. Hu, J. Ramasco and A. Vespignani. Multiscale mobility networks and the spatial spreading of infectious diseases. PNAS 2009.
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- David Kempe, Jon Kleinberg, and Eva Tardos. Maximizing the spread of influence through a social network. SIGKDD 2003.
- Joao Gama Oliveira and Albert-Lazlo Barabasi. Darwin and Einstein correspondence patterns . Nature, 2005.
- P. S. Dodds and D. J. Watts. Universal behavior in a generalized model of contagion. PRL 2004.
- Y. Matsubara, Y. Sakurai, B. A. Prakash, L. Li, C. Faloutsos. Rise and Fall Patterns of Information Diffusion: Model and Implications. SIGKDD, 2012.
- D. Romero, B. Meeder, J. Kleinberg. Differences in the Mechanics of Information Diffusion Across Topics: Idioms, Political Hashtags, and Complex Contagion on Twitter. WWW, 2011.
- The Lotka-Volterra Model. Wikipedia.
- S. Myers and J. Leskovec. Clash of the Contagions: Cooperation and Competition in Information Diffusion. ICDM 2012.
- A. Beutel, B. A. Prakash, R. Rosenfeld and C. Faloutsos. Interacting Viruses in Networks: Can Both Survive?. SIGKDD 2012.
- Madhav Marathe and Anil Vullikanti. Computational Epidemiology, CACM 2013
- N. Dimitrov and L. Meyers. Section 5. Mathematical Approaches to Infectious Disease Prediction and Control, INFORMS 2010.
- A. Aleta et al. Modelling the impact of testing, contact tracing and household quarantine on second waves of COVID-19. Nature Human Behavior 2020.
- K. Eames, S. Bansal, S. Frost and S. Riley. Six challenges in measuring contact networks for use in modelling. Epidemics, 2015.
- P. S. Bearman, J. Moody, and K. Stoval. Chains of affection: The structure of adolescent romantic and sexual networks AJS 2004.
- P. Sapiezynski, A. Stopczynski, D. D. Lassen, and S. Lehmann Interaction data from the copenhagen networks study. Nature Scientific Data, 2019.
- A. Hess, K. A. Hummel, W. N. Gansterer, G. Haring. Data-driven Human Mobility Modeling: A Survey and Engineering Guidance for Mobile Networking. ACM Computing Surveys, 2016.
- N. Christakis and J. Fowler. Social Network Sensors for Early Detection of Contagious Outbreaks. PLoS One 2010.
- H. Shao et al. Forecasting the Flu: Designing Social Network Sensors for Epidemics. SIGKDD epiDAMIK 2018.
- J. Leskovec, A. Krause, C. Guestrin, C. Faloutsos, J. VanBriesen, N. Glance. Cost-effective Outbreak Detection in Networks. SIGKDD, 2007.
- A. Krause and D. Golovin. Sections 1 and 2. Submodular Function Maximization. Survey, in Practical Algorithms, 2014.
- Bijaya Adhikari, B. Lewis, A. Vullikanti, J. M. Jimenez, and B. A. Prakash. Fast and Near-Optimal Monitoring for Healthcare Acquired Infection Outbreaks. PLoS Computational Biology 2019.
- Daniel Neill. Subset Scanning for Event and Pattern Detection. Survey in Encyclopedia of Geographic Systems. 2017