INDEMICS: An Interactive High-Performance Computing Framework for Data Intensive Epidemic Modeling

We describe the design and prototype implementation of Indemics (_Interactive; Epi_demic; _Simulation;)—a modeling environment utilizing high-performance computing technologies for supporting complex epidemic simulations. Indemics can support policy analysts and epidemiologists interested in planning and control of pandemics. Indemics goes beyond traditional epidemic simulations by providing a simple and powerful way to represent and analyze policy-based as well as individual-based adaptive interventions. Users can also stop the simulation at any point, assess the state of the simulated system, and add additional interventions. Indemics is available to end-users via a web-based interface. Detailed performance analysis shows that Indemics greatly enhances the capability and productivity of simulating complex intervention strategies with a marginal decrease in performance. We also demonstrate how Indemics was applied in some real case studies where complex interventions were implemented

Early Warning Analysis for Social Diffusion Events

There is considerable interest in developing predictive capabilities for social diffusion processes, for instance to permit early identification of emerging contentious situations, rapid detection of disease outbreaks, or accurate forecasting of the ultimate reach of potentially viral ideas or behaviors. This paper proposes a new approach to this predictive analytics problem, in which analysis of meso-scale network dynamics is leveraged to generate useful predictions for complex social phenomena. We begin by deriving a stochastic hybrid dynamical systems (S-HDS) model for diffusion processes taking place over social networks with realistic topologies; this modeling approach is inspired by recent work in biology demonstrating that S-HDS offer a useful mathematical formalism with which to represent complex, multi-scale biological network dynamics. We then perform formal stochastic reachability analysis with this S-HDS model and conclude that the outcomes of social diffusion processes may depend crucially upon the way the early dynamics of the process interacts with the underlying network's community structure and core-periphery structure. This theoretical finding provides the foundations for developing a machine learning algorithm that enables accurate early warning analysis for social diffusion events. The utility of the warning algorithm, and the power of network-based predictive metrics, are demonstrated through an empirical investigation of the propagation of political memes over social media networks. Additionally, we illustrate the potential of the approach for security informatics applications through case studies involving early warning analysis of large-scale protests events and politically-motivated cyber attacks

Rule-based epidemic models

Rule-based models generalise reaction-based models with reagents that have internal state and may be bound together to form complexes, as in chemistry. An important class of system that would be intractable if expressed as reactions or ordinary differential equations can be efficiently simulated when expressed as rules. In this paper we demonstrate the utility of the rule-based approach for epidemiological modelling presenting a suite of seven models illustrating the spread of infectious disease under different scenarios: wearing masks, infection via fomites and prevention by hand-washing, the concept of vector-borne diseases, testing and contact tracing interventions, disease propagation within motif-structured populations with shared environments such as schools, and superspreading events. Rule-based models allow to combine transparent modelling approach with scalability and compositionality and therefore can facilitate the study of aspects of infectious disease propagation in a richer context than would otherwise be feasible

Spreading processes in Multilayer Networks

Several systems can be modeled as sets of interconnected networks or networks with multiple types of connections, here generally called multilayer networks. Spreading processes such as information propagation among users of an online social networks, or the diffusion of pathogens among individuals through their contact network, are fundamental phenomena occurring in these networks. However, while information diffusion in single networks has received considerable attention from various disciplines for over a decade, spreading processes in multilayer networks is still a young research area presenting many challenging research issues. In this paper we review the main models, results and applications of multilayer spreading processes and discuss some promising research directions.Comment: 21 pages, 3 figures, 4 table

Leveraging social networks for understanding the evolution of epidemics

<p>Abstract</p> <p>Background</p> <p>To understand how infectious agents disseminate throughout a population it is essential to capture the social model in a realistic manner. This paper presents a novel approach to modeling the propagation of the influenza virus throughout a realistic interconnection network based on actual individual interactions which we extract from online social networks. The advantage is that these networks can be extracted from existing sources which faithfully record interactions between people in their natural environment. We additionally allow modeling the characteristics of each individual as well as customizing his daily interaction patterns by making them time-dependent. Our purpose is to understand how the infection spreads depending on the structure of the contact network and the individuals who introduce the infection in the population. This would help public health authorities to respond more efficiently to epidemics.</p> <p>Results</p> <p>We implement a scalable, fully distributed simulator and validate the epidemic model by comparing the simulation results against the data in the 2004-2005 New York State Department of Health Report (NYSDOH), with similar temporal distribution results for the number of infected individuals. We analyze the impact of different types of connection models on the virus propagation. Lastly, we analyze and compare the effects of adopting several different vaccination policies, some of them based on individual characteristics -such as age- while others targeting the super-connectors in the social model.</p> <p>Conclusions</p> <p>This paper presents an approach to modeling the propagation of the influenza virus via a realistic social model based on actual individual interactions extracted from online social networks. We implemented a scalable, fully distributed simulator and we analyzed both the dissemination of the infection and the effect of different vaccination policies on the progress of the epidemics. The epidemic values predicted by our simulator match real data from NYSDOH. Our results show that our simulator can be a useful tool in understanding the differences in the evolution of an epidemic within populations with different characteristics and can provide guidance with regard to which, and how many, individuals should be vaccinated to slow down the virus propagation and reduce the number of infections.</p

Report on DIMACS Working Group Meeting: Mathematical Sciences Methods for the Study of Deliberate Releases of Biological Agents and their Consequences

55 pages, 1 article*Report on DIMACS Working Group Meeting: Mathematical Sciences Methods for the Study of Deliberate Releases of Biological Agents and their Consequences* (Castillo-Chavez, Carlos; Roberts, Fred S.) 55 page