Simulation of an SEIR infectious disease model on the dynamic contact network of conference attendees

The spread of infectious diseases crucially depends on the pattern of contacts among individuals. Knowledge of these patterns is thus essential to inform models and computational efforts. Few empirical studies are however available that provide estimates of the number and duration of contacts among social groups. Moreover, their space and time resolution are limited, so that data is not explicit at the person-to-person level, and the dynamical aspect of the contacts is disregarded. Here, we want to assess the role of data-driven dynamic contact patterns among individuals, and in particular of their temporal aspects, in shaping the spread of a simulated epidemic in the population. We consider high resolution data of face-to-face interactions between the attendees of a conference, obtained from the deployment of an infrastructure based on Radio Frequency Identification (RFID) devices that assess mutual face-to-face proximity. The spread of epidemics along these interactions is simulated through an SEIR model, using both the dynamical network of contacts defined by the collected data, and two aggregated versions of such network, in order to assess the role of the data temporal aspects. We show that, on the timescales considered, an aggregated network taking into account the daily duration of contacts is a good approximation to the full resolution network, whereas a homogeneous representation which retains only the topology of the contact network fails in reproducing the size of the epidemic. These results have important implications in understanding the level of detail needed to correctly inform computational models for the study and management of real epidemics

PocketCare: Tracking the Flu with Mobile Phones using Partial Observations of Proximity and Symptoms

Mobile phones provide a powerful sensing platform that researchers may adopt to understand proximity interactions among people and the diffusion, through these interactions, of diseases, behaviors, and opinions. However, it remains a challenge to track the proximity-based interactions of a whole community and then model the social diffusion of diseases and behaviors starting from the observations of a small fraction of the volunteer population. In this paper, we propose a novel approach that tries to connect together these sparse observations using a model of how individuals interact with each other and how social interactions happen in terms of a sequence of proximity interactions. We apply our approach to track the spreading of flu in the spatial-proximity network of a 3000-people university campus by mobilizing 300 volunteers from this population to monitor nearby mobile phones through Bluetooth scanning and to daily report flu symptoms about and around them. Our aim is to predict the likelihood for an individual to get flu based on how often her/his daily routine intersects with those of the volunteers. Thus, we use the daily routines of the volunteers to build a model of the volunteers as well as of the non-volunteers. Our results show that we can predict flu infection two weeks ahead of time with an average precision from 0.24 to 0.35 depending on the amount of information. This precision is six to nine times higher than with a random guess model. At the population level, we can predict infectious population in a two-week window with an r-squared value of 0.95 (a random-guess model obtains an r-squared value of 0.2). These results point to an innovative approach for tracking individuals who have interacted with people showing symptoms, allowing us to warn those in danger of infection and to inform health researchers about the progression of contact-induced diseases

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

Optimal treatment allocations in space and time for on-line control of an emerging infectious disease

A key component in controlling the spread of an epidemic is deciding where, whenand to whom to apply an intervention.We develop a framework for using data to informthese decisionsin realtime.We formalize a treatment allocation strategy as a sequence of functions, oneper treatment period, that map up-to-date information on the spread of an infectious diseaseto a subset of locations where treatment should be allocated. An optimal allocation strategyoptimizes some cumulative outcome, e.g. the number of uninfected locations, the geographicfootprint of the disease or the cost of the epidemic. Estimation of an optimal allocation strategyfor an emerging infectious disease is challenging because spatial proximity induces interferencebetween locations, the number of possible allocations is exponential in the number oflocations, and because disease dynamics and intervention effectiveness are unknown at outbreak.We derive a Bayesian on-line estimator of the optimal allocation strategy that combinessimulation–optimization with Thompson sampling.The estimator proposed performs favourablyin simulation experiments. This work is motivated by and illustrated using data on the spread ofwhite nose syndrome, which is a highly fatal infectious disease devastating bat populations inNorth America

Data on face-to-face contacts in an office building suggests a low-cost vaccination strategy based on community linkers

Empirical data on contacts between individuals in social contexts play an important role in providing information for models describing human behavior and how epidemics spread in populations. Here, we analyze data on face-to-face contacts collected in an office building. The statistical properties of contacts are similar to other social situations, but important differences are observed in the contact network structure. In particular, the contact network is strongly shaped by the organization of the offices in departments, which has consequences in the design of accurate agent-based models of epidemic spread. We consider the contact network as a potential substrate for infectious disease spread and show that its sparsity tends to prevent outbreaks of rapidly spreading epidemics. Moreover, we define three typical behaviors according to the fraction $f$ of links each individual shares outside its own department: residents, wanderers and linkers. Linkers ($f\sim 50\%$) act as bridges in the network and have large betweenness centralities. Thus, a vaccination strategy targeting linkers efficiently prevents large outbreaks. As such a behavior may be spotted a priori in the offices' organization or from surveys, without the full knowledge of the time-resolved contact network, this result may help the design of efficient, low-cost vaccination or social-distancing strategies