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During an epidemic, it can be difficult to get an estimate of the actual number of people infected at any given time. This is due to multiple reasons, including some cases being asymptomatic and sick people not seeking healthcare for mild symptoms, among others. Large scale random sampling of the population for testing can be expensive, especially in the early stages of an epidemic, when tests are scarce. Here we show how an adaptive prevalence testing method can be developed to obtain a good estimate of the disease burden by learning to intelligently allocate a small number of tests for random testing of the population. Our approach uses a combination of an agent-based simulation and deep learning in an active sensing paradigm. We show that it is possible to get a good state estimate with relatively minimal prevalence testing, and that the trained system adapts quickly and performs well even if the disease parameters change. 

ABSTRACT Evacuation plans are designed to move people to safety in case of a disaster. It mainly consists of two components: routing and scheduling. Joint optimization of these two components with the goal of minimizing total evacuation time is a computationally hard problem, specifically when the problem instance is large. Moreover, often in disaster situations, there is uncertainty regarding the passability of roads throughout the evacuation time period. In this paper, we present a way to model the time-varying risk associated with roads in disaster situations. We also design a heuristic method based on the well known Large Neighborhood Search framework to perform the joint optimization task. We use real-world road network and population data from Harris County in Houston, Texas and apply our heuristic to find evacuation routes and schedules for the area. We show that the proposed method is able to find good solutions within a reasonable amount of time. We also perform agent-based simulations of the evacuation using these solutions to evaluate their quality and efficacy. 

As the complexity of our food systems increases, they also become susceptible to unanticipated natural and human-initiated events. Commodity trade networks are a critical component of our food systems in ensuring food availability. We develop a generic data-driven framework to construct realistic agricultural commodity trade networks. Our work is motivated by the need to study food flows in the context of biological invasions. These networks are derived by fusing gridded, administrative-level, and survey datasets on production, trade, and consumption. Further, they are periodic temporal networks reflecting seasonal variations in production and trade of the crop. We apply this approach to create networks of tomato flow for two regions – Senegal and Nepal. Using statistical methods and network analysis, we gain insights into spatiotemporal dynamics of production and trade. Our results suggest that agricultural systems are increasingly vulnerable to attacks through trade of commodities due to their vicinity to regions of high demand and seasonal variations in production and flows. 

This research measures the epidemiological and economic impact of COVID-19 spread in the US under different mitigation scenarios, comprising of non-pharmaceutical interventions. A detailed disease model of COVID-19 is combined with a model of the US economy to estimate the direct impact of labor supply shock to each sector arising from morbidity, mortality, and lockdown, as well as the indirect impact caused by the interdependencies between sectors. During a lockdown, estimates of jobs that are workable from home in each sector are used to modify the shock to labor supply. Results show trade-os between economic losses, and lives saved and infections averted are non-linear in compliance to social distancing and the duration of lockdown. Sectors that are worst hit are not the labor-intensive sectors such as Agriculture and Construction, but the ones with high valued jobs such as Professional Services, even after the teleworkability of jobs is accounted for. Additionally, the findings show that a low compliance to interventions can be overcome by a longer shutdown period and vice versa to arrive at similar epidemiological impact but their net effect on economic loss depends on the interplay between the marginal gains from averting infections and deaths, versus the marginal loss from having healthy workers stay at home during the shutdown. 

Computational epidemiology aims to develop computer models and decision support systems that understand, predict, and control a disease’s spatiotemporal diffusion throughout a population. Researchers can use these models to forecast an epidemic’s future course, allocate scarce resources and assess depletion of current resources, infer disease parameters, and evaluate various interventions. Individual behavior and public policy are critical in understanding and controlling infectious diseases, and computational techniques provide a potentially powerful study tool. The COVID-19 pandemic has had significant social, health, economic, and political ramifications worldwide, and its impact will undoubtedly continue to grow in the coming months. Here we outline an approach to support the COVID-19 response with examples that are rooted in network science and data-driven modeling. 

Computational epidemiology aims to develop computer models and decision support systems that understand, predict, and control a disease’s spatiotemporal diffusion throughout a population. Researchers can use these models to forecast an epidemic’s future course, allocate scarce resources and assess depletion of current resources, infer disease parameters, and evaluate various interventions. Individual behavior and public policy are critical in understanding and controlling infectious diseases, and computational techniques provide a potentially powerful study tool. The COVID-19 pandemic has had significant social, health, economic, and political ramifications worldwide, and its impact will undoubtedly continue to grow in the coming months.Here we outline an approach to support the COVID-19 response with examples that are rooted in network science and data-driven modeling. 

We study allocation of COVID-19 vaccines to individuals based on the structural properties of their underlying social contact network. Even optimistic estimates suggest that most countries will likely take 6 to 24 months to vaccinate their citizens. These time estimates and the emergence of new viral strains urge us to find quick and effective ways to allocate the vaccines and contain the pandemic. While current approaches use combinations of age-based and occupation-based prioritizations, our strategy marks a departure from such largely aggregate vaccine allocation strategies. We propose a novel agent-based modeling approach motivated by recent advances in (i) science of real-world networks that point to efficacy of certain vaccination strategies and (ii) digital technologies that improve our ability to estimate some of these structural properties. Using a realistic representation of a social contact network for the Commonwealth of Virginia, combined with accurate surveillance data on spatio-temporal cases and currently accepted models of within- and between-host disease dynamics, we study how a limited number of vaccine doses can be strategically distributed to individuals to reduce the overall burden of the pandemic. We show that allocation of vaccines based on individuals' degree (number of social contacts) and total social proximity time is significantly more effective than the currently used age-based allocation strategy in terms of number of infections, hospitalizations and deaths. Our results suggest that in just two months, by March 31, 2021, compared to age-based allocation, the proposed degree-based strategy can result in reducing an additional 56{110k infections, 3.2{5.4k hospitalizations, and 700{900 deaths just in the Commonwealth of Virginia. Extrapolating these results for the entire US, this strategy can lead to 3{6 million fewer infections, 181{306k fewer hospitalizations, and 51{62k fewer deaths compared to age-based allocation. The overall strategy is robust even: (i) if the social contacts are not estimated correctly; (ii) if the vaccine efficacy is lower than expected or only a single dose is given; (iii) if there is a delay in vaccine production and deployment; and (iv) whether or not non-pharmaceutical interventions continue as vaccines are deployed. For reasons of implementability, we have used degree, which is a simple structural measure and can be easily estimated using several methods, including the digital technology available today. These results are significant, especially for resource-poor countries, where vaccines are less available, have lower efficacy, and are more slowly distributed. 

Global airline networks play a key role in the global importation of emerging infectious diseases. Detailed information on air traffic between international airports has been demonstrated to be useful in retrospectively validating and prospectively predicting case emergence in other countries. In this paper, we use a well-established metric known as effective distance on the global air traffic data from IATA to quantify risk of emergence for different countries as a consequence of direct importation from China, and compare it against arrival times for the first 24 countries. Using this model trained on official first reports from WHO, we estimate time of arrival (ToA) for all other countries. We then incorporate data on airline suspensions to recompute the effective distance and assess the effect of such cancellations in delaying the estimated arrival time for all other countries. Finally we use the infectious disease vulnerability indices to explain some of the estimated reporting delays.