Epidemic Spread Modeling for COVID-19 Using Cross-fertilization of Mobility Data

We present an individual-centric model for COVID-19 spread in an urban setting. We first analyze patient and route data of infected patients from January 20, 2020, to May 31, 2020, collected by the Korean Center for Disease Control & Prevention (KCDC) and discover how infection clusters develop as a function of time. This analysis offers a statistical characterization of mobility habits and patterns of individuals at the beginning of the pandemic. While the KCDC data offer a wealth of information, they are also by their nature limited. To compensate for their limitations, we use detailed mobility data from Berlin, Germany after observing that mobility of individuals is surprisingly similar in both Berlin and Seoul. Using information from the Berlin mobility data, we cross-fertilize the KCDC Seoul data set and use it to parameterize an agent-based simulation that models the spread of the disease in an urban environment. After validating the simulation predictions with ground truth infection spread in Seoul, we study the importance of each input parameter on the prediction accuracy, compare the performance of our model to state-of-the-art approaches, and show how to use the proposed model to evaluate different what-if counter-measure scenarios. IEEE

GeoSpread: An Epidemic Spread Modeling Tool for COVID-19 Using Mobility Data

We present an individual-centric agent-based model and a flexible tool, GeoSpread, for studying and predicting the spread of viruses and diseases in urban settings. Using COVID-19 data collected by the Korean Center for Disease Control & Prevention (KCDC), we analyze patient and route data of infected people from January 20, 2020, to May 31, 2020, and discover how infection clusters develop as a function of time. This analysis offers a statistical characterization of population mobility and is used to parameterize GeoSpread to capture the spread of the disease. We validate simulation predictions from GeoSpread with ground truth and we evaluate different what-if counter-measure scenarios to illustrate the usefulness and flexibility of the tool for epidemic modeling. © 2022 Owner/Author.

Forecasting the spread of SARS-CoV-2 in the campania region using genetic programming.

Coronavirus disease 19 (COVID-19) is an infectious disease caused by the SARS-CoV-2 virus, which is responsible for the ongoing global pandemic. Stringent measures have been adopted to face the pandemic, such as complete lockdown, shutting down businesses and trade, as well as travel restrictions. Nevertheless, such solutions have had a tremendous economic impact. Although the use of recent vaccines seems to reduce the scale of the problem, the pandemic does not appear to finish soon. Therefore, having a forecasting model about the COVID-19 spread is of paramount importance to plan interventions and, then, to limit the economic and social damage. In this paper, we use Genetic Programming to evidence dependences of the SARS-CoV-2 spread from past data in a given Country. Namely, we analyze real data of the Campania Region, in Italy. The resulting models prove their effectiveness in forecasting the number of new positives 10/15 days before, with quite a high accuracy. The developed models have been integrated into the context of SVIMAC-19, an analytical-forecasting system for the containment, contrast, and monitoring of Covid-19 within the Campania Region.

Network Based Framework to Compare Vaccination Strategies

We propose a network based framework to model spread of disease. We study the evolution and control of spread of virus using the standard SIR-like rules while incorporating the various available models for social interaction. The dynamics of the framework has been compared with the real-world data of COVID-19 spread in India. This framework is further used to compare vaccination strategies. © 2021, Springer Nature Switzerland AG.

Genetic algorithm with cross-validation-based epidemic model and application to the early diffusion of COVID-19 in Algeria.

A dynamical epidemic model optimized using a genetic algorithm and a cross-validation method to overcome the overfitting problem is proposed. The cross-validation procedure is applied so that available data are split into a training subset used to fit the algorithm's parameters, and a smaller subset used for validation. This process is tested on Italy, Spain, Germany, and South Korea cases before being applied to Algeria. Interestingly, our study reveals an inverse relationship between the size of the training sample and the number of generations required in the genetic algorithm. Moreover, the enhanced compartmental model presented in this work has proven to be a reliable tool to estimate key epidemic parameters and the non-measurable asymptomatic infected portion of the susceptible population to establish a realistic nowcast and forecast of the epidemic's evolution. The model is employed to study the COVID-19 outbreak dynamics in Algeria between February 25th, 2020, and May 24th, 2020. The basic reproduction number and effective reproduction number on May 24th, after three months of the outbreak, are estimated to be 3.78 (95% CI 3.033-4.53) and 0.651 (95% CI 0.539-0.761), respectively. Disease incidence, CFR, and IFR are also calculated. Numerical programs developed for this study are made publicly accessible for reproduction and further use.

DeepCOVIDNet: An Interpretable Deep Learning Model for Predictive Surveillance of COVID-19 Using Heterogeneous Features and Their Interactions.

In this paper, we propose a deep learning model to forecast the range of increase in COVID-19 infected cases in future days and we present a novel method to compute equidimensional representations of multivariate time series and multivariate spatial time series data. Using this novel method, the proposed model can both take in a large number of heterogeneous features, such as census data, intra-county mobility, inter-county mobility, social distancing data, past growth of infection, among others, and learn complex interactions between these features. Using data collected from various sources, we estimate the range of increase in infected cases seven days into the future for all U.S. counties. In addition, we use the model to identify the most influential features for prediction of the growth of infection. We also analyze pairs of features and estimate the amount of observed second-order interaction between them. Experiments show that the proposed model obtains satisfactory predictive performance and fairly interpretable feature analysis results; hence, the proposed model could complement the standard epidemiological models for national-level surveillance of pandemics, such as COVID-19. The results and findings obtained from the deep learning model could potentially inform policymakers and researchers in devising effective mitigation and response strategies. To fast-track further development and experimentation, the code used to implement the proposed model has been made fully open source.

Epidemiological Predictive Modeling of COVID-19 Infection: Development, Testing, and Implementation on the Population of the Benelux Union.

Since the outbreak of coronavirus disease-2019 (COVID-19), the whole world has taken interest in the mechanisms of its spread and development. Mathematical models have been valuable instruments for the study of the spread and control of infectious diseases. For that purpose, we propose a two-way approach in modeling COVID-19 spread: a susceptible, exposed, infected, recovered, deceased (SEIRD) model based on differential equations and a long short-term memory (LSTM) deep learning model. The SEIRD model is a compartmental epidemiological model with included components: susceptible, exposed, infected, recovered, deceased. In the case of the SEIRD model, official statistical data available online for countries of Belgium, Netherlands, and Luxembourg (Benelux) in the period of March 15 2020 to March 15 2021 were used. Based on them, we have calculated key parameters and forward them to the epidemiological model, which will predict the number of infected, deceased, and recovered people. Results show that the SEIRD model is able to accurately predict several peaks for all the three countries of interest, with very small root mean square error (RMSE), except for the mild cases (maximum RMSE was 240.79 ± 90.556), which can be explained by the fact that no official data were available for mild cases, but this number was derived from other statistics. On the other hand, LSTM represents a special kind of recurrent neural network structure that can comparatively learn long-term temporal dependencies. Results show that LSTM is capable of predicting several peaks based on the position of previous peaks with low values of RMSE. Higher values of RMSE are observed in the number of infected cases in Belgium (RMSE was 535.93) and Netherlands (RMSE was 434.28), and are expected because of thousands of people getting infected per day in those countries. In future studies, we will extend the models to include mobility information, variants of concern, as well as a medical intervention, etc. A prognostic model could help us predict epidemic peaks. In that way, we could react in a timely manner by introducing new or tightening existing measures before the health system is overloaded.

Accuracy of State-Level Surveillance during Emerging Outbreaks of Respiratory Viruses: A Model-Based Assessment.

It is long perceived that the more data collection, the more knowledge emerges about the real disease progression. During emergencies like the H1N1 and the severe acute respiratory syndrome coronavirus 2 pandemics, public health surveillance requested increased testing to address the exacerbated demand. However, it is currently unknown how accurately surveillance portrays disease progression through incidence and confirmed case trends. State surveillance, unlike commercial testing, can process specimens based on the upcoming demand (e.g., with testing restrictions). Hence, proper assessment of accuracy may lead to improvements for a robust infrastructure. Using the H1N1 pandemic experience, we developed a simulation that models the true unobserved influenza incidence trend in the State of Michigan, as well as trends observed at different data collection points of the surveillance system. We calculated the growth rate, or speed at which each trend increases during the pandemic growth phase, and we performed statistical experiments to assess the biases (or differences) between growth rates of unobserved and observed trends. We highlight the following results: 1) emergency-driven high-risk perception increases reporting, which leads to reduction of biases in the growth rates; 2) the best predicted growth rates are those estimated from the trend of specimens submitted to the surveillance point that receives reports from a variety of health care providers; and 3) under several criteria to queue specimens for viral subtyping with limited capacity, the best-performing criterion was to queue first-come, first-serve restricted to specimens with higher hospitalization risk. Under this criterion, the lab released capacity to subtype specimens for each day in the trend, which reduced the growth rate bias the most compared to other queuing criteria. Future research should investigate additional restrictions to the queue.

Estimation of COVID-19 epidemic curves using genetic programming algorithm.

This paper investigates the possibility of the implementation of Genetic Programming (GP) algorithm on a publicly available COVID-19 data set, in order to obtain mathematical models which could be used for estimation of confirmed, deceased, and recovered cases and the estimation of epidemiology curve for specific countries, with a high number of cases, such as China, Italy, Spain, and USA and as well as on the global scale. The conducted investigation shows that the best mathematical models produced for estimating confirmed and deceased cases achieved R2 scores of 0.999, while the models developed for estimation of recovered cases achieved the R2 score of 0.998. The equations generated for confirmed, deceased, and recovered cases were combined in order to estimate the epidemiology curve of specific countries and on the global scale. The estimated epidemiology curve for each country obtained from these equations is almost identical to the real data contained within the data set.