We present a demonstration of a highly scalable, spatially explicit infectious disease simulation that models the spread of disease across all 220,000+ census block groups in the United States using a compartmental Susceptible-Infectious-Recovered (SIR) epidemiological framework. To achieve this unprecedented scale and resolution, our system leverages efficient sparse matrix and vector operations alongside statistical approximations of large numbers of independent random events via Poisson and Normal distributions. The resulting simulation produces realistic spatiotemporal dynamics that align with empirical patterns observed in major epidemics, including the COVID-19 outbreak. Our live demonstration at the conference will highlight the simulation's computational efficiency and interactive capabilities. Starting from the conference venue in Minneapolis, participants will be able to configure disease parameters and observe the geographic spread of infection in real time, offering both an educational and analytical perspective on pandemic modeling.

Massive datasets related to infectious diseases became available after the COVID-19 pandemic, supporting data-driven approaches in modeling and forecasting infectious diseases. However, these approaches are known to exacerbate data biases present in the training data such as having certain demographic groups being over or underrepresented in the data. Such data collection biases may propagate through the modeling and prediction pipelines to decision-making, and the consequences are relatively unknown. Therefore, efforts are needed to understand how data collection bias affects data-driven infectious disease models. This datasets and benchmarks paper provides a suite of datasets, each corresponding to a simulated disease spread among a population of 5000 simulated agents over 90 days in Atlanta and San Francisco. For each dataset, we provide not only the full (simulated ground truth) of the disease spread in terms of when, where, and by whom the disease spreads, but also information on which cases are observed when different types and degrees of data collection bias are applied. The agents' characteristics, check-ins, and social network data are also available to support downstream tasks. Additionally, we also describe how to use the simulation to re-generate the data and to generate new datasets in different regions and with different parameters. With the provided datasets and the simulation tools, researchers studying the spread of infectious diseases may better understand, account for, and correct the systematic bias caused by the inherent real-world data bias, and hence improve the prediction of infectious diseases.

Agent-based models (ABMs) simulate the behaviors, interactions, and disease transmission between individual "agents" within their environment, enabling the investigation of the underlying processes driving disease dynamics and how these processes may be influenced by policy interventions. Despite the critical role that characteristics such as health attitudes and vaccination status play in disease outcomes, the initialization of agent populations with these variables is often oversimplified, overlooking statistical relationships between attitudes and other characteristics or lacking spatial heterogeneity. Leveraging population synthesis methods to create populations with realistic health attitudes and protective behaviors for spatial ABMs has yet to be fully explored. Therefore, this study introduces a novel application for generating synthetic populations with protective behaviors and associated attitudes using public health surveys instead of traditional individual-level survey datasets from the census. We test our approach using two different public health surveys to create two synthetic populations representing individuals aged 18 and over in Virginia, U.S., and their COVID-19 vaccine attitudes and uptake as of December 2021. Results show that integrating public health surveys into synthetic population generation processes preserves the statistical relationships between vaccine uptake and attitudes in different demographic groups while capturing spatial heterogeneity at fine scales. This approach can support disease simulations that aim to explore how real populations might respond to interventions and how these responses may lead to demographic or geographic health disparities. Our study also demonstrates the potential for initializing agents with variables relevant to public health domains that extend beyond infectious diseases, ultimately advancing data-driven ABMs for geographically targeted decision-making.

The increased availability of datasets during the COVID-19 pandemic enabled machine-learning approaches for modeling and forecasting infectious diseases. However, such approaches are known to amplify the bias in the data they are trained on. Bias in such input data like clinical case data for COVID-19 is difficult to measure due to disparities in testing availability, reporting standards, and healthcare access among different populations and regions. Furthermore, the way such biases may propagate through the modeling pipeline to decision-making is relatively unknown. Therefore, we present a system that leverages a highly detailed agent-based model (ABM) of infectious disease spread in a city to simulate the collection of biased clinical case data where the bias is known. Our system allows users to load either a pre-selected region or select their own (using OpenStreetMap data for the environment and census data for the population), specify population and infectious disease parameters, and the degree(s) to which different populations will be overrep-resented or underrepresented in the case data. In addition to the system, we provide a large number of benchmark datasets that produce case data at different levels of bias for different regions. We hope that infectious disease modelers will use these datasets to investigate how well their models are robust to data bias or whether their model is overfit to biased data.

Since the onset of the COVID-19 pandemic, mil-lions of coronavirus sequences have been rapidly deposited in publicly available repositories. The sequences have been used primarily to monitor the evolution and transmission of the virus. In addition, the data can be combined with spatiotemporal information and mapped over space and time to understand transmission dynamics further. For example, the first COVID-19 cases in Australia were genetically related to the dominant strain in Wuhan, China, and spread via international travel. These data are currently available through the Global Initiative on Sharing Avian Influenza Data (GISAID) yet generally remains an untapped resource for data scientists to analyze such multi-dimensional data. Therefore, in this study, we demonstrate a system named Phyloview, a highly interactive visual environment that can be used to examine the spatiotemporal evolution of COVID-19 (from-to) over time using the case study of Louisiana, USA. PhyloView (powered by ArcGIsInsights) facilitates the visualization and exploration of the different dimensions of the phylogenetic data and can be layered with other types of spatiotemporal data for further investigation. Our system has the potential to be shared as a model to be used by health officials that can access relevant data through GISAID, visualize, and analyze it. Such data is essential for a better understanding, predicting, and responding to infectious diseases.

Agent-based models (ABM) are used to represent a variety of complex systems by simulating the local interactions between system components from which observable spatial patterns at the system-level emerge. Thus, the degree to which these interactions are represented correctly must be evaluated. Networks can be used to discretely represent and quantify interactions between system components and the emergent system structure. Therefore, the main objective of this study is to develop and implement a novel validation approach called the NEtworks for ABM Testing (NEAT) that integrates geographic information science, ABM approaches, and spatial network representations to simulate complex systems as measurable and dynamic spatial networks. The simulated spatial network structures are measured using graph theory and compared with empirical regularities of observed real networks. The approach is implemented to validate a theoretical ABM representing the spread of influenza in the City of Vancouver, Canada. Results demonstrate that the NEAT approach can validate whether the internal model processes are represented realistically, thus better enabling the use of ABMs in decision-making processes.