arXiv subjects

Joy Kitson

Publications and source records attributed to Joy Kitson.

5 recordsLinked to original sources

arXiv2025

Simulating nationwide coupled disease and fear spread in an agent-based model

Human cognitive responses, behavioral responses, and disease dynamics co-evolve over the course of any disease outbreak, and can result in complex feedbacks. We present a dynamic agent-based model that explicitly couples the spread of disease with the spread of fear surrounding the disease, implemented within the EpiCast simulation framework. EpiCast models transmission across a realistic synthetic population, capturing individual-level interactions. In our model, fear propagates through both in-person contact and broadcast media, prompting individuals to adopt protective behaviors that reduce disease spread. In order to better understand these coupled dynamics, we create and compare a range of compartmental surrogate models to analyze the impact of including various disease states. Additionally, we compare a range of behavioral scenarios within EpiCast, varying the level and intensity of fear and behavioral change. Our results show that the addition of asymptomatic, exposed, and pre-symptomatic disease states can impact both the rate at which an outbreak progresses and its overall trajectory. Moreover, the combination of non-local fear spread via broadcasters and strong behavioral responses by fearful individuals generally leads to multiple epidemic waves, an outcome that occurs only within a narrow parameter range when fear spreads purely through local contact. Accounting for the coupled spread of fear and disease is critical for understanding disease dynamics and designing timely, targeted responses to emerging infectious threats.

q-bio.PE↗

arXiv2025

Epicast 2.0: A large-scale, demographically detailed, agent-based model for simulating respiratory pathogen spread in the United States

The recent history of respiratory pathogen epidemics, including those caused by influenza and SARS-CoV-2, has highlighted the urgent need for advanced modeling approaches that can accurately capture heterogeneous disease dynamics and outcomes at the national scale, thereby enhancing the effectiveness of resource allocation and decision-making. In this paper, we describe Epicast 2.0, an agent-based model that utilizes a highly detailed, synthetic population and high-performance computing techniques to simulate respiratory pathogen transmission across the entire United States. This model replicates the contact patterns of over 320 million agents as they engage in daily activities at school, work, and within their communities. Epicast 2.0 supports vaccination and an array of non-pharmaceutical interventions that can be promoted or relaxed via highly granular, user specified policies. We illustrate the model's capabilities using a wide range of outbreak scenarios, highlighting the model's varied dynamics as well as its extensive support for policy exploration. This model provides a robust platform for conducting what if scenario analysis and providing insights into potential strategies for mitigating the impacts of infectious diseases.

q-bio.PE↗

arXiv2024

Taking GPU Programming Models to Task for Performance Portability

Portability is critical to ensuring high productivity in developing and maintaining scientific software as the diversity in on-node hardware architectures increases. While several programming models provide portability for diverse GPU systems, they don't make any guarantees about performance portability. In this work, we explore several programming models -- CUDA, HIP, Kokkos, RAJA, OpenMP, OpenACC, and SYCL, to assess the consistency of their performance across NVIDIA and AMD GPUs. We use five proxy applications from different scientific domains, create implementations where missing, and use them to present a comprehensive comparative evaluation of the performance portability of these programming models. We provide a Spack scripting-based methodology to ensure reproducibility of experiments conducted in this work. Finally, we analyze the reasons for why some programming models underperform in certain scenarios and in some cases, present performance optimizations to the proxy applications.

cs.DC↗

arXiv2024

Pandemics In Silico: Scaling an Agent-Based Simulation on Realistic Social Contact Networks

Preventing the spread of infectious diseases requires implementing interventions at various levels of government and evaluating the potential impact and efficacy of those preemptive measures. Agent-based modeling can be used for detailed studies of epidemic diffusion and possible interventions. Modeling of epidemic diffusion in large social contact networks requires the use of parallel algorithms and resources. In this work, we present Loimos, a scalable parallel framework for simulating epidemic diffusion. Loimos uses a hybrid of time-stepping and discrete-event simulation to model disease spread, and is implemented on top of an asynchronous, many-task runtime. We demonstrate that Loimos is to able to achieve significant speedups while scaling to large core counts. In particular, Loimos is able to simulate 200 days of a COVID-19 outbreak on a digital twin of California in about 42 seconds, for an average of 4.6 billion traversed edges per second (TEPS), using 4096 cores on Perlmutter at NERSC.

cs.DC↗

arXiv2019

SOMOSPIE: A modular SOil MOisture SPatial Inference Engine based on data driven decisions

The current availability of soil moisture data over large areas comes from satellite remote sensing technologies (i.e., radar-based systems), but these data have coarse resolution and often exhibit large spatial information gaps. Where data are too coarse or sparse for a given need (e.g., precision agriculture), one can leverage machine-learning techniques coupled with other sources of environmental information (e.g., topography) to generate gap-free information and at a finer spatial resolution (i.e., increased granularity). To this end, we develop a spatial inference engine consisting of modular stages for processing spatial environmental data, generating predictions with machine-learning techniques, and analyzing these predictions. We demonstrate the functionality of this approach and the effects of data processing choices via multiple prediction maps over a United States ecological region with a highly diverse soil moisture profile (i.e., the Middle Atlantic Coastal Plains). The relevance of our work derives from a pressing need to improve the spatial representation of soil moisture for applications in environmental sciences (e.g., ecological niche modeling, carbon monitoring systems, and other Earth system models) and precision agriculture (e.g., optimizing irrigation practices and other land management decisions).

cs.LG↗