Studying Contagious Disease Spread: An ABM Framework

In the past we have written about the use of synthetic populations and their use in agent-based models. We are finding such synthetic populations to be extremely useful in the creation or initialization of agent-based models. To give you a sense of how we are utilizing such synthetic populations at the 7th ACM SIGSPATIAL International Workshop on Geospatial Simulation (GeoSim 2024),   Na (Richard) Jiang and myself have a new paper entitled  "Studying Contagious Disease Spread Utilizing Synthetic Populations Inspired by COVID-19: An Agent-based Modeling Framework." 

In the paper we show how we can we utilize a method to create the geographically-explicit synthetic population along with capturing their social networks and how this can be used to study  contagious disease spread (and various lineages of the disease) in Western New York. If this sounds of interest, below you can read the abstract from the paper, see some of the results and find the full reference and the link to the paper. While the model itself and the data needed to run it is available at https://osf.io/zrtuj/

Abstract

The COVID-19 pandemic has reshaped societies and brought to the forefront simulation as a tool to explore the spread of the diseases including that of agent-based modeling. Efforts have been made to ground these models on the world around us using synthetic populations that attempt to mimic the population at large. However, we would argue that many of these synthetic populations and therefore the models using them, miss the social connections which were paramount to the spread of the pandemic. Our argument being is that contagious diseases mainly spread through people interacting with each other and therefore the social connections need to be captured. To address this, we create a geographically-explicit synthetic population along with its social network for the Western New York (WNY) Area. This synthetic population is then used to build a framework to explore a hypothetical contagious disease inspired by various of COVID-19. We show simulation results from two scenarios utilizing this framework, which demonstrates the utility of our approach capturing the disease dynamics. As such we show how basic patterns of life along with interactions driven by social networks can lead to the emergence of disease outbreaks and pave the way for researchers to explore the next pandemic utilizing agent-based modeling with geographically explicit social networks.

Keywords: Agent-based Modeling, Synthetic Populations, Social Networks, COVID-19, Disease Modeling.

Single Lineage Results: (a) Overall SEIR Dynamic; (b) Contact Tracing Example.

Western New York Commuting Pattern.

Disease Dynamics when Two Lineages are Introduced.

Reference: 

Jiang N., Crooks, A.T. (2024), Studying Contagious Disease Spread Utilizing Synthetic Populations Inspired by COVID-19: An Agent-based Modeling Framework, Proceedings of the 7th ACM SIGSPATIAL International Workshop on Geospatial Simulation (GeoSim 2024), Atlanta, GA., pp. 29-32. (pdf)

Agent-Based Models and Geography

Just a quick post, In recently released Encyclopedia of Human Geography edited by Barney Warf we were asked to write a short chapter entitled "Agent-based Models and Geography" In the chapter we discuss how over  the last several decades, agent-based modeling has gained widespread adoption in geography.and introduce the reader to what are agent-based models, how they have developed and types of geographical applications that can be explored with them, especially when linked to Geographical Information Systems (GIS). The chapter concludes with a brief summary along with a discussion of challenges and opportunities with agent-based modeling (ABM). If this sounds of interest, below you can find the full reference and link to the chapter. 

Example application domains for agent-based models over various spatial and temporal scales. For more examples and further details can be found at https://www.gisagents.org/

Full Referece:

Crooks, A.T. and Jiang, N. (2024), Agent-based Models and Geography, in Warf, B. (ed.), The Encyclopedia of Human Geography, Springer, Cham, Switzerland, https://doi.org/10.1007/978-3-031-25900-5_258-1. (pdf)

An Agent-based model of COVID-19 Vaccine uptake in New York State

In the past we have explored how agent-based modeling can be used to study vaccine uptake and what is the mechanism underlying the diffusion of different vaccine opinions in hybrid spaces (e.g., physical, relational and cyber) can affect individuals’ vaccination decisions. But this prior work was limited to  just one small area. However, we know that urban and rural communities have different levels of digital connectivity and we were wondering if our initial findings are applicable to other counties which are more urban or to a larger study area. To explore this, at the 7th ACM SIGSPATIAL International Workshop on Geospatial Simulation (GeoSim 2024)  we (Fuzhen Yin, Na Jiang, Lucie Laurian and myself) have a paper entitled "Agent-based Modeling of COVID-19 Vaccine uptake in New York State: Information Diffusion in Hybrid Spaces". 

This paper significantly extends our previous work in a number of ways. First we move from a single rural county to the entire state of New York which has 62 counties which differ substantially in  socioeconomic status. Furthermore, we move from a small population of 120,000 to over 20 million agents. By doing so, it allows us to compare vaccination uptakes in different areas (e.g., urban versus rural communities, second home destinations versus college towns). We also use  different parameters to initialize hybrid spaces for urban and rural populations to understand how individuals' preferences on hybrid spaces affect information diffusion and vaccination rates at a macro level. Lastly, we updated the decision-making rules for minors (i.e., ages under 18) that allows us to better simulate young population groups. In the sense that we make the assumption that minors need to have at least one of their guardians in the family network vaccinated already before they can take vaccines. By extending the model  we can can accurately simulate the vaccination rates for New York state (mean absolute error=6.93) and for the majority of counties within it (81%).

If this sounds of interest, below you can read the abstract of our paper, see our various hybrid spaces over the New York state along with our updated model logic and the aggregate results. The full reference and the link to the paper can be found at the bottom of the post. While the model itself, which was created in Mesa and the data needed to run the model can be found at: https://osf.io/3khyq/. We share our modeling scripts, input data and results at  for interested readers to reproduce or extend our work as they see fit but also to conform with the FAIR principles (findable, accessible, interoperable and reusable),

Abstract

During the COVID-19 pandemic, social media become an important hub for public discussions on vaccination. However, it is unclear how the rise of cyber space (i.e., social media) combined with traditional relational spaces (i.e., social circles), and physical space (i.e., spatial proximity) together affect the diffusion of vaccination opinions and produce different impacts on urban and rural population's vaccination uptake. This research builds an agent-based model utilizing the Mesa framework to simulate individuals' opinion dynamics towards COVID-19 vaccines, their vaccination uptake and the emergent vaccination rates at a macro level for New York State (NYS). By using a spatially explicit synthetic population, our model can accurately simulate the vaccination rates for NYS (mean absolute error=6.93) and for the majority of counties within it (81\%). This research contributes to the modeling literature by simulating individuals vaccination behaviors which are important for disease spread and transmission studies. Our study extends geo-simulations into hybrid-space settings (i.e., physical, relational, and cyber spaces).

Keywords: Agent-based modeling, GIS, Information diffusion, Hybrid spaces, Social networks, Health informatics, Vaccines, COVID-19. 

Schematic representation of hybrid spaces. Physical space includes family and group quarter network. Relational space represents people's social circles in work, school and daycare. Cyber space is a social media network. This figure only display 2% of total population in NYS (around 200,000 agents) for visualization process.

Modeling process and structure: from data to agent-behaviors.

Mapping the differences (i.e., mean absolute error (MAE)) in vaccination rate between simulated and ground truth data. 

Reference: 

Yin, F., Jiang, Na., Crooks, A.T., Laurian, L. (2024), Agent-based Modeling of Covid-19 Vaccine Uptake in New York State: Information Diffusion in Hybrid Spaces, Proceedings of the 7th ACM SIGSPATIAL International Workshop on Geospatial Simulation (GeoSim 2024), Atlanta, GA., pp. 11-20. (pdf)

Retention in Higher Education: An Agent-Based Model

The effects of educational attainment on individuals and society have been the subject of much research. However, there is still a need to study what factors matter the most, and what is worth investing more time and resources into, and how new methods of analysis can provide additional ways of looking into some of the challenges faced by higher education. 

To this end at the 2024 International Conference of the Computational Social Science Society of the Americas (CSSSA), Amira Al-Khulaidy Stine and myself had a paper entitled "Retention in Higher Education: An Agent-Based Model of Social Interactions and Motivated Agent Behavior."  In the paper we introduce an agent-based model which explores retention where we focus on students and their levels of motivation (i.e., "grit"), their immediate connections (i.e., sense of belonging) and institutional support. At the same time we capture institutional locales (i.e., urban and rural) and their selectivity. Taken all together the model explores how these factors impact student success outcomes and retention.  We find students level of motivation is a reliable factor in determining student outcome which is inline with others, but the model also suggests that for certain student populations (i.e., those that have average motivation and mid range GPAs), their sense of belonging represented though their social connections with other students and institutional support (i.e., hubs of support)  can be more important. 

If this sounds of interest below we have the abstract to the paper, along with some images relating the data that was used to inform aspects of the model, the graphical user interface of model, its logic and some of the results that emerge from it. While at the bottom of the post you can find the full citation and a the link to the paper itself. The model itself which was developed in NetLogo, along with a detailed Overview, Design concepts, and Details (ODD) document can be found at https://www.comses.net/codebase-release/53302b0a-0a97-463a-8498-d604cb246e4c/.

Abstract:

In the United States, educational attainment and student retention in higher education are two of the main focuses of higher education research. Institutions are constantly looking for ways to identify areas of improvement across different aspects of the student experience on university campuses. This paper combines Department of Education data over a 10 year period, U.S. Census data, and higher education theory on student retention, to build an agent-based model of student behavior. Furthermore we model student social interactions with their peers along with considering environmental components (e.g., urban vs. rural campuses) and institution personnel to explore the elements that increase the likelihood of student retention. Results suggest that both social interactions and environmental components make a difference in student retention. Suggesting that higher education institutions should consider new ways to accommodate learning needs that promote better student outcomes.

Keywords: Agent-Based Model, College Campuses, Higher Education, Department of Education,  Social Interactions, Student Retention.

Student retention 2007-2021 by institutional support and urbanicity for Urban, Suburban, Town, and Rural areas.

Model Graphical User Interface.

Process Overview and Model Logic.

Retention results for Urban (left) and Rural (right) settings of low support and low sense of belonging while high motivation (grit).

Referece: 

Stine, A.A. and Crooks, A.T. (2024), Retention in Higher Education: An Agent-Based Model of Social Interactions and Motivated Agent Behavior, Proceedings of the 2024 International Conference of the Computational Social Science Society of the Americas, Santa Fe, NM. (pdf)

Call for Abstracts - AAG 2025: Geo-simulation Sessions

Building upon last year’s successful sessions related to geosimulation, were various topics and issues from across the urban, social and environmental fields and the resulting application areas. More excitingly, we are witnessing the emergence of the integration of cutting-edge techniques (e.g., machine learning and generative AI) which is energizing the geosimulation community as they offer new approaches for advancing geosimulations. 

This year, the 2025 AAG Annual Meeting will take place in Detroit, Michigan from March 24 to March 28. We are continuing to organize sessions on "Geosimulations for Addressing Societal Challenges," and we encourage you to submit abstracts if this area aligns with your research interests.

Session Description:

There is an urgent need for research that promotes sustainability in an era of societal challenges ranging from climate change, population growth, aging and wellbeing to that of pandemics. These need to be directly fed into policy. We, as a Geosimulation community, have the skills and knowledge to use the latest theory, models and evidence to make a positive and disruptive impact. These include agent-based modeling, microsimulation and increasingly, machine learning methods. However, there are several key questions that we need to address which we seek to cover in this session. For example, What do we need to be able to contribute to policy in a more direct and timely manner? What new or existing research approaches are needed? How can we make sure they are robust enough to be used in decision making? How can geosimulation be used to link across citizens, policy and practice and respond to these societal challenges? What are the cross-scale local trade-offs that will have to be negotiated as we re-configure and transform our urban and rural environments? How can spatial data (and analysis) be used to support the co-production of truly sustainable solutions, achieve social buy-in and social acceptance? And thereby co-produce solutions with citizens and policy makers.

We are particularly interested in presentations that will discuss issues relating to:

• Agent-based modeling and microsimulation techniques for responding to societal challenges;
• Agent-based models used for policy formation;
• Data driven modeling;
• Utilizing machine modeling for geosimulation;
• Creating really big models using exascale computation;
• Model validation and assessment;
• Participatory methods for agent-based modeling;
• Approaches to connect and share (open source) data and models;
• Revealing, quantifying, and reducing socio-economic inequalities with Geosimulation.

Next Steps:

If this sounds of interest, please e-mail the abstract and keywords with your expression of intent to Richard Jiang (njiang8@buffalo.edu) by October 29 (2 days before the AAG session deadline). Please make sure that your abstract conforms to the AAG guidelines in relation to title, word limit and keywords and as specified at: https://aag.secure-platform.com/aag2025/page/abstracts/abstract-guidelines An abstract should be no more than 250 words that describe the presentation’s purpose, methods, and conclusions.

Timeline:

• October 29, 2024: Please send abstract and keywords with your expression of intent to Richard Jiang (njiang8@buffalo.edu) 
• October 30th, 2024: Session finalization and author notification 
• October 31, 2024: Final abstract submission to AAG, via https://aag.secure-platform.com/aag2025.  All participants must register individually via this site. Upon registration you will be given a participant number (PIN). Send the PIN and a copy of your final abstract to Richard Jiang. Neither the organizers nor the AAG will edit the abstracts. 
• February 6, 2025: Final Abstract/Session Editing and Presentation Conversion deadlines for AAG, via https://aag.secure-platform.com/aag2025. 
• March 24-28 2025: AAG in Detroit.

Organizers

• Alison Heppenstall, University of Glasgow, Scotland.
• Andrew Crooks, University at Buffalo, USA.
• Na (Richard) Jiang, University at Buffalo, USA.
• Fuzhen Yin, University of Colorado, Colorado Springs, USA.
• Raja Sengupta, McGill University, Canada.
• Suzana Dragicevic, Simon Fraser University, Canada.
• Boyu Wang, University at Buffalo, USA.
• Sarah Wise, University College London, England.