Neural Universal Differential Equation Hypernetwork Surrogates for Agent-Based Disease Models
Presentation for SIAM CSE 2025 on new surrogate modeling for epidemiological agent-based models
Robertson, Connor James [Sandia National Laborator↗
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The Chicago Social Interaction Model (ChiSIM)
ChiSIM is a framework for implementing agent-based models that simulate the mixing of a synthetic population. In a ChiSIM based model, each agent, that is, each person in the simulated population, resides in a place (a household, dormitory or retirement home/long term care facility, for example), and moves among other places such as workplaces, homes, clinics, and community resources. Agents typically move between places according to their domain specific activity profile, such that each agent has a profile that determines at what times throughout the day they occupy a particular location. Once in a place, an agent mixes with other agents in some model or domain-specific way. For example, an agent may expose other agents to a disease in an epidemiological model.
Ozik, Jonathan↗
System Analysis Modeling and Intermodal Transportation for Commercial Spent Nuclear Fuel
The United States Department of Energy (DOE) has long term goals to develop solutions for managing the nation’s spent nuclear fuel (SNF) and high-level waste (HLW) inventory. The Integrated Waste Management (IWM) program under the DOE office of Nuclear Energy (DOE-NE) is employing system-level engineering and analysis principles to inform potential future waste management system architectures. Managing the spent nuclear waste requires the use of system-level analysis software that takes various aspects of the fuel cycle into account like waste generation, on-site/centralized storage, transportation infrastructure, and long-term disposal. The Next Generation System Analysis Model (NGSAM) is an agent-based model that was developed to simulate the transportation and storage of SNF and HLW. As an agent-based model, NGSAM has the capability to detail the interaction and movement of individual components and groups, such as rail cars and casks. The SNF inventory from commercial nuclear reactors is currently in temporary storage at multiple locations spread across the United States. Shipping of SNF from these locations relies on one of three transportation modes: rail, heavy-haul truck, or barge. Out of the three modes identified, rail is generally the most preferred due to the size of the canisters and casks the SNF would be shipped in. However, under some scenarios, a direct rail route might not be readily available to a reactor site or improving the rail infrastructure at shutdown sites might be too cost-prohibitive for utilities to opt for a direct rail transfer. Under such scenarios, using a barge or heavy haul truck to de-inventory the site and transfer the SNF to a nearby intermodal transfer site with adequate rail infrastructure where the payload could be transferred to a rail car might prove to be an attractive option. This work initially presents the various intermodal transportation options that could be used to transfer SNF from reactor sites to rail cars. This is followed by exploring the operational steps in each of these modes to move the SNF from a reactor site and transfer it to a rail car. This work also presents the procedure of implementing the intermodal transfer methodology in NGSAM using various Java methods. Finally, the process times for accomplishing each of the individual steps are furnished. The implementation ideology, assumptions, and future steps are presented in this work.
Gadey, Harish Reddy↗
Evaluating efficacy of indoor non-pharmaceutical interventions against COVID-19 outbreaks with a coupled spatial-SIR agent-based simulation framework
Contagious respiratory diseases, such as COVID-19, depend on sufficiently prolonged exposures for the successful transmission of the underlying pathogen. It is important that organizations evaluate the efficacy of non-pharmaceutical interventions aimed at mitigating viral transmission among their personnel. We have developed a operational risk assessment simulation framework that couples a spatial agent-based model of movement with an agent-based SIR model to assess the relative risks of different intervention strategies. By applying our model on MIT’s Stata center, we assess the impacts of three possible dimensions of intervention: one-way vs unrestricted movement, population size allowed onsite, and frequency of leaving designated work location for breaks. We find that there is no significant impact made by one-way movement restrictions over unrestricted movement. Instead, we find that reducing the frequency at which individuals leave their workstations combined with lowering the number of individuals admitted below the current recommendations lowers the likelihood of highly connected individuals within the contact networks that emerge, which in turn lowers the overall risk of infection. We discover three classes of possible interventions based on their epidemiological effects. By assuming a direct relationship between data on secondary attack rates and transmissibility in the agent-based SIR model, we compare relative infection risk of four respiratory illnesses, MERS, SARS, COVID-19, and Measles, within the simulated area, and recommend appropriate intervention guidelines.
60 APPLIED LIFE SCIENCES↗
Nested active learning for efficient model contextualization and parameterization: pathway to generating simulated populations using multi-scale computational models
There is increasing interest in the use of mechanism-based multi-scale computational models (such as agent-based models (ABMs)) to generate simulated clinical populations in order to discover and evaluate potential diagnostic and therapeutic modalities. The description of the environment in which a biomedical simulation operates (model context) and parameterization of internal model rules (model content) requires the optimization of a large number of free parameters. In this work, we utilize a nested active learning (AL) workflow to efficiently parameterize and contextualize an ABM of systemic inflammation used to examine sepsis. Contextual parameter space was examined using four parameters external to the model’s rule set. The model’s internal parameterization, which represents gene expression and associated cellular behaviors, was explored through the augmentation or inhibition of signaling pathways for 12 signaling mediators associated with inflammation and wound healing. We have implemented a nested AL approach in which the clinically relevant (CR) model environment space for a given internal model parameterization is mapped using a small Artificial Neural Network (ANN). The outer AL level workflow is a larger ANN that uses AL to efficiently regress the volume and centroid location of the CR space given by a single internal parameterization. We have reduced the number of simulations required to efficiently map the CR parameter space of this model by approximately 99%. In addition, we have shown that more complex models with a larger number of variables may expect further improvements in efficiency.
97 MATHEMATICS AND COMPUTING↗
Modern Warfare: An M and S Examination of the Dynamic Impact of Warlords and Insurgents on State Stability
9/11 changed the world as we knew it. Part of this change was to redirect the military of the United States away from focusing primarily on conventional conflict to a primary focus on unconventional or irregular conflict. This change required a tremendous learning effort by the military and their supporting research and development community. This learning effort included relearning of old but largely forgotten lessons as well as acquiring newly discovered knowledge. During the process of our immediate 9/11 response, we identified that we were engaged in Iraq and Afghanistan in an insurgency. Subsequently, our focus converged upon the description of insurgencies and the requirements for counterinsurgency. This paper argues that emerging conditions now allow the re-evaluation of the type of conflict occurring today and into the foreseeable future: that we, including the modeling and simulation world, emerge from a singular focus on orthodox insurgencies and start to consider the consequences and opportunities of the complexity of current conflicts. As an example of complexity, this paper will use the relatively common phenomenon of the Warlord or Warlordism. The paper will provide a definition of this phenomenon and then describe the implications for modelers. The paper will conclude by demonstrating the impact of incorporating this one rather prosaic complexity into an insurgency model, using agent based modeling (ABM).
Jones, Phillip N.↗
Exploring PV Circularity by Modeling Socio-Technical Dynamics of Modules’ End-of-Life Management
The circular economy (CE) tackles environmental and resource scarcity issues by maximizing value retention in the economy. The concept implies design strategies such as reducing the use of materials or improving products’ durability and end-of-life (EOL) strategies, for example, reusing products and components and recycling materials. With an estimated 80 million tons of global cumulative EOL photovoltaic (PV) modules, applying CE principles to the PV industry could alleviate resource scarcity issues while also providing economic benefits. However, transitioning to a CE may imply changes in organizations and consumer behaviors. In this context, assessment of CE strategies may require accounting for behavioral change, a requirement that methods from complex system science such as agent-based modeling meet. Thus, this paper uses an agent-based modeling (ABM) approach to study circularity in the photovoltaics supply chain. Four types of agents are represented in the ABM: PV owners, installers, recyclers, and manufacturers. Moreover, five possible EOL options – including three CE strategies – are modeled. Departing from traditional techno-economic analysis, the model includes techno-economic factors as well as social factors to model EOL management decisions. Results show that each dollar decrease in the recycling fees improves the recycling rate by roughly 1.1%. However, excluding social factors underestimates the effect that lower recycling prices have on material circularity.
agent-based modeling↗
Exploring PV Circularity by Modeling Socio-Technical Dynamics of Modules' End-of-Life Management: Preprint
The circular economy (CE) tackles environmental and resource scarcity issues by maximizing value retention in the economy. The concept implies design strategies such as reducing the use of materials or improving products’ durability and end-of-life (EOL) strategies such as reusing products and components and recycling materials. With an estimated 80 million tons of global cumulative EOL photovoltaic (PV) modules, applying CE principles to the PV industry could alleviate resource scarcity issues while also providing economic benefits. However, transitioning to a CE may imply changes in organizations and consumer behaviors. In this context, assessment of CE strategies may require accounting for behavioral change, a requirement that methods from complex system science such as agent-based modeling meet. Thus, this paper uses an agent-based modeling (ABM) approach to study circularity in the photovoltaics supply chain. Four types of agents are represented in the ABM: PV owners, installers, recyclers, and manufacturers. Moreover, five possible EOL options – including three CE strategies – are modeled. Departing from traditional techno-economic analysis, the model includes techno-economic factors as well as social factors to model EOL management decisions. Results show that each dollar decrease in the recycling fees improves the recycling rate by roughly 1.1%. However, excluding social factors underestimates the effect that lower recycling prices have on material circularity.
28 EE - Advanced Manufacturing Office (EE-5A)↗
Moving the needle: Employing deep reinforcement learning to push the boundaries of coarse-grained vaccine models
Highly mutable infectious disease pathogens (hm-IDPs) such as HIV and influenza evolve faster than the human immune system can contain them, allowing them to circumvent traditional vaccination approaches and causing over one million deaths annually. Agent-based models can be used to simulate the complex interactions that occur between immune cells and hm-IDP-like proteins (antigens) during affinity maturation—the process by which antibodies evolve. Compared to existing experimental approaches, agent-based models offer a safe, low-cost, and rapid route to study the immune response to vaccines spanning a wide range of design variables. However, the highly stochastic nature of affinity maturation and vast sequence space of hm-IDPs render brute force searches intractable for exploring all pertinent vaccine design variables and the subset of immunization protocols encompassed therein. To address this challenge, we employed deep reinforcement learning to drive a recently developed agent-based model of affinity maturation to focus sampling on immunization protocols with greater potential to improve the chosen metrics of protection, namely the broadly neutralizing antibody (bnAb) titers or fraction of bnAbs produced. Using this approach, we were able to coarse-grain a wide range of vaccine design variables and explore the relevant design space. Our work offers new testable insights into how vaccines should be formulated to maximize protective immune responses to hm-IDPs and how they can be minimally tailored to account for major sources of heterogeneity in human immune responses and various socioeconomic factors. Our results indicate that the first 3 to 5 immunizations, depending on the metric of protection, should be specially tailored to achieve a robust protective immune response, but that beyond this point further immunizations require only subtle changes in formulation to sustain a durable bnAb response.
60 APPLIED LIFE SCIENCES↗
Genetic programming for understanding cognitive biases that generate polarization in social networks
Recent studies have applied agent-based models to infer human-interpretable explanations of individual-scale behaviors that generate macro-scale patterns in complex social systems. Genetic programming has proven to be an ideal explainable AI tool for this purpose, where primitives may be expressed in an interpretable fashion and assembled into agent rules. Evolutionary model discovery (EMD) is a tool that combines genetic programming and random forest feature importance analysis, to infer individual-scale, human-interpretable explanations from agent-based models. We deploy EMD to investigate the cognitive biases behind the emergence of ideological polarization within a population. An agent-based model is developed to simulate a social network, where agents are able to create or sever links with one another, and update an internal ideological stance based on their neighbors' stances. Agent rules govern these actions and constitute of cognitive biases. A set of 7 cognitive biases are included as genetic program primitives in the search for rules that generate hyper-polarization among the population of agents. We find that heterogeneity in cognitive biases is more likely to generate polarized social networks. Highly polarized social networks are likely to emerge when individuals with confirmation bias are exposed to those with either attentional bias, egocentric bias, or cognitive dissonance.
Gunaratne, Chathika↗
Demographic Microsimulator for Integrated Urban Systems: Adapting Panel Survey of Income Dynamics to Capture the Continuum of Life
Agent-based models (ABMs) in transportation modeling simulate activity and travel decisions at the disaggregate level of households and individuals. To do this, ABMs require detailed and realistic information on agents’ socioeconomic and demographic characteristics. Various synthetic population generators have been proposed to address this need. However, most of those currently in practice are cross-sectional in nature and do not account for the dynamics within households and individuals as they progress through life events over time. This is a major shortcoming, as literature has shown that transportation decisions are affected by the transition between and co-occurrence of life cycle events. While some demographic evolution simulators have been proposed to address this issue, they are developed using cross-sectional data and capture only a small set of life cycle events and their interdependence. Addressing these drawbacks, we propose a demographic microsimulator (DEMOS) that captures the “continuum of life” by considering a range of household- and individual-level life cycle events. DEMOS is developed using the Panel Survey of Income Dynamics, one of the world’s longest-running longitudinal surveys. The DEMOS submodels consider key life cycle events that are influenced by agents’ demographic variables. DEMOS is applied to evolve the population of the San Francisco Bay Area over a 9-year horizon. Results demonstrate how DEMOS generates life trajectories and how DEMOS outputs match the observed demographic trends. DEMOS is expected to enable longitudinal analysis in the context of ABMs and expand ABMs analyses relating to dynamic processes such as household-level vehicle transactions.
Demographic evolution↗
Meta Biome: a multiscale model integrating agent-based and metabolic networks to reveal spatial regulation in gut mucosal microbial communities
ABSTRACT Mucosal microbial communities (MMCs) are complex ecosystems near the mucosal layers of the gut essential for maintaining health and modulating disease states. Despite advances in high-throughput omics technologies, current methodologies struggle to capture the dynamic metabolic interactions and spatiotemporal variations within MMCs. In this work, we presentMetaBiome, a multiscale model integrating agent-based modeling (ABM), finite volume methods, and constraint-based models to explore the metabolic interactions within these communities. Integrating ABM allows for the detailed representation of individual microbial agents each governed by rules that dictate cell growth, division, and interactions with their surroundings. Through a layered approach—encompassing microenvironmental conditions, agent information, and metabolic pathways—we simulated different communities to showcase the potential of the model. Using ourin-silicoplatform, we explored the dynamics and spatiotemporal patterns of MMCs in the proximal small intestine and the cecum, simulating the physiological conditions of the two gut regions. Our findings revealed how specific microbes adapt their metabolic processes based on substrate availability and local environmental conditions, shedding light on spatial metabolite regulation and informing targeted therapies for localized gut diseases.MetaBiome provides a detailed representation of microbial agents and their interactions, surpassing the limitations of traditional grid-based systems. This work marks a significant advancement in microbial ecology, as it offers new insights into predicting and analyzing microbial communities. IMPORTANCE Our study presents a novel multiscale model that combines agent-based modeling, finite volume methods, and genome-scale metabolic models to simulate the complex dynamics of mucosal microbial communities in the gut. This integrated approach allows us to capture spatial and temporal variations in microbial interactions and metabolism that are difficult to study experimentally. Key findings from our model include the following: (i) prediction of metabolic cross-feeding and spatial organization in multi-species communities, (ii) insights into how oxygen gradients and nutrient availability shape community composition in different gut regions, and (iii) identification of spatiallyregulated metabolic pathways and enzymes inE. coli. We believe this work represents a significant advance in computational modeling of microbial communities and provides new insights into the spatial regulation of gut microbiome metabolism. The multiscale modeling approach we have developed could be broadly applicable for studying other complex microbial ecosystems.
Microbiology↗
A population data-driven workflow for COVID-19 modeling and learning
CityCOVID is a detailed agent-based model that represents the behaviors and social interactions of 2.7 million residents of Chicago as they move between and colocate in 1.2 million distinct places, including households, schools, workplaces, and hospitals, as determined by individual hourly activity schedules and dynamic behaviors such as isolating because of symptom onset. Disease progression dynamics incorporated within each agent track transitions between possible COVID-19 disease states, based on heterogeneous agent attributes, exposure through colocation, and effects of protective behaviors of individuals on viral transmissibility. Throughout the COVID-19 epidemic, CityCOVID model outputs have been provided to city, county, and state stakeholders in response to evolving decision-making priorities, while incorporating emerging information on SARS-CoV-2 epidemiology. Here we demonstrate our efforts in integrating our high-performance epidemiological simulation model with large-scale machine learning to develop a generalizable, flexible, and performant analytical platform for planning and crisis response.
97 MATHEMATICS AND COMPUTING↗
Application of the DNAS framework expansion to occupant population synthesis
Research in occupant behaviour is now using a more elaborate framework of building occupant interaction. Researchers often face challenges in collecting data, particularly for the data to meet the minimum number of required data points and the data interoperability requirements. Researchers address the first issue with the synthetic population and the latter with data ontologies. While synthetic population is commonly used to address the first issue, data ontology development is used to address the latter. The two solutions are complementary to each other. One of the known ontologies in building occupant behaviour research is the Drivers-Needs-Actions-Systems (DNAS) ontology, which has been used by building modelers to describe energy-related occupant behaviour. This paper describes the ontology-based synthetic population generation that can be used in the agent-based modeling (ABM) applications. This paper considers multiple data sources, including ASHRAE Thermal Comfort DB II and IEA Annex 66 data sets. A case study of an office building is used to present the workflow of DNAS framework expansion, synthetic population generation, and agent-based modeling.
Chandra Putra, Handi↗
Food And Agriculture Supply Chain Model
This model is part of an LDRD effort to investigate the connection of food and agriculture supply chain and the critical infrastructure. The model was built for a small number of farmers, shippers, processing companies and retailers as proof of concept to illustrate supply chain impacts. In this model, the emphasis is on understanding the climate change impacts on the food supply chain. The model uses agent-based modeling method in combination with machine learning. It also connects logistic simulation with economic principles such as price change caused by supply and demand, and consumer substitution effect based on price comparisons of two substitutable commodities.
Nguyen, Thuy↗
People who inject drugs in metropolitan Chicago: A meta-analysis of data from 1997-2017 to inform interventions and computational modeling toward hepatitis C microelimination
Progress toward hepatitis C virus (HCV) elimination in the United States is not on track to meet targets set by the World Health Organization, as the opioid crisis continues to drive both injection drug use and increasing HCV incidence. A pragmatic approach to achieving this is using a microelimination approach of focusing on high-risk populations such as people who inject drugs (PWID). Computational models are useful in understanding the complex interplay of individual, social, and structural level factors that might alter HCV incidence, prevalence, transmission, and treatment uptake to achieve HCV microelimination. However, these models need to be informed with realistic sociodemographic, risk behavior and network estimates on PWID. We conducted a meta-analysis of research studies spanning 20 years of research and interventions with PWID in metropolitan Chicago to produce parameters for a synthetic population for realistic computational models (e.g., agent-based models). We then fit an exponential random graph model (ERGM) using the network estimates from the meta-analysis in order to develop the network component of the synthetic population.
60 APPLIED LIFE SCIENCES↗
Coupled social and infrastructure approaches for enhancing solar energy adoption. Final Report
The goal of this project was to work with rural electric cooperatives to facilitate the diffusion of solar energy adoption in households located in the rural and semi-urban areas of Virginia by identifying social and behavioral factors that might be unique to rural regions; and develop a model to calculate the solar adoption propensity score for household based on their demographics, social and behavioral characteristics which would provide an objective metric to cooperatives that can be further used to do targeted marketing of rooftop solar panels. This was achieved through the following tasks: (1) Conducted a survey of the members of Virginia electric cooperatives to identify demographic, social, financial and behavioral attributes of individuals who are likely to adopt rooftop solar panels. (2) Developed a highly detailed, data-driven, agent-based model of the population of Virginia, focusing on the rural regions. (3) Developed diffusion models that use social, behavioral, and demographic factors, and peer effects to study their impact on solar adoption in rural areas. (4) Built a prototype tool based on the diffusion model to help study market segmentation in rural areas and made it available to National Rural Electric Cooperative Association (NRECA). (5) Results and recommendations derived from the model were provided to NRECA to be shared with participating cooperatives. (6) Results were published in peer reviewed journals, conference proceedings and book chapters, and ideas disseminated through presentations and newsletters. There were several important methodological contributions made under this project which are detailed in the published papers, including: (1) Built a decision-adjusted model for predicting adoptors with imbalanced training data; (2) designed seeding strategies to maximize adoption given a fixed budget; (3) built a methodology to compare different agent based models; (4) created models to identify important factors that influence decision to adopt solar panels; and (5) built a methodology for building household profiles of solar generation to study the duck curve phenomenon. The team included members from the University of Virginia (lead), National Rural Electric Cooperative Association (NRECA), Arizona State University, Virginia Tech and Sandia National Laboratory. Note that no individual entity or stakeholder has incentive to promote solar in rural regions. Most of the research and work focuses around urban regions where the potential for growth in solar adoption is higher due to higher population density. This puts rural areas at a disadvantage. By improving the diffusion of solar adoption in rural parts of the country, we can not only provide clean energy to rural areas but also promote job growth and improves energy independence.
14 SOLAR ENERGY↗
Model-Drive Architecture for Agent-Based Systems
The Model Driven Architecture (MDA) approach uses a platform-independent model to define system functionality, or requirements, using some specification language. The requirements are then translated to a platform-specific model for implementation. An agent architecture based on the human cognitive model of planning, the Cognitive Agent Architecture (Cougaar) is selected for the implementation platform. The resulting Cougaar MDA prescribes certain kinds of models to be used, how those models may be prepared and the relationships of the different kinds of models. Using the existing Cougaar architecture, the level of application composition is elevated from individual components to domain level model specifications in order to generate software artifacts. The software artifacts generation is based on a metamodel. Each component maps to a UML structured component which is then converted into multiple artifacts: Cougaar/Java code, documentation, and test cases.
Gradanin, Denis↗