Bayesian calibration and exploration of agent-based epidemiological models (Poster)
poster for ASCR PI meeting
Ray, Jaideep [Sandia National Laboratories (SNL-CA↗
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Bayesian calibration and exploration of agent-based epidemiological models
Abstract for a poster to be presented at ASCR PI meeting.
Ray, Jaideep [Sandia National Laboratories (SNL-CA↗
Improved School and Workplace Interactions in ExaEpi, an Agent–Based Epidemiological Model
Explore the source record for details and available documents.
Biological and medical sciences↗
Towards verifiable cancer digital twins: tissue level modeling protocol for precision medicine
Cancer exhibits substantial heterogeneity, manifesting as distinct morphological and molecular variations across tumors, which frequently undermines the efficacy of conventional oncological treatments. Developments in multiomics and sequencing technologies have paved the way for unraveling this heterogeneity. Nevertheless, the complexity of the data gathered from these methods cannot be fully interpreted through multimodal data analysis alone. Mathematical modeling plays a crucial role in delineating the underlying mechanisms to explain sources of heterogeneity using patient-specific data. Intra-tumoral diversity necessitates the development of precision oncology therapies utilizing multiphysics, multiscale mathematical models for cancer. This review discusses recent advancements in computational methodologies for precision oncology, highlighting the potential of cancer digital twins to enhance patient-specific decision-making in clinical settings. We review computational efforts in building patient-informed cellular and tissue-level models for cancer and propose a computational framework that utilizes agent-based modeling as an effective conduit to integrate cancer systems models that encode signaling at the cellular scale with digital twin models that predict tissue-level response in a tumor microenvironment customized to patient information. Furthermore, we discuss machine learning approaches to building surrogates for these complex mathematical models. These surrogates can potentially be used to conduct sensitivity analysis, verification, validation, and uncertainty quantification, which is especially important for tumor studies due to their dynamic nature.
60 APPLIED LIFE SCIENCES↗
A mesoscopic link-transmission-model able to track individual vehicles
Macroscopic traffic flow is a common choice for large-scale traffic simulations. These models do not provide individual-specific metrics as outputs. However, this treatment is necessary in agent-based-models, as in, for example, assigning routes based on personal characteristics. Here, in this paper, we propose an extension of the link-transmission-model, an efficient and yet accurate discretization of the Lighthill-Whitham-Richards (LWR) model, which allow vehicles to be tracked individually while keeping the main features of the underlying model. The extension comprises modifying the link and node models to ensure that the flow between links is always at discrete levels. Therefore, every unit of flow is associated with one individual vehicle moving from its current to its next link. An upper bound of the discretization error is provided. We show that the proposed model resembles its continuous counterpart on lane drop, merge, and diverge cases. In addition, we apply the model into three different networks to validate its applicability in large networks. Finally, we also confirm the parameter transferability between continuous and discrete models and that both can well reproduce field data.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
National Modeling of Geothermal District Energy Systems with Ambient-Temperature Loops Using dGeo: Preprint
Geothermal district energy systems (DES) with ambient-temperature loops, also known as thermal energy networks, are one option for decarbonizing space heating and cooling loads. Geothermal fifth-generation DES include an "ambient" temperature thermal loop that connects heat pumps at each building with thermal balancing sources such as geothermal borehole fields. Heating and cooling are provided via a water-source heat pump at each end-user. This project seeks to analyze the nationwide potential for ambient-temperature loop districts by creating a new module within the Distributed Geothermal Market Demand Model (dGeo). dGeo is an agent-based modeling tool for distributed geothermal resources; it can investigate potential on a nationwide or statewide scale using geospatial data for all 50 states and thermal demands for existing buildings. This process allows for high-level estimates of technical and economic potential for ambient-temperature loop districts across the United States. Using GHEDesigner, a lookup table was created to size borehole fields for different thermal loads and ground conditions experienced across the country. A cost and financing structure, along with incentives, were applied. Cost estimates include costs for the distribution network, borehole field installation and operation, and circulation pump operation, while savings are calculated based on agent energy bills. This newly developed module can be used for assessing which areas of the country have the highest potential for agent benefits from ambient-temperature loop installation and assess the impact of different costing and pricing future scenarios. While the code is still under development and nationwide simulations are ongoing, initial results for two states are provided. Future work includes expanding the module to consider mixed residential and commercial districts and considering multiple costing scenarios.
ambient temperature loop↗
National Modeling of Geothermal District Energy Systems with Ambient-Temperature Loops Using dGeo
Geothermal district energy systems (DES) with ambient-temperature loops, also known as thermal energy networks, are one option for decarbonizing space heating and cooling loads. Geothermal fifth-generation DES include an "ambient" temperature thermal loop that connects heat pumps at each building with thermal balancing sources such as geothermal borehole fields. Heating and cooling are provided via a water-source heat pump at each end-user. This project seeks to analyze the nationwide potential for ambient-temperature loop districts by creating a new module within the Distributed Geothermal Market Demand Model (dGeo). dGeo is an agent-based modeling tool for distributed geothermal resources; it can investigate potential on a nationwide or statewide scale using geospatial data for all 50 states and thermal demands for existing buildings. This process allows for high-level estimates of technical and economic potential for ambient-temperature loop districts across the United States. A lookup table was created using GHEDesigner to size borehole fields for different thermal loads and ground conditions experienced across the country. A cost and financing structure, along with incentives, were applied. Cost estimates include costs for the distribution network, borehole field installation and operation, and circulation pump operation, while savings are calculated based on energy bills for building owners (agents). This newly developed module can be used for assessing which areas of the country have the highest potential for agent benefits from ambient-temperature loop installation and assess the impact of future cost and price scenarios. Initial results for statewide analysis (for Vermont) and nationwide (for United States) are provided. Future work includes expanding the module to consider mixed residential and commercial districts as well as evaluating multiple cost scenarios.
ambient-temperature loop↗
Filling the cellulosic bio-economy gap by utilizing a wedge approach combined with stakeholder collaboration
The price gap between the market and breakeven prices of cellulosic biomass for farmers represents a significant barrier to the development of a low-carbon cellulosic bioeconomy. Using a bottom-up, agent-based modeling tool that replicates the behaviors and interactions of key stakeholders, this study analyzes the emergence of a cellulosic bioeconomy at the local scale through a wedge approach that examines an integrated portfolio of multiple policy options, including subsidies for small-scale bioproducts and environmental credits. Here, the role of collaboration among multiple stakeholders, such as biomass producers (farmers), bio-refinery industry, government, and society, is assessed for filling the price gap. Using the Sangamon River Basin as a case study site, we evaluate the effectiveness of the wedge approach by comparing simulation results from multiple scenarios, each incorporating different combinations of bioeconomy wedges, with and without stakeholder collaboration. Results underscore that active collaboration among stakeholders acts as a catalyst enlarging the effectiveness of bioeconomy wedges. Including the carbon credits and environmental value in the policy portfolio is found to bridge the price gap through collective contributions from diverse stakeholders, where the cellulosic biofuel and bioproduct industry plays a pivotal role. Although this study is conducted at the local watershed scale, the methodology and findings offer valuable insights for market development in other watersheds and the potential scaling of local markets to regional and national levels.
09 BIOMASS FUELS↗
Assessing the behavioral realism of energy system models in light of the consumer adoption literature
Effective policymaking to achieve net zero greenhouse gas emissions demands an understanding of the complex drivers of, and barriers to, consumer adoption behavior via behaviorally realistic energy system models. Existing models tend to oversimplify by focusing on homogenized financial factors while neglecting consumer heterogeneity and non-monetary influences. This study develops and applies a comprehensive framework for evaluating the behavioral realism of consumer adoption models, informed by the adoption literature. It introduces a typology for factors influencing low-carbon technology adoption decisions: monetary and non-monetary factors relating to household characteristics, psychology, technological attributes, and contextual conditions. Next, reviews of the consumer adoption and decision-making literature identify the most influential adoption factor categories for distributed solar photovoltaics, electric vehicles, and air-source heat pumps. Finally, the extent to which a selection of energy system models accounts for these adoption factors is assessed. Existing models predominantly emphasize the economic aspects of technology, which are generally identified as the most important factors. Where the models fall short — in considering moderately important factor categories — sector-specific and agent-based models can offer more behaviorally realistic insights. This study sheds light on which types of factors are most important for consumer adoption decisions and investigates how well current models rise to the challenge of behavioral realism. The end-to-end analysis presented enables internally consistent comparisons across models and energy technologies. This research advances timely conversations on consumer adoption. It could inform more behaviorally realistic energy system modeling, and thereby more effective decarbonization policymaking.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
National Security Programs - Cyber: MMAREJBLIGE – Modular Multi Agent Grid Emulation for Joined Breakdowns in Linked Generative Emulations - 23-0644
Modular Multi Agent Grid Emulations for Joined Breakdowns in Linked Generative Emulations (MMAREJBLIGE) introduces an agent-based modeling framework into real-time cyber-physical emulation to achieve a context-aware environment that introduces operator/attacker/external-condition variability to improve emulation fidelity and testing rigor. We detail our agent framework design, internal communication via message passing, and time synchronization, as well as the individual components of the system. We include a brief analysis of several scenarios run on a real-time, hardware-in-the-loop, Industrial Control Systems (ICS) test-bed which include normal operation, physical disruption, disruption with mitigation, and disruption with mitigation during a cyber denial-of-service (DOS) attack.
42 ENGINEERING↗
Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities
Abstract The gut microbiome plays a major role in human health; however, little is known about the structural arrangement of microbes and factors governing their distribution. In this work, we present an in silico agent-based model (ABM) to conceptually simulate the dynamics of gut mucosal bacterial communities. We explored how various types of metabolic interactions, including competition, neutralism, commensalism, and mutualism, affect community structure, through nutrient consumption and metabolite exchange. Results showed that, across scenarios with different initial species abundances, cross-feeding promotes species coexistence. Morphologically, competition and neutralism resulted in segregation, while mutualism and commensalism fostered high intermixing. In addition, cooperative relations resulted in community properties with little sensitivity to the selective uptake of metabolites produced by the host. Moreover, metabolic interactions strongly influenced colonization success following the invasion of newcomer species. These results provide important insights into the utility of ABM in deciphering complex microbiome patterns.
Biotechnology & Applied Microbiology↗
mosartwmpy sample input data; 1980 - 1985
Sample input data spanning the years 1980-1985 for running the `mosartwmpy` water routing and management model: https://github.com/IMMM-SFA/mosartwmpy. More information is available in the README.md. Changelog: v0.0.8: Update with new CAP_MIN reservoir parameter, corresponds with mosartwmpy v1.0.0 v0.0.7: new reservoir files with corrected locations based on an exhaustive review by Dan Broman for the 9505 project; corresponding long term mean demand and flow files updated based on VIC4 simulations using Daymet forcing. v0.0.6: updates reservoir parameters to indicate which reservoirs should follow generic operating rules and which should follow ISTARF data-driven operating rules. v0.0.5: adds supporting files for running the Farmer Agent Based Model of adaptive water demand.
Bracken, Cameron [Pacific Northwest National Labor↗
Cascading economic losses from port disruptions under capacity constrained multimodal freight networks
This study quantifies how throughput disruptions at major seaports cascade through capacity-constrained multimodal freight networks and interregional production systems. We couple an agent-based model (ABM) multimodal freight simulation that resolves rerouting, terminal queueing, and inventory drawdown under binding modal and facility capacities with a multiregional output loss input-output (MRIIM) model that propagates realized delivery shortfalls across regions and sectors. The framework is demonstrated for the Port of Los Angeles using Freight Analysis Framework flows and Bureau of Economic Analysis input-output accounts and is evaluated over a 52-week horizon under deterministic sector targeted shocks and stochastic disruption realizations with uncertain severity and duration. Results indicate nonlinear amplification: realized national losses concentrate in manufacturing and transportation/warehousing even when exogenous port shocks are dispersed, suggesting that congestion spillback and limited short-run substitution can dominate the initial shock allocation. We further evaluate a tabular reinforcement-learning (Q-learning) intervention layer that selects among a small set of implementable system level levers (truck-to-rail and truck-to-barge shift settings) without overriding shipper routing, finding that such interventions reduce total losses for moderate disruptions but yield diminishing returns once substitute modes approach capacity. By linking operational freight behavior to system wide impacts under uncertainty, the proposed ABM-MRIIM pipeline provides a reusable workflow for port disruption stress testing, identification of structurally critical sectors/corridors, and evaluation of resilience interventions under realistic capacity limits.
42 ENGINEERING↗
Organizational Resilience in the Context of Information Quality: An Agent-Based Simulation of Structural and Cognitive Influences
This study examines how organizational structure and stress levels affect decision-making with poor quality information. Using an agent-based model, it finds loosely structured organizations are timely but less effective at filtering bad information, while tightly structured ones are slower but better at filtering. The research highlights a trade-off between timeliness and robustness and suggests an optimal stress level for decision-making efficacy.
99 GENERAL AND MISCELLANEOUS↗
BEAM CORE: A Flexible Ecosystem for Freight, Demographics, and Vehicle Analysis
The Behavior, Energy, Autonomy, and Mobility Comprehensive Regional Evaluator (BEAM CORE) is an open-source, modular ecosystem of highly refined, agent-based modeling tools developed by Lawrence Berkeley National Laboratory and the National Laboratory of the Rockies. Organizations such as metropolitan planning organizations, agencies, and companies can use BEAM CORE to analyze freight movement and optimize logistics solutions, assess the impacts of emerging freight technologies or e-commerce trends, model dynamic population growth and evolution, and understand the drivers and impacts of electric vehicle adoption across households in a given region. Users can choose from a flexible suite of modeling modules according to their needs and priorities. The modules integrate with travel demand models to support enhanced analysis of diverse scenarios involving freight movement, vehicle technologies, and other key factors relevant to regional planning.
33 ADVANCED PROPULSION SYSTEMS↗
Calibration verification for stochastic agent-based disease spread models
Accurate disease spread modeling is crucial for identifying the severity of outbreaks and planning effective mitigation efforts. To be reliable when applied to new outbreaks, model calibration techniques must be robust. However, current methods frequently forgo calibration verification (a stand-alone process evaluating the calibration procedure) and instead use overall model validation (a process comparing calibrated model results to data) to check calibration processes, which may conceal errors in calibration. In this work, we develop a stochastic agent-based disease spread model to act as a testing environment as we test two calibration methods using simulation-based calibration, which is a synthetic data calibration verification method. The first calibration method is a Bayesian inference approach using an empirically-constructed likelihood and Markov chain Monte Carlo (MCMC) sampling, while the second method is a likelihood-free approach using approximate Bayesian computation (ABC). Simulation-based calibration suggests that there are challenges with the empirical likelihood calculation used in the first calibration method in this context. These issues are alleviated in the ABC approach. Despite these challenges, we note that the first calibration method performs well in a synthetic data model validation test similar to those common in disease spread modeling literature. We conclude that stand-alone calibration verification using synthetic data may benefit epidemiological researchers in identifying model calibration challenges that may be difficult to identify with other commonly used model validation techniques.
60 APPLIED LIFE SCIENCES↗
Modeling and Calibration of Supplier Selection Problem in Freight Agent-Based Simulations
Freight transportation modeling often struggles with data limitations, especially in accurately representing complex supplier selection processes and their impact on network flows. This research addresses this critical gap by developing a large-scale, calibrated agent-based model for supplier selection, complemented by a probabilistic heuristic for international shipments. Our approach integrates trade relationships between industry sectors, transportation costs, and a supplier-rating model adapted from existing literature. The model’s core objective is to minimize the discrepancy between modeled and observed commodity flows while ensuring a close match to regional shipping distance distributions. Implemented and tested across four major U.S. metropolitan areas—Atlanta, Chicago, Dallas–Fort Worth, and Los Angeles—the model demonstrates high fidelity in replicating observed freight patterns. Key findings reveal consistent alignment with national shipping distance trends and highlight significant spatial variations in commodity trade assignments and demand across the study regions. This behaviorally informed and transport-sensitive framework is designed to approximate real-world decision making, providing a robust tool for policymakers and planners to evaluate targeted interventions, assess infrastructure investments, and enhance supply chain resilience in the face of disruptions.
Ismael, Abdelrahman (ORCID:0000000303712110)↗
Comparing Delay-, Distance-, and Cordon-Based Congestion Pricing Strategies Via Large-Scale Simulation
This study compares the impacts of delay-, distance-, and cordon-based congestion pricing strategies for Austin, Texas, using the POLARIS agent-based activity-based travel demand simulation model. This approach enables agent-level heterogeneity and realistic choice options (including destination, mode, and activity scheduling) for dynamic traffic assignment and congestion feedbacks across a major metro region, which are features lacking in past work. To ensure comparability, distance-based tolls were set to generate the same revenue as delay-based tolling of $3.5 M/day, averaging $1.17/resident/day or $0.42/vehicle-trip. Delay-based pricing delivers 44% lower network delay and 13% lower VHT compared to the no-toll baseline, levels unmatched by other pricing strategies. At the height of the AM peak, drivers pay up to $0.13/mile on average, though most links in the network remain untolled. Distance-based pricing is the most effective at reducing VMT (by 4%), but VHT reductions (of 6%) primarily stem from drivers selecting closer destinations, achieving only one-fourth the delay reduction of delay-based pricing. Across various implementations of delay- and distance-based pricing, the results suggest that spatial variations of tolls are far more important than temporal variations. Cordon tolls produce minimal impacts at the network-wide level, but offer substantial delay reductions inside the cordon. Other major findings include: 1) delay-based pricing increases trip-making during the PM peak period due to backward shifts in discretionary-activity start times by higher-income residents; and 2) tolls’ spatial impacts, including changes in network flows and tolls paid by residents, vary substantially between delay- and distance-based pricing strategies.
Agent-based modeling↗