Developing Surrogates for Epidemic Agent-Based Models via Scientific Machine Learning
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Nguyen, Kyle Cuongthe [Sandia National Laboratorie↗
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Beyond the List: Bioagent-Agnostic Signatures Could Enable a More Flexible and Resilient Biodefense Posture Than an Approach Based on Priority Agent Lists Alone
As of 2021, the biothreat policy and research communities organize their efforts around lists of priority agents, which elides consideration of novel pathogens and biotoxins. For example, the Select Agents and Toxins list is composed of agents that historic biological warfare programs had weaponized or that have previously caused great harm during natural outbreaks. Similarly, lists of priority agents promulgated by the World Health Organization and the National Institute of Allergy and Infectious Diseases are composed of previously known pathogens and biotoxins. To fill this gap, we argue that the research/scientific and biodefense/biosecurity communities should categorize agents based on how they impact their hosts to augment current list-based paradigms. Specifically, we propose integrating the results of multi-omics studies to identify bioagent-agnostic signatures (BASs) of disease—namely, patterns of biomarkers that accurately and reproducibly predict the impacts of infection or intoxication without prior knowledge of the causative agent. Here, we highlight three pathways that investigators might exploit as sources of signals to construct BASs and their applicability to this framework. The research community will need to forge robust interdisciplinary teams to surmount substantial experimental, technical, and data analytic challenges that stand in the way of our long-term vision. However, if successful, our functionality-based BAS model could present a means to more effectively surveil for and treat known and novel agents alike.
59 BASIC BIOLOGICAL SCIENCES↗
Managing autonomous materials labs with multi-agent AI and its implications for the science of science
Self-driving lab systems (aka, autonomous experimentation) accelerate research - letting scientists learn faster, spend less resources, and fail smarter in well defined, narrow studies. The next-generation materials lab combines self-driving systems to tackle broader challenges - orchestrating complex research campaigns while optimizing lab resources. We propose that agent-based and agentic artificial intelligence will be an integral part of next-generation lab management and discuss potential implementation scenarios. Additionally, digital and physical sandboxes will allow scientists to evaluate diverse and dynamic research and lab management strategies. Beyond the immediate benefit to lab optimization, such sandboxes will enable realistic computational studies of the philosophy of science (i.e., science of science) to achieve higher level scientific efficiencies.
Computer science↗
ATEAM4Py: An Efficient and Scalable Python-Based Model for Charging Demand
This report details the development and implementation of ATEAM4Py, a Python-based simulation model that projects demand for battery electric vehicle (BEV) charging based on adoption trends and consumer behavior. With Exelon’s support, Argonne National Laboratory converted the original Java-based Agent-based Transportation Energy Analysis Model (ATEAM) into Python, resulting in a faster and more efficient tool for forecasting the timing, location, and scale of charging demand growth. ATEAM4Py tackles key challenges in simulation efficiency and runtime, supporting the strategic development of cost-effective grid capacity expansion strategies and ensuring reliable service for stakeholders.
33 ADVANCED PROPULSION SYSTEMS↗
Analysis of Organophosphorus-Based Nerve Agent Degradation Products by Gas Chromatography-Mass Spectrometry (GC-MS): Current Derivatization Reactions in the Analytical Chemist’s Toolbox
The field of gas chromatography-mass spectrometry (GC-MS) in the analysis of chemical warfare agents (CWAs), specifically those involving the organophosphorus-based nerve agents (OPNAs), is a continually evolving and dynamic area of research. The ever-present interest in this field within analytical chemistry is driven by the constant threat posed by these lethal CWAs, highlighted by their use during the Tokyo subway attack in 1995, their deliberate use on civilians in Syria in 2013, and their use in the poisoning of Sergei and Yulia Skripal in Great Britain in 2018 and Alexei Navalny in 2020. These events coupled with their potential for mass destruction only serve to stress the importance of developing methods for their rapid and unambiguous detection. Although the direct detection of OPNAs is possible by GC-MS, in most instances, the analytical chemist must rely on the detection of the products arising from their degradation. To this end, derivatization reactions mainly in the form of silylations and alkylations employing a vast array of reagents have played a pivotal role in the efficient detection of these products that can be used retrospectively to identify the original OPNA.
sarin↗
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↗
Carbon fiber/epoxy vitrimer composite patch cured with bio‐based curing agents for one‐step repair metallic sheet and its recyclability
Abstract Vitrimers have gained a great deal of attention from researchers, yet research on its application is still lacking. This study, a novel bio‐based vitrimer was developed from epoxy (EP) and bio‐based curing agents, that is, cashew nut shell liquid (CNSL) and citric acid (CA), and then reinforced by carbon fiber. The vitrimers with different ratios of acid to epoxy (R ratio) at 0.30–0.40 contained ester and ether linkages. All EP/CA/CNSL vitrimers showed the stress relaxation over 70–100°C due to transesterification. The vitrimers were applied as polymer matrices for the carbon fiber composites and then used as repair patches. By using the carbon fiber‐reinforced vitrimer with the R ratio of 0.30, patch repair on a damaged alloy sheet revealed that approximately 98% of the tensile strength of the damaged alloy sheet was recovered. The vitrimer can be dissolved from carbon fiber composite to recover carbon fiber. The recovered carbon fiber retained good tensile strength compared to the pristine composite. Based on this study, the EP/CA/CNSL vitrimers showed the comparable thermomechanical properties with the epoxy vitrimer cured by the petroleum‐based curing agent. The vitrimer composite patch could therefore be an alternative new repair method to extend the service life of damaged structures.
Lorwanishpaisarn, Narubeth↗
Application of Gaussian Bayes classifier to differentiate chlorine-based chemical agents
The Portable Isotopic Neutron Spectroscopy (PINS) is a commercialized system developed by Idaho National Laboratory (INL) to examine chemical warfare agents (CWA) non-destructively, utilizing Prompt Gamma Neutron Activation Analysis (PGNAA) techniques. The PINS system takes advantage of a high-resolution gamma-ray spectrum from a mechanically-cooled high-purity germanium (HPGe) detector. One of the difficult technical challenges is to discriminate the chlorine-based chemical agents. Especially, CN, CNB, CNS and CG have similar chemical compositions to make it hard to discriminate them with a higher confidence. Current identification algorithms for PINS systems with 252-Cf sources have been improved and updated continuously as more field data became available, and new algorithms was studied to complement the current algorithms by adopting the Gaussian Bayes classifier. These new algorithms were intended to be applied to a subset of chlorine-based chemical agents, and their main goal is discriminate CN, CNB, CNS and CG with their ratios of the chlorine neutron inelastic 1763keV peak to the chlorine thermal neutron capture 1959keV peak, which is referred to as the “Cl i/c” or “clic” ratio in this study. The Cl i/c ratios were assumed to follow Gaussian distributions with the means and the standard deviations unique to their corresponding chemical agents. The prior probabilities of these four chemical agents were optimized with a collection of field data to achieve the best performance in terms of precision or positive predictive value (PPV). Finally, their posterior probabilities as functions of the Cl i/c ratio were implemented in the current version of PINS analysis software in order to be tested with more field data.
38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
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↗
LIGHT DUTY VEHICLE CHOICE MODELS EXAMINING ALTERNATIVE FUEL TECHNOLOGY PREFERENCES AMONG COMMERCIAL FLEET OWNERS
Agent-based transportation models are critical tool for evaluating energy use, emissions and mobility impacts of transportation. In this context, vehicle ownership models are critical for linking agent activities to their impacts on the transportation system. However, no agent-based freight transportation models to date has been developed that predicts the fuel technology that is preferred by establishments when purchasing a Light Duty Vehicle (LDV) for business purposes. This research addresses this gap by using recently collected survey data to estimate a discrete choice model that can be applied in the agent-based context.
commercial↗
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↗
EMIS Agent Simulation Model (Electricity Markets Investment Suite) [SWR-19-56]
The Electricity Markets Investment Suite Agent-based Simulation (EMIS-AS) model is an agent-based model developed at NREL for simulating annual investment and retirement decisions of heterogeneous investors in the electricity sector. EMIS-AS is designed to capture the evolution of the electricity generation portfolio resulting from the interactions of heterogeneous investors under different policy and market designs. EMIS-AS not only allows end-users to customize market products and rules, but also to capture investors' heterogeneous financing parameters, technology preferences, beliefs about the future (forecasts), ability to update those forecasts, and risk preferences under uncertainty.
Anwar, Mahammad Bashar↗
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↗
The Highly Integrated Vehicle Ecosystem (HIVE): A Platform for Managing the Operations of On-Demand Vehicle Fleets
This paper introduces the Highly Integrated Vehicle Ecosystem (HIVE), a transportation modeling tool developed by within the Center for Integrated Mobility Sciences (CIMS) group at the National Renewable Energy Laboratory (NREL). HIVE is an agent-based supply/demand model for Mobility on Demand (MoD) which mixes agent-based modeling and centralized dispatch for automated and human-driven fleets and ride hail passengers. Research questions using HIVE span multiple categories, including intelligent fleet planning (assessing fleet, battery, and infrastructure investment decisions), intelligent fleet control (charge management, vehicle dispatching) and strategic business model decision-making (depot-based full-time drivers versus gig-based drivers, human-driven versus automated). The components of the HIVE model are explained and then HIVE is demonstrated in a case study using demand data from the New York City Taxi & Limousine Commission data set.
33 ADVANCED PROPULSION SYSTEMS↗