Latest papers on Agent-Based Modeling in PubMed

This repository is an Example using GitHub Actions [egga] for the Advanced Programming with R class. The project consists of a quarto document updated once a week or whenever there’s a push or pull request. It performs a search on PubMed looking for the latest papers about Agent-Based Models. The last update was on 2025-03-23 00:55:06.

1. Associations between long-term air pollution exposure and mortality and cardiovascular morbidity: A comparison of mobility-integrated and residential-only exposure assessment.

   Ndiaye A, Vienneau D, Flückiger B, Probst-Hensch N, Jeong A, Imboden M, Schmitz O, Lu M, Vermeulen R, Kyriakou K, Shen Y, Karssenberg D, de Hoogh K, Hoek G.

   Environ Int. 2025 Mar 16;198:109387. doi: 10.1016/j.envint.2025.109387. Online ahead of print.

   We evaluated two major pollutants, NO(2) and PM(2.5), and four health outcomes, natural and cause-specific mortality and coronary and cerebrovascular events. Agent-based modeling (ABM) was used to simulate the mobility patterns of the participants in the EPIC …

2. Emergence of ion-channel-mediated electrical oscillations in Escherichia coli biofilms.

   Akabuogu E, Carneiro da Cunha Martorelli V, Krašovec R, Roberts IS, Waigh TA.

   Elife. 2025 Mar 21;13:RP92525. doi: 10.7554/eLife.92525.

   The electrical phenomena are explained using Hodgkin-Huxley and 3D fire-diffuse-fire agent-based models. These data demonstrate that electrical wavefronts based on potassium ions are a mechanism by which signaling occurs in Gram-negative biofilms and as such …

3. Modelling the mitigation of anti-vaccine opinion propagation to suppress epidemic spread: A computational approach.

   Alahmadi S, Hoyle R, Head M, Brede M.

   PLoS One. 2025 Mar 20;20(3):e0318544. doi: 10.1371/journal.pone.0318544. eCollection 2025.

   This study investigates strategies to mitigate anti-vaccine social contagion through effective counter-campaigns that disseminate positive vaccine information and encourage vaccine uptake, aiming to reduce the size of epidemics. In a coupled agent-based model …

4. Competing social contagions with opinion-dependent infectivity.

   Sampson CR, Restrepo JG.

   Phys Rev E. 2025 Feb;111(2-1):024313. doi: 10.1103/PhysRevE.111.024313.

   Moreover, disinformation often spreads in direct competition with corresponding true information. To model these phenomena, we develop a model for two competing beliefs spreading on a social network, where individuals have an internal opinion that models thei …

5. Incorporating Additional Evidence as Prior Information to Resolve Non-Identifiability in Bayesian Disease Model Calibration: A Tutorial.

   Semochkina D, Walsh CD.

   Stat Med. 2025 Mar 15;44(6):e70039. doi: 10.1002/sim.70039.

   This study explores the use of the Bayesian framework to provide a natural way to calibrate models and address non-identifiability in a probabilistic fashion in the context of disease modeling. …These approaches are applied to two common disease models: a b …

6. Synthetic population generation with public health characteristics for spatial agent-based models.

   Von Hoene E, Roess A, Kavak H, Anderson T.

   PLoS Comput Biol. 2025 Mar 17;21(3):e1012439. doi: 10.1371/journal.pcbi.1012439. Online ahead of print.

   Agent-based models (ABMs) simulate the behaviors, interactions, and disease transmission between individual “agents” within their environment, enabling the investigation of the underlying processes driving disease dynamics and how these processes may be influ …

7. Investigating resilience in the childcare context through the agent-based paradigm.

   Duan H, Tian B, Levine DT, Kaul H.

   Child Abuse Negl. 2025 Mar 15;163:107402. doi: 10.1016/j.chiabu.2025.107402. Online ahead of print.

   This paper explores the study of the complex dynamics of team resilience in the context of CPP and how agent-based modelling (ABM) can be used to systematically investigate resilience. Specifically, we explore the attributes of ABM that make it ideal to captu …

8. Supporting decision-making for industrial symbioses using a hybrid modelling approach and its application to wastewater treatment.

   Chen O, Mustafee N, Evans B, Khoury M, Vamvakeridou-Lyroudia L, Chen AS, Djordjević S, Savić D.

   Water Sci Technol. 2025 Mar;91(5):501-523. doi: 10.2166/wst.2025.022. Epub 2025 Feb 17.

   Operations Research (OR) - particularly computer modelling and simulation techniques - can help mitigate risks in InSym implementation by enabling an experimental approach to decision-making. This paper presents a hybrid modelling framework to support InSym decision …

9. Advances in computational modeling of cytokine and growth factor dynamics in bone healing: a scoping review.

   Hedayatzadeh Razavi A, Nafisi N, Velasquez-Hammerle M, Shariyate MJ, Khak M, Mirahmadi A, McNichol M, Rodrogiuez EK, Nazarian A.

   Biomech Model Mechanobiol. 2025 Mar 14. doi: 10.1007/s10237-025-01938-7. Online ahead of print.

   Through a systematic analysis of 71 studies, this review identifies and categorizes the modeling methodologies used, including mathematical, finite element, agent-based, mechanobiological, pharmacobiological, and hybrid approaches. The findings highlight the …

10. Incorporating social determinants of health into agent-based models of HIV transmission: methodological challenges and future directions.

    Hotton AL, Nascimento de Lima P, Fadikar A, Collier NT, Khanna AS, Motley DN, Tatara E, Rimer S, Almirol E, Pollack HA, Schneider JA, Lempert RJ, Ozik J.

    Front Epidemiol. 2025 Feb 27;5:1533119. doi: 10.3389/fepid.2025.1533119. eCollection 2025.

    Because they allow for both detailed and large-scale simulations of counterfactual experiments, agent-based models (ABMs) can demonstrate the potential impact of combinations of interventions that may otherwise be infeasible to evaluate in empirical settings …

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