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 2025-08-17 01:01:51.

1. Learned Insignificance of Credibility Signs.

   Kainz V, Sulik J, Utz S, Enßlin T.

   Cogn Sci. 2025 Aug;49(8):e70102. doi: 10.1111/cogs.70102.

   Crucially, we show how this happens even when individuals engage in rational belief updating and have access to objective cues of deception. Using an agent-based model, the Reputation Game Simulation, we show that mere misinformation is not the problem: The d …

2. Cognitively-plausible reinforcement learning in epidemiological agent-based simulations.

   Mitsopoulos K, Baker L, Lebiere C, Pirolli P, Orr M, Vardavas R.

   Front Epidemiol. 2025 Jul 28;5:1563731. doi: 10.3389/fepid.2025.1563731. eCollection 2025.

   To accurately reflect these dynamics, epidemiological simulation models should endogenously account for both disease transmission and behavioral dynamics. Traditional agent-based models (ABMs) often rely on simplified rules to represent behavior, limit …

3. Bifurcation in the healing or fibrotic response in a network model of fibrosis: role of the initial injury structure.

   Israel E, Hall JK, Deng Y, Bates JHT, Suki B.

   Front Netw Physiol. 2025 Jul 25;5:1589216. doi: 10.3389/fnetp.2025.1589216. eCollection 2025.

   METHODS: In this study, we investigated a previously published agent-based spring network model of PF that exhibited bifurcation behavior between healing and fully developed fibrosis as network members were gradually stiffened. …

4. Tolerant integrated reciprocity sustains cooperation in a noisy environment.

   Yamamoto H, Okada I, Suzuki T.

   Sci Rep. 2025 Aug 7;15(1):28912. doi: 10.1038/s41598-025-14538-3.

   However, the existing literature has paid limited attention to the contextual factors and mechanisms supporting the coexistence of direct and indirect reciprocity. This study proposes and analyses a model of integrated reciprocity that combines personal experiences with re …

5. Agent-based modelling of the early stages of actin polymerisation required to drive endocytosis in Saccharomyces cerevisiae.

   Hancock LP, Allwood EG, Palmer JS, Ayscough KR, Williamson MP.

   Sci Rep. 2025 Aug 7;15(1):28951. doi: 10.1038/s41598-025-14248-w.

   Its complexity means that many aspects remain poorly understood. We have developed an agent-based model covering key components of actin filament generation in endocytosis in Saccharomyces cerevisiae. …The model yields relative rates and affinities f …

6. Topological classification of tumour-immune interactions and dynamics.

   Yang J, Fang H, Dhesi J, Yoon IHR, Bull JA, Byrne HM, Harrington HA, Grindstaff G.

   J Math Biol. 2025 Aug 5;91(3):25. doi: 10.1007/s00285-025-02253-6.

   To demonstrate the approach, synthetic data are generated from an agent-based model with varying parameters. We compare the performance of topological summaries in predicting-with logistic regression at various time steps-whether tumour niches surrounding blo …

7. Modelling Mobility of Hunter-Gatherer Populations: A Dynamic Simulation Approach Based on Cellular Automata.

   Hewitt RJ, Alcaraz-Castaño M, Hernandez VC, Morley MW.

   J Archaeol Method Theory. 2025;32(4):57. doi: 10.1007/s10816-025-09726-4. Epub 2025 Aug 2.

   Most least cost models also assume that origin points, destination points, or both, are known in advance, limiting their utility for exploring movement potential in landscapes where evidence for occupation is scarce. This research addresses these limitations through an …

8. Modeling of hepatitis B virus infection spread in primary human hepatocytes.

   Shi Z, Tsuge M, Collier N, Takeuchi Y, Uchida T, Rutter CM, Teraoka Y, Uprichard SL, Ishida Y, Tateno C, Ozik J, Dahari H, Chayama K.

   J Virol. 2025 Aug 4:e0092725. doi: 10.1128/jvi.00927-25. Online ahead of print.

   We characterized HBV DNA kinetics in primary human hepatocytes (PHHs) over 32 days post-inoculation (p.i.) and modified our in-vivo agent-based modeling (ABM) to gain insights into the HBV lifecycle and spread in vitro. …In this study, we characterize HBV v …

9. Assessing carbon-neutral supercapacitors in renewable energy systems with self-improving agent-based molecular fuzzy intelligent algorithms.

   Castillo O, Dinçer H, Yüksel S, Eti S.

   Sci Rep. 2025 Aug 2;15(1):28234. doi: 10.1038/s41598-025-12924-5.

   To fill this gap, this study proposes an original decision-making model to determine the importance levels of variables affecting the performance of these devices and to present appropriate investment strategies. The proposed model includes the integrated use of Ent …

10. A computational framework for agent-based assessment of multiple environmental exposures.

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

    J Expo Sci Environ Epidemiol. 2025 Aug 2. doi: 10.1038/s41370-025-00799-7. Online ahead of print.

    BACKGROUND: Agent-based assessment of long-term personal exposure to environmental factors accounts for spatio-temporal variation in exposures along daily activity tracks of individuals. …METHODS: We design an agent-based methodology that addresses t …

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