Latest papers on Agent-Based Modeling in PubMed

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This repository is an Example using GitHub Actions [egge] 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 2026-09-08 16:25:04.14939.

  1. Stochastic thermodynamics of social imitation beyond energetics.

    Irisarri L, Trigal L, Toral R, Manzano G.

    Nat Commun. 2026 Aug 8;17(1):9542. doi: 10.1038/s41467-026-76212-0.

    Similarly to Landauer’s principle, it constrains spontaneous changes in agent attributes (opinions, cultural traits, etc.) and their informational entropy. We illustrate this framework to toy agent-based models of social imitation with non-trivial phase diagr …

  2. A multi-agent quantitative microbial risk assessment of raw milk cheeses: from farm-level practices to consumer risk.

    Guillier L, Chaix E, Auvray F, Collineau L, Desriac N, Mtimet N, Oswald E, Dubois-Brissonnet F, Membré JM.

    J Food Prot. 2026 Sep 5:100913. doi: 10.1016/j.jfp.2026.100913. Online ahead of print.

    In this study, we developed an innovative agent-based Quantitative Microbial Risk Assessment (QMRA) model that explicitly represents farms, animals, cheese batches, and consumers as individual agents. …Grounded in extensive knowledge of the French raw milk …

  3. Elements on the move: How ungulate migration expands Alpine biogeochemical footprints.

    Ferraro KM, Corradini A, Hawkinson V, Chanel O, Figuières C, Bramoullé Y, Vanderlocht C, Ossi F, Righetti D, Schmitz OJ, Cagnacci F.

    J Anim Ecol. 2026 Sep 5. doi: 10.1111/1365-2656.70340. Online ahead of print.

    Yet the relationship between animal movement and element distribution remains poorly characterized. We developed a spatially explicit agent-based model to test how migratory versus resident red deer (Cervus elaphus) influence nitrogen redistribution across an …

  4. Age-Associated Primordial Follicle Density in Human Ovarian Cortical Tissue from Post-Pubertal Females Undergoing Ovarian Tissue Cryopreservation and Transplantation: A Descriptive Analysis.

    Erden M, Celik S, Oktay KH.

    Fertil Steril. 2026 Sep 4:S0015-0282(26)01748-6. doi: 10.1016/j.fertnstert.2026.08.1131. Online ahead of print.

    SUBJECTS: Ovarian cortical tissue from 33 post-pubertal individuals aged 16-43 years obtained from organ donors and patients undergoing ovarian tissue cryopreservation, without prior exposure to intensive alkylating agent-based chemotherapy. EXPOSURE: Age at ovarian …

  5. Slovotvir: Grassroots reform of the Ukrainian language reveals the role of drift and selection in language change.

    Koshevoy A, Sobchuk O, Morin O.

    PNAS Nexus. 2026 Sep 3;5(9):pgag258. doi: 10.1093/pnasnexus/pgag258. eCollection 2026 Sep.

    This pre-registered study examines lexical evolution in the Ukrainian language using data from Slovotvir, a crowdsourcing platform where over 4,000 users proposed and ranked translations of foreign-origin words over 9 years. We rely on an agent-based model co …

  6. Unmasking bias in the evidence ecosystem: a panoramic analysis of 311,751 meta-analyses using an artificial intelligence agent-based approach.

    Chen X, She Z, Yang S, Chu M, Zhou Y.

    J Glob Health. 2026 Sep 4;16:03029. doi: 10.7189/jogh.16.03029.

    In this viewpoint, we aimed to evaluate the feasibility of large language models in automating meta-analysis workflows and develop the Meta-Analysis Screening, Transformation and Evaluation Review Agent (MASTER) agent; establish a large-scale Unified Meta-Analysis Reposito …

  7. How AI Can Advance Mathematical Biology: Opportunities, Challenges, and Future Directions.

    Rabiei K, Rempala GA, Laubenbacher R, Hao W.

    Bull Math Biol. 2026 Sep 3;88(10):175. doi: 10.1007/s11538-026-01744-x.

    Mathematical biology has long relied on mechanistic models, including ordinary and partial differential equations, stochastic systems, and agent-based models, to study biological processes across scales. …As a result, artificial intelligence (AI) and …

  8. Agent-based modeling of tumor microenvironment suppression reveals the dominant barriers to anti-tumor immunity.

    Dehkordi SH, Arabameri A.

    Comput Biol Med. 2026 Sep 3;214:111906. doi: 10.1016/j.compbiomed.2026.111906. Online ahead of print.

    Cancer progression is driven by a tumor microenvironment (TME) that suppresses anti-tumor immunity through structural, cellular, and metabolic barriers. We developed a computational model to compare the relative impact of four major suppressive mechanisms: extracellular ma …

  9. AI agent-based discovery of antimicrobial peptides against multidrug-resistant gram-negative bacterial infection.

    Zhang Y, Zhang X, Chen X, Chen J, Kong L, Ma H.

    Eur J Med Chem. 2026 Aug 28;319:119279. doi: 10.1016/j.ejmech.2026.119279. Online ahead of print.

    In terms of bactericidal mechanism, AMP-ZJLC586 can reduce the production of bacterial ATP by inhibiting the synthesis of lipopolysaccharide and the enzyme activity of respiratory chain, and oxidative stress response and SOS response at the same time. In the sepsis mouse model …

  10. From assistant to collaborator: A systematic review of the evolution of artificial intelligence in end-stage renal disease care and management.

    Wang M, Hong C, Huang Z, Shao F, Gu Y.

    PLOS Digit Health. 2026 Sep 2;5(9):e0001635. doi: 10.1371/journal.pdig.0001635. eCollection 2026 Sep.

    A three-stage analytical framework was applied to chart the technological evolution of AI in ESRD care: (1) rule-based assistive tools, (2) data-driven learning systems, and (3) emerging large language model- and agent-based cognitive systems. A total of 100 …