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 2026-04-12 00:15:08.

1. Automated extraction and optimization of protein purification protocols using multi-agent large language models.

   Ye J, DeRocher A, Khim M, Subramanian S, Cron L, Myler PJ, Phan IQ.

   bioRxiv [Preprint]. 2026 Mar 11:2026.03.03.709341. doi: 10.64898/2026.03.03.709341.

   Recent advances in Large Language Models (LLMs) present new opportunities for automating critical bottlenecks in scientific workflows such as literature reviews or protocol design. …While this system reduces complex analysis time from hours to minutes, we identify the la …

2. Tumor-immune trajectory context connects static tissue architecture to clinical outcomes.

   Cramer EM, Heiland R, da Rocha HL, Bergman DR, Gray JW, Mills GB, Fertig EJ, Macklin P, Heiser LM, Chang YH.

   bioRxiv [Preprint]. 2026 Apr 2:2026.03.26.714521. doi: 10.64898/2026.03.26.714521.

   Here, we introduce a trajectory-centric framework that reconstructs continuous TME dynamics by integrating agent-based mathematical modeling and simulation with state space analysis. This approach yields a mechanistically constrained reference landscape built …

3. Model recapitulates regenerative limb blastema formation through local softening of the wounded epithelium.

   Finkbeiner S, Brew-Smith A, Wang X, Fu DT, Monaghan J, Copos C.

   bioRxiv [Preprint]. 2026 Mar 13:2026.03.11.711112. doi: 10.64898/2026.03.11.711112.

   This study introduces a computational tool to examine how the outgrowth results from the interaction of two tissue layers: the bulk (mesenchyme) and the overlying epithelium. We developed a novel hybrid agent-based modeling framework and an accompanying param …

4. Modelling infectious disease transmission dynamics in conference environments: An agent-based approach.

   Liu X, Deng Y, Huang J, Zhang Y, Lei J.

   Math Biosci Eng. 2026 Mar 10;23(4):1096-1120. doi: 10.3934/mbe.2026041.

   Our model captures the activities of individual attendees within the conference venue, including meetings, rest breaks, and meal breaks. …Moreover, the restroom environment poses an additional avenue for potential infection transmission. Employing an agent-base …

5. Spatio-temporal agent-based modelling of malaria.

   Walker CR, Anwar MN, Bräuninger L, Richards J, Ataide R, Thang ND, Thang NX, Canavati S, Flegg JA.

   Epidemics. 2026 Apr 4;55:100909. doi: 10.1016/j.epidem.2026.100909. Online ahead of print.

   We show the impact of these factors by developing a stochastic spatiotemporal agent-based malaria model that captures the impact of spatially distributed interventions on malaria transmission. Our model uses spatiotemporal estimates of mosquito climati …

6. Leveraging Large Language Models for Contextual Prioritization of Contaminants of Emerging Concern in Chemical Mixtures.

   Cheng F, Li Q, He L, Li H, Brooks BW, Yu Z, You J.

   Environ Sci Technol. 2026 Apr 9. doi: 10.1021/acs.est.6c01342. Online ahead of print.

   While recent advances in nontarget analysis enable the generation of extensive chemical inventories, key bottlenecks have shifted to postidentification interpretation within heterogeneous data. Here, we present an agent-based workflow that integrates large language …

7. e3SIM: Epidemiological-ecological-evolutionary simulation framework for genomic epidemiology.

   Xu P, Liang S, Hahn A, Zhao V, Lo WT’, Haller BC, Sobkowiak B, Chitwood MH, Colijn C, Cohen T, Rhee KY, Messer PW, Wells MT, Clark AG, Kim J.

   Methods Ecol Evol. 2026 Apr;17(4):1051-1059. doi: 10.1111/2041-210x.70278. Epub 2026 Mar 5.

   Infectious disease dynamics result from the complex interplay of epidemiological, ecological and evolutionary (epi-eco-evo) processes. Accurately modelling these coupled processes is crucial for understanding pathogen spread and informing public health strategies. …This …

8. From non-agentic large language models to multi-agent systems in emergency medicine: a scoping review.

   Kim H, Jo S, Lim MH, Choi DH.

   Clin Exp Emerg Med. 2026 Apr 8. doi: 10.15441/ceem.26.136. Online ahead of print.

   OBJECTIVE: This study aimed to conduct a scoping review of studies on non-agentic large language models (LLMs), LLM-based agents, and multi-agent systems reported in emergency medicine, and to identify current research trends and major gaps by analyzing their clinical appl …

9. Mobility On Demand: What About the Weekend?

   Kagho GO, Balac M, Axhausen KW.

   Transp Res Rec. 2025 Aug 15;2679(11):68-84. doi: 10.1177/03611981251346454. eCollection 2025 Nov.

   However, existing simulations predominantly focus on modeling average working days, characterized by high and predictable travel demand. This approach overlooks the distinct travel patterns observed during weekends. …This study compares the differences in travel demand p …

10. A reproducible pipeline for activity-based travel demand generation in England.

    Mahfouz H, Greenbury SF, Zhang B, Lynn S, Cheng T.

    Environ Plan B Urban Anal City Sci. 2025 Sep 19;52(9):2326-2339. doi: 10.1177/23998083251379620. eCollection 2025 Nov.

    Agent-based transport models are gaining popularity due to their ability to model features such as heterogenous individual behaviour, household dependencies, and new dynamic modes of travel. Such models require as input disaggregate population d …

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