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 2024-05-26 00:40:42.
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Feedback between stochastic gene networks and population dynamics enables cellular decision-making.
Piho P, Thomas P.
Sci Adv. 2024 May 24;10(21):eadl4895. doi: 10.1126/sciadv.adl4895. Epub 2024 May 24.
Such noise arises from fluctuations in reactions synthesizing proteins and plays a crucial role in how cells make decisions and respond to stress or drugs. We propose a general stochastic agent-based model for growing populations capturing the feedback betwee …
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The Efficacy and Safety of Tandem Transplant Versus Single Stem Cell Transplant for Multiple Myeloma Patients: A Systematic Review and Meta-Analysis.
Chen YH, Fogel L, Sun AY, Yang C, Patel R, Chang WC, Chen PH, Jhou HJ, Chen YC, Dai MS, Lee CH.
Diagnostics (Basel). 2024 May 16;14(10):1030. doi: 10.3390/diagnostics14101030.
The primary outcomes were progression-free survival (PFS), overall survival (OS), overall response rate (ORR), complete response rate (CRR), and treatment-related mortality (TRM). We used a random-effects model to calculate pooled hazard ratios (HRs) and relative risks (RR …
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CCTFv2: Modeling Cyber Competitions.
Qolomany B, Calay TJ, Hossain L, Mulahuwaish A, Bou Abdo J.
Entropy (Basel). 2024 Apr 30;26(5):384. doi: 10.3390/e26050384.
This work follows a cross-validating two-approach methodology. The first is the computational modeling of cyber competitions using Agent-Based Modeling. Team members are modeled, in NetLogo, as collaborating agents competing over a network in a …
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Understanding the Role of Naive Learners in Cultural Change.
Chimento M, Aplin LM.
Am Nat. 2024 Jun;203(6):695-712. doi: 10.1086/730110. Epub 2024 Apr 15.
We conducted a formal exploration of this hypothesis using a generative model that concurrently simulated its two key ingredients: social transmission and reinforcement learning. …These effects depended on network and learning parameters. Our model provides formal …
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Modelling techniques in cholera epidemiology: A systematic and critical review.
Anteneh LM, Lokonon BE, Kakaï RG.
Math Biosci. 2024 May 20;373:109210. doi: 10.1016/j.mbs.2024.109210. Online ahead of print.
About 52%, 21%, and 9%, of the studies, were based on compartmental (e.g., SIRB), statistical (time series and regression), and spatial (spatiotemporal clustering) models, respectively, while the rest of the analysed studies used other modelling approaches such as n …
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Growth-induced collective bending and kinetic trapping of cytoskeletal filaments.
Banerjee DS, Freedman SL, Murrell MP, Banerjee S.
Cytoskeleton (Hoboken). 2024 May 22. doi: 10.1002/cm.21877. Online ahead of print.
To understand how filament growth shapes the emergent architecture of actin networks, we developed a minimal agent-based model coupling filament mechanics and growth in a limiting subunit pool. …
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Novel multi-cluster workflow system to support real-time HPC-enabled epidemic science: Investigating the impact of vaccine acceptance on COVID-19 spread.
Bhattacharya P, Machi D, Chen J, Hoops S, Lewis B, Mortveit H, Venkatramanan S, Wilson ML, Marathe A, Porebski P, Klahn B, Outten J, Vullikanti A, Xie D, Adiga A, Brown S, Barrett C, Marathe M.
J Parallel Distrib Comput. 2024 Sep;191:104899. doi: 10.1016/j.jpdc.2024.104899. Epub 2024 May 4.
MacKenzie is a novel HPC meta-scheduler that can execute US-scale simulation models and associated workflows that typically present significant big data challenges. …We use a 288 million node synthetic social contact network (digital twin) spanning all 50 US states plus …
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Untangling the stranglehold through mathematical modelling of Streptococcus equi subspecies equi transmission.
Houben RMAC, Newton JR, van Maanen C, Waller AS, Sloet van Oldruitenborgh-Oosterbaan MM, Heesterbeek JAP.
Prev Vet Med. 2024 May 17;228:106230. doi: 10.1016/j.prevetmed.2024.106230. Online ahead of print.
A compartmental deterministic model was constructed. Parameter values were estimated from current literature wherever possible. …In some of worst-case scenarios, vaccination alone would not suffice to prevent major outbreaks from occurring. A stochastic agent-b …
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Using an epidemiological model to explore the interplay between sharing and advertising in viral videos.
Li Y, Shao L.
Sci Rep. 2024 May 18;14(1):11351. doi: 10.1038/s41598-024-61814-9.
We mathematically analyze the global stability of the system and propose an agent-based modeling approach to evaluate the efficiency of sharing and advertising. We further provide a case study of music videos on YouTube to show the validity of our model …
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Mathematical modeling of hypoxia and adenosine to explore tumor escape mechanisms in DC-based immunotherapy.
Ghiyabi E, Arabameri A, Charmi M.
Sci Rep. 2024 May 18;14(1):11387. doi: 10.1038/s41598-024-62209-6.
However, challenges include understanding dynamics, optimal vaccine dosages, and timing. Mathematical models, including agent-based, diffusion, and ordinary differential equations, address these challenges. Here, we employ these models for the first ti …
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