23 papers · ranked by Valyu relevance
Abdulrahman M El-Sayed, Peter Scarborough, Lars Seemann, Sandro Galea
'Sandro Galea'] The past five years have seen a growth in the interest in systems approaches in epidemiologic research. These approaches may be particularly appropriate for social epidemiology. Social network analysis and agent-based models (ABMs) are two approaches that have been used in the epidemiologic literature.…
Lukas Breitwieser, Ahmad Hesam, Jean de Montigny, Vasileios Vavourakis + 9 more
Computer simulation is an indispensable tool for studying complex biological systems. In particular, agent-based modeling is an attractive method to describe biophysical dynamics. However, two barriers limit faster progress. First, simulators do not always take full advantage of parallel and heterogeneous hardware.…
Gael Pérez-Rodríguez, Martín Pérez-Pérez, Daniel Glez-Peña, Florentino Fdez-Riverola + 2 more
'Florentino Fdez-Riverola' 'Nuno F. Azevedo' 'Anália Lourenço'] Agent-based modelling is being used to represent biological systems with increasing frequency and success. This paper presents the implementation of a new tool for biomolecular reaction modelling in the open source Multiagent Simulator of Neighborhoods…
Lukas Johannes Breitwieser
D E S I G N A N D A N A LY S I S O F A N E X T R E M E - S C A L E , H I G H - P E R F O R M A N C E , A N D M O D U L A R A G E N T - B A S E D S I M U L AT I O N P L AT F O R M
Rosaria Conte, Mario Paolucci
In the first part of the paper, the field of agent-based modeling (ABM) is discussed focusing on the role of generative theories, aiming at explaining phenomena by growing them. After a brief analysis of the major strengths of the field some crucial weaknesses are analyzed. In particular, the generative power of ABM is…
Sean L. Wu, Andrew J. Dolgert, Joseph A. Lewnard, John M. Marshall + 1 more
After more than a century of sustained work by mathematicians, biologists, epidemiologists, probabilists, and other experts, dynamic models have become a vital tool for understanding and describing epidemics and disease transmission systems. Such models fulfill a variety of crucial roles including data integration…
Atsushi Niida, Takanori Hasegawa, Satoru Miyano
An essential step in the analysis of agent-based simulation is sensitivity analysis, which namely examines the dependency of parameter values on simulation results. Although a number of approaches have been proposed for sensitivity analysis, they still have limitations in exhaustivity and interpretability. In this…
Erica Cau, Andrea Failla, Valentina Pansanella, Giulio Rossetti
This book chapter covers the evolution of social simulation from classical agent-based models, in which agents interact according to explicitly defined behavioral rules, to AI-enhanced simulations based on Large Language Models and, ultimately, Social Digital Twins: high-fidelity, data-driven representations of…
Anna Klabunde, Frans Willekens
We review agent-based models (ABM) of human migration with respect to their decision-making rules. The most prominent behavioural theories used as decision rules are the random utility theory, as implemented in the discrete choice model, and the theory of planned behaviour. We identify the critical choices that must be…
Jameson Miller, Miles Parker, Robert B. Bourret, Morgan C. Giddings + 1 more
'Michael Otto'] We report the application of agent-based modeling to examine the signal transduction network and receptor arrays for chemotaxis in Escherichia coli, which are responsible for regulating swimming behavior in response to environmental stimuli. Agent-based modeling is a stochastic and bottom-up approach…
Affan Shoukat, Seyed M. Moghadas
Modelling and computational methods have been essential in advancing quantitative science, especially in the past two decades with the availability of vast amount of complex, voluminous, and heterogeneous data. In particular, there has been a surge of interest in agent-based modelling, largely due to its capabilities…
Alexander Kott, Bruce Skarin
For the purposes of this paper, we define insurgency as an organized movement that uses armed violence to overthrow a country's government while often hiding within the civilian population and using civilians to perform combat support functions. The use of civilian population differentiates insurgency from the regular…
Vitor B. Pinheiro, Thomas E. Gorochowski
Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier…
Maik Larooij, Petter Törnberg
Recent advances in Large Language Models (LLMs) have revitalized interest in Agent-Based Models (ABMs) by enabling “generative” simulations, with agents that can plan, reason, and interact through natural language. These developments promise greater realism and expressive power, but also revive long-standing concerns…
Juliette Griffié, Ruby Peters, Dylan M. Owen
Molecular clustering at the plasma membrane has long been identified as a key process and is associated with regulating signalling pathways across cell types. Recent advances in microscopy, in particular the rise of super-resolution, have allowed the experimental observation of nanoscale molecular clusters in the…
Florian Cogoni, David Bernard, Roxana Kazhen, Salvatore Valitutti + 2 more
Agent-based models are commonly used in biology to study tissue-scale phenomena by reproducing the individual behavior of the cells. They offer the possibility to study cellular biology at the individual cell scale to explore the basic behavior of cells which are responsible of the emergence of more complex phenomena…
Rong Pan
Public policy making has direct and indirect impacts on social behaviors. However, using system dynamics model alone to assess these impacts fails to consider the interactions among social elements, thus may produce doubtful conclusions. In this study, we examine the political science theory of greed and grievance in…
Gavin Fullstone, Cristiano Guttà, Amatus Beyer, Markus Rehm
Agent-based modelling is particularly adept at modelling complex features of cell signalling pathways, where heterogeneity, stochastic and spatial effects are important, thus increasing our understanding of decision processes in biology in such scenarios. However, agent-based modelling often is computationally…
Authors not listed
Agentic artificial intelligence (AI) is poised to redefine how science is conducted, automating not just data analysis but the entire research lifecycle, from hypothesis generation to validation. Yet most current AI agents remain domain-bound, tailored to specific applications such as materials synthesis or quantum…
Hossein Sabzian, Alireza Aliahmadi, Adel Azar, Madjid Mirzaee
Economic inequality is one of the pivotal issues for most of economic and social policy makers across the world to insure the sustainable economic growth and justice. In the mainstream school of economics, namely neoclassical theories, economic issues are dealt with in a mechanistic manner. Such a mainstream framework…
Authors not listed
Machine olfaction—the artificial replication of the sense of smell—faces significant challenges due to the absence of large, standardized training datasets. Unlike vision, language, and audio models, which benefit from extensive corpora such as ImageNet, GLUE, and AudioSet, olfaction lacks scaled equivalents and…
Authors not listed
We have developed Aitomia – a platform powered by AI to assist in performing AI-driven atomistic and quantum chemical (QC) simulations. This evolving intelligent assistant platform is equipped with chatbots and AI agents to help experts and guide non-experts in setting up and running atomistic simulations, monitoring…
Monika Vogler, Jonas Busk, Hamidreza Hajiyani, Peter Bjørn Jørgensen + 9 more
The future of materials science is borderless, cooperative, and distributed across the globe. This necessitates flexible, reconfigurable software defined research workflows, which we herein demonstrate by integrating multiple disciplines and modalities. Our brokering approach to research orchestration exposes entire…