Related papers: Converting a Systems Dynamic Model to an Agent-bas…
Advances in synthetic biology allow us to engineer bacterial collectives with pre-specified characteristics. However, the behavior of these collectives is difficult to understand, as cellular growth and division as well as extra-cellular…
Morphogen gradients play an essential role in the spatial regulation of cell patterning during early development. The classical mechanism of morphogen gradient formation involves the diffusion of morphogens away from a localized source…
We present an Equation/Variable free machine learning (EVFML) framework for the control of the collective dynamics of complex/multiscale systems modelled via microscopic/agent-based simulators. The approach obviates the need for…
Multi-agent simulations enables the modeling and analyses of the dynamic behaviors and interactions of autonomous entities evolving in complex environments. Agent-based models (ABM) are widely used to study emergent phenomena arising from…
We study the asymptotic behaviors of stochastic cell fate decision between proliferation and differentiation. We propose a model of a self-replicating Langevin system, where cells choose their fate (i.e. proliferation or differentiation)…
Morphogens are secreted signaling molecules that mediate tissue patterning and growth of embryonic tissues. They are secreted in a localized region and spread through the tissue to form a graded concentration profile. We present a…
Most of the grand challenges of humanity today involve complex agent-based systems, such as epidemiology, economics or ecology. However, remains as a pending task the challenge of identifying the general principles underlying their…
Agent-based models provide a constructive approach to studying emergent dynamics in life-like systems composed of interacting, adaptive agents. Financial markets serve as a canonical example of such systems, where collective price dynamics…
The potential power provided and possibilities presented by computation graphs has steered most of the available modeling techniques to re-implementing, utilization and including the complex nature of System Biology (SB). To model the…
Based on recent experiments with time-lapse fluorescent imaging, we propose a cellular automaton model for the dynamics of vascular endothelial cells (ECs) in angiogenic morphogenesis. The model successfully reproduces cell mixing behavior,…
When modeling of tumor-driven angiogenesis, a major source of analytical and computational complexity is the strong coupling between the kinetic parameters of the relevant stochastic branching-and-growth of the capillary network, and the…
Risk management resulting from the actions and states of the different elements making up a operating room is a major concern during a surgical procedure. Agent-based simulation shows an interest through its interaction concepts,…
Agent Based Modeling (ABM) has become a widespread approach to model complex interactions. In this chapter after briefly summarizing some features of ABM the different approaches in modeling spatial interactions are discussed. It is…
A discrete time stochastic model for a multiagent system given in terms of a large collection of interacting Markov chains is studied. The evolution of the interacting particles is described through a time inhomogeneous transition…
This chapter presents the main lines of agent based modeling in the field of medical research. The general diagram consists of a cohort of patients (virtual or real) whose evolution is observed by means of so-called evolution models.…
Self-organisation of individuals within large collectives occurs throughout biology. Mathematical models can help elucidate the individual-level mechanisms behind these dynamics, but analytical tractability often comes at the cost of…
Large-Scale Multi-Agent Systems (LS-MAS) consist of several autonomous components, interacting in a non-trivial way, so that the emerging behaviour of the ensemble depends on the individual dynamics of the components and their reciprocal…
The study of system complexity primarily has two objectives: to explore underlying patterns and to develop theoretical explanations. Pattern exploration seeks to clarify the mechanisms behind the emergence of system complexity, while…
In this paper, we analyze the behavior of a multi-agent system driven by the interactions of agents within a competitive environment. To achieve this, we describe the transition probabilities that underlie the system's stochastic nature. We…
This article extends the preprint "Characterizing Agent-Based Model Dynamics via $\epsilon$-Machines and Kolmogorov-Style Complexity" by introducing diffusion models as orthogonal and complementary tools for characterizing the output of…