相关论文: SIMMUNE, a tool for simulating and analyzing immun…

This work proposes a theoretical framework using a systemic modeling paradigm to implement computational agents in the simulation of organizations. The potential of its use is demonstrated in the modeling of supply chains. Finally, research…

Simflowny is an open platform which automatically generates parallel code of scientific dynamical models for different simulation frameworks. Here we present major upgrades on this software to support an extended set of families of models,…

Simulating consumer decision-making is vital for designing and evaluating marketing strategies before costly real-world deployment. However, post-event analyses and rule-based agent-based models (ABMs) struggle to capture the complexity of…

Intelligent agents offer a new and exciting way of understanding the world of work. Agent-Based Simulation (ABS), one way of using intelligent agents, carries great potential for progressing our understanding of management practices and how…

The challenges posed by epidemics and pandemics are immense, especially if the causes are novel. This article introduces a versatile open-source simulation framework designed to model intricate dynamics of infectious diseases across diverse…

Agent-based modeling is indispensable for studying complex systems across many domains. However, existing simulation platforms exhibit two major issues: performance and modularity. Low performance prevents simulations with a large number of…

Virtual cell modeling aims to predict cellular responses to diverse perturbations but faces challenges from biological complexity, multimodal data heterogeneity, and the need for interdisciplinary expertise. We introduce CellForge, a…

Characterizing the dynamic interactive patterns of complex systems helps gain in-depth understanding of how components interrelate with each other while performing certain functions as a whole. In this study, we present a novel multimodal…

SALMON (Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience, http://salmon-tddft.jp) is a software package for the simulation of electron dynamics and optical properties of molecules, nanostructures, and crystalline solids…

We review different aspects of the simulation of spiking neural networks. We start by reviewing the different types of simulation strategies and algorithms that are currently implemented. We next review the precision of those simulation…

Simulation ensembles are a common tool in physics for understanding how a model outcome depends on input parameters. We analyze an active particle system, where each particle can use energy from its surroundings to propel itself. A…

We present a method based on a time domain simulation of wave propagation that allows studying the optical response of a broad range of dielectric photonic structures. This method is particularly suitable for dealing with complex biological…

The discovery of causal relationships from high-dimensional data is a major open problem in bioinformatics. Machine learning and feature attribution models have shown great promise in this context but lack causal interpretation. Here, we…

The integration of multiple viewpoints became an increasingly popular approach to deal with agent-based simulations. Despite their disparities, recent approaches successfully manage to run such multi-level simulations. Yet, are they doing…

Control of an inflammatory immune response is still an ongoing research. Here, a strategy consisting of manipulating a pro and anti-inflammatory mediator is considered. Already existing and promising model-based techniques suffer…

We model the immune surveillance of a pathogen which passes through $n$ immunologically distinct stages. The biological parameters of this system induce a partial order on the stages, and this, in turn, determines which stages will be…

Large language models (LLMs) and vision-language models (VLMs) have the potential to transform biological research by enabling autonomous experimentation. Yet, their application remains constrained by rigid protocol design, limited…

Process mining techniques including process discovery, conformance checking, and process enhancement provide extensive knowledge about processes. Discovering running processes and deviations as well as detecting performance problems and…

Simulation is used extensively in autonomous systems, particularly in robotic manipulation. By far, the most common approach is to train a controller in simulation, and then use it as an initial starting point for the real system. We…

Emergence is a phenomenon taken for granted in science but also still not well understood. We have developed a model of artificial genetic evolution intended to allow for emergence on genetic, population and social levels. We present the…