Related papers: Weak Independence and Coupled Parallelism in Biolo…
The major biochemical networks of the living cell, the network of interacting genes and the network of biochemical reactions, are highly interdependent, however, they have been studied mostly as separate systems so far. In the last years an…
A compositional Petri net-based semantics is given to a simple language allowing pointer manipulation and parallelism. The model is then applied to give a notion of validity to the judgements made by concurrent separation logic that…
Spiking neural networks (SNNs) promise energy-efficient computation by mimicking biological neural dynamics, yet existing plasticity rules focus on isolated spike pairs and fail to leverage the synchronous activity patterns that drive…
In this work, we propose an interdependent, multilayer network model and percolation process that matches infrastructures better than previous models by allowing some nodes to survive when their interdependent neighbors fail. We consider a…
Across scientific disciplines, thresholded pairwise measures of statistical dependence between time series are taken as proxies for the interactions between the dynamical units of a network. Yet such correlation measures often fail to…
Despite their widespread utility across domains, basic network models face fundamental limitations when applied to complex biological systems, particularly in neuroscience. This paper critically examines these limitations and explores…
Mobile computing systems, service-based systems and some other systems with mobile interacting components have recently received much attention. However, because of their characteristics such as mobility and disconnection, it is difficult…
We suggest a novel approach to treating symbiotic relations between biological species or social entities. The main idea is the characterisation of symbiotic relations of coexisting species through their mutual influence on their respective…
The analysis of biological networks has benefited from the richness of Boolean networks (BNs) and the associated theory. These results have been further fortified in recent years by the emergence of Most Permissive (MP) semantics, combining…
The free energy principle (FEP) is a mathematical framework that describes how biological systems self-organize and survive in their environment. This principle provides insights on multiple scales, from high-level behavioral and cognitive…
We propose a framework for the specification of behaviour-preserving reconfigurations of systems modelled as Petri nets. The framework is based on open nets, a mild generalisation of ordinary Place/Transition nets suited to model open…
A critical task in systems biology is the identification of genes that interact to control cellular processes by transcriptional activation of a set of target genes. Many methods have been developed to use statistical correlations in…
Petri nets provide accurate analogues to chemical reaction networks, with places representing individual molecules (the resources of the system) and transitions representing chemical reactions which convert educt molecules into product…
We investigate the dynamics of two models of biological networks with purely suppressive interactions between the units; species interacting via niche competition and neurons via inhibitory synaptic coupling. In both of these cases,…
In the modelling and analysis of large, real systems, the main problem in their efficient processing is the size of the global model. One of the popular approaches that address this issue is the decomposition of such global model into much…
This article focuses on comparing the notions of home spaces and invariants, in Transition Systems and more particularly, in Petri Nets as well as a variety of derived Petri Nets. After recalling basic notions of Petri Nets and semiflows,…
This is the second of two papers dedicated to the relationship between population models of competition and biodiversity. Here we consider species assembly models where the population dynamics is kept far from fixed points through the…
In this talk we are concerned with the intrinsic similarities and differences between Petri nets on the one hand, and membrane systems and reaction systems on the other hand.
The protein-protein interaction (PPI) network provides an overview of the complex biological reactions vital to an organism's metabolism and survival. Even though in the past PPI network were compared across organisms in detail, there has…
Simple nonlinear dynamical systems with multiple stable stationary states are often taken as models for switchlike biological systems. This paper considers the interaction of multiple such simple multistable systems when they are embedded…