Related papers: Pathway Realisability in Chemical Networks

In living cells, chemical reactions are connected by sharing their products and substrates, and form complex networks, e.g. metabolic pathways. Here we developed a theory to predict the sensitivity, i.e. the responses of concentrations and…

The Metaverse emerges by integrating highly-distributed, complex, and interconnecting technologies. These technologies need to be formally verified and evaluated through formal modelling before executing them in real-world applications, in…

We introduce the notion of a network's conduciveness, a probabilistically interpretable measure of how the network's structure allows it to be conducive to roaming agents, in certain conditions, from one portion of the network to another.…

Signalling pathways are abstractions that help life scientists structure the coordination of cellular activity. Cross-talk between pathways accounts for many of the complex behaviours exhibited by signalling pathways and is often critical…

Link prediction is a popular research area with important applications in a variety of disciplines, including biology, social science, security, and medicine. The fundamental requirement of link prediction is the accurate and effective…

Can we objectively distinguish chemical systems that are able to process meaningful information from those that are not suitable for information processing? Here, we present a formal method to assess the semantic capacity of a chemical…

The development of chemical reaction models aids understanding and prediction in areas ranging from biology to electrochemistry and combustion. A systematic approach to building reaction network models uses observational data not only to…

Graph reachability is the task of understanding whether two distinct points in a graph are interconnected by arcs to which in general a semantic is attached. Reachability has plenty of applications, ranging from motion planning to routing.…

Assessing the synthesizability of inorganic materials is a grand challenge for accelerating their discovery using computations. Synthesis of a material is a complex process that depends not only on its thermodynamic stability with respect…

Pathway idea is a switching mechanism by which one can go from one functional form to another, and to yet another. It is shown that through a parameter $\alpha$, called the pathway parameter, one can connect generalized type-1 beta family…

We consider paths in weighted and directed temporal networks, introducing tools to compute sets of paths of high probability. We quantify the relative importance of the most probable path between two nodes with respect to the whole set of…

Reactions forming a pathway can be rewritten by making explicit the different molecular components involved in them. A molecular component represents a biological entity (e.g. a protein) in all its states (free, bound, degraded, etc.). In…

This paper develops a structural theory of unique shortest paths in real-weighted graphs. Our main goal is to characterize exactly which sets of node sequences, which we call path systems, can be realized as unique shortest paths in a graph…

The concept of multilayer networks has become recently integrated into complex systems modeling since it encapsulates a very general concept of complex relationships. Biological pathways are an example of complex real-world networks, where…

The concept of robustness of regulatory networks has been closely related to the nature of the interactions among genes, and the capability of pattern maintenance or reproducibility. Defining this robustness property is a challenging task,…

Neural networks achieve outstanding accuracy in classification and regression tasks. However, understanding their behavior still remains an open challenge that requires questions to be addressed on the robustness, explainability and…

In a temporal network causal paths are characterized by the fact that links from a source to a target must respect the chronological order. In this article we study the causal paths structure in temporal networks of human face to face…

Motivated by the increasing appeal of robots in information-gathering missions, we study multi-agent path planning problems in which the agents must remain interconnected. We model an area by a topological graph specifying the movement and…

To a considerable extent, the continuing importance and popularity of complex networks as models of real-world structures has been motivated by scale free degree distributions as well as the respectively implied hubs. Being related to…

Binary relations are one of the standard ways to encode, characterise and reason about graphs. Relation algebras provide equational axioms for a large fragment of the calculus of binary relations. Although relations are standard tools in…