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Methods from statistical physics, such as those involving complex networks, have been increasingly used in quantitative analysis of linguistic phenomena. In this paper, we represented pieces of text with different levels of simplification…

We investigate the ability of algorithms developed for reverse engineering of transcriptional regulatory networks to reconstruct metabolic networks from high-throughput metabolite profiling data. For this, we generate synthetic metabolic…

In this review we establish various connections between complex networks and symmetry. While special types of symmetries (e.g., automorphisms) are studied in detail within discrete mathematics for particular classes of deterministic graphs,…

Characterization of real-world complex systems increasingly involves the study of their topological structure using graph theory. Among global network properties, small-world property, consisting in existence of relatively short paths…

We discuss chemical reaction networks and metabolic pathways based on stoichiometric network analysis, and introduce deformed toric ideal constraints by the algebraic geometrical approach. This paper concerns steady state flux of chemical…

How biological networks achieve robust control despite relying on imperfect, local information remains an important open question. Here, we identify thermodynamic constraints that can curtail non-equilibrium steady-state responses so…

We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a…

Synchronization, in which individual dynamical units keep in pace with each other in a decentralized fashion, depends both on the dynamical units and on the properties of the interaction network. Yet, the role played by the network has…

Many real-world systems are composed of many individual components that interact with one another in a complex pattern to produce diverse behaviors. Understanding how to intervene in these systems to guide behaviors is critically important…

In this work, we explore the state-space formulation of a network process to recover, from partial observations, the underlying network topology that drives its dynamics. To do so, we employ subspace techniques borrowed from system…

The collective dynamics of interacting dynamical units on a network crucially depends on the properties of the network structure. Rather than considering large but finite graphs to capture the network, one often resorts to graph limits and…

With the emergence of graph databases, the task of frequent subgraph discovery has been extensively addressed. Although the proposed approaches in the literature have made this task feasible, the number of discovered frequent subgraphs is…

The application of network techniques to the analysis of neural data has greatly improved our ability to quantify and describe these rich interacting systems. Among many important contributions, networks have proven useful in identifying…

Complex networks encountered in biology are often characterized by significant structural diversity. Whether it be differences in the three-dimensional structure of allosteric proteins, or the variation among the micro-scale structures of…

Autocatalytic Sets are reaction networks theorised as networks at the basis of life. Their main feature is the ability of spontaneously emerging and self-reproducing. The Reflexively and Food-generated theory provides a formal definition of…

This paper deals with dynamical networks for which the relations between node signals are described by proper transfer functions and external signals can influence each of the node signals. We are interested in graph-theoretic conditions…

A procedure is developed and tested to recover the distribution of connectivity of an a priori unknown network, by sampling the dynamics of an ensemble made of reactive walkers. The relative weight between reaction and relocation is gauged…

Control of complex processes is a major goal of network analyses. Most approaches to control nonlinearly coupled systems require the network topology and/or network dynamics. Unfortunately, neither the full set of participating nodes nor…

Through detailed analysis of scores of publicly available data sets corresponding to a wide range of large-scale networks, from communication and road networks to various forms of social networks, we explore a little-studied geometric…

This paper addresses the problem of identifying the topology of an unknown, weighted, directed network running a consensus dynamics. We propose a methodology to reconstruct the network topology from the dynamic response when the system is…