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After more than a century of concerted effort, physics still lacks basic principles of spontaneous self-organization. To appreciate why, we first state the problem, outline historical approaches, and survey the present state of the physics…
The molecular biology revolution of the last seventy five years has transformed our view of living systems. Scientific explanations of biological phenomena are now synonymous with the identification of the genes, proteins, and signaling…
Many real-world dynamic systems, both natural and artificial, are understood to be performing computations. For artificial dynamic systems, explicitly designed to perform computation - such as digital computers - by construction, we can…
The concept of structured occurrence nets is an extension of that of occurrence nets which are directed acyclic graphs that represent causality and concurrency information concerning a single execution of a distributed system. The formalism…
Contemporary complexity theory has been instrumental in providing novel rigorous definitions for some classic philosophical concepts, including emergence. In an attempt to provide an account of emergence that is consistent with complexity…
Cancers remain the lead cause of disease-related, pediatric death in North America. The emerging field of complex systems has redefined cancer networks as a computational system with intractable algorithmic complexity. Herein, a tumor and…
Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and postgenomics data sets. Indeed, biological entities are not isolated, but are components of complex…
The interaction of distinct units in physical, social, biological and technological systems naturally gives rise to complex network structures. Networks have constantly been in the focus of research for the last decade, with considerable…
This chapter discusses the interplay between structure and dynamics in complex networks. Given a particular network with an endowed dynamics, our goal is to find partitions aligned with the dynamical process acting on top of the network. We…
We create a novel optimisation technique inspired by natural ecosystems, where the optimisation works at two levels: a first optimisation, migration of genes which are distributed in a peer-to-peer network, operating continuously in time;…
Complex networks are universal, arising in fields as disparate as sociology, physics, and biology. In the past decade, extensive research into the properties and behaviors of complex systems has uncovered surprising commonalities among the…
A procedure to characterize chaotic dynamical systems with concepts of complex networks is pursued, in which a dynamical system is mapped onto a network. The nodes represent the regions of space visited by the system, while edges represent…
The study of complex systems has attracted widespread attention from researchers in the fields of natural sciences, social sciences, and engineering. Prediction is one of the central issues in this field. Although most related studies have…
Empirical studies of graphs have contributed enormously to our understanding of complex systems. Known today as network science, what was originally a theoretical study of graphs has grown into a more scientific exploration of communities…
Quantum cybernetics and its connections to complex quantum systems science is addressed from the perspective of complex quantum computing systems. In this way, the notion of an autonomous quantum computing system is introduced in regards to…
Directed networks are essential for representing complex systems, capturing the asymmetry of interactions in fields such as neuroscience, transportation, and social networks. Directionality reveals how influence, information, or resources…
The design and operation of systems are conventionally viewed as a sequential decision-making process that is informed by data from physical experiments and simulations. However, the integration of these high-dimensional and heterogeneous…
We view Digital Ecosystems to be the digital counterparts of biological ecosystems, exploiting the self-organising properties of biological ecosystems, which are considered to be robust, self-organising and scalable architectures that can…
The increasing recognition of the association between adverse human health conditions and many environmental substances as well as processes has led to the need to monitor them. An important problem that arises in environmental statistics…
We show that, in contrast to classical random graph models, many real-world complex systems -- including a variety of biological regulatory networks and technological networks such as the internet -- spontaneously self-organize to a richly…