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In this work, we perform an exploratory study on synthesizing deep neural networks using biological synaptic strength distributions, and the potential influence of different distributions on modelling performance particularly for the…
A model of cellular metabolism due to S. Kauffman is analyzed. It consists of a network of Boolean gates randomly assembled according to a probability distribution. It is shown that the behavior of the network depends very critically on…
Networks are widely used in science and technology to represent relationships between entities, such as social or ecological links between organisms, enzymatic interactions in metabolic systems, or computer infrastructure. Statistical…
For decades, complex networks, such as social networks, biological networks, chemical networks, technological networks, have been used to study the evolution and dynamics of different kinds of complex systems. These complex systems can be…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
Many real life networks present an average path length logarithmic with the number of nodes and a degree distribution which follows a power law. Often these networks have also a modular and self-similar structure and, in some cases -…
To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…
The whole complex process to obtain a protein encoded by a gene is difficult to include in a mathematical model. There are many models for describing different aspects of a genetic network. Finding a better model is one of the most…
The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the…
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…
Extracting understanding from the growing ``sea'' of biological and socio-economic data is one of the most pressing scientific challenges facing us. Here, we introduce and validate an unsupervised method that is able to accurately extract…
An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…
In recent years, methods from network science are gaining rapidly interest in economics and finance. A reason for this is that in a globalized world the interconnectedness among economic and financial entities are crucial to understand and…
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…
Complex Systems were identified and studied in different fields, such as physics, biology, and economics. These systems exhibit exciting properties such as self-organization, robust order, and emergence. In recent years, software systems…
The relationship between the regulatory design and the functionality of molecular networks is a key issue in biology. Modules and motifs have been associated to various cellular processes, thereby providing anecdotal evidence for…
We interpret the subgraph centrality as the partition function of a network. The entropy, the internal energy and the Helmholtz free energy are defined for networks and molecular graphs on the basis of graph spectral theory. Various…
Complex software systems are among most sophisticated human-made systems, yet only little is known about the actual structure of 'good' software. We here study different software systems developed in Java from the perspective of network…
Generative mechanisms which lead to empirically observed structure of networked systems from diverse fields like biology, technology and social sciences form a very important part of study of complex networks. The structure of many…
Adaptive networks appear in many biological applications. They combine topological evolution of the network with dynamics in the network nodes. Recently, the dynamics of adaptive networks has been investigated in a number of parallel…