Related papers: A simple model to study phylogeographies and speci…
Predicting the fate of ecologies is a daunting, albeit extremely important, task. As part of this task one needs to develop an understanding of the organization, hierarchies, and correlations among the species forming the ecology. Focusing…
This dissertation presents a multifaceted look into the structural decomposition of permutation classes. The theory of permutation patterns is a rich and varied field, and is a prime example of how an accessible and intuitive definition…
We propose a modeling framework for growing multiplexes where a node can belong to different networks. We define new measures for multiplexes and we identify a number of relevant ingredients for modeling their evolution such as the coupling…
The structure of real-world networks is usually difficult to characterize owing to the variation of topological scales, the nondyadic complex interactions, and the fluctuations in the network. We aim to address these problems by introducing…
The process of pattern formation for a multi-species model anchored on a time varying network is studied. A non homogeneous perturbation superposed to an homogeneous stable fixed point can amplify, as follows a novel mechanism of…
A network is a typical expressive form of representing complex systems in terms of vertices and links, in which the pattern of interactions amongst components of the network is intricate. The network can be static that does not change over…
It was recently shown that a large class of phylogenetic networks, the `labellable' networks, is in bijection with the set of `expanding' covers of finite sets. In this paper, we show how several prominent classes of phylogenetic networks…
This paper presents a statistically sound method for using likelihood to assess potential models of network evolution. The method is tested on data from five real networks. Data from the internet autonomous system network, from two photo…
Modes of speciation have been the subject of a century's debate. Traditionally, most speciations are believed to be caused by spatial separation of populations (allopatry). Recent observations (Meyer 1990, Schliewen 1994, Schliewen 2001,…
We introduce a novel approach to description of networks/graphs. It is based on an analogue physical model which is dynamically evolved. This evolution depends on the connectivity matrix and readily brings out many qualitative features of…
When dealing with evolving or multi-dimensional complex systems, network theory provides with elegant ways of describing their constituting components, through respectively time-varying and multi-layer complex networks. Nevertheless, the…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
We review the recent fast progress in statistical physics of evolving networks. Interest has focused mainly on the structural properties of random complex networks in communications, biology, social sciences and economics. A number of giant…
We provide a framework for modeling social network formation through conditional multinomial logit models from discrete choice and random utility theory, in which each new edge is viewed as a "choice" made by a node to connect to another…
The ability to compare complex systems can provide new insight into the fundamental nature of the processes captured in ways that are otherwise inaccessible to observation. Here, we introduce the $n$-tangle method to directly compare two…
Many real-world networks, ranging from subway systems to polymer structures and fungal mycelia, do not form by the incremental addition of individual nodes but instead grow through the successive extension and intersection of lines or…
Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…
Researchers worldwide have drawn inspiration from nature to optimize network design and dynamics. Some of the wonders of the living world exhibit remarkable abilities in generating efficient and resilient spatial structures. By mimicking…
We propose a new method for quantitative characterization of spatial network-like patterns with loops, such as surface fracture patterns, leaf vein networks and patterns of urban streets. Such patterns are not well characterized by purely…