Related papers: Evolution of spatially embedded branching trees wi…
Life systems are complex and hierarchical, with diverse components at different scales, yet they sustain themselves, grow, and evolve over time. How can a theory of such complex biological states be developed? Here we note that for a…
We have simulated the evolution of age structured populations whose individuals represented by their diploid genomes were distributed on a square lattice. The environmental conditions on the whole territory changed simultaneously in the…
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…
We consider an individual-based spatially structured population for Darwinian evolution in an asexual population. The individuals move randomly on a bounded continuous space according to a reflected brownian motion. The dynamics involves…
A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree…
Message passing neural networks iteratively generate node embeddings by aggregating information from neighboring nodes. With increasing depth, information from more distant nodes is included. However, node embeddings may be unable to…
Motivated by results of Henry, Pralat and Zhang (PNAS 108.21 (2011): 8605-8610), we propose a general scheme for evolving spatial networks in order to reduce their total edge lengths. We study the properties of the equilbria of two networks…
This paper considers generalised network, intended as networks where (a) the edges connecting the nodes are nonlinear, and (b) stochastic processes are continuously indexed over both vertices and edges. Such topological structures are…
We consider branching processes with interaction in continuous time, both with values in the integers and in the reals (in the second case we restrict ourselves to continuous processes), which model the evolution of the size of a…
Disentangling the mechanisms underlying the social network evolution is one of social science's unsolved puzzles. Preferential attachment is a powerful mechanism explaining social network dynamics, yet not able to explain all scaling-laws…
Many real-world complex networks arise as a result of a competition between growth and rewiring processes. Usually the initial part of the evolution is dominated by growth while the later one rather by rewiring. The initial growth allows…
In this article, we construct a generalization of the Blum-Fran\c{c}ois Beta-splitting model for evolutionary trees, which was itself inspired by Aldous' Beta-splitting model on cladograms. The novelty of our approach allows for asymmetric…
When three species compete cyclically in a well-mixed, stochastic system of $N$ individuals, extinction is known to typically occur at times scaling as the system size $N$. This happens, for example, in rock-paper-scissors games or…
Shape is one of the important characteristics for the structures observed in living organisms. Whereas biologists have proposed models where the shape is controlled on a molecular level [1], physicists, following Turing [2] and d'Arcy…
Results of experimental investigation are presented of evolutionary dynamics of several stochastic pattern formation and growth models designed by modifications of the famous mathematical Game of Life. The modifications are two-fold: Game…
In this paper we show that all infinite trees which have bounded coordination and whose surface is negligible with respect to the volume in the limit of large distances (so that they can be embedded in a finite-dimensional euclidean space)…
The first main result of this paper is that the law of the (rescaled) two-dimensional uniform spanning tree is tight in a space whose elements are measured, rooted real trees continuously embedded into Euclidean space. Various properties of…
A branching process in a Markovian environment consists of an irreducible Markov chain on a set of "environments" together with an offspring distribution for each environment. At each time step the chain transitions to a new random…
The investigation of dynamical processes on networks has been one focus for the study of contagion processes. It has been demonstrated that contagions can be used to obtain information about the embedding of nodes in a Euclidean space.…
There have been many studies to examine whether one trait is correlated with another trait across a group of present-day species (for example, do species with larger brains tend to have longer gestation times. Since the introduction of the…