Related papers: Types of Stickiness in BHV Phylogenetic Tree Space…
Phylogenetic trees provide a fundamental representation of evolutionary relationships, yet the combinatorial explosion of possible tree topologies renders inference computationally challenging. Classical approaches to characterizing tree…
The stochastic motion in a nonhomogeneous medium with traps is studied and diffusion properties of that system are discussed. The particle is subjected to a stochastic stimulation obeying a general L\'evy stable statistics and experiences…
Frequency-dependent selection reflects the interaction between different species as they battle for limited resources in their environment. In a stochastic evolutionary game the species relative fitnesses guides the evolutionary dynamics…
We experimentally investigate the response of a sheared granular medium in a Couette geometry. The apparatus exhibits the expected stick-slip motion and we probe it in the very intermittent regime resulting from low driving. Statistical…
Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the (unknown) subset of current species that will still be present at some future time, then this…
A considerable number of systems have recently been reported in which Brownian yet non-Gaussian dynamics was observed. These are processes characterised by a linear growth in time of the mean squared displacement, yet the probability…
We compare the observed probability distribution function of the transmission in the \HI\ Lyman-alpha forest, measured from the UVES 'Large Programme' sample at redshifts z=[2,2.5,3], to results from the GIMIC cosmological simulations. Our…
We study a topology on a space of functions, called sticking topology, with the property to be the weakest among the topologies preserving continuity. In suitable frameworks, this topology preserves borelianity, local integrability, right…
Two surfaces are "sticky" if breaking their mutual contact requires a finite tensile force. At low fractal dimensions D, there is consensus stickiness does not depend on the upper truncation frequency of roughness spectrum (or…
Settling velocity statistics for dilute, non-Brownian suspensions of polydisperse spheres having a log-normal size distribution are analysed by Stokesian Dynamics, as a function of the total volume fraction and width of the size…
This study develops and analyzes a stochastic differential equation (SDE) model for the dynamics of hepatitis B virus (HBV) infection. While deterministic frameworks have yielded important insights into viral behavior, they cannot…
Recently, multi-scale notions of local homology (a variant of persistent homology) have been used to study the local structure of spaces around a given point from a point cloud sample. Current reconstruction guarantees rely on constructing…
Sticky diffusion models a Markovian particle experiencing reflection and temporary adhesion phenomena at the boundary. Numerous numerical schemes exist for approximating stopped or reflected stochastic differential equations (SDEs), but…
We investigate mixed eigenstates in systems with sharply-divided phase space, using different piecewise-linear maps whose regular-chaotic boundaries are formed by marginally unstable periodic orbits (MUPOs) or by quasi-periodic orbits. With…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
Persistent homology computes the multiscale topology of a data set by using a sequence of discrete complexes. In this paper, we propose that persistent homology may be a useful tool for studying the structure of the landscape of string…
Evolutionary relationships between species are represented by phylogenetic trees, but these relationships are subject to uncertainty due to the random nature of evolution. A geometry for the space of phylogenetic trees is necessary in order…
Inferring dependencies between complex biological traits while accounting for evolutionary relationships between specimens is of great scientific interest yet remains infeasible when trait and specimen counts grow large. The…
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…
Reconstructing the evolutionary history relating a collection of molecular sequences is the main subject of modern Bayesian phylogenetic inference. However, the commonly used Markov chain Monte Carlo methods can be inefficient due to the…