Related papers: A model of macro-evolution as a branching process …
The impact of environmental fluctuation on species diversity is studied with a model of the evolutionary ecology of microorganisms. We show that environmental fluctuation induces evolutionary branching and assures the consequential…
In this paper, we propose an evolving network model growing fast in units of module, based on the analysis of the evolution characteristics in real complex networks. Each module is a small-world network containing several interconnected…
A method for creating a forest of model trees to fit samples of a function defined on images is described in several steps: down-sampling the images, determining a tree's hyperplanes, applying convolutions to the hyperplanes to handle small…
We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is…
We present a generalization of the Yule model for macroevolution in which, for the appearance of genera, we consider point processes with the order statistics property, while for the growth of species we use nonlinear time-fractional pure…
We study a model of a branching process subject to selection, modeled by giving each family an individual fitness acting as a branching rate, and mutation, modeled by resampling the fitness of a proportion of offspring in each generation.…
Interpretation of empirical results based on a taxa's lifetime distribution shows apparently conflicting results. Species' lifetime is reported to be exponentially distributed, whereas higher order taxa, such as families or genera, follow a…
We introduce a new model of random tree that grows like a random recursive tree, except at some exceptional "doubling events" when the tree is replaced by two copies of itself attached to a new root. We prove asymptotic results for the size…
Latent space models for network data characterize each node through a vector of latent features whose pairwise similarities define the edge probabilities among the pairs of nodes. Although this formulation has led to successful…
Scientific studies in many areas of biology routinely employ evolutionary analyses based on the probabilistic inference of phylogenetic trees from molecular sequence data. Evolutionary processes that act at the molecular level are highly…
This paper proposes an attributed network growth model. Despite the knowledge that individuals use limited resources to form connections to similar others, we lack an understanding of how local and resource-constrained mechanisms explain…
The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small world property of real…
Natural evolution gives the impression of leading to an open-ended process of increasing diversity and complexity. If our goal is to produce such open-endedness artificially, this suggests an approach driven by evolutionary metaphor. On the…
We consider a class of Crump-Mode-Jagers processes with interaction, constructed by removing a newly born offspring with a probability that depends on the age structure of the population at its birth time. We prove a law of large numbers…
We model evolution of plants in a world, made up of different locations, with multiple environments (mutually exclusive and collectively exhaustive subsets of locations). Each environment (landmass) has temperature, rainfall, and other…
We present a stochastic model for the size of a taxon in paleobiology, in which we allow for the evolution of new taxon members, and both individual and catastrophic extinction events. The model uses ideas from the theory of birth and death…
We define the beta diffusion tree, a random tree structure with a set of leaves that defines a collection of overlapping subsets of objects, known as a feature allocation. A generative process for the tree structure is defined in terms of…
The evolution of structure in biology is driven by accretion and change. Accretion brings together disparate parts to form bigger wholes. Change provides opportunities for growth and innovation. Here we review patterns and processes that…
Network models have been widely used to study diverse systems and analyze their dynamic behaviors. Given the structural variability of networks, an intriguing question arises: Can we infer the type of system represented by a network based…
Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative…