Related papers: Analysis of evolution through competitive selectio…
Selection, the tendency of some traits to become more frequent than others in a population under the influence of some (natural or artificial) agency, is a key component of Darwinian evolution and countless other natural and social…
Diffusion models are powerful generative models that produce high-quality samples from complex data. While their infinite-data behavior is well understood, their generalization with finite data remains less clear. Classical learning theory…
We obtain general inequalities constraining the difference between the average of an arbitrary function of a phenotypic trait, which includes the fitness landscape of the trait itself, in the presence or in the absence of natural selection.…
Multi-model inference covers a wide range of modern statistical applications such as variable selection, model confidence set, model averaging and variable importance. The performance of multi-model inference depends on the availability of…
Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial…
The Allen-Cahn equation, coupled with dynamic boundary conditions, has recently received a good deal of attention. The new issue of this paper is the setting of a rather general mass constraint which may involve either the solution inside…
More than ever, today we are left with the abundance of molecular data outpaced by the advancements of the phylogenomic methods. Especially in the case of presence of many genes over a set of species under the phylogeny question, more…
A growing number of experimental evidence shows that it is general for a ligand binding protein to have a potential for allosteric regulation and for further evolution. In addition, such proteins generically change their conformation upon…
The problem of natural selection in dispersal-structured populations consisting of individuals characterized by different diffusion coefficients is studied. The competition between the organisms is taken into account through the assumption…
Dynamical systems driven by strong external signals are ubiquituous in nature and engineering. Here we study "echo state networks", networks of a large number of randomly connected nodes, which represent a simple model of a neural network,…
In the course of various biological processes, specific DNA-binding proteins must find a particular target sequence/protein or a damaged site on the DNA efficiently. DNA-binding proteins perform this task based on diffusion. Yet,…
A general framework of evolutionary dynamics under heterogeneous populations is presented. The framework allows continuously many types of heterogeneous agents, heterogeneity both in payoff functions and in revision protocols and the entire…
The entanglement of population dynamics, evolution, and adaptive radiation for species competing for resources is studied. For resource harvesting, we modify the model used in Ref. Phys. Rev. Lett. 118 048103 and introduce new resource…
Understanding how genes influence phenotype across species is a fundamental challenge in genetic engineering, which will facilitate advances in various fields such as crop breeding, conservation biology, and personalized medicine. However,…
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…
The theory of life history evolution provides a powerful framework to understand the evolutionary dynamics of pathogens in both epidemic and endemic situations. This framework, however, relies on the assumption that pathogen populations are…
We present a simple physical model that recapitulates several features of biological evolution, while being based only on thermally-driven attachment and detachment of elementary building blocks. Through its dynamics, this model samples a…
Protein domains are found on genomes with notable statistical distributions, which bear a high degree of similarity. Previous work has shown how these distributions can be accounted for by simple models, where the main ingredients are…
Horizontal gene transfer consists in exchanging genetic materials between microorganisms during their lives. This is a major mechanism of bacterial evolution and is believed to be of main importance in antibiotics resistance. We consider a…
Machine learning models that are developed with invariance to certain types of data transformations have demonstrated superior generalization performance in practice. However, the underlying mechanism that explains why invariance leads to…