相关论文: Path integral formulation and Feynman rules for ph…
A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in…
For taxonomic levels higher than species, the abundance distributions of number of subtaxa per taxon tend to approximate power laws, but often show strong deviationns from such a law. Previously, these deviations were attributed to…
We introduce a filtration-based framework for studying when and why adding taxa improves phylodynamic inference, by constructing a natural ordering of observed tips and applying sequential Bayesian analysis to the resulting filtration. We…
We are interested in the study of models describing the evolution of a polymorphic population with mutation and selection in the specific scales of the biological framework of adaptive dynamics. The population size is assumed to be large…
Phylogeny is the field of modelling the temporal discrete dynamics of speciation. Complex models can nowadays be studied using the Approximate Bayesian Computation approach which avoids likelihood calculations. The field's progression is…
We investigate a simple quantitative genetics model subjet to a gradual environmental change from the viewpoint of the phylogenies of the living individuals. We aim to understand better how the past traits of their ancestors are shaped by…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
Rate variation among the sites of a molecular sequence is commonly found in applications of phylogenetic inference. Several approaches exist to account for this feature but they do not usually enable the investigator to pinpoint the sites…
One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of…
Probabilistic solutions of the so called Schr\"{o}dinger boundary data problem provide for a unique Markovian interpolation between any two strictly positive probability densities designed to form the input-output statistics data for the…
The parameters of many classes of birth-death processes cannot be inferred uniquely from phylogenetic trees: infinitely many parameter combinations yield the same distribution of phylogenetic trees. Here, we show that parameter…
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…
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 study the evolution of sexual and asexual populations in general fitness landscapes. We find deep relations between the mathematics of biological evolution and the formalism of quantum mechanics. We give the general structure of the…
We consider a class of piecewise-deterministic Markov processes where the state evolves according to a linear dynamical system. This continuous time evolution is interspersed by discrete events that occur at random times and change (reset)…
Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…
Stem cells, through their ability to produce daughter stem cells and differentiate into specialized cells, are essential in the growth, maintenance, and repair of biological tissues. Understanding the dynamics of cell populations in the…
Phylogenetic invariants are equations that vanish on algebraic varieties associated with Markov processes that model molecular substitutions on phylogenetic trees. For practical applications, it is essential to understand these equations…
We present a method of dimensional reduction for the general Markov model of sequence evolution on a phylogenetic tree. We show that taking certain linear combinations of the associated random variables (site pattern counts) reduces the…
As an alternative but unified and more fundamental description for quantum physics, Feynman path integrals generalize the classical action principle to a probabilistic perspective, under which the physical observables' estimation translates…