相关论文: Brownian motion tree models are toric
Stochastic transport due to a velocity field modeled by the superposition of small-scale divergence free vector fields activated by Fractional Gaussian Noises (FGN) is numerically investigated. We present two non-trivial contributions: the…
We explicitly describe the tropicalization of a cluster variety of finite type C, realizing it as the space of axially symmetric phylogenetic trees. We also find all occurring sign patterns of coordinates, for both the cluster variety and…
Fickian yet non-Gaussian diffusion is a ubiquitous phenomenon observed in various biological and soft matter systems. This anomalous dynamics is typically attributed to heterogeneous environments inducing spatiotemporal variations in the…
Probability estimation of tree topologies is one of the fundamental tasks in phylogenetic inference. The recently proposed subsplit Bayesian networks (SBNs) provide a powerful probabilistic graphical model for tree topology probability…
The Yule model and the coalescent model are two neutral stochastic models for generating trees in phylogenetics and population genetics, respectively. Although these models are quite different, they lead to identical distributions…
The probability that two randomly selected phylogenetic trees of the same size are isomorphic is found to be asymptotic to a decreasing exponential modulated by a polynomial factor. The number of symmetrical nodes in a random phylogenetic…
In phylogenomics, species-tree methods must contend with two major sources of noise; stochastic gene-tree variation under the multispecies coalescent model (MSC) and finite-sequence substitutional noise. Fast agglomerative methods such as…
The Robinson-Foulds (RF) distance is by far the most widely used measure of dissimilarity between trees. Although the distribution of these distances has been investigated for twenty years, an algorithm that is explicitly polynomial time…
We study the problem of parameter estimation for the homogenization limit of multiscale systems involving fractional dynamics. In the case of stochastic multiscale systems driven by Brownian motion, it has been shown that in order for the…
In this work, we prove a version of H\"{o}rmander's theorem for a stochastic evolution equation driven by a trace-class fractional Brownian motion with Hurst exponent $\frac{1}{2} < H < 1$ and an analytic semigroup on a given separable…
We give a geometric description of the positivity of the Frobenius-trace kernel on a $\mathbb{Q}$-factorial projective toric variety. To do so, we define its Frobenius support as well as the notions of $F$-effectiveness for divisors and…
We study the relation between the integer tropical points of a cluster variety (satisfying the full Fock-Goncharov conjecture) and the totally positive part of the tropicalization of an ideal presenting the corresponding cluster algebra.…
We study the problem of optimal transport in tropical geometry and define the Wasserstein-$p$ distances in the continuous metric measure space setting of the tropical projective torus. We specify the tropical metric -- a combinatorial…
The Brown-Resnick max-stable process has proven to be well-suited for modeling extremes of complex environmental processes, but in many applications its likelihood function is intractable and inference must be based on a composite…
Many statistical models are algebraic in that they are defined by polynomial constraints or by parameterizations that are polynomial or rational maps. This opens the door for tools from computational algebraic geometry. These tools can be…
We analyse a maximum-likelihood approach for combining phylogenetic trees into a larger `supertree'. This is based on a simple exponential model of phylogenetic error, which ensures that ML supertrees have a simple combinatorial description…
The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…
This paper announces results on the behavior of some important algebraic and topological invariants --- Euler characteristic, arithmetic genus, and their intersection homology analogues; the signature, etc. --- and their associated…
We analyze the problem of maximum likelihood estimation for Gaussian distributions that are multivariate totally positive of order two (MTP2). By exploiting connections to phylogenetics and single-linkage clustering, we give a simple proof…
Dynamic programming approaches have long been applied to fit models of univariate and multivariate trait evolution on phylogenetic trees for discrete and continuous traits, and more recently adapted to phylogenetic networks with…