相关论文: Brownian motion tree models are toric

Contraction properties of transport maps between probability measures play an important role in the theory of functional inequalities. The actual construction of such maps, however, is a non-trivial task and, so far, relies mostly on the…

We introduce a biologically natural, mathematically tractable model of random phylogenetic network to describe evolution in the presence of hybridization. One of the features of this model is that the hybridization rate of the lineages…

Using exhaustion properties of invariant plurisubharmonic functions along with basic combinatorial information on toric varieties convergence results for sequences of distribution functions \phi_n=|s_N| / |s_N|_{L^2} for sections s_N\in…

This paper presents a new multi-query motion planning algorithm for linear Gaussian systems with the goal of reaching a Euclidean ball with high probability. We develop a new formulation for ball-shaped ambiguity sets of Gaussian…

The ratio of two densities provides a direct characterization of their differences. We consider the two-sample comparison problem by estimating this ratio given i.i.d. observations from two distributions. To this end, we propose additive…

We give a combinatorial description of the toric ideal of invariants of the Cavender-Farris-Neyman model with a molecular clock (CFN-MC) on a rooted binary phylogenetic tree and prove results about the polytope associated to this toric…

Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…

The Brownian tree, also known as the continuum random tree, is a canonical random compact, geodesic $\mathbf R$-tree that arises as the universal scaling limit for numerous models of discrete random trees. A key quasisymmetric invariant of…

For any affine variety equipped with coordinates, there is a surjective, continuous map from its Berkovich space to its tropicalisation. Exploiting torus actions, we develop techniques for finding an explicit, continuous section of this…

Tensor models are natural generalizations of matrix models. The interactions and observables in the case of unitary invariant models are generalizations of matrix traces. Some notable interactions in the literature include the melonic ones,…

We investigate the toric geometry of two families of generalised determinantal varieties arising from permutations: Matrix Schubert varieties ($\overline{X_w}$) and Kazhdan-Lusztig varieties ($\mathcal{N}_{v,w}$). Matrix Schubert varieties…

Efforts to reconstruct phylogenetic trees and understand evolutionary processes depend fundamentally on stochastic models of speciation and mutation. The simplest continuous-time model for speciation in phylogenetic trees is the Yule…

A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting.…

Gaussian graphical models are semi-algebraic subsets of the cone of positive definite covariance matrices. They are widely used throughout natural sciences, computational biology and many other fields. Computing the vanishing ideal of the…

We revisit the representation theory in type $A$used previously to establish that the dissimilarity vectors of phylogenetic trees are points on the tropical Grassmannian variety. We use a different version of this construction to show that…

This is a survey article on trees, with a modest number of proofs to give a flavor of the way these topologies can be efficiently handled. Trees are defined in set-theorist fashion as partially ordered sets in which the elements below each…

The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…

Ultrametric matrices have a rich structure that is not apparent from their definition. Notably, the subclass of strictly ultrametric matrices are covariance matrices of certain weighted rooted binary trees. In applications, these matrices…

We determine the long time behavior and the exact order of the tail probability for the maximal displacement of a branching Brownian motion in Euclidean space in terms of the principal eigenvalue of the associated Schr\"odinger type…

Phylogenetic trees constitute an interesting class of objects for stochastic processes due to the non-standard nature of the space they inhabit. In particular, many statistical applications require the construction of Markov processes on…