Related papers: Nested tree space: a geometric framework for co-ph…
We consider the compact space of pairs of nested partitions of $\mathbb N$, where by analogy with models used in molecular evolution, we call "gene partition" the finer partition and "species partition" the coarser one. We introduce the…
Using the theory of Properly Embedded Graphs developed in an earlier work we define an involutory duality on the set labeled non-crossing trees that lifts the obvious duality in the set of unlabeled non-crossing trees. The set of…
THIS IS A CORRECTED VERSION INCLUDING AN APPENDED CORRIGENDUM. Best match graphs arise naturally as the first processing intermediate in algorithms for orthology detection. Let $T$ be a phylogenetic (gene) tree $T$ and $\sigma$ an…
Rooted phylogenetic networks are rooted acyclic digraphs. They are used to model complex evolution where hybridization, recombination and other reticulation events play important roles. A rigorous definition of network compression is…
We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…
We consider fixed-point equations for probability distributions on isometry classes of measured metric spaces. The construction is required to be recursive and tree-like, but we allow loops for the geodesics between points in the support of…
The edge-product space of phylogenetic trees is a regular CW complex whose maximal closed cells correspond to trivalent trees with leaves labeled by a finite set $X$. The face poset of this cell decomposition is isomorphic to the Tuffley…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
Any nested Archimedean copula is defined starting from a rooted phylogenetic tree, for which a new class of nonparametric estimators is presented. An estimator from this new class relies on a two-step procedure where first a binary tree is…
Since Darwin, species trees have been used as a simplified description of the relationships which summarize the complicated network $N$ of reality. Recent evidence of hybridization and lateral gene transfer, however, suggest that there are…
The compression of geometric structures is a relatively new field of data compression. Since about 1995, several articles have dealt with the coding of meshes, using for most of them the following approach: the vertices of the mesh are…
We present a general class of geometric network growth mechanisms by homogeneous attachment in which the links created at a given time $t$ are distributed homogeneously between a new node and the exising nodes selected uniformly. This is…
Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…
A closed-form formula is derived for the number of occurrences of matches of a multiset of patterns among all ordered (plane-planted) trees with a given number of edges. A pattern looks like a tree, with internal nodes and leaves, but also…
Nested parentheses are forms in an algebra which define orders of evaluations. A class of well-formed sets of associated opening and closing parentheses is well studied in conjunction with Dyck paths and Catalan numbers. Nested parentheses…
We define and study a model of winding for non-colliding particles in finite trees. We prove that the asymptotic behavior of this statistic satisfies a central limiting theorem, analogous to similar results on winding of bounded particles…
The Learnable Tree Filter presents a remarkable approach to model structure-preserving relations for semantic segmentation. Nevertheless, the intrinsic geometric constraint forces it to focus on the regions with close spatial distance,…
Phylogenetic networks generalize phylogenetic trees in order to model reticulation events. Although the comparison of phylogenetic trees is well studied, and there are multiple ways to do it in an efficient way, the situation is much…
The concept of reiterated $\Sigma$-convergence (and more generally of multiscale $\Sigma$-convergence) is extended to framework of Orlicz-Sobolev spaces, in order to deals with homogenization of multiscales problems in general deterministic…
The nature inspired algorithms are becoming popular due to their simplicity and wider applicability. In the recent past several such algorithms have been developed. They are mainly bio-inspired, swarm based, physics based and…