相关论文: Compactifications of phylogenetic systems and spec…

We study a new invariant of circular planar electrical networks, well known to phylogeneticists: the circular split system. We use our invariant to answer some open questions about levels of complexity of networks and their related…

A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree…

We construct a compactification of the space of circular planar electrical networks studied by Curtis-Ingerman-Morrow and De Verdiere-Gitler-Vertigan, using cactus networks. We embed this compactification as a linear slice of the totally…

We introduce and investigate the space of \emph{equidistant} $X$-\emph{cactuses}. These are rooted, arc weighted, phylogenetic networks with leaf set $X$, where $X$ is a finite set of species, and all leaves have the same distance from the…

Phylogenetic networks are a generalization of evolutionary or phylogenetic trees that are commonly used to represent the evolution of species which cross with one another. A special type of phylogenetic network is an {\em $X$-cactus}, which…

In this paper we relate a well-known in symplectic geometry compactification of the space of symmetric bilinear forms considered as a chart of the Lagrangian Grassmannian to the specific compactifications of the space of electrical networks…

Cactus networks were introduced by Lam as a generalization of planar electrical networks. He defined a map from these networks to the Grassmannian Gr($n+1,2n$) and showed that the image of this map, $\mathcal X_n$ lies inside the totally…

The first part of this paper deals with electrical networks and symplectic reductions. We consider two operations on electrical networks (the "trace map" and the "gluing map") and show that they correspond to symplectic reductions. We also…

Ranked tree-child networks are a recently introduced class of rooted phylogenetic networks in which the evolutionary events represented by the network are ordered so as to respect the flow of time. This class includes the well-studied…

Phylogenetic networks are an important way to represent evolutionary histories that involve reticulations such as hybridization or horizontal gene transfer, yet fundamental questions such as how many networks there are that satisfy certain…

In this paper, we build on recent results by Chauve et al. (2014) and Bahrani and Lumbroso (2017), which combined the split-decomposition, as exposed by Gioan and Paul, with analytic combinatorics, to produce new enumerative results on…

Phylogenetic networks are generalizations of trees that allow for the modeling of non-tree like evolutionary processes. Split networks give a useful way to construct networks with intuitive distance structures induced from the associated…

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…

Phylogenetics begins with reconstructing biological family trees from genetic data. Since Nature is not limited to tree-like histories, we use networks to organize our data, and have discovered new polytopes, metric spaces, and simplicial…

A classic problem in data analysis is studying the systems of subsets defined by either a similarity or a dissimilarity function on $X$ which is either observed directly or derived from a data set. For an electrical network there are two…

We define a graph network to be a coupled cell network where there are only one type of cell and one type of symmetric coupling between the cells. For a difference-coupled vector field on a graph network system, all the cells have the same…

The space $ \ft_n = \C^n/\C $ of $n$ points on the line modulo translation has a natural compactification $ \overline \ft_n $ as a matroid Schubert variety. In this space, pairwise distances between points can be infinite; it is natural to…

A cactus representation of a graph, introduced by Dinitz et al. in 1976, is an edge sparsifier of $O(n)$ size that exactly captures all global minimum cuts of the graph. It is a central combinatorial object that has been a key ingredient in…

The object of this paper is to transform a set of local chain complexes to a single global complex using an equivalence relation of congruence of cells, solving topologically the numerical inaccuracies of floating-point arithmetics. While…

The $r$-th cactus variety of a subvariety $X$ in a projective space generalizes the $r$-th secant variety of $X$ and it is defined using linear spans of finite subschemes of $X$ of degree $r$. One of its original purposes was to study the…