相关论文: All that Glisters is not Galled

In recent decades, phylogenetic networks have become a standard tool in modeling evolutionary processes. Nevertheless, basic combinatorial questions about them are still largely open. For instance, even the asymptotic counting problem for…

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In a recent series of papers devoted to the…

In networks that grow by isotropic redirection (IR), a new node selects an initial target node uniformly at random and attaches to a randomly chosen neighbor of the target. The emerging networks exhibit leaf proliferation, in which the…

In the gelation theory it has been implicitly assumed that (I) a cyclic bond is a finite bond that returns to itself; (II) cyclic bonds distribute at random in network structures. In this paper these two assumptions are reexamined from a…

The derivation trees of a tree adjoining grammar provide a first insight into the sentence semantics, and are thus prime targets for generation systems. We define a formalism, feature-based regular tree grammars, and a translation from…

Phylogenetic trees and networks are graphs used to model evolutionary relationships, with trees representing strictly branching histories and networks allowing for events in which lineages merge, called reticulation events. While the…

We introduce a new class of networks that grow by enhanced redirection. Nodes are introduced sequentially, and each either attaches to a randomly chosen target node with probability 1-r or to the ancestor of the target with probability r,…

We investigate the new, Turing-complete class of layered systems, whose lefthand sides of rules can only be overlapped at a multiset of disjoint or equal positions. Layered systems define a natural notion of rank for terms: the maximal…

Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…

A normal network is uniquely determined by the set of phylogenetic trees that it displays. Given a set $\mathcal{P}$ of rooted binary phylogenetic trees, this paper presents a polynomial-time algorithm that reconstructs the unique binary…

Semi-directed phylogenetic networks have recently emerged as a class of phylogenetic networks sitting between rooted (directed) and unrooted (undirected) phylogenetic networks as they contain both directed as well as undirected edges. While…

An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…

Tree sets are posets with additional structure that generalize tree-like objects in graphs, matroids, or other combinatorial structures. They are a special class of abstract separation systems. We study infinite tree sets and how they…

Garside groups are a natural lattice-theoretic generalisation of the braid groups and spherical type Artin--Tits groups. Here we show that the class of Garside groups is closed under some free products with cyclic amalgamated subgroups. We…

The modular decomposition of a graph $G$ is a natural construction to capture key features of $G$ in terms of a labeled tree $(T,t)$ whose vertices are labeled as "series" ($1$), "parallel" ($0$) or "prime". However, full information of $G$…

The modular decomposition of a graph $G$ is a natural construction to capture key features of $G$ in terms of a labeled tree $(T,t)$ whose vertices are labeled as "series" ($1$), "parallel" ($0$) or "prime". However, full information of $G$…

Percolation theory can be used to describe the structural properties of complex networks using the generating function formulation. This mapping assumes that the network is locally tree-like and does not contain short-range loops between…

We minimize a linear combination of the Willmore and the length functional among networks in $\mathbb{R}^d$ belonging to a given class determined by the number of curves, the order of the junctions and the angles between curves at the…

Many complex networks in nature have directed links, a property that affects the network's navigability and large-scale topology. Here we study the percolation properties of such directed scale-free networks with correlated in- and…

Phylogenetic networks generalize phylogenetic trees by representing reticulate evolution. Tree-based networks and their support trees have been extensively studied, but not all networks are tree-based. To measure how far such networks are…