Related papers: Labeling and folding multi-labeled trees
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
In this paper we solve the ancestry-labeling scheme problem which aims at assigning the shortest possible labels (bit strings) to nodes of rooted trees, so that ancestry queries between any two nodes can be answered by inspecting their…
As part of work to connect phylogenetics with machine learning, there has been considerable recent interest in vector encodings of phylogenetic trees. We present a simple new "ordered leaf attachment" (OLA) method for uniquely encoding a…
This article presents a unified bijective scheme between planar maps and blossoming trees, where a blossoming tree is defined as a spanning tree of the map decorated with some dangling half-edges that enable to reconstruct its faces. Our…
Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…
A tree $T$ on $2^n$ vertices is called set-sequential if the elements in $V(T)\cup E(T)$ can be labeled with distinct nonzero $(n+1)$-dimensional $01$-vectors such that the vector labeling each edge is the component-wise sum modulo $2$ of…
For a given graph, the unlabeled subgraphs $G-v$ are called the cards of $G$ and the deck of $G$ is the multiset $\{G-v: v \in V(G)\}$. Wendy Myrvold [Ars Combinatoria, 1989] showed that a non-connected graph and a connected graph both on…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two…
We describe a combinatorial approach for investigating properties of rational numbers. The overall approach rests on structural bijections between rational numbers and familiar combinatorial objects, namely rooted trees. We emphasize that…
We develop a novel probabilistic approach for multi-label classification that is based on the mixtures-of-experts architecture combined with recently introduced conditional tree-structured Bayesian networks. Our approach captures different…
In biology, a phylogenetic tree is a tool to represent the evolutionary relationship between species. Unfortunately, the classical Schr\"oder tree model is not adapted to take into account the chronology between the branching nodes. In…
We introduce a notion of finite sampling consistency for phylogenetic trees and show that the set of finitely sampling consistent and exchangeable distributions on n leaf phylogenetic trees is a polytope. We use this polytope to show that…
In mathematical phylogenetics, the time-consistent galled trees provide a simple class of rooted binary network structures that can be used to represent a variety of different biological phenomena. We study the enumerative combinatorics of…
Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…
Tutte founded the theory of enumeration of planar maps in a series of papers in the 1960s. Rooted non-separable planar maps are in bijection with West-2-stack-sortable permutations, beta(1,0)-trees introduced by Cori, Jacquard and Schaeffer…
Phylogenomics commonly aims to construct evolutionary trees from genomic sequence information. One way to approach this problem is to first estimate event-labeled gene trees (i.e., rooted trees whose non-leaf vertices are labeled by…
A labeling scheme for nearest common ancestors assigns a distinct binary string, called the label, to every node of a tree, so that given the labels of two nodes (and no further information about the topology of the tree) we can compute the…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
In evolutionary biology, biologists often face the problem of constructing a phylogenetic tree on a set $X$ of species from a multiset $\Pi$ of partitions corresponding to various attributes of these species. One approach that is used to…