Related papers: Vector encoding of phylogenetic trees by ordered l…
This paper contains a classification of countable lower 1-transitive linear orders. The notion of lower 1-transitivity generalises that of 1-transitivity for linear orders, and is essential for the structure theory of 1-transitive trees.…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
Reconstructing the evolutionary past of a family of genes is an important aspect of many genomic studies. To help with this, simple operations on a set of sequences called orthology relations may be employed. In addition to being…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods 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 this paper, we present and study a new…
Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…
Given two messages - as linear sequences of letters, it is immediate to determine whether one can be transformed into the other by simple substitution cipher of the letters. On the other hand, if the letters are carried as labels on nodes…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
Understanding the learning process and the embedded computation in transformers is becoming a central goal for the development of interpretable AI. In the present study, we introduce a hierarchical filtering procedure for data models of…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
Every encoding has priori information if the encoding represents any semantic information of the unverse or object. Encoding means mapping from the unverse to the string or strings of digits. The semantic here is used in the model-theoretic…
Embeddings of graphs into distributions of trees that preserve distances in expectation are a cornerstone of many optimization algorithms. Unfortunately, online or dynamic algorithms which use these embeddings seem inherently randomized and…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
An ordered labeled tree is a tree in which the nodes are labeled and the left-to-right order among siblings is relevant. The edit distance between two ordered labeled trees is the minimum cost of changing one tree into the other through a…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
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 this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
The study describes a class of integer labelings of the Fibonacci tree, the tree of descent introduced by Fibonacci. In these labelings, Fibonacci sequences appear along ascending branches of the tree, and it is shown that the labels at any…