Related papers: Vector encoding of phylogenetic trees by ordered l…
Recently, a new vector encoding, Ordered Leaf Attachment (OLA), was introduced that represents $n$-leaf phylogenetic trees as $n-1$ length integer vectors by recording the placement location of each leaf. Both encoding and decoding of trees…
Good representations for phylogenetic trees and networks are important for optimizing storage efficiency and implementation of scalable methods for the inference and analysis of evolutionary trees for genes, genomes and species. We…
Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called \textsc{Tree Containment}, arises when validating networks constructed by phylogenetic…
The degree distribution of an ordered tree $T$ with $n$ nodes is $\vec{n} = (n_0,\ldots,n_{n-1})$, where $n_i$ is the number of nodes in $T$ with $i$ children. Let $\mathcal{N}(\vec{n})$ be the number of trees with degree distribution…
Visual localization algorithms have achieved significant improvements in performance thanks to recent advances in camera technology and vision-based techniques. However, there remains one critical caveat: all current approaches that are…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
We study the enumeration of spinal tree-child phylogenetic networks, a rigid family of tree-child networks in which all internal vertices lie on a single root--to--leaf path. We provide two complementary combinatorial frameworks. First, we…
Billey et al. [arXiv:1507.04976] have recently discovered a surprisingly simple formula for the number $a_n(\sigma)$ of leaf-labelled rooted non-embedded binary trees (also known as phylogenetic trees) with $n\geq 1$ leaves, fixed (for the…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art…
LRM-Trees are an elegant way to partition a sequence of values into sorted consecutive blocks, and to express the relative position of the first element of each block within a previous block. They were used to encode ordinal trees and to…
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…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
In 1989 Erd\H{o}s and Sz\'ekely showed that there is a bijection between (i) the set of rooted trees with $n+1$ vertices whose leaves are bijectively labeled with the elements of $[\ell]=\{1,2,\dots,\ell\}$ for some $\ell \leq n$, and (ii)…
This note presents an encoding and a decoding algorithms for a forest of (labelled) rooted uniform hypertrees and hypercycles in linear time, by using as few as $n - 2$ integers in the range $[1,n]$. It is a simple extension of the…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the…
In the present work we propose an unsupervised ensemble method consisting of oblique trees that can address the task of auto-encoding, namely Oblique Forest AutoEncoders (briefly OF-AE). Our method is a natural extension of the eForest…
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…