Related papers: Length-minimizing LED Trees
We introduce tree dimension and its leveled variant in order to measure the complexity of leaf sets in binary trees. We then provide a tight upper bound on the size of such sets using leveled tree dimension. This, in turn, implies both the…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…
Comparing and computing distances between phylogenetic trees are important biological problems, especially for models where edge lengths play an important role. The geodesic distance measure between two phylogenetic trees with edge lengths…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
In the Euclidean Steiner Tree problem, we are given as input a set of points (called terminals) in the $\ell_2$-metric space and the goal is to find the minimum-cost tree connecting them. Additional points (called Steiner points) from the…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
Borrowing inspiration from Marcone and Mont\'{a}lban's one-one correspondence between the class of signed trees and the equimorphism classes of indecomposable scattered linear orders, we find a subclass of signed trees which has an…
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…
The enormous amount of data to be represented using large graphs exceeds in some cases the resources of a conventional computer. Edges in particular can take up a considerable amount of memory as compared to the number of nodes. However,…
In conservation biology, phylogenetic diversity (PD) provides a way to quantify the impact of the current rapid extinction of species on the evolutionary `Tree of Life'. This approach recognises that extinction not only removes species but…
Given two sets of points in the plane, $P$ of $n$ terminals and $S$ of $m$ Steiner points, a Steiner tree of $P$ is a tree spanning all points of $P$ and some (or none or all) points of $S$. A Steiner tree with length of longest edge…
This paper addresses the problem of finding a representation of a subtree distance, which is an extension of the tree metric. We show that a minimal representation is uniquely determined by a given subtree distance, and give a linear time…
The minimum linear arrangement problem on a network consists of finding the minimum sum of edge lengths that can be achieved when the vertices are arranged linearly. Although there are algorithms to solve this problem on trees in polynomial…
We give a dynamic programming solution to find the minimum cost of a diameter constrained Steiner tree in case of directed graphs. Then we show a simple reduction from undirected version to the directed version to realize an algorithm of…
Among other results, we prove the following theorem about Steiner minimal trees in $d$-dimensional Euclidean space: if two finite sets in $\mathbb{R}^d$ have unique and combinatorially equivalent Steiner minimal trees, then there is a…
The Gilbert-Pollak Conjecture \citep{gilbert1968steiner}, also known as the Steiner Ratio Conjecture, states that for any finite point set in the Euclidean plane, the Steiner minimum tree has length at least $\sqrt{3}/2 \approx 0.866$ times…
In this paper we consider variational problems involving 1-dimensional connected sets in the Euclidean plane, such as the classical Steiner tree problem and the irrigation (Gilbert-Steiner) problem. We relate them to optimal partition…
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…
We study periodic tessellations of the Euclidean space with unequal cells arising from the minimization of perimeter functionals. Existence results and qualitative properties of minimizers are discussed for different classes of problems,…
This paper addresses a graph optimization problem, called the Witness Tree problem, which seeks a spanning tree of a graph minimizing a certain non-linear objective function. This problem is of interest because it plays a crucial role in…