Related papers: Length-minimizing LED Trees
In phylogenetics, a key problem is to construct evolutionary trees from collections of characters where, for a set X of species, a character is simply a function from X onto a set of states. In this context, a key concept is convexity,…
We study the problem of constructing phylogenetic trees for a given set of species. The problem is formulated as that of finding a minimum Steiner tree on $n$ points over the Boolean hypercube of dimension $d$. It is known that an optimal…
Metric embedding has become a common technique in the design of algorithms. Its applicability is often dependent on how high the embedding's distortion is. For example, embedding finite metric space into trees may require linear distortion…
Given a graph G = (V,E) with a root r in V, positive capacities {c(e)|e in E}, and non-negative lengths {l(e)|e in E}, the minimum-length (rooted) edge capacitated Steiner tree problem is to find a tree in G of minimum total length, rooted…
In this paper we present a mathematical framework on linking of embeddings of compact topological spaces into Euclidean spaces and separability of linked embeddings under a specific class of dimension reduction maps. As applications of the…
This paper is concerned with model order reduction of parametric Partial Differential Equations (PDEs) using tree-based library approximations. Classical approaches are formulated for PDEs on Hilbert spaces and involve one single linear…
In this paper we provide an approximation \`a la Ambrosio-Tortorelli of some classical minimization problems involving the length of an unknown one-dimensional set, with an additional connectedness constraint, in dimension two. We introduce…
This paper studies Minimum Spanning Trees under incomplete information for its vertices. We assume that no information is available on the precise placement of vertices so that it is only known that vertices belong to some neighborhoods…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
In this study, we investigate the application of Semidefinite Programming (SDP) to phylogenetics. SDP is a powerful optimization framework that seeks to optimize a linear objective function over the cone of positive semidefinite matrices.…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
Trees with labelled leaves and with all other vertices of degree three play an important role in systematic biology and other areas of classification. A classical combinatorial result ensures that such trees can be uniquely reconstructed…
A polyhedral convex set optimization problem is given by a set-valued objective mapping from the $n$-dimensional to the $q$-dimensional Euclidean space whose graph is a convex polyhedron. This problem can be seen as the most elementary…
The class of self-nested trees presents remarkable compression properties because of the systematic repetition of subtrees in their structure. In this paper, we provide a better combinatorial characterization of this specific family of…
Minimal spanning trees on infinite vertex sets are investigated. A criterion for minimality of a spanning tree having a finite length is obtained, which generalizes the corresponding classical result for finite sets. It is given an analytic…
Large tree structures are ubiquitous and real-world relational datasets often have information associated with nodes (e.g., labels or other attributes) and edges (e.g., weights or distances) that need to be communicated to the viewers. Yet,…
The Minimum Linear Arrangement problem (MLA) consists of finding a mapping $\pi$ from vertices of a graph to distinct integers that minimizes $\sum_{\{u,v\}\in E}|\pi(u) - \pi(v)|$. In that setting, vertices are often assumed to lie on a…
Cubicity of a graph $G$ is the smallest dimension $d$, for which $G$ is a unit disc graph in ${\mathbb{R}}^d$, under the $l^\infty$ metric, i.e. $G$ can be represented as an intersection graph of $d$-dimensional (axis-parallel) unit…
We define a search problem on trees that closely captures the backtracking behavior of all current practical graph isomorphism algorithms. Given two trees with colored leaves, the goal is to find two leaves of matching color, one in each of…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…