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In comparison to phylogenetic trees, phylogenetic networks are more suitable to represent complex evolutionary histories of species whose past includes reticulation such as hybridisation or lateral gene transfer. However, the reconstruction…
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…
Large computer networks are an essential part of modern technology, and quite often information needs to be broadcast to all the computers in the network. If all computers work perfectly all the time, this is simple. Suppose, however, that…
The Spanning Tree Congestion (STC) problem is the following NP-hard problem: given a graph $G$, construct a spanning tree $T$ of $G$ minimizing its maximum edge congestion where the congestion of an edge $e\in T$ is the number of edges $uv$…
A phylogenetic network is a graph-theoretical tool that is used by biologists to represent the evolutionary history of a collection of species. One potential way of constructing such networks is via a distance-based approach, where one is…
In this paper, we propose new learning algorithms for approximating high-dimensional functions using tree tensor networks in a least-squares setting. Given a dimension tree or architecture of the tensor network, we provide an algorithm that…
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…
In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all…
There exist several methods dealing with the reconstruction of rooted phylogenetic networks explaining different evolutionary histories given by rooted binary phylogenetic trees. In practice, however, due to insufficient information of the…
We consider a variant of treewidth that we call clique-partitioned treewidth in which each bag is partitioned into cliques. This is motivated by the recent development of FPT-algorithms based on similar parameters for various problems. With…
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…
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…
The perfect phylogeny is one of the most used models in different areas of computational biology. In this paper we consider the problem of the Persistent Perfect Phylogeny (referred as P-PP) recently introduced to extend the perfect…
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.…
We derive fundamental lower bounds on the connectivity and the memory requirements of deep neural networks guaranteeing uniform approximation rates for arbitrary function classes in $L^2(\mathbb R^d)$. In other words, we establish a…
In the Steiner Tree Augmentation Problem (STAP), we are given a graph $G = (V,E)$, a set of terminals $R \subseteq V$, and a Steiner tree $T$ spanning $R$. The edges $L := E \setminus E(T)$ are called links and have non-negative costs. The…
The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard phylogenetic tree model by also…
Characterization of joint probability distribution for large networks of random variables remains a challenging task in data science. Probabilistic graph approximation with simple topologies has practically been resorted to; typically 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…
Reliability is one of the important measures of how well the system meets its design objective, and mathematically is the probability that a system will perform satisfactorily for at least a given period of time. When the system is…