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We present approximation algorithms for the following NP-hard optimization problems related to bottleneck spanning trees in metric spaces. 1. The disjoint bottleneck spanning tree problem: Given $n$ pairs of points in a metric space, find…
Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…
The generation of trees with a specified tree edit distance has significant applications across various fields, including computational biology, structured data analysis, and image processing. Recently, generative networks have been…
A fringe subtree of a rooted tree is a subtree consisting of one of the nodes and all its descendants. In this paper, we are specifically interested in the number of non-isomorphic trees that appear in the collection of all fringe subtrees…
The Treewidth-2 Vertex Deletion problem asks whether a set of at most $t$ vertices can be removed from a graph, such that the resulting graph has treewidth at most two. A graph has treewidth at most two if and only if it does not contain a…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
The path-difference metric is one of the oldest distances for the comparison of fully resolved phylogenetic trees, but its statistical properties are still quite unknown. In this paper we compute the mean value of the square of the…
Graph-structured data arise ubiquitously in many application domains. A fundamental problem is to quantify their similarities. Graph kernels are often used for this purpose, which decompose graphs into substructures and compare these…
We propose a novel architecture for Graph Neural Networks that is inspired by the idea behind Tree Kernels of measuring similarity between trees by taking into account their common substructures, named fragments. By imposing a series of…
Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized. However, from a biological point of view…
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…
The early development of a zygote can be mathematically described by a developmental tree. To compare developmental trees of different species, we need to define distances on trees. If children cells after a division are not…
We consider the problem of \emph{pruning} a classification tree, that is, selecting a suitable subtree that balances bias and variance, in common situations with inhomogeneous training data. Namely, assuming access to mostly data from a…
We study distorted metrics on binary trees in the context of phylogenetic reconstruction. Given a binary tree $T$ on $n$ leaves with a path metric $d$, consider the pairwise distances $\{d(u,v)\}$ between leaves. It is well known that these…
When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic of a larger collection of sequences. For example, one may…
The Subtree Isomorphism problem asks whether a given tree is contained in another given tree. The problem is of fundamental importance and has been studied since the 1960s. For some variants, e.g., ordered trees, near-linear time algorithms…
Rooted phylogenetic networks are often used to represent conflicting phylogenetic signals. Given a set of clusters, a network is said to represent these clusters in the "softwired" sense if, for each cluster in the input set, at least one…
Let $G$ be an undirected graph. We say that $G$ contains a ladder of length $k$ if the $2 \times (k+1)$ grid graph is an induced subgraph of $G$ that is only connected to the rest of $G$ via its four cornerpoints. We prove that if all the…