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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…
This work presents novel algorithms for learning Bayesian network structures with bounded treewidth. Both exact and approximate methods are developed. The exact method combines mixed-integer linear programming formulations for structure…
One strategy for reconstruction of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the…
Inspired by the seminal works of Khuller et al. (STOC 1994) and Chan (SoCG 2003) we study the bottleneck version of the Euclidean bounded-degree spanning tree problem. A bottleneck spanning tree is a spanning tree whose largest edge-length…
Supertree methods are tree reconstruction techniques that combine several smaller gene trees (possibly on different sets of species) to build a larger species tree. The question of interest is whether the reconstructed supertree converges…
For a tree with the given sequence of vertex degrees the spectral radius of its terminal distance matrix is shown to be bounded from below by the the average row sum of the terminal distance matrix of the, so called, BFS-tree (also known as…
We study two problems that seek a subtree $T$ of a graph $G=(V,E)$ such that $T$ satisfies a certain property and has minimal maximum degree. - In the Min-Degree Group Steiner Tree problem we are given a collection ${\cal S}$ of groups…
Minimum $k$-Section denotes the NP-hard problem to partition the vertex set of a graph into $k$ sets of sizes as equal as possible while minimizing the cut width, which is the number of edges between these sets. When $k$ is an input…
Tree size ($\rm{TS}$) is an interesting measure of complexity for multiqubit states: not only is it in principle computable, but one can obtain lower bounds for it. In this way, it has been possible to identify families of states whose…
This paper addresses the following questions for a given tree $T$ and integer $d\geq2$: (1) What is the minimum number of degree-$d$ subtrees that partition $E(T)$? (2) What is the minimum number of degree-$d$ subtrees that cover $E(T)$? We…
Given a set of points, we define a minimum Steiner point tree to be a tree interconnecting these points and possibly some additional points such that the length of every edge is at most 1 and the number of additional points is minimized. We…
Phylogenetic networks are directed acyclic graphs that depict the genomic evolution of related taxa. Reticulation nodes in such networks (nodes with more than one parent) represent reticulate evolutionary events, such as recombination,…
Treewidth is an important structural graph parameter that quantifies how closely a graph resembles a tree-like structure. It has applications in many algorithmic and combinatorial problems. In this paper, we study the treewidth of outer…
In the \emph{$k$-Diameter-Optimally Augmenting Tree Problem} we are given a tree $T$ of $n$ vertices as input. The tree is embedded in an unknown \emph{metric} space and we have unlimited access to an oracle that, given two distinct…
Estimating phylogenetic trees, which depict the relationships between different species, from aligned sequence data (such as DNA, RNA, or proteins) is one of the main aims of evolutionary biology. However, tree reconstruction criteria like…
Optimal transport provides a metric which quantifies the dissimilarity between probability measures. For measures supported in discrete metric spaces, finding the optimal transport distance has cubic time complexity in the size of the…
In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide…
Quartet Reconstruction, the task of recovering a phylogenetic tree from smaller trees on four species called \textit{quartets}, is a well-studied problem in theoretical computer science with far-reaching connections to statistics, graph…
The notion of $\mathcal{H}$-treewidth, where $\mathcal{H}$ is a hereditary graph class, was recently introduced as a generalization of the treewidth of an undirected graph. Roughly speaking, a graph of $\mathcal{H}$-treewidth at most $k$…
Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we…