Related papers: A kernel for the maximum agreement forest problem …
We introduce a graph partitioning problem motivated by computational topology and propose two algorithms that produce approximate solutions. Specifically, given a weighted, undirected graph $G$ and a positive integer $k$, we desire to find…
Given a rooted tree and a ranking of its leaves, what is the minimum number of inversions of the leaves that can be attained by ordering the tree? This variation of the problem of counting inversions in arrays originated in mathematical…
A complete description is given of how minimal trees on atoms of the algebra of subsets $\mathfrak{A}_k$ generated by minimal spanning $k$-component forests of a weighted digraph $V$ determine the form of these forests and how forests grow…
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 study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of $m$ binary trees with…
We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem…
We prove that the size of the largest common subtree between two uniform, independent, leaf-labelled random binary trees of size $n$ is typically less than $n^{1/2-\varepsilon}$ for some $\varepsilon>0$. Our proof relies on the coupling…
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…
For a set of graphs $\mathcal{F}$, the extremal number $ex(n;\mathcal{F})$ is the maximum number of edges in a graph of order $n$ not containing any subgraph isomorphic to some graph in $\mathcal{F}$. If $\mathcal{F}$ contains a graph on…
In this paper, we focus on the prediction phase of a random forest and study the problem of representing a bag of decision trees using a smaller bag of decision trees, where we only consider binary decision problems on the binary domain and…
Frequent tree mining asks us to enumerate tree patterns that occur frequently in a database of rooted trees. This problem is motivated by tree-structured data in bioinformatics, such as glycans and pseudoknot-free RNA secondary structures.…
Tree search algorithms, such as branch-and-bound, are the most widely used tools for solving combinatorial and nonconvex problems. For example, they are the foremost method for solving (mixed) integer programs and constraint satisfaction…
It is known that any two trees on the same $n$ leaves can be displayed by a network with $n-2$ reticulations, and there are two trees that cannot be displayed by a network with fewer reticulations. But how many reticulations are needed to…
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…
We consider the problem of exploring an unknown tree with a team of $k$ initially colocated mobile agents. Each agent has limited energy and cannot, as a result, traverse more than $B$ edges. The goal is to maximize the number of nodes…
In the Multiagent Path Finding problem (MAPF for short), we focus on efficiently finding non-colliding paths for a set of $k$ agents on a given graph $G$, where each agent seeks a path from its source vertex to a target. An important…
Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…
We consider \textsc{Cliques or Trees Vertex Deletion}, which is a hybrid of two fundamental parameterized problems: \textsc{Cluster Vertex Deletion} and \textsc{Feedback Vertex Set}. In this problem, we are given an undirected graph $G$ and…
A new 2-parameter family of central structures in trees, called central forests, is introduced. Minieka's $m$-center problem and McMorris's and Reid's central-$k$-tree can be seen as special cases of central forests in trees. A central…