Related papers: Split-or-decompose: Improved FPT branching algorit…
This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which…
In phylogenetics, distances are often used to measure the incongruence between a pair of phylogenetic trees that are reconstructed by different methods or using different regions of genome. Motivated by the maximum parsimony principle in…
Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…
The reconstruction of the history of evolutionary genome-wide events among a set of related organisms is of great biological interest. A simplified model that captures only content modifying operations was introduced recently. It allows the…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop…
We revisit the Maximum Node-Disjoint Paths problem, the natural optimization version of Node-Disjoint Paths, where we are given a graph $G$, $k$ pairs of vertices $(s_i, t_i)$ and an integer $\ell$, and are asked whether there exist at…
In recent years, significant progress has been made on algorithms for learning optimal decision trees, primarily in the context of binary features. Extending these methods to continuous features remains substantially more challenging due to…
In this thesis, Minimal Partitioning (MP) algorithm, an innovative algorithm for enumerating all the spanning trees in an undirected graph is presented. While MP algorithm uses a computational tree graph to traverse all possible spanning…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
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…
Algorithms for computing or approximating optimal decompositions for decompositional parameters such as treewidth or clique-width have so far traditionally been tailored to specific width parameters. Moreover, for mim-width, no efficient…
Deciding whether a collection of unrooted trees is compatible is a fundamental problem in phylogenetics. Two different graph-theoretic characterizations of tree compatibility have recently been proposed. In one of these, tree compatibility…
For a phylogenetic tree, the phylogenetic diversity of a set A of taxa is the total weight of edges on paths to A. Finding small sets of maximal diversity is crucial for conservation planning, as it indicates where limited resources can be…
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…
Structural parameters of graphs, such as treewidth, play a central role in the study of the parameterized complexity of graph problems. Motivated by the study of parametrized algorithms on phylogenetic networks, scanwidth was introduced…
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a…
The minimum degree spanning tree (MDST) problem requires the construction of a spanning tree $T$ for graph $G=(V,E)$ with $n$ vertices, such that the maximum degree $d$ of $T$ is the smallest among all spanning trees of $G$. In this paper,…
Random Forests (RF) is a popular machine learning method for classification and regression problems. It involves a bagging application to decision tree models. One of the primary advantages of the Random Forests model is the reduction in…
Unmanned Aerial Vehicles (UAVs) are increasingly used for reforestation and forest monitoring, including seed dispersal in hard-to-reach terrains. However, a detailed understanding of the forest floor remains a challenge due to high natural…