Related papers: Computing nearest neighbour interchange distances …
We consider the problem of reconfiguring non-crossing spanning trees on point sets. For a set $P$ of $n$ points in general position in the plane, the flip graph $F(P)$ has a vertex for each non-crossing spanning tree on $P$ and an edge…
{\em Reoptimization} is a setting in which we are given an (near) optimal solution of a problem instance and a local modification that slightly changes the instance. The main goal is that of finding an (near) optimal solution of the…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…
Nearest neighbor (kNN) methods have been gaining popularity in recent years in light of advances in hardware and efficiency of algorithms. There is a plethora of methods to choose from today, each with their own advantages and…
Despite the recent progress in genome sequencing and assembly, many of the currently available assembled genomes come in a draft form. Such draft genomes consist of a large number of genomic fragments (scaffolds), whose order and/or…
Hyperbolicity is a graph parameter which indicates how much the shortest-path distance metric of a graph deviates from a tree metric. It is used in various fields such as networking, security, and bioinformatics for the classification of…
A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. While the most traditional…
We significantly improve known time bounds for solving the minimum cut problem on undirected graphs. We use a ``semi-duality'' between minimum cuts and maximum spanning tree packings combined with our previously developed random sampling…
Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to measure the dissimilarity of the two trees.…
Chordal graphs form one of the most studied graph classes. Several graph problems that are NP-hard in general become solvable in polynomial time on chordal graphs, whereas many others remain NP-hard. For a large group of problems among the…
Crossing minimization is one of the central problems in graph drawing. Recently, there has been an increased interest in the problem of minimizing crossings between paths in drawings of graphs. This is the metro-line crossing minimization…
The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…
Recursive partitioning is the core of several statistical methods including CART, random forest, and boosted trees. Despite the popularity of tree based methods, to date, there did not exist methods for combining multiple trees into a…
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…
We compare the performance of three nearest neighbor search algorithms: the Orchard, ball tree, and VP-tree algorithms. These algorithms are commonly used for nearest-neighbor searches and are known for their efficiency in large datasets.…
Given a graph, the sparsest cut problem asks for a subset of vertices whose edge expansion (the normalized cut given by the subset) is minimized. In this paper, we study a generalization of this problem seeking for $ k $ disjoint subsets of…
Rotation distance between rooted binary trees is the minimum number of simple rotations needed to transform one tree into the other. Computing the rotation distance between a pair of rooted trees can be quickly reduced in cases where there…
Nearest-neighbor search dominates the asymptotic complexity of sampling-based motion planning algorithms and is often addressed with k-d tree data structures. While it is generally believed that the expected complexity of nearest-neighbor…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…