Related papers: Lower bounding edit distances between permutations
Given a permutation pi, the application of prefix reversal f^(i) to pi reverses the order of the first i elements of pi. The problem of Sorting By Prefix Reversals (also known as pancake flipping), made famous by Gates and Papadimitriou…
In this paper we study several variations of the \emph{pancake flipping problem}, which is also well known as the problem of \emph{sorting by prefix reversals}. We consider the variations in the sorting process by adding with prefix…
We initiate the study of sorting permutations using prefix block-interchanges, which exchange any prefix of a permutation with another non-intersecting interval. The goal is to transform a given permutation into the identity permutation…
Considering a pair of genomes, the goal of rearrangement distance problems is to estimate how distant these genomes are from each other based on genome rearrangements. Seminal works in genome rearrangements assumed that both genomes being…
A permutation array $A$ is a set of permutations on a finite set $\Omega$, say of size $n$. Given distinct permutations $\pi, \sigma\in \Omega$, we let $hd(\pi, \sigma) = |\{ x\in \Omega: \pi(x) \ne \sigma(x) \}|$, called the Hamming…
Sorting by reversals is an important problem in inferring the evolutionary relationship between two genomes. The problem of sorting unsigned permutation has been proven to be NP-hard. The best guaranteed error bounded is the 3/2-…
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…
We consider the problems of finding optimal identifying codes, (open) locating-dominating sets and resolving sets of an interval or a permutation graph. In these problems, one asks to find a subset of vertices, normally called a…
The genome rearrangement problem computes the minimum number of operations that are required to sort all elements of a permutation. A block-interchange operation exchanges two blocks of a permutation which are not necessarily adjacent and…
Genome rearrangement has been an active area of research in computational comparative genomics for the last three decades. While initially mostly an interesting algorithmic endeavor, now the practical application by applying rearrangement…
We survey permutation-based methods for approximate k-nearest neighbor search. In these methods, every data point is represented by a ranked list of pivots sorted by the distance to this point. Such ranked lists are called permutations. The…
We address the problem of computing distances between rankings that take into account similarities between candidates. The need for evaluating such distances is governed by applications as diverse as rank aggregation, bioinformatics, social…
Given a generator set $S$ of the symmetric group ${\rm{Sym}}_n$, every permutation $\pi\in {\rm{Sym}_n}$ is a word (product of elements) of $S$. A positive integer $d(\pi)$ is associated with each $\pi\in{\rm{Sym}_n}$ taking the length of…
In this work, we study theoretical models of \emph{programmable matter} systems. The systems under consideration consist of spherical modules, kept together by magnetic forces and able to perform two minimal mechanical operations (or…
Finding the minimum distance of linear codes is an NP-hard problem. Traditionally, this computation has been addressed by means of the design of algorithms that find, by a clever exhaustive search, a linear combination of some generating…
Of the many modern approaches to calculating evolutionary distance via models of genome rearrangement, most are tied to a particular set of genomic modelling assumptions and to a restricted class of allowed rearrangements. The "position…
We continue the study of Adin, Alon and Roichman [arXiv:2502.14398, 2025] on the number of steps required to sort $n$ labelled points on a circle by transpositions. Imagine that the vertices of a cycle of length $n$ are labelled by the…
In the context of the genome rearrangement problem, we analyze two well known models, namely the reversal and the prefix reversal models, by exploiting the connection with the notion of permutation pattern. More specifically, for any $k$,…
We explore various techniques to compress a permutation $\pi$ over n integers, taking advantage of ordered subsequences in $\pi$, while supporting its application $\pi$(i) and the application of its inverse $\pi^{-1}(i)$ in small time. Our…
Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…