Related papers: Lower bounding edit distances between permutations
We introduce Permutation and Structured Perturbation Inference (PSPI), a new problem formulation that abstracts many graph matching tasks that arise in systems biology. PSPI can be viewed as a robust formulation of the permutation inference…
We investigate the symmetry of circular genome rearrangement models, discuss the implementation of a new representation-theoretic method of calculating evolutionary distances between circular genomes, and give the results of some initial…
We investigate lossy compression (source coding) of data in the form of permutations. This problem has direct applications in the storage of ordinal data or rankings, and in the analysis of sorting algorithms. We analyze the rate-distortion…
Motivated by Bourque and Pevzner's simulation study of the parsimony method for studying genome rearrangement, Berestycki and Durrett used techniques from random graph theory to prove that the minimum parsimony distance after iterating the…
Permutation codes have recently garnered substantial research interest due to their potential in various applications including cloud storage systems, genome resequencing and flash memories. In this paper, we study the theoretical bounds…
We address the problem of reasoning on graph transformations featuring actions such as \emph{addition} and \emph{deletion} of nodes and edges, node \emph{merging} and \emph{cloning}, node or edge \emph{labelling} and edge…
We study sorting by queues that can rearrange their content by applying permutations from a predefined set. These new sorting devices are called shuffle queues and we investigate those of them corresponding to sets of permutations defining…
Reconfiguration graphs provide a way to represent relationships among solutions to a problem, and have been studied in many contexts. We investigate the reconfiguration graphs corresponding to minimum PSD forcing sets and minimum skew…
Communication is a major factor determining the performance of algorithms on current computing systems; it is therefore valuable to provide tight lower bounds on the communication complexity of computations. This paper presents a lower…
Base polytopes of polymatroids, also known as generalized permutohedra, are polytopes whose edges are parallel to a vector of the form $\mathbf{e}_i - \mathbf{e}_j$. We consider the following computational problem: Given two vertices of a…
An edit distance is a measure of the minimum cost sequence of edit operations to transform one structure into another. Edit distance is most commonly encountered within the context of strings, where Wagner and Fischer's string edit distance…
The ''trace reconstruction'' problem asks, given an unknown binary string $x$ and a channel that repeatedly returns ''traces'' of $x$ with each bit randomly deleted with some probability $p$, how many traces are needed to recover $x$? There…
We consider single-source shortest path algorithms that perform a sequence of relaxation steps whose ordering depends only on the input graph structure and not on its weights or the results of prior steps. Each step examines one edge of the…
We give a positive answer to a question raised by Davis et al. ({\em Discrete Mathematics} 341, 2018), concerning permutations with the same pinnacle set. Given $\pi\in S_n$, a {\em pinnacle} of $\pi$ is an element $\pi_i$ ($i\neq 1,n$)…
The graph edit distance is used for comparing graphs in various domains. Due to its high computational complexity it is primarily approximated. Widely-used heuristics search for an optimal assignment of vertices based on the distance…
For a graph with edge ordering, a linear order on the edge set, we obtain a permutation of vertices by considering the edges as transpositions of endvertices. It is known from D\'enes' results that the permutation of a tree is a full cyclic…
We introduce a new sorting device for permutations which makes use of a pop stack augmented with a bypass operation. This results in a sorting machine, which is more powerful than the usual Popstacksort algorithm and seems to have never…
In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness.…
The edit distance between two graphs is a widely used measure of similarity that evaluates the smallest number of vertex and edge deletions/insertions required to transform one graph to another. It is NP-hard to compute in general, and a…
Let $\Gamma$ be a Cayley graph of the permutation group generated by a transposition tree $T$ on $n$ vertices. In an oft-cited paper \cite{Akers:Krishnamurthy:1989} (see also \cite{Hahn:Sabidussi:1997}), it is shown that the diameter of the…