Related papers: Lower bounding edit distances between permutations

In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…

In the \textsc{Coloring Reconfiguration} problem, we are given two proper $k$-colorings of a graph and asked to decide whether one can be transformed into the other by repeatedly applying a specified recoloring rule, while maintaining a…

New bounds on the cardinality of permutation codes equipped with the Ulam distance are presented. First, an integer-programming upper bound is derived, which improves on the Singleton-type upper bound in the literature for some lengths.…

The move structure represents permutations with long contiguously permuted intervals in compressed space with optimal query time. They have become an important feature of compressed text indexes using space proportional to the number of…

Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…

In graph theory, a tree is one of the more popular families of graphs with a wide range of applications in computer science as well as many other related fields. While there are several distance measures over the set of all trees, we…

A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for reconstructing trees, it is crucial to understand the size and structure of the…

We introduce the cycle intersection graph of a graph, an adaptation of the cycle graph of a graph, and use the structure of these graphs to prove an upper bound for the decycling number of all even graphs. This bound is shown to be…

We show that for any permutation $\pi$ there exists an integer $k_{\pi}$ such that every permutation avoiding $\pi$ as a pattern is a product of at most $k_{\pi}$ separable permutations. In other words, every strict class $\mathcal C$ of…

We show that global constraints on finite domains like all-different can be reformulated into answer set programs on which we achieve arc, bound or range consistency. These reformulations offer a number of other advantages beyond providing…

We study aspects of the enumeration of permutation classes, sets of permutations closed downwards under the subpermutation order. First, we consider monotone grid classes of permutations. We present procedures for calculating the generating…

A permutation $\pi: [n] \rightarrow [n]$ is a Baxter permutation if and only if it does not contain either of the patterns $2-41-3$ and $3-14-2$. Baxter permutations are one of the most widely studied subclasses of general permutation due…

This work presents a method to adaptively refine reduced-order models \emph{a posteriori} without requiring additional full-order-model solves. The technique is analogous to mesh-adaptive $h$-refinement: it enriches the reduced-basis space…

Variants of the coordinate descent approach for minimizing a nonlinear function are distinguished in part by the order in which coordinates are considered for relaxation. Three common orderings are cyclic (CCD), in which we cycle through…

Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into…

A permutation array(or code) of length $n$ and distance $d$, denoted by $(n,d)$ PA, is a set of permutations $C$ from some fixed set of $n$ elements such that the Hamming distance between distinct members $\mathbf{x},\mathbf{y}\in C$ is at…

In this paper, we examine the computational complexity of enumeration in certain genome rearrangement models. We first show that the Pairwise Rearrangement problem in the Single Cut-and-Join model (Bergeron, Medvedev, & Stoye, J. Comput.…

In this paper, we consider two fundamental cut approximation problems on large graphs. We prove new lower bounds for both problems that are optimal up to logarithmic factors. The first problem is to approximate cuts in balanced directed…

We consider the problem of determining the maximum number of moves required to sort a permutation of $[n]$ using cut-and-paste operations, in which a segment is cut out and then pasted into the remaining string, possibly reversed. We give…

This paper proves strong lower bounds for distributed computing in the CONGEST model, by presenting the bit-gadget: a new technique for constructing graphs with small cuts. The contribution of bit-gadgets is twofold. First, developing…