Related papers: Sorting by Transpositions is Difficult
We consider the well-studied pattern counting problem: given a permutation $\pi \in \mathbb{S}_n$ and an integer $k > 1$, count the number of order-isomorphic occurrences of every pattern $\tau \in \mathbb{S}_k$ in $\pi$. Our first result…
This paper proposes a new algorithm for generating all permutations of multisets. The method uses transpositions only and adjacent transpositions are favoured. The algorithm requires a strong homogeneous transposition condition:…
The study of genome rearrangement has many flavours, but they all are somehow tied to edit distances on variations of a multi-graph called the breakpoint graph. We study a weighted 2-break distance on Eulerian 2-edge-colored multi-graphs,…
We characterise and enumerate permutations that are sortable by n-4 passes through a stack. We conjecture the number of permutations sortable by n-5 passes, and also the form of a formula for the general case n-k, which involves a…
Drawing on a problem posed by Hertzsprung in 1887, we say that a given permutation $\pi\in\mathcal{S}_n$ contains the Hertzsprung pattern $\sigma\in\mathcal{S}_k$ if there is factor $\pi(d+1)\pi(d+2)\cdots\pi(d+k)$ of $\pi$ such that…
Recently, different works proposed a new way to mine patterns in databases with pathological size. For example, experiments in genome biology usually provide databases with thousands of attributes (genes) but only tens of objects…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
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…
String consensus problems aim at finding a string that minimizes some given distance with respect to an input set of strings. In particular, in the Closest string problem, we are given a set of strings of equal length and a radius $d$. The…
Let $s$ be West's deterministic stack-sorting map. A well-known result (West) is that any length $n$ permutation can be sorted with $n-1$ iterations of $s.$ In 2020, Defant introduced the notion of highly-sorted permutations -- permutations…
The Permutation Pattern Matching problem, asking whether a pattern permutation $\pi$ is contained in a permutation $\tau$, is known to be NP-complete. In this paper we present two polynomial time algorithms for special cases. The first…
Given a set $Y$ of decreasing plane trees and a permutation $\pi$, how many trees in $Y$ have $\pi$ as their postorder? Using combinatorial and geometric constructions, we provide a method for answering this question for certain sets $Y$…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
Many machine learning tasks require finding per-part correspondences between objects. In this work we focus on low-level correspondences - a highly ambiguous matching problem. We propose to use a hierarchical semantic representation of the…
Genome rearrangement is a common model for molecular evolution. In this paper, we consider the Pairwise Rearrangement problem, which takes as input two genomes and asks for the number of minimum-length sequences of permissible operations…
We study the token swapping problem, in which we are given a graph with an initial assignment of one distinct token to each vertex, and a final desired assignment (again with one token per vertex). The goal is to find the minimum length…
The interval count problem, a classical question in the study of interval orders, was introduced by Ronald Graham in the 1980s. This problem asks: given an interval order $P$, what is the minimum number of distinct interval lengths required…
A lazy transposition $(a,b,p)$ is the random permutation that equals the identity with probability $1-p$ and the transposition $(a,b)\in S_n$ with probability $p$. How long must a sequence of independent lazy transpositions be if their…
In sorting situations where the final destination of each item is known, it is natural to repeatedly choose items and place them where they belong, allowing the intervening items to shift by one to make room. (In fact, a special case of…
Many matching, tracking, sorting, and ranking problems require probabilistic reasoning about possible permutations, a set that grows factorially with dimension. Combinatorial optimization algorithms may enable efficient point estimation,…