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 $π\in S_n$, a {\em pinnacle} of $π$ is an element $π_i$ ($i\neq 1,n$) such that $π_{i-1}<π_i>π_{i+1}$. The question is: given $π,π'\in S_n$ with the same pinnacle set $S$, is there a sequence of operations that transforms $π$ into $π'$ such that all the intermediate permutations have pinnacle set $S$? We introduce {\em balanced reversals}, defined as reversals that do not modify the pinnacle set of the permutation to which they are applied. Then we show that $π$ may be sorted by balanced reversals (i.e. transformed into a standard permutation $\Id_S$), implying that $π$ may be transformed into $π'$ using at most $4n-2\min\{p,3\}$ balanced reversals, where $p=|S|\geq 1$. In case $p=0$, at most $2n-1$ balanced reversals are needed.
We introduce an algorithm to determine when a sorting operation, such as stack-sort or bubble-sort, outputs a given pattern. The algorithm provides a new proof of the description of West-2-stack-sortable permutations, that is permutations that are completely sorted when passed twice through a stack, in terms of patterns. We also solve the long-standing problem of describing West-3-stack-sortable permutations. This requires a new type of generalized permutation pattern we call a decorated pattern.
Pop-Stack Sorting is an algorithm that takes a permutation as an input and sorts its elements. It consists of several steps. At one step, the algorithm reads the permutation it has to process from left to right and reverses each of its maximal decreasing subsequences of consecutive elements. It terminates at the first step that outputs the identity permutation. In this note, we answer a question of Defant on the running time of Pop-Stack Sorting on the uniform random permutation $σ_n$. More precisely, we show that there is a constant $c > 0.5$ such that asymptotically almost surely, the algori…
A sequence of reversals that takes a signed permutation to the identity is perfect if at no step a common interval is broken. Determining a parsimonious perfect sequence of reversals that sorts a signed permutation is NP-hard. Here we show that, despite this worst-case analysis, with probability one, sorting can be done in polynomial time. Further, we find asymptotic expressions for the average length and number of reversals in commuting permutations, an interesting sub-class of signed permutations.
Previous compact representations of permutations have focused on adding a small index on top of the plain data $<π(1), π(2),...π(n)>$, in order to efficiently support the application of the inverse or the iterated permutation. In this paper we initiate the study of techniques that exploit the compressibility of the data itself, while retaining efficient computation of $π(i)$ and its inverse. In particular, we focus on exploiting {\em runs}, which are subsets (contiguous or not) of the domain where the permutation is monotonic. Several variants of those types of runs arise in real applications …
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 using as few such operations as possible. We give a 2-approximation algorithm for this problem, show how to obtain improved lower and upper bounds on the corresponding distance, and determine the largest possible value for that distance.
LRM-Trees are an elegant way to partition a sequence of values into sorted consecutive blocks, and to express the relative position of the first element of each block within a previous block. They were used to encode ordinal trees and to index integer arrays in order to support range minimum queries on them. We describe how they yield many other convenient results in a variety of areas, from data structures to algorithms: some compressed succinct indices for range minimum queries; a new adaptive sorting algorithm; and a compressed succinct data structure for permutations supporting direct and …
In genome rearrangements, the mutational event transposition swaps two adjacent blocks of genes in one chromosome. The Transposition Distance Problem (TDP) aims to find the minimum number of transpositions required to transform one chromosome into another, both represented as permutations. The TDP can be reduced to the problem of Sorting by Transpositions (SBT). SBT is $\mathcal{NP}$-hard and the best approximation algorithm with a $1.375$ ratio was proposed by Elias and Hartman. Their algorithm employs simplification, a technique used to transform an input permutation $π$ into a simple permut…
Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence of reversals that do not break any common interval. Bérard et al. (2007) make use of strong interval trees to describe an algorithm for sorting signed permutations by reversals. Combinatorial properties of this family of trees are essential to the algorithm analysis. Here, we use the expected value of certain tree parameters to prove that the average run-time of the algorithm is at worst, poly…
The (classical) problem of characterizing and enumerating permutations that can be sorted using two stacks connected in series is still largely open. In the present paper we address a related problem, in which we impose restrictions both on the procedure and on the stacks. More precisely, we consider a greedy algorithm where we perform the rightmost legal operation (here "rightmost" refers to the usual representation of stack sorting problems). Moreover, the first stack is required to be $σ$-avoiding, for some permutation $σ$, meaning that, at each step, the elements maintained in the stack av…
We introduce a sorting machine consisting of $k+1$ stacks in series: the first $k$ stacks can only contain elements in decreasing order from top to bottom, while the last one has the opposite restriction. This device generalizes \cite{SM}, which studies the case $k=1$. Here we show that, for $k=2$, the set of sortable permutations is a class with infinite basis, by explicitly finding an antichain of minimal nonsortable permutations. This construction can easily be adapted to each $k \ge 3$. Next we describe an optimal sorting algorithm, again for the case $k=2$. We then analyze two types of le…
A complete set of filters $F_n$ for the optimal-depth $n$-input sorting network problem is such that if there exists an $n$-input sorting network of depth $d$ then there exists one of the form $C \oplus C'$ for some $C \in F_n$. Previous work on the topic presents a method for finding complete set of filters $R_{n, 1}$ and $R_{n, 2}$ that consists only of networks of depths one and two respectively, whose outputs are minimal and representative up to permutation and reflection. Our main contribution is a practical approach for finding a complete set of filters $R_{n, 3}$ containing only network…
Pancake flipping, a famous open problem in computer science, can be formalised as the problem of sorting a permutation of positive integers using as few prefix reversals as possible. In that context, a prefix reversal of length k reverses the order of the first k elements of the permutation. The burnt variant of pancake flipping involves permutations of signed integers, and reversals in that case not only reverse the order of elements but also invert their signs. Although three decades have now passed since the first works on these problems, neither their computational complexity nor the maxim…
In the 60's, Knuth introduced stack-sorting and serial compositions of stacks. In particular, one significant question arise out of the work of Knuth: how to decide efficiently if a given permutation is sortable with 2 stacks in series? Whether this problem is polynomial or NP-complete is still unanswered yet. In this article we introduce 2-stack pushall permutations which form a subclass of 2-stack sortable permutations and show that these two classes are closely related. Moreover, we give an optimal O(n^2) algorithm to decide if a given permutation of size n is 2-stack pushall sortable and d…
A wide range of applications, most notably in comparative genomics, involve the computation of a shortest sorting sequence of operations for a given permutation, where the set of allowed operations is fixed beforehand. Such sequences are useful for instance when reconstructing potential scenarios of evolution between species, or when trying to assess their similarity. We revisit those problems by adding a new constraint on the sequences to be computed: they must \emph{avoid} a given set of \emph{forbidden intermediates}, which correspond to species that cannot exist because the mutations that …
Together with a characteristic function, idempotent permutations uniquely determine idempotent maps, as well as their linearly ordered arrangement simultaneously. Furthermore, in-place linear time transformations are possible between them. Hence, they may be important for succinct data structures, information storing, sorting and searching. In this study, their combinatorial interpretation is given and their application on sorting is examined. Given an array of n integer keys each in [1,n], if it is allowed to modify the keys in the range [-n,n], idempotent permutations make it possible to obt…
The set of all permutations with $n$ symbols is a symmetric group denoted by $S_n$. A transposition tree, $T$, is a spanning tree over its $n$ vertices $V_T=${$1, 2, 3, \ldots n$} where the vertices are the positions of a permutation $π$ and $π$ is in $S_n$. $T$ is the operation and the edge set $E_T$ denotes the corresponding generator set. The goal is to sort a given permutation $π$ with $T$. The number of generators of $E_T$ that suffices to sort any $π\in S_n$ constitutes an upper bound. It is an upper bound, on the diameter of the corresponding Cayley graph $Γ$ i.e. $diam(Γ)$. A precise u…
Sorting a Permutation by Transpositions (SPbT) is an important problem in Bioinformtics. In this paper, we improve the running time of the best known approximation algorithm for SPbT. We use the permutation tree data structure of Feng and Zhu and improve the running time of the 1.375 Approximation Algorithm for SPbT of Elias and Hartman to $O(n\log n)$. The previous running time of EH algorithm was $O(n^2)$.
In comparative genomics, a transposition is an operation that exchanges two consecutive sequences of genes in a genome. The transposition distance, that is, the minimum number of transpositions needed to transform a genome into another, is, according to numerous studies, a relevant evolutionary distance. The problem of computing this distance when genomes are represented by permutations, called the Sorting by Transpositions problem, has been introduced by Bafna and Pevzner in 1995. It has naturally been the focus of a number of studies, but the computational complexity of this problem has rema…
University of Bonn（波恩大学）；Fraunhofer IAIS（弗劳恩霍夫智能分析与信息系统研究所）
We show that the fundamental tasks of sorting lists and building search trees or heaps can be modeled as quadratic unconstrained binary optimization problems (QUBOs). The idea is to understand these tasks as permutation problems and to devise QUBOs whose solutions represent appropriate permutation matrices. We discuss how to construct such QUBOs and how to solve them using Hopfield nets or adiabatic) quantum computing. In short, we show that neurocomputing methods or quantum computers can solve problems usually associated with abstract data structures.
We prove several combinatorial properties of suffix arrays, including a characterization of suffix arrays through a bijection with a certain well-defined class of permutations. Our approach is based on the characterization of Burrows-Wheeler arrays given in [1], that we apply by reducing suffix sorting to cyclic shift sorting through the use of an additional sentinel symbol. We show that the characterization of suffix arrays for a special case of binary alphabet given in [2] easily follows from our characterization. Based on our results, we also provide simple proofs for the enumeration result…
A number of fields, including the study of genome rearrangements and the design of interconnection networks, deal with the connected problems of sorting permutations in "as few moves as possible", using a given set of allowed operations, or computing the number of moves the sorting process requires, often referred to as the \emph{distance} of the permutation. These operations often act on just one or two segments of the permutation, e.g. by reversing one segment or exchanging two segments. The \emph{cycle graph} of the permutation to sort is a fundamental tool in the theory of genome rearrange…
This paper studies problems of inferring order given noisy information. In these problems there is an unknown order (permutation) $π$ on $n$ elements denoted by $1,...,n$. We assume that information is generated in a way correlated with $π$. The goal is to find a maximum likelihood $π^*$ given the information observed. We will consider two different types of observations: noisy comparisons and noisy orders. The data in Noisy orders are permutations given from an exponential distribution correlated with π(this is also called the Mallow's model). The data in Noisy Comparisons is a signal given f…
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 reversals other similar operations such as prefix transpositions and prefix transreversals. These type of sorting problems have applications in interconnection networks and computational biology. We first study the problem of sorting unsigned permutations by prefix reversals and prefix transpositions and present a 3-approximation algorithm for this problem. Then we…
In-place associative integer sorting technique was developed, improved and specialized for distinct integers. The technique is suitable for integer sorting. Hence, given a list S of n integers S[0...n-1], the technique sorts the integers in ascending or descending order. It replaces bucket sort, distribution counting sort and address calculation sort family of algorithms and requires only constant amount of additional memory for storing counters and indices beside the input list. The technique was inspired from one of the ordinal theories of "serial order in behavior" and explained by the anal…
Sorted data is usually easier to compress than unsorted permutations of the same data. This motivates a simple compression scheme: specify the sorted permutation of the data along with a representation of the sorted data compressed recursively. The sorted permutation can be specified by recording the decisions made by quicksort. If the size of the data is known, then the quicksort decisions describe the data at a rate that is nearly as efficient as the minimal prefix-free code for the distribution, which is bounded by the entropy of the distribution. This is possible even though the distributi…
