Polynomial-time sortable stacks of burnt pancakes

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 maximal number of prefix reversals needed to sort a permutation is yet known. In this work, we prove a new lower bound for sorting burnt pancakes, and show that an important class of permutations, known as "simple permutations", can be optimally sorted in polynomial time.Comment: Accepted pending minor revisio

Pancake Flipping is Hard

Pancake Flipping is the problem of sorting a stack of pancakes of different sizes (that is, a permutation), when the only allowed operation is to insert a spatula anywhere in the stack and to flip the pancakes above it (that is, to perform a prefix reversal). In the burnt variant, one side of each pancake is marked as burnt, and it is required to finish with all pancakes having the burnt side down. Computing the optimal scenario for any stack of pancakes and determining the worst-case stack for any stack size have been challenges over more than three decades. Beyond being an intriguing combinatorial problem in itself, it also yields applications, e.g. in parallel computing and computational biology. In this paper, we show that the Pancake Flipping problem, in its original (unburnt) variant, is NP-hard, thus answering the long-standing question of its computational complexity.Comment: Corrected reference

Sorting signed permutations by short operations

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Background: During evolution, global mutations may alter the order and the orientation of the genes in a genome. Such mutations are referred to as rearrangement events, or simply operations. In unichromosomal genomes, the most common operations are reversals, which are responsible for reversing the order and orientation of a sequence of genes, and transpositions, which are responsible for switching the location of two contiguous portions of a genome. The problem of computing the minimum sequence of operations that transforms one genome into another - which is equivalent to the problem of sorting a permutation into the identity permutation - is a well-studied problem that finds application in comparative genomics. There are a number of works concerning this problem in the literature, but they generally do not take into account the length of the operations (i.e. the number of genes affected by the operations). Since it has been observed that short operations are prevalent in the evolution of some species, algorithms that efficiently solve this problem in the special case of short operations are of interest. Results: In this paper, we investigate the problem of sorting a signed permutation by short operations. More precisely, we study four flavors of this problem: (i) the problem of sorting a signed permutation by reversals of length at most 2; (ii) the problem of sorting a signed permutation by reversals of length at most 3; (iii) the problem of sorting a signed permutation by reversals and transpositions of length at most 2; and (iv) the problem of sorting a signed permutation by reversals and transpositions of length at most 3. We present polynomial-time solutions for problems (i) and (iii), a 5-approximation for problem (ii), and a 3-approximation for problem (iv). Moreover, we show that the expected approximation ratio of the 5-approximation algorithm is not greater than 3 for random signed permutations with more than 12 elements. Finally, we present experimental results that show that the approximation ratios of the approximation algorithms cannot be smaller than 3. In particular, this means that the approximation ratio of the 3-approximation algorithm is tight.During evolution, global mutations may alter the order and the orientation of the genes in a genome. Such mutations are referred to as rearrangement events, or simply operations. In unichromosomal genomes, the most common operations are reversals, which a10117CAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIORFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)FAPESP [2014/04718-6]CNPq [303947/2008-0, 477692/2012-5]CNPq [477692/2012-5, 306730/2012-0, 483370/2013-4]FAPESP [2013/08293-7]SEM INFORMAÇÃO2014/04718-6; 2013/08293-7303947/2008-0; 477692/2012-5; 306730/2012-0; 477692/2012-5; 483370/2013-

Sorting by Block Moves

The research in this thesis is focused on the problem of Block Sorting, which has applications in Computational Biology and in Optical Character Recognition (OCR). A block in a permutation is a maximal sequence of consecutive elements that are also consecutive in the identity permutation. BLOCK SORTING is the process of transforming an arbitrary permutation to the identity permutation through a sequence of block moves. Given an arbitrary permutation π and an integer m, the Block Sorting Problem, or the problem of deciding whether the transformation can be accomplished in at most m block moves has been shown to be NP-hard. After being known to be 3-approximable for over a decade, block sorting has been researched extensively and now there are several 2-approximation algorithms for its solution. This work introduces new structures on a permutation, which are called runs and ordered pairs, and are used to develop two new approximation algorithms. Both the new algorithms are 2-approximation algorithms, yielding the approximation ratio equal to the current best. This work also includes an analysis of both the new algorithms showing they are 2-approximation algorithms

Reversal Distances for Strings with Few Blocks or Small Alphabets

International audienceWe study the String Reversal Distance problem, an extension of the well-known Sorting by Reversals problem. String Reversal Distance takes two strings S and T as input, and asks for a minimum number of reversals to obtain T from S. We consider four variants: String Reversal Distance, String Prefix Reversal Distance (in which any reversal must include the first letter of the string), and the signed variants of these problems, namely Signed String Reversal Distance and Signed String Prefix Reversal Distance. We study algorithmic properties of these four problems, in connection with two parameters of the input strings: the number of blocks they contain (a block being maximal substring such that all letters in the substring are equal), and the alphabet size Σ. For instance, we show that Signed String Reversal Distance and Signed String Prefix Reversal Distance are NP-hard even if the input strings have only one letter