Related papers: Sorting by Transpositions is Difficult
In this article, we give a polynomial algorithm to decide whether a given permutation $\sigma$ is sortable with two stacks in series. This is indeed a longstanding open problem which was first introduced by Knuth. He introduced the stack…
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…
Given a generator set $S$ of the symmetric group ${\rm{Sym}}_n$, every permutation $\pi\in {\rm{Sym}_n}$ is a word (product of elements) of $S$. A positive integer $d(\pi)$ is associated with each $\pi\in{\rm{Sym}_n}$ taking the length of…
Computing the reversal distances of signed permutations is an important topic in Bioinformatics. Recently, a new lower bound for the reversal distance was obtained via the plane permutation framework. This lower bound appears different from…
Gibbons and Korach studied a fundamental problem in 1997: given an observed sequence of reads and writes of a multi-threaded program, does there exist an interleaving which is sequentially consistent? Apart from applications in testing…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
In the context of the genome rearrangement problem, we analyze two well known models, namely the reversal and the prefix reversal models, by exploiting the connection with the notion of permutation pattern. More specifically, for any $k$,…
The task of learning to map an input set onto a permuted sequence of its elements is challenging for neural networks. Set-to-sequence problems occur in natural language processing, computer vision and structure prediction, where…
Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are more likely than larger inversions. Deletions may arise in…
In the evolution of a genome, the gene sequence is sometimes rearranged, for example by transposition of two adjacent gene blocks. In biocombinatorics, one tries to reconstruct these rearrangement incidents from the resulting permutation.…
A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogeny. All the existing measures are defined on genomes without duplicates. However, we know…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
Given a countable set X (usually taken to be the natural numbers or the integers), an infinite permutation \pi of X is a linear ordering of X. This paper investigates the combinatorial complexity of the infinite permutation on the natural…
A linear list is a collection of items that can be accessed sequentially. The cost of a request is the number of items that need to be examined before the desired item is located, i.e., the distance of the requested item from the beginning…
Sorting is one of the most used and well investigated algorithmic problem [1]. Traditional postulation supposes the sorting data archived, and the elementary operation as comparisons of two numbers. In a view of appearance of new processors…
We prove that it is NP-hard to properly PAC learn decision trees with queries, resolving a longstanding open problem in learning theory (Bshouty 1993; Guijarro-Lavin-Raghavan 1999; Mehta-Raghavan 2002; Feldman 2016). While there has been a…
Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence…
Dokos et. al. studied the distribution of two statistics over permutations $\mathfrak{S}_n$ of $\{1,2,\dots, n\}$ that avoid one or more length three patterns. A permutation $\sigma\in\mathfrak{S}_n$ contains a pattern…
In this paper, we study the problem of sorting unichromosomal linear genomes by prefix double-cut-and-joins (or DCJs) in both the signed and the unsigned settings. Prefix DCJs cut the leftmost segment of a genome and any other segment, and…
There is a deep connection between permutations and trees. Certain sub-structures of permutations, called sub-permutations, bijectively map to sub-trees of binary increasing trees. This opens a powerful tool set to study enumerative and…