Related papers: A simple framework on sorting permutations
V. Levenshtein first proposed the sequence reconstruction problem in 2001. This problem studies the model where the same sequence from some set is transmitted over multiple channels, and the decoder receives the different outputs. Assume…
The ability to estimate the evolutionary distance between extant genomes plays a crucial role in many phylogenomic studies. Often such estimation is based on the parsimony assumption, implying that the distance between two genomes can be…
Random permutation set (RPS) is a recently proposed framework designed to represent order-structured uncertain information. Measuring the distance between permutation mass functions is a key research topic in RPS theory (RPST). This paper…
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…
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…
Measuring the distance between two bacterial genomes under the inversion process is usually done by assuming all inversions to occur with equal probability. Recently, an approach to calculating inversion distance using group theory was…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
We look at geometric limits of large random non-uniform permutations. We mainly consider two theories for limits of permutations: permuton limits, introduced by Hoppen, Kohayakawa, Moreira, Rath, and Sampaio to define a notion of scaling…
The Genome Median Problem is an important problem in phylogenetic reconstruction under rearrangement models. It can be stated as follows: given three genomes, find a fourth that minimizes the sum of the pairwise rearrangement distances…
On the string of finite length, a (genomic) transposition is defined as the operation of exchanging two consecutive substrings. The minimum number of transpositions needed to transform one into the other is the transposition distance, that…
This paper initiates a limit theory of permutation valued processes, building on the recent theory of permutons. We apply this to study the asymptotic behaviour of random sorting networks. We prove that the Archimedean path, the conjectured…
A permutation graph is the intersection graph of a set of segments between two parallel lines. In other words, they are defined by a permutation $\pi$ on $n$ elements, such that $u$ and $v$ are adjacent if an only if $u<v$ but…
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.…
We address the problem of finding the minimum decomposition of a permutation in terms of transpositions with non-uniform cost. For arbitrary non-negative cost functions, we describe polynomial-time, constant-approximation decomposition…
The genome rearrangement problem computes the minimum number of operations that are required to sort all elements of a permutation. A block-interchange operation exchanges two blocks of a permutation which are not necessarily adjacent and…
We study complexity of rearrangement problems in the generalized breakpoint model and settle several open questions. The model was introduced by Tannier et al. (2009) who showed that the median problem is solvable in polynomial time in the…
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…
Evolutionary algorithms solve problems by simulating the evolution of a population of candidate solutions. We focus on evolving permutations for ordering problems like the traveling salesperson problem (TSP), as well as assignment problems…
This research is concerned with evolution equations and their forward-backward discretizations. Our first contribution is an estimation for the distance between iterates of sequences generated by forward-backward schemes, useful in the…
We consider the problem of upper bounding the number of circular transpositions needed to sort a permutation. It is well known that any permutation can be sorted using at most $n(n-1)/2$ adjacent transpositions. We show that, if we allow…