Related papers: Sorting by Transpositions is Difficult
This article studies the poset of simple permutations with respect to the pattern involvement. We specify results on critically indecomposable posets obtained by Schmerl and Trotter to simple permutations and prove that if $\sigma, \pi$ are…
The 3SUM problem represents a class of problems conjectured to require $\Omega (n^2)$ time to solve, where $n$ is the size of the input. Given two polygons $P$ and $Q$ in the plane, we show that some variants of the decision problem,…
Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and…
Comtet introduced the notion of indecomposable permutations in 1972. A permutation is indecomposable if and only if it has no proper prefix which is itself a permutation. Indecomposable permutations were studied in the literature in various…
Training deep neural networks (DNNs) is computationally expensive, which is problematic especially when performing duplicated or similar training runs in model ensemble or fine-tuning pre-trained models, for example. Once we have trained…
The problem of genealogy of permutations has been solved partially by Stefan (odd order) and Acosta-Hum\'anez & Bernhardt (power of two). It is well known that Sharkovskii's theorem shows the relationship between the cardinal of the set of…
Given a real number beta>1, a permutation pi of length n is realized by the beta-shift if there is some x in [0,1] such that the relative order of the sequence x,f(x),...,f^{n-1}(x), where f(x) is the factional part of beta*x, is the same…
The input to the token swapping problem is a graph with vertices $v_1, v_2, \ldots, v_n$, and $n$ tokens with labels $1, 2, \ldots, n$, one on each vertex. The goal is to get token $i$ to vertex $v_i$ for all $i= 1, \ldots, n$ using a…
Given two genomes with duplicate genes, \textsc{Zero Exemplar Distance} is the problem of deciding whether the two genomes can be reduced to the same genome without duplicate genes by deleting all but one copy of each gene in each genome.…
Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…
A permutation whose any prefix has no more descents than ascents is called a ballot permutation. In this paper, we present a decomposition of ballot permutations that enables us to construct a bijection between ballot permutations and odd…
Given a countable set X (usually taken to be the natural numbers or integers), an infinite permutation, \pi, of X is a linear ordering of X. This paper investigates the combinatorial complexity of infinite permutations on the natural…
Track finding in particle data is a challenging pattern recognition problem in High Energy Physics. It takes as inputs a point cloud of space points and labels them so that space points created by the same particle have the same label. The…
Breakpoint graphs are ubiquitous structures in the field of genome rearrangements. Their cycle decomposition has proved useful in computing and bounding many measures of (dis)similarity between genomes, and studying the distribution of…
The computation of genomic distances has been a very active field of computational comparative genomics over the last 25 years. Substantial results include the polynomial-time computability of the inversion distance by Hannenhalli and…
Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot…
Reordering poses a major challenge in machine translation (MT) between two languages with significant differences in word order. In this paper, we present a novel reordering approach utilizing sparse features based on dependency word pairs.…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
Permutations are usually enumerated by size, but new results can be found by enumerating them by inversions instead, in which case one must restrict one's attention to indecomposable permutations. In the style of the seminal paper by Simion…
Our work is motivated by Bourque and Pevzner's (2002) simulation study of the effectiveness of the parsimony method in studying genome rearrangement, and leads to a surprising result about the random transposition walk on the group of…