Related papers: Permutation patterns in genome rearrangement probl…
Following a question of J. Cooper, we study the expected number of occurrences of a given permutation pattern $q$ in permutations that avoid another given pattern $r$. In some cases, we find the pattern that occurs least often, (resp. most…
We give an account on what is known on the subject of permutation matchings, which are bijections of a finite regular semigroup that map each element to one of its inverses. This includes partial solutions to some open questions, including…
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…
We consider the problem of training generative models with deep neural networks as generators, i.e. to map latent codes to data points. Whereas the dominant paradigm combines simple priors over codes with complex deterministic models, we…
We introduce and study a new notion of patterns in Stirling and $k$-Stirling permutations, which we call block patterns. We prove a general result which allows us to compute generating functions for the occurrences of various block patterns…
Packing density is a permutation occurrence statistic which describes the maximal number of permutations of a given type that can occur in another permutation. In this article we focus on containment of sets of permutations. Although this…
We analyse the statistical properties of genealogical trees in a neutral model of a closed population with sexual reproduction and non-overlapping generations. By reconstructing the genealogy of an individual from the population evolution,…
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…
We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward…
A model of pattern formation in living systems is presented. The pattern is achieved by the sequential interaction of two signaling pathways. The coupling of the pattern to the (thick) epithelial sheet changes is given, when the Gauss…
Understanding the metric structure of permutation families is fundamental to combinatorics and has applications in social choice theory, bioinformatics, and coding theory. We study permutation families defined by restriction…
We construct generating trees with one, two, and three labels for some classes of permutations avoiding generalized patterns of length 3 and 4. These trees are built by adding at each level an entry to the right end of the permutation,…
We consider the question of computing the distribution of a permutation statistics over restricted permutations via enumeration schemes. The restricted permutations are those avoiding sets of vincular patterns (which include both classical…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…
We introduce and study the writhe of a permutation, a circular variant of the well-known inversion number. This simple permutation statistics has several interpretations, which lead to some interesting properties. For a permutation sampled…
Researchers in genetics and other life sciences commonly use permutation tests to evaluate differences between groups. Permutation tests have desirable properties, including exactness if data are exchangeable, and are applicable even when…
Sorting a permutation by reversals is a famous problem in genome rearrangements. Since 1997, quite some biological evidence were found that in many genomes the reversed regions are usually flanked by a pair of inverted repeats. This type of…
We count the number of occurrences of restricted patterns of length 3 in permutations with respect to length and the number of cycles. The main tool is a bijection between permutations in standard cycle form and weighted Motzkin paths.
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 pancake problem is concerned with sorting a permutation (a stack of pancakes of different diameter) using only prefix reversals (spatula flips). Although the problem description belies simplicity, an exact formula for the maximum number…