Related papers: Sorting permutations with a transposition tree
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
In this paper we study several problems concerning the number of homomorphisms of trees. We give an algorithm for the number of homomorphisms from a tree to any graph by the Transfer-matrix method. By using this algorithm and some…
An independent edge set of graph $G$ is a matching, and is maximal if it is not a proper subset of any other matching of $G$. The number of all the maximal matchings of $G$ is denoted by $\Psi(G)$. In this paper, an algorithm to count…
An algorithm is presented for unranking permutations in transposition order: Given a seed s\in N, the algorithm produces a permutation P(s) that differs from the permutation P(s+1) by the transposition of two elements.
We investigate the complexity of finding a transformation from a given spanning tree in a graph to another given spanning tree in the same graph via a sequence of edge flips. The exchange property of the matroid bases immediately yields…
Given a graph $G$ and two spanning trees $T$ and $T'$ in $G$, Spanning Tree Reconfiguration asks whether there is a step-by-step transformation from $T$ to $T'$ such that all intermediates are also spanning trees of $G$, by exchanging an…
The subject of pattern avoiding permutations has its roots in computer science, namely in the problem of sorting a permutation through a stack. A formula for the number of permutations of length n that can be sorted by passing it twice…
Permutation codes have recently garnered substantial research interest due to their potential in various applications including cloud storage systems, genome resequencing and flash memories. In this paper, we study the theoretical bounds…
Tree transductions are binary relations of finite trees. For tree transductions defined by non-deterministic top-down tree transducers, inclusion, equivalence and synthesis problems are known to be undecidable. Adding origin semantics to…
The circular peak set of a permutation $\sigma$ is the set $\{\sigma(i)\mid \sigma(i-1)<\sigma(i)>\sigma(i+1)\}$. In this paper, we focus on the enumeration problems for permutations by circular peak sets. Let $cp_n(S)$ denote the number of…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
We show that for any permutation $\pi$ there exists an integer $k_{\pi}$ such that every permutation avoiding $\pi$ as a pattern is a product of at most $k_{\pi}$ separable permutations. In other words, every strict class $\mathcal C$ of…
Given a set $Y$ of decreasing plane trees and a permutation $\pi$, how many trees in $Y$ have $\pi$ as their postorder? Using combinatorial and geometric constructions, we provide a method for answering this question for certain sets $Y$…
For a graph with edge ordering, a linear order on the edge set, we obtain a permutation of vertices by considering the edges as transpositions of endvertices. It is known from D\'enes' results that the permutation of a tree is a full cyclic…
Sorting a Permutation by Transpositions (SPbT) is an important problem in Bioinformtics. In this paper, we improve the running time of the best known approximation algorithm for SPbT. We use the permutation tree data structure of Feng and…
Billey et al. [arXiv:1507.04976] have recently discovered a surprisingly simple formula for the number $a_n(\sigma)$ of leaf-labelled rooted non-embedded binary trees (also known as phylogenetic trees) with $n\geq 1$ leaves, fixed (for the…
The VC-dimension of a family P of n-permutations is the largest integer k such that the set of restrictions of the permutations in P on some k-tuple of positions is the set of all k! permutation patterns. Let r_k(n) be the maximum size of a…
Consider a rooted tree $T$ with leaf-set $[n]$, and with all non-leaf vertices having out-degree $2$, at least. A rooted tree $\mathcal T$ with leaf-set $S\subset [n]$ is induced by $S$ in $T$ if $\mathcal T$ is the lowest common ancestor…
Given a set $I \subseteq \mathbb{N}$, consider the sequences $\{d_n(I)\},\{p_n(I)\}$ where for any $n$, $d_n(I)$ and $p_n(I)$ respectively count the number of permutations in the symmetric group $\mathfrak{S}_n$ whose descent set…
Given a 2-edge connected, unweighted, and undirected graph $G$ with $n$ vertices and $m$ edges, a $\sigma$-tree spanner is a spanning tree $T$ of $G$ in which the ratio between the distance in $T$ of any pair of vertices and the…