Related papers: Edit Distance between Unlabeled Ordered Trees
Metric learning has the aim to improve classification accuracy by learning a distance measure which brings data points from the same class closer together and pushes data points from different classes further apart. Recent research has…
For each positive integer $k$, we consider five well-studied posets defined on the set of Dyck paths of semilength $k$. We prove that uniquely sorted permutations avoiding various patterns are equinumerous with intervals in these posets.…
The log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple non-mixture models of sequence evolution. Here we prove that the log-det distance, coupled…
We extend earlier work of the same author to enumerate alternating permutations avoiding the permutation pattern 2143. We use a generating tree approach to construct a recursive bijection between the set A_{2n}(2143) of alternating…
In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide…
A number of fields, including the study of genome rearrangements and the design of interconnection networks, deal with the connected problems of sorting permutations in "as few moves as possible", using a given set of allowed operations, or…
We define a class L_{n, k} of permutations that generalizes alternating (up-down) permutations and give bijective proofs of certain pattern-avoidance results for this class. As a special case of our results, we give two bijections between…
Tree comparison metrics have proven to be an invaluable aide in the reconstruction and analysis of phylogenetic (evolutionary) trees. The path-length distance between trees is a particularly attractive measure as it reflects differences in…
The early development of a zygote can be mathematically described by a developmental tree. To compare developmental trees of different species, we need to define distances on trees. If children cells after a division are not…
The tree edit distance (TED) between two rooted ordered trees with $n$ nodes labeled from an alphabet $\Sigma$ is the minimum cost of transforming one tree into the other by a sequence of valid operations consisting of insertions, deletions…
We study the number of 231-avoiding permutations with $j$-descents and maximum drop is less than or equal to $k$ which we denote by $a_{n,231,j}^{(k)}$. We show that $a_{n,231,j}^{(k)}$ also counts the number of Dyck paths of length $2n$…
We consider the problem of estimating species trees from unrooted gene tree topologies in the presence of incomplete lineage sorting, a common phenomenon that creates gene tree heterogeneity in multilocus datasets. One popular class of…
Metric learning has the aim to improve classification accuracy by learning a distance measure which brings data points from the same class closer together and pushes data points from different classes further apart. Recent research has…
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,…
Several measures exist for string similarity, including notable ones like the edit distance and the indel distance. The former measures the count of insertions, deletions, and substitutions required to transform one string into another,…
The problem of computing the edit-distance between a string and a finite automaton arises in a variety of applications in computational biology, text processing, and speech recognition. This paper presents linear-space algorithms for…
Recently, Babson and Steingrimsson have introduced generalised permutation patterns that allow the requirement that two adjacent letters in a pattern must be adjacent in the permutation. We consider pattern avoidance for such patterns, and…
This paper considers the enumeration of ternary trees (i.e. rooted ordered trees in which each vertex has 0 or 3 children) avoiding a contiguous ternary tree pattern. We begin by finding recurrence relations for several simple tree…
A $k$-universal permutation, or $k$-superpermutation, is a permutation that contains all permutations of length $k$ as patterns. The problem of finding the minimum length of a $k$-superpermutation has recently received significant attention…
In this paper we consider the enumeration of binary trees avoiding non-contiguous binary tree patterns. We begin by computing closed formulas for the number of trees avoiding a single binary tree pattern with 4 or fewer leaves and compare…