Related papers: On the rotation distance between binary trees
Plane increasing trees are rooted labeled trees embedded into the plane such that the sequence of labels is increasing on any branch starting at the root. Relaxed binary trees are a subclass of unlabeled directed acyclic graphs. We…
A compacted binary tree is a directed acyclic graph encoding a binary tree in which common subtrees are factored and shared, such that they are represented only once. We show that the number of compacted binary trees of size $n$ grows…
The in-order traversal provides a natural correspondence between binary trees with a decreasing vertex labeling and endofunctions on a finite set. By suitably restricting the vertex labeling we arrive at a class of trees that we call…
Simultaneous diagonal flips in plane triangulations are investigated. It is proved that every $n$-vertex triangulation with at least six vertices has a simultaneous flip into a 4-connected triangulation, and that it can be computed in O(n)…
In this article, we propose tree edit distance with variables, which is an extension of the tree edit distance to handle trees with variables and has a potential application to measuring the similarity between mathematical formulas,…
In this short note we prove that, given two (not necessarily binary) rooted phylogenetic trees T_1, T_2 on the same set of taxa X, where |X|=n, the hybridization number of T_1 and T_2 can be computed in time O^{*}(2^n) i.e. O(2^{n}…
A spanning tree of an unweighted graph is a minimum average stretch spanning tree if it minimizes the ratio of sum of the distances in the tree between the end vertices of the graph edges and the number of graph edges. We consider the…
Geometric graphs appear in many real-world data sets, such as road networks, sensor networks, and molecules. We investigate the notion of distance between embedded graphs and present a metric to measure the distance between two geometric…
Binary trees are fundamental objects in models of evolutionary biology and population genetics. Here, we discuss some of their combinatorial and structural properties as they depend on the tree class considered. Furthermore, the process by…
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…
Let $T$ be a tree on $n$ vertices whose edge weights are positive definite matrices of order $s$. The squared distance matrix of $T$, denoted by $\Delta$, is the $ns \times ns$ block matrix with $\Delta_{ij}=d(i,j)^2$, where $d(i,j)$ is the…
In this work we define a novel edit distance for trees considered with some abstract weights on the edges. The metric is driven by the idea of considering trees as topological summaries in the context of persistence and topological data…
We compute a number of distance-dependent universal scaling functions characterizing the distance statistics of large maps of genus one. In particular, we obtain explicitly the probability distribution for the length of the shortest…
A spanning tree of a graph $G$ is a connected acyclic spanning subgraph of $G$. We consider enumeration of spanning trees when $G$ is a $2$-tree, meaning that $G$ is obtained from one edge by iteratively adding a vertex whose neighborhood…
We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of $m$ binary trees with…
We present new and improved fixed-parameter algorithms for computing maximum agreement forests (MAFs) of pairs of rooted binary phylogenetic trees. The size of such a forest for two trees corresponds to their subtree prune-and-regraft…
The Gromov-Hausdorff (GH) distance is a natural way to measure distance between two metric spaces. We prove that it is $\mathrm{NP}$-hard to approximate the Gromov-Hausdorff distance better than a factor of $3$ for geodesic metrics on a…
This paper introduces a new combinatorial framework for modeling the growth of binary trees through a discrete evolution process that incorporates a growing rule and an extinction rule. Building upon the theory of increasingly labeled…
In this paper we introduce and study three new measures for efficient discriminative comparison of phylogenetic trees. The NNI navigation dissimilarity $d_{nav}$ counts the steps along a "combing" of the Nearest Neighbor Interchange (NNI)…
The matching distance is a computationally tractable topological measure to compare multi-filtered simplicial complexes. We design efficient algorithms for approximating the matching distance of two bi-filtered complexes to any desired…