Related papers: A rearrangement distance for fully-labelled trees
We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling…
We give a short and direct proof of a remarkable identity that arises in the enumeration of labeled trees with respect to their indegree sequence, where all edges are oriented from the vertex with lower label towards the vertex with higher…
Computing the similarity between two data points plays a vital role in many machine learning algorithms. Metric learning has the aim of learning a good metric automatically from data. Most existing studies on metric learning for…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
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…
Weight-balanced trees are a popular form of self-balancing binary search trees. Their popularity is due to desirable guarantees, for example regarding the required work to balance annotated trees. While usual weight-balanced trees perform…
The diagnosis and segmentation of tumors using any medical diagnostic tool can be challenging due to the varying nature of this pathology. Magnetic Reso- nance Imaging (MRI) is an established diagnostic tool for various diseases and…
The largest common embeddable subtree problem asks for the largest possible tree embeddable into two input trees and generalizes the classical maximum common subtree problem. Several variants of the problem in labeled and unlabeled rooted…
The unordered tree edit distance is a natural metric to compute distances between trees without intrinsic child order, such as representations of chemical molecules. While the unordered tree edit distance is MAX SNP-hard in principle, it is…
Comparative analysis of scalar fields is an important problem with various applications including feature-directed visualization and feature tracking in time-varying data. Comparing topological structures that are abstract and succinct…
A classical result, fundamental to evolutionary biology, states that an edge-weighted tree $T$ with leaf set $X$, positive edge weights, and no vertices of degree 2 can be uniquely reconstructed from the set of leaf-to-leaf distances…
Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x…
Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into…
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…
Rotation distance between rooted binary trees is the minimum number of simple rotations needed to transform one tree into the other. Computing the rotation distance between a pair of rooted trees can be quickly reduced in cases where there…
We investigate the tractability of a simple fusion of two fundamental structures on graphs, a spanning tree and a perfect matching. Specifically, we consider the following problem: given an edge-weighted graph, find a minimum-weight…
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…
In the longest plane spanning tree problem, we are given a finite planar point set $\mathcal{P}$, and our task is to find a plane (i.e., noncrossing) spanning tree for $\mathcal{P}$ with maximum total Euclidean edge length. Despite more…
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…
A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. While the most traditional…