Related papers: Measuring similarity between two mixture trees usi…
Comparing the ranking of candidates by different voters is an important topic in social and information science with a high relevance from the point of view of practical applications. In general, ties and pairs of incomparable candidates…
Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…
Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to measure the dissimilarity of the two 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…
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…
Recent theoretical work has demonstrated that Neighbor Joining applied to concatenated DNA sequences is a statistically consistent method of species tree reconstruction. This brief note compares the accuracy of this approach to other…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
The purpose of this paper is to extend the definition of Frechet distance which measures the distance between two curves to a distance (Frechet-Like distance) which measures the similarity between two rooted trees. The definition of…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
A common approach to implementing similarity search applications is the usage of distance functions, where small distances indicate high similarity. In the case of metric distance functions, metric index structures can be used to accelerate…
In many situations, the choice of an adequate similarity measure or metric on the feature space dramatically determines the performance of machine learning methods. Building automatically such measures is the specific purpose of…
Gromov-Hausdorff (GH) distance is a natural way to measure the distortion between two metric spaces. However, there has been only limited algorithmic development to compute or approximate this distance. We focus on computing the…
A variety of algorithms have been proposed for reconstructing trees that show the evolutionary relationships between species by comparing differences in genetic data across present-day taxa. If the leaf-to-leaf distances in a tree can be…
Inspired by [4] we present a new algorithm for uniformly random generation of ordered trees in which all occuring outdegrees can be specified by a given sequence of numbers. The method can be used for random generation of binary or n-ary…
This paper give a simple linear-time algorithm that, given a weighted digraph, finds a spanning tree that simultaneously approximates a shortest-path tree and a minimum spanning tree. The algorithm provides a continuous trade-off: given the…
Dynamic tree data structures maintain a forest while supporting insertion and deletion of edges and a broad set of queries in $O(\log n)$ time per operation. Such data structures are at the core of many modern algorithms. Recent work has…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
We consider the tree consensus problem, an important problem in bioinformatics. Given a rooted tree $t$ and another tree $T$, one would like to incorporate compatible information from $T$ to $t$. This problem is a subproblem in the tree…