Related papers: A rearrangement distance for fully-labelled trees
This paper addresses the problem of finding a representation of a subtree distance, which is an extension of the tree metric. We show that a minimal representation is uniquely determined by a given subtree distance, and give a linear time…
A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…
We consider the problem of constructing an an optimal-weight tree from the 3*(n choose 4) weighted quartet topologies on n objects, where optimality means that the summed weight of the embedded quartet topologiesis optimal (so it can be the…
Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here the rooted triple and quartet metrizations are introduced, and applied to formulate novel fast methods of…
The quartet distance is a measure of similarity used to compare two unrooted phylogenetic trees on the same set of $n$ leaves, defined as the number of subsets of four leaves related by a different topology in both trees. After a series of…
A labeling scheme for nearest common ancestors assigns a distinct binary string, called the label, to every node of a tree, so that given the labels of two nodes (and no further information about the topology of the tree) we can compute the…
We show that reconstructing a tree from order information on triples is NP-hard. This is in contrast to the case for ultra-metrics and for subtree information on quadruples which are both known to allow polynomial time reconstruction.
The class of self-nested trees presents remarkable compression properties because of the systematic repetition of subtrees in their structure. In this paper, we provide a better combinatorial characterization of this specific family of…
We provide time- and sample-efficient algorithms for learning and testing latent-tree Ising models, i.e. Ising models that may only be observed at their leaf nodes. On the learning side, we obtain efficient algorithms for learning a…
We derive tractable criteria for the consistency of Bayesian tree reconstruction procedures, which constitute a central class of algorithms for inferring common ancestry among DNA sequence samples in phylogenetics. Our results encompass…
Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…
We present a complete classification of the deterministic distributed time complexity for a family of graph problems: binary labeling problems in trees. These are locally checkable problems that can be encoded with an alphabet of size two…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
Many natural language processing (NLP) applications require the computation of similarities between pairs of syntactic or semantic trees. Many researchers have used tree edit distance for this task, but this technique suffers from the…
The history of gene families - which are equivalent to \emph{event-labeled} gene trees - can be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The…
Topological structures such as the merge tree provide an abstract and succinct representation of scalar fields. They facilitate effective visualization and interactive exploration of feature-rich data. A merge tree captures the topology of…
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…
Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…
Given a distance matrix consisting of pairwise distances between species, a distance-based phylogenetic reconstruction method returns a tree metric or equidistant tree metric (ultrametric) that best fits the data. We investigate…
Distance-based unsupervised text classification is a method within text classification that leverages the semantic similarity between a label and a text to determine label relevance. This method provides numerous benefits, including fast…