Related papers: Relating Interleaving and Fr\'echet Distances via …
We present a scalable approach for range and $k$ nearest neighbor queries under computationally expensive metrics, like the continuous Fr\'echet distance on trajectory data. Based on clustering for metric indexes, we obtain a dynamic tree…
Persistent homology is a way of determining the topological properties of a data set. It is well known that each persistence module admits the structure of a representation of a finite totally ordered set. In previous work, the authors…
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…
Adapting a definition given by Bjerkevik and Lesnick for multiparameter persistence modules, we introduce an $\ell^p$-type extension of the interleaving distance on merge trees. We show that our distance is a metric, and that it…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
Merge trees are a type of topological descriptors that record the connectivity among the sublevel sets of scalar fields. They are among the most widely used topological tools in visualization. In this paper, we are interested in sketching a…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
Kondo et al. (DS 2014) proposed methods for computing distances between unordered rooted trees by transforming an instance of the distance computing problem into an instance of the integer programming problem. They showed that the tree edit…
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…
An added edge to a graph is called an inset edge. Predicting k inset edges which minimize the average distance of a graph is known to be NP-Hard. However, when k = 1 the complexity of the problem is polynomial. In this paper, some tools for…
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 study the problem of learning hypergraphs with shortest-path queries (SP-queries), and present the first provably optimal online algorithm for a broad and natural class of hypertrees that we call orderly hypertrees. Our online algorithm…
We introduce a new variation of Tree Encoding with Nested Intervals, find connections with Materialized Path, and suggest a method for moving parts of the hierarchy.
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…
In this work we answer an open question asked by Johnson--Scoville. We show that each merge tree is represented by a discrete Morse function on a path. Furthermore, we present explicit constructions for two different but related kinds of…
We consider the genealogy tree for a critical branching process conditioned on non-extinction. We enumerate vertices in each generation of the tree so that for each two generations one can define a monotone map describing the…
The Hausdorff distance is a relatively new measure of similarity of graphs. The notion of the Hausdorff distance considers a special kind of a common subgraph of the compared graphs and depends on the structural properties outside of the…
Ranked tree-child networks are a recently introduced class of rooted phylogenetic networks in which the evolutionary events represented by the network are ordered so as to respect the flow of time. This class includes the well-studied…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
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…