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Evolutionary relationships between species are usually inferred through phylogenetic analysis, which provides phylogenetic trees computed from allelic profiles built by sequencing specific regions of the sequences and abstracting them to…
Building a spanning tree, minimum spanning tree (MST), and BFS tree in a distributed network are fundamental problems which are still not fully understood in terms of time and communication cost. x The first work to succeed in computing a…
Search trees on trees (STTs) generalize the fundamental binary search tree (BST) data structure: in STTs the underlying search space is an arbitrary tree, whereas in BSTs it is a path. An optimal BST of size $n$ can be computed for a given…
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…
The tree edit distance (TED) between two rooted ordered trees with $n$ nodes labeled from an alphabet $\Sigma$ is the minimum cost of transforming one tree into the other by a sequence of valid operations consisting of insertions, deletions…
Recent years have witnessed a surge of biological interest in the minimum spanning tree (MST) problem for its relevance to automatic model construction using the distances between data points. Despite the increasing use of MST algorithms…
Merge trees are a type of graph-based topological summary that tracks the evolution of connected components in the sublevel sets of scalar functions. They enjoy widespread applications in data analysis and scientific visualization. In this…
The goal of this paper is to study the similarity between sequences using a distance between the \emph{context} trees associated to the sequences. These trees are defined in the framework of \emph{Sparse Probabilistic Suffix Trees} (SPST),…
An important problem in geometric computing is defining and computing similarity between two geometric shapes, e.g. point sets, curves and surfaces, etc. Important geometric and topological information of many shapes can be captured by…
SpectralNet is a graph clustering method that uses neural network to find an embedding that separates the data. So far it was only used with $k$-nn graphs, which are usually constructed using a distance metric (e.g., Euclidean distance).…
We consider the classical tree edit distance between ordered labeled trees, which is defined as the minimum-cost sequence of node edit operations that transform one tree into another. The state-of-the-art solutions for the tree edit…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
It was recently observed by de Vienne et al. that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on…
We present approximation algorithms for the following NP-hard optimization problems related to bottleneck spanning trees in metric spaces. 1. The disjoint bottleneck spanning tree problem: Given $n$ pairs of points in a metric space, find…
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…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
A merge tree is a fundamental topological structure used to capture the sub-level set (and similarly, super-level set) topology in scalar data analysis. The interleaving distance is a theoretically sound, stable metric for comparing merge…
We study the connections between sorting and the binary search tree (BST) model, with an aim towards showing that the fields are connected more deeply than is currently appreciated. While any BST can be used to sort by inserting the keys…
Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. But, as far as…
The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small world property of real…