Related papers: An $O(n \log n)$ time Algorithm for computing the …
The problem of comparing trees representing the evolutionary histories of cancerous tumors has turned out to be crucial, since there is a variety of different methods which typically infer multiple possible trees. A departure from the…
We show how to compute the edit distance between two strings of length n up to a factor of 2^{\~O(sqrt(log n))} in n^(1+o(1)) time. This is the first sub-polynomial approximation algorithm for this problem that runs in near-linear time,…
We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
Distances on merge trees facilitate visual comparison of collections of scalar fields. Two desirable properties for these distances to exhibit are 1) the ability to discern between scalar fields which other, less complex topological…
Let $P$ be a path graph of $n$ vertices embedded in a metric space. We consider the problem of adding a new edge to $P$ such that the diameter of the resulting graph is minimized. Previously (in ICALP 2015) the problem was solved in…
There are several interrelated notions of discrete curvature on graphs. Many approaches utilize the optimal transportation metric on its probability simplex or the distance matrix of the graph. In this survey article, we compute formulas…
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…
We study a path-planning problem amid a set $\mathcal{O}$ of obstacles in $\mathbb{R}^2$, in which we wish to compute a short path between two points while also maintaining a high clearance from $\mathcal{O}$; the clearance of a point is…
Phylogenetic tree comparison metrics are an important tool in the study of evolution, and hence the definition of such metrics is an interesting problem in phylogenetics. In a paper in Taxon fifty years ago, Sokal and Rohlf proposed to…
We show that the cophylogenetic distance, k-interval cospeciation, is distinct from other metrics and accounts for global congruence between locally incongruent trees. The growth of the neighborhood of trees which satisfy the largest…
The paper presents a discrete variation of the Frechet distance between closed curves, which can be seen as an approximation of the continuous measure. A rather straightforward approach to compute the discrete Frechet distance between two…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
Optimal transport provides a metric which quantifies the dissimilarity between probability measures. For measures supported in discrete metric spaces, finding the optimal transport distance has cubic time complexity in the size of the…
Given a graph $G = (V, E)$, we wish to compute a spanning tree whose maximum vertex degree, i.e. tree degree, is as small as possible. Computing the exact optimal solution is known to be NP-hard, since it generalizes the Hamiltonian path…
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…
Tree rotations (left and right) are basic local deformations allowing to transform between two unlabeled binary trees of the same size. Hence, there is a natural problem of practically finding such transformation path with low number of…
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 present fixed-parameter tractability algorithms for both the undirected and directed versions of the Spanning Tree Isomorphism Problem, parameterized by the size $k$ of a redundant set. A redundant set is a collection of…
Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Here, based on an idea of Bruen and Bryant, we propose and analyze a new distance measure: the Maximum Parsimony (MP)…
The Fr\'echet distance is a commonly used similarity measure between curves. It is known how to compute the continuous Fr\'echet distance between two polylines with $m$ and $n$ vertices in $\mathbb{R}^d$ in $O(mn (\log \log n)^2)$ time;…