Related papers: Least Squares Methods for Equidistant Tree Reconst…
We develop a time-optimal $O(mn^2)$-time algorithm to construct the subtree prune-regraft (SPR) graph on a collection of m phylogenetic trees with n leaves. This improves on the previous bound of $O(mn^3)$. Such graphs are used to better…
Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we…
Many metric learning tasks, such as triplet learning, nearest neighbor retrieval, and visualization, are treated primarily as embedding tasks where the ultimate metric is some variant of the Euclidean distance (e.g., cosine or Mahalanobis),…
The Euclidean Steiner tree problem asks to find a min-cost metric graph that connects a given set of \emph{terminal} points $X$ in $\mathbb{R}^d$, possibly using points not in $X$ which are called Steiner points. Even though near-linear…
Given a set of points in the Euclidean plane, the Euclidean \textit{$\delta$-minimum spanning tree} ($\delta$-MST) problem is the problem of finding a spanning tree with maximum degree no more than $\delta$ for the set of points such the…
We propose a unifying algorithm for non-smooth non-convex optimization. The algorithm approximates the objective function by a convex model function and finds an approximate (Bregman) proximal point of the convex model. This approximate…
Phylogenetic trees are leaf-labelled trees, where the leaves correspond to extant species (taxa), and the internal vertices represent ancestral species. The evolutionary history of a set of species can be explained by more than one…
The nni-distance is a well-known distance measure for phylogenetic trees. We construct an efficient parallel approximation algorithm for the nni-distance in the CRCW-PRAM model running in O(log n) time on O(n) processors. Given two…
We present improved learning-augmented algorithms for finding an approximate minimum spanning tree (MST) for points in an arbitrary metric space. Our work follows a recent framework called metric forest completion (MFC), where the learned…
The problem of recovering the configuration of points from their partial pairwise distances, referred to as the Euclidean Distance Matrix Completion (EDMC) problem, arises in a broad range of applications, including sensor network…
Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…
Embedding graphs in a geographical or latent space, i.e.\ inferring locations for vertices in Euclidean space or on a smooth manifold or submanifold, is a common task in network analysis, statistical inference, and graph visualization. We…
Proximity graph-based methods have emerged as a leading paradigm for approximate nearest neighbor (ANN) search in the system community. This paper presents fresh insights into the theoretical foundation of these methods. We describe an…
We introduce a decomposition method for the distributed calculation of exact Euclidean Minimum Spanning Trees in high dimensions (where sub-quadratic algorithms are not effective), or more generalized geometric-minimum spanning trees of…
Given access to the vertex set $V$ of a connected graph $G=(V,E)$ and an oracle that given two vertices $u,v\in V$, returns the shortest path distance between $u$ and $v$, how many queries are needed to reconstruct $E$? Firstly, we show…
Motivation: Word-based or `alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate. Most of these methods calculate pairwise distances for a set of input…
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 recurring theme in the least squares approach to phylogenetics has been the discovery of elegant combinatorial formulas for the least squares estimates of edge lengths. These formulas have proved useful for the development of efficient…
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…
Given a 2-edge connected, unweighted, and undirected graph $G$ with $n$ vertices and $m$ edges, a $\sigma$-tree spanner is a spanning tree $T$ of $G$ in which the ratio between the distance in $T$ of any pair of vertices and the…