Related papers: Least Squares Methods for Equidistant Tree Reconst…
The number of the non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the nearest…
Tree rearrangements such as Nearest Neighbor Interchange (NNI) and Subtree Prune and Regraft (SPR) are commonly used to explore phylogenetic treespace. Computing distances based on them, however, is often intractable, so the efficiently…
Balanced minimum evolution (BME) is a statistically consistent distance-based method to reconstruct a phylogenetic tree from an alignment of molecular data. In 2000, Pauplin showed that the BME method is equivalent to optimizing a linear…
A classic problem in unsupervised learning and data analysis is to find simpler and easy-to-visualize representations of the data that preserve its essential properties. A widely-used method to preserve the underlying hierarchical structure…
The metric space of phylogenetic trees defined by Billera, Holmes, and Vogtmann, which we refer to as BHV space, provides a natural geometric setting for describing collections of trees on the same set of taxa. However, it is sometimes…
This paper studies numerical methods for the approximation of elliptic PDEs with lognormal coefficients of the form $-{\rm div}(a\nabla u)=f$ where $a=\exp(b)$ and $b$ is a Gaussian random field. The approximant of the solution $u$ is an…
Short spanning trees subject to additional constraints are important building blocks in various approximation algorithms. Especially in the context of the Traveling Salesman Problem (TSP), new techniques for finding spanning trees with…
Nuclear Magnetic Resonance (NMR) Spectroscopy is a widely used technique to predict the native structure of proteins. However, NMR machines are only able to report approximate and partial distances between pair of atoms. To build the…
The Neighbor-Joining algorithm is a popular distance-based phylogenetic method that computes a tree metric from a dissimilarity map arising from biological data. Realizing dissimilarity maps as points in Euclidean space, the algorithm…
We provide efficient constant factor approximation algorithms for the problems of finding a hierarchical clustering of a point set in any metric space, minimizing the sum of minimimum spanning tree lengths within each cluster, and in the…
We give a greedy learning algorithm for reconstructing an evolutionary tree based on a certain harmonic average on triplets of terminal taxa. After the pairwise distances between terminal taxa are estimated from sequence data, the algorithm…
Given an undirected, weighted graph, the minimum spanning tree (MST) is a tree that connects all of the vertices of the graph with minimum sum of edge weights. In real world applications, network designers often seek to quickly find a…
Balanced minimum evolution is a distance-based criterion for the reconstruction of phylogenetic trees. Several algorithms exist to find the optimal tree with respect to this criterion. One approach is to minimize a certain linear functional…
Uniform cost-distance Steiner trees minimize the sum of the total length and weighted path lengths from a dedicated root to the other terminals. They are applied when the tree is intended for signal transmission, e.g. in chip design or…
The Gromov-Hausdorff (GH) distance is a natural way to measure distance between two metric spaces. We prove that it is $\mathrm{NP}$-hard to approximate the Gromov-Hausdorff distance better than a factor of $3$ for geodesic metrics on a…
The subtree prune-and-regraft (SPR) distance metric is a fundamental way of comparing evolutionary trees. It has wide-ranging applications, such as to study lateral genetic transfer, viral recombination, and Markov chain Monte Carlo…
A rearrangement operation makes a small graph-theoretical change to a phylogenetic network to transform it into another one. For unrooted phylogenetic trees and networks, popular rearrangement operations are tree bisection and reconnection…
In this paper, we provide a simple convergence analysis of proximal gradient algorithm with Bregman distance, which provides a tighter bound than existing result. In particular, for the problem of minimizing a class of convex objective…
The (unweighted) tree edit distance problem for $n$ node trees asks to compute a measure of dissimilarity between two rooted trees with node labels. The current best algorithm from more than a decade ago runs in $O(n ^ 3)$ time [Demaine,…
Consider~\(n\) nodes~\(\{X_i\}_{1 \leq i \leq n}\) independently distributed in the unit square~\(S,\) each according to a distribution~\(f.\) Nodes~\(X_i\) and~\(X_j\) are joined by an edge if the Euclidean distance~\(d(X_i,X_j)\) is less…