Related papers: The Neighbor-Net Algorithm

Neighborhood finders and nearest neighbor queries are fundamental parts of sampling based motion planning algorithms. Using different distance metrics or otherwise changing the definition of a neighborhood produces different algorithms with…

This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which…

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…

One of the approaches for the nearest neighbor search problem is to build a network which nodes correspond to the given set of indexed objects. In this case the search of the closest object can be thought as a search of a node in a network.…

\begin{abstract} Greedy permutations, also known as Gonzalez Orderings or Farthest Point Traversals are a standard way to approximate $k$-center clustering and have many applications in sampling and approximating metric spaces. A greedy…

We study the problem of minimizing a sum of convex objective functions where the components of the objective are available at different nodes of a network and nodes are allowed to only communicate with their neighbors. The use of…

Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…

We address the question of finding the community structure of a complex network. In an earlier effort [H. Zhou, {\em Phys. Rev. E} (2003)], the concept of network random walking is introduced and a distance measure defined. Here we…

Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the…

Many distributed learning techniques have been motivated by the increasing size of datasets and their inability to fit into main memory on a single machine. We propose an algorithm that finds the nearest neighbor in a graph locally without…

Data-driven neighborhood definitions and graph constructions are often used in machine learning and signal processing applications. k-nearest neighbor~(kNN) and $\epsilon$-neighborhood methods are among the most common methods used for…

It is a critical issue to compute the shortest paths between nodes in networks. Exact algorithms for shortest paths are usually inapplicable for large scale networks due to the high computational complexity. In this paper, we propose a…

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…

The Neighbor Joining Algorithm is among the most fundamental algorithmic results in computational biology. However, its definition and correctness proof are not straightforward. In particular, ''the question ''what does the NJ method seek…

k-nearest neighbor graph is a fundamental data structure in many disciplines such as information retrieval, data-mining, pattern recognition, and machine learning, etc. In the literature, considerable research has been focusing on how to…

We start with a review of the pervasiveness of the nearest neighbor search problem and techniques used to solve it along with some experimental results. In the second chapter, we show reductions between two different classes of geo- metric…

Phylogenetic networks are notoriously difficult to reconstruct. Here we suggest that it can be useful to view unknown genetic distance along edges in phylogenetic networks as analogous to unknown resistance in electric circuits. This…

In an earlier paper we introduced a special kind of k-width junction tree, called k-th order t-cherry junction tree in order to approximate a joint probability distribution. The approximation is the best if the Kullback-Leibler divergence…

The growing amount of applications that generate vast amount of data in short time scales render the problem of partial monitoring, coupled with prediction, a rather fundamental one. We study the aforementioned canonical problem under the…

Visualization of the adjacency matrix enables us to capture macroscopic features of a network when the matrix elements are aligned properly. Community structure, a network consisting of several densely connected components, is a…