Related papers: Efficient Parallel Computation of Nearest Neighbor…
There are few, if any, algorithms in statistical phylogenetics which are used more heavily than Felsenstein's 1973 pruning method for computing the likelihood of a tree. We present LvD, (Likelihood via Decomposition), an alternative to…
Given two strings of length $n$ over alphabet $\Sigma$, and an upper bound $k$ on their edit distance, the algorithm of Myers (Algorithmica'86) and Landau and Vishkin (JCSS'88) computes the unweighted string edit distance in…
In this paper, we present a new hybrid algorithm for the time integration of collisional N-body systems. In this algorithm, gravitational force between two particles is divided into short-range and long-range terms, using a…
A consensus tree is a phylogenetic tree that captures the similarity between a set of conflicting phylogenetic trees. The problem of computing a consensus tree is a major step in phylogenetic tree reconstruction. It also finds applications…
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…
Computing a Single-Linkage Dendrogram (SLD) is a key step in the classic single-linkage hierarchical clustering algorithm. Given an input edge-weighted tree $T$, the SLD of $T$ is a binary dendrogram that summarizes the $n-1$ clusterings…
The phylogenetic Mean Pairwise Distance (MPD) is one of the most popular measures for computing the phylogenetic distance between a given group of species. More specifically, for a phylogenetic tree T and for a set of species R represented…
The graph edit distance is used for comparing graphs in various domains. Due to its high computational complexity it is primarily approximated. Widely-used heuristics search for an optimal assignment of vertices based on the distance…
An algorithm is proposed for constructing directed spanning forests of the minimum weight, in which the maximum possible degree of affinity between the minimum forests is preserved when the number of trees changes. The correctness of the…
We consider the ``minimum degree spanning tree'' problem. As input, we receive an undirected, connected graph $G=(V, E)$ with $n$ nodes and $m$ edges, and our task is to find a spanning tree $T$ of $G$ that minimizes $\max_{u \in V}…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…
In this paper we present algorithms for a number of problems in geometric pattern matching where the input consist of a collections of segments in the plane. Our work consists of two main parts. In the first, we address problems and…
Exact nearest neighbor search is a computationally intensive process, and even its simpler sibling -- vector retrieval -- can be computationally complex. This is exacerbated when retrieving vectors which have high-dimension $d$ relative to…
Time series are ubiquitous in domains ranging from medicine to marketing and finance. Frequent Pattern Mining (FPM) from a time series has thus received much attention. Recently, it has been studied under the order-preserving (OP) matching…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
We describe a $O(\log n )$-approximation algorithm for computing the homotopic \Frechet distance between two polygonal curves that lie on the boundary of a triangulated topological disk. Prior to this work, algorithms were known only for…
We study approximate-near-neighbor data structures for time series under the continuous Fr\'echet distance. For an attainable approximation factor $c>1$ and a query radius $r$, an approximate-near-neighbor data structure can be used to…
We present a near-linear time algorithm that approximates the edit distance between two strings within a polylogarithmic factor; specifically, for strings of length n and every fixed epsilon>0, it can compute a (log n)^O(1/epsilon)…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
K-nearest neighbor (kNN) search has wide applications in many areas, including data mining, machine learning, statistics and many applied domains. Inspired by the success of ensemble methods and the flexibility of tree-based methodology, we…