Related papers: An $O(n \log n)$ time Algorithm for computing the …
Good representations for phylogenetic trees and networks are important for optimizing storage efficiency and implementation of scalable methods for the inference and analysis of evolutionary trees for genes, genomes and species. We…
As well known the rotation distance D(S,T) between two binary trees S, T of n vertices is the minimum number of rotations of pairs of vertices to transform S into T. We introduce the new operation of chain rotation on a tree, involving two…
Linear rank-width is a linearized variation of rank-width, and it is deeply related to matroid path-width. In this paper, we show that the linear rank-width of every $n$-vertex distance-hereditary graph, equivalently a graph of rank-width…
This work briefly explores the possibility of approximating spatial distance (alternatively, similarity) between data points using the Isolation Forest method envisioned for outlier detection. The logic is similar to that of isolation: the…
The edit distance between two rooted ordered trees with $n$ nodes labeled from an alphabet~$\Sigma$ is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling…
Let $G$ be a unit disk graph in the plane defined by $n$ disks whose positions are known. For the case when $G$ is unweighted, we give a simple algorithm to compute a shortest path tree from a given source in $O(n\log n)$ time. For the case…
The shortest augmenting path technique is one of the fundamental ideas used in maximum matching and maximum flow algorithms. Since being introduced by Edmonds and Karp in 1972, it has been widely applied in many different settings.…
Metrics for merge trees that are simultaneously stable, informative, and efficiently computable have so far eluded researchers. We show in this work that it is possible to devise such a metric when restricting merge trees to ordered domains…
We describe the first strongly subquadratic time algorithm with subexponential approximation ratio for approximately computing the Fr\'echet distance between two polygonal chains. Specifically, let $P$ and $Q$ be two polygonal chains with…
Given a plane undirected graph $G$ with non-negative edge weights and a set of $k$ terminal pairs on the external face, it is shown in Takahashi et al. (Algorithmica, 16, 1996, pp. 339-357) that the union $U$ of $k$ non-crossing shortest…
The space of phylogenetic trees arises naturally in tropical geometry as the tropical Grassmannian. Tropical geometry therefore suggests a natural notion of a tropical path between two trees, given by a tropical line segment in the tropical…
This thesis presents analysis of the properties and run-time of the Rapidly-exploring Random Tree (RRT) algorithm. It is shown that the time for the RRT with stepsize $\epsilon$ to grow close to every point in the $d$-dimensional unit cube…
We give an O(sqrt n log n)-query quantum algorithm for evaluating size-n AND-OR formulas. Its running time is poly-logarithmically greater after efficient preprocessing. Unlike previous approaches, the algorithm is based on a quantum walk…
The tree-cut width of a graph is a graph parameter defined by Wollan [J. Comb. Theory, Ser. B, 110:47-66, 2015] with the help of tree-cut decompositions. In certain cases, tree-cut width appears to be more adequate than treewidth as an…
We present a randomized algorithm for reconstructing directed rooted trees of $n$ nodes and node degree at most $d$, by asking at most $O(dn\log^2 n)$ path queries. Each path query takes as input an origin node and a target node, and…
Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…
In molecular systematics, evolutionary trees are reconstructed from sequences at the tips under simple models of site substitution. A central question is how much sequence data is required to reconstruct a tree accurately? The answer…
Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to measure the dissimilarity of the two trees.…
Computing the Fr\'echet distance between two polygonal curves takes roughly quadratic time. In this paper, we show that for a special class of curves the Fr\'echet distance computations become easier. Let $P$ and $Q$ be two polygonal curves…
Let $T=t_0 ... t_{n-1}$ be a text and $P = p_0 ... p_{m-1}$ a pattern taken from some finite alphabet set $\Sigma$, and let $\dist$ be a metric on $\Sigma$. We consider the problem of calculating the sum of distances between the symbols of…