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We study the problem of computing the triplet distance between two rooted unordered trees with $n$ labeled leafs. Introduced by Dobson 1975, the triplet distance is the number of leaf triples that induce different topologies in the two…
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…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…
We present a new approximation algorithm for the treewidth problem which finds an upper bound on the treewidth and constructs a corresponding tree decomposition as well. Our algorithm is a faster variation of Reed's classical algorithm. For…
Evolutionary scenarios displaying reticulation events are often represented by rooted phylogenetic networks. Due to biological reasons, those events occur very rarely, and, thus, networks containing a minimum number of such events,…
Univariate polynomial root-finding is a classical subject, still important for modern computing. Frequently one seeks just the real roots of a polynomial with real coefficients. They can be approximated at a low computational cost if the…
This paper give a simple linear-time algorithm that, given a weighted digraph, finds a spanning tree that simultaneously approximates a shortest-path tree and a minimum spanning tree. The algorithm provides a continuous trade-off: given the…
Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Recently, a new distance measure has been proposed: the Maximum Parsimony (MP) distance. This is based on the…
We study approximation algorithms for the forest cover and bounded forest cover problems. A probabilistic $2+\epsilon$ approximation algorithm for the forest cover problem is given using the method of dual fitting. A deterministic algorithm…
We analyze a probabilistic algorithm for matching shapes modeled by planar regions under translations and rigid motions (rotation and translation). Given shapes $A$ and $B$, the algorithm computes a transformation $t$ such that with high…
Linear model trees are regression trees that incorporate linear models in the leaf nodes. This preserves the intuitive interpretation of decision trees and at the same time enables them to better capture linear relationships, which is hard…
The syntactic structure of a sentence is often represented using syntactic dependency trees. The sum of the distances between syntactically related words has been in the limelight for the past decades. Research on dependency distances led…
The focus of this paper is the analysis of real-time systems with recursion, through the development of good theoretical techniques which are implementable. Time is modeled using clock variables, and recursion using stacks. Our technique…
This paper presents a detailed comparison of a recently proposed algorithm for optimizing decision trees, tree alternating optimization (TAO), with other popular, established algorithms. We compare their performance on a number of…
In recent years, non-parametric methods utilizing random walks on graphs have been used to solve a wide range of machine learning problems, but in their simplest form they do not scale well due to the quadratic complexity. In this paper, a…
In the first part of the paper, we present an (1+\mu)-approximation algorithm to the minimum-spanning tree of points in a planar arrangement of lines, where the metric is the number of crossings between the spanning tree and the lines. The…
The Aho, Hopcroft and Ullman (AHU) algorithm has been the state of the art since the 1970s for determining in linear time whether two unordered rooted trees are isomorphic or not. However, it has been criticized (by Campbell and Radford)…
This paper proposes a bidirectional rapidly-exploring random trees (RRT) algorithm to solve the motion planning problem for hybrid systems. The proposed algorithm, called HyRRT-Connect, propagates in both forward and backward directions in…
Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…
Rebalancing schemes for dynamic binary search trees are numerous in the literature, where the goal is to maintain trees of low height, either in the worst-case or expected sense. In this paper we study randomized rebalancing schemes for…