Related papers: An $O(n \log n)$ time Algorithm for computing the …
Cartesian tree pattern matching consists of finding all the factors of a text that have the same Cartesian tree than a given pattern. There already exist theoretical and practical solutions for the exact case. In this paper, we propose the…
The early development of a zygote can be mathematically described by a developmental tree. To compare developmental trees of different species, we need to define distances on trees. If children cells after a division are not…
Several problems that are NP-hard on general graphs are efficiently solvable on graphs with bounded treewidth. Efforts have been made to generalize treewidth and the related notion of pathwidth to digraphs. Directed treewidth, DAG-width and…
In the PATH COVER problem, one asks to cover the vertices of a graph using the smallest possible number of (not necessarily disjoint) paths. While the variant where the paths need to be pairwise vertex-disjoint, which we call PATH…
In graph theory, a tree is one of the more popular families of graphs with a wide range of applications in computer science as well as many other related fields. While there are several distance measures over the set of all trees, we…
In this paper, we present a distributed algorithm to compute various parameters of a tree such as the process number, the edge search number or the node search number and so the pathwidth. This algorithm requires n steps, an overall…
Motivated by classic tree algorithms, in 1995 we designed a bottom-up $O(n)$ algorithm to compute the determinant of a tree's adjacency matrix $A$. In 2010 an $O(n)$ algorithm was found for constructing a diagonal matrix congruent to $A +…
Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…
We present a dynamic data structure that maintains a tree decomposition of width at most $9k+8$ of a dynamic graph with treewidth at most $k$, which is updated by edge insertions and deletions. The amortized update time of our data…
Distance based algorithms are a common technique in the construction of phylogenetic trees from taxonomic sequence data. The first step in the implementation of these algorithms is the calculation of a pairwise distance matrix to give a…
We address the problem of computing distances between rankings that take into account similarities between candidates. The need for evaluating such distances is governed by applications as diverse as rank aggregation, bioinformatics, social…
Given two binary trees on $N$ labeled leaves, the quartet distance between the trees is the number of disagreeing quartets. By permuting the leaves at random, the expected quartets distance between the two trees is…
Feature tracking in time-varying scalar fields is a fundamental task in scientific computing. Topological descriptors, which summarize important features of data, have proved to be viable tools to facilitate this task. The merge tree is a…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
We present the first dynamic algorithms for Dyck and tree edit distances with subpolynomial update times. Dyck edit distance measures how far a parenthesis string is from a well-parenthesized expression, while tree edit distance quantifies…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
This paper studies graphs that have two tree decompositions with the property that every bag from the first decomposition has a bounded-size intersection with every bag from the second decomposition. We show that every graph in each of the…
We present a simple $O(n^4)$-time algorithm for computing optimal search trees with two-way comparisons. The only previous solution to this problem, by Anderson et al., has the same running time, but is significantly more complicated and is…