Related papers: Efficient chaining of seeds in ordered trees
Given a pattern x of length m and a text y of length n, both over an ordered alphabet, the order-preserving pattern matching problem consists in finding all substrings of the text with the same relative order as the pattern. It is an…
We introduce a new metric of match, called Cartesian tree matching, which means that two strings match if they have the same Cartesian trees. Based on Cartesian tree matching, we define single pattern matching for a text of length n and a…
We give an algorithm to enumerate the results on trees of monadic second-order (MSO) queries represented by nondeterministic tree automata. After linear time preprocessing (in the input tree), we can enumerate answers with linear delay (in…
The class of self-nested trees presents remarkable compression properties because of the systematic repetition of subtrees in their structure. In this paper, we provide a better combinatorial characterization of this specific family of…
We study compact straight-line embeddings of trees. We show that perfect binary trees can be embedded optimally: a tree with $n$ nodes can be drawn on a $\sqrt n$ by $\sqrt n$ grid. We also show that testing whether a given binary tree has…
We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We…
For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…
In this article, we give a precise mathematical meaning to `linear? time' that matches experimental behaviour of the algorithm. The sorting algorithm is not our own, it is a variant of radix sort with counting sort as a subroutine. The true…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
In this paper, an stochastic queue core problem on a tree, which seeks to find a core in an M/G/1 operating environment is investigated. Let T = (V,E) be a tree, an stochastic queue core of T is assumed to be a path P, for which the…
In this paper, we consider the problem of identifying patterns of interest in colored strings. A colored string is a string where each position is assigned one of a finite set of colors. Our task is to find substrings of the colored string…
We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling…
We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is…
Decompositions of networks are useful not only for structural exploration. They also have implications and use in analysis and computational solution of processes (such as the Ising model, percolation, SIR model) running on a given network.…
Inspired by [4] we present a new algorithm for uniformly random generation of ordered trees in which all occuring outdegrees can be specified by a given sequence of numbers. The method can be used for random generation of binary or n-ary…
An arc-annotated string is a string of characters, called bases, augmented with a set of pairs, called arcs, each connecting two bases. Given arc-annotated strings $P$ and $Q$ the arc-preserving subsequence problem is to determine if $P$…
We consider the problem of laying out a tree with fixed parent/child structure in hierarchical memory. The goal is to minimize the expected number of block transfers performed during a search along a root-to-leaf path, subject to a given…
We present a comprehensive classical and parameterized complexity analysis of decision tree pruning operations, extending recent research on the complexity of learning small decision trees. Thereby, we offer new insights into the…
The cellular tree classifier model addresses a fundamental problem in the design of classifiers for a parallel or distributed computing world: Given a data set, is it sufficient to apply a majority rule for classification, or shall one…
An ordered labeled tree is a tree in which the nodes are labeled and the left-to-right order among siblings is relevant. The edit distance between two ordered labeled trees is the minimum cost of changing one tree into the other through a…