Related papers: Efficient chaining of seeds in ordered trees
The notion of the cover is a generalization of a period of a string, and there are linear time algorithms for finding the shortest cover. The seed is a more complicated generalization of periodicity, it is a cover of a superstring of a…
A seed in a word is a relaxed version of a period in which the occurrences of the repeating subword may overlap. We show a linear-time algorithm computing a linear-size representation of all the seeds of a word (the number of seeds might be…
The tree inclusion problem is, given two node-labeled trees $P$ and $T$ (the ``pattern tree'' and the ``target tree''), to locate every minimal subtree in $T$ (if any) that can be obtained by applying a sequence of node insertion operations…
Given two rooted, labeled trees $P$ and $T$ the tree path subsequence problem is to determine which paths in $P$ are subsequences of which paths in $T$. Here a path begins at the root and ends at a leaf. In this paper we propose this…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called \textsc{Tree Containment}, arises when validating networks constructed by phylogenetic…
Trees are useful entities allowing to model data structures and hierarchical relationships in networked decision systems ubiquitously. An ordered tree is a rooted tree where the order of the subtrees (children) of a node is significant. In…
Tree containment problem is a fundamental problem in phylogenetic study, as it is used to verify a network model. It asks whether a given network contain a subtree that resembles a binary tree. The problem is NP-complete in general, even in…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
Algorithms to find optimal alignments among strings, or to find a parsimonious summary of a collection of strings, are well studied in a variety of contexts, addressing a wide range of interesting applications. In this paper, we consider…
Dual-tree algorithms are a widely used class of branch-and-bound algorithms. Unfortunately, developing dual-tree algorithms for use with different trees and problems is often complex and burdensome. We introduce a four-part logical split:…
The order preserving pattern matching (OPPM) problem is, given a pattern string $p$ and a text string $t$, find all substrings of $t$ which have the same relative orders as $p$. In this paper, we consider two variants of the OPPM problem…
One of the important features of an interconnection network is its ability to efficiently simulate programs or parallel algorithms written for other architectures. Such a simulation problem can be mathematically formulated as a graph…
We study the problem of connecting the parts of a multipartite graph using a minimum number of edges under a matching constraint. We introduce interconnection trees, defined as matchings whose projections onto the quotient graph form a…
Sorting is a foundational problem in computer science that is typically employed on sequences or total orders. More recently, a more general form of sorting on partially ordered sets (or posets), where some pairs of elements are…
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…
Recently Kubica et al. (Inf. Process. Let., 2013) and Kim et al. (submitted to Theor. Comp. Sci.) introduced order-preserving pattern matching. In this problem we are looking for consecutive substrings of the text that have the same "shape"…