Related papers: Efficient chaining of seeds in ordered trees

Path partition problems on trees have found various applications. In this paper, we present an $O(n \log n)$ time algorithm for solving the following variant of path partition problem: given a rooted tree of $n$ nodes $1, \ldots, n$, where…

Phylogenetic networks are used to represent evolutionary scenarios in biology and linguistics. To find the most probable scenario, it may be necessary to compare candidate networks, to distinguish different networks, and to see when one…

The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…

Computing an optimal chain of fragments is a classical problem in string algorithms, with important applications in computational biology. There exist two efficient dynamic programming algorithms solving this problem, based on different…

This paper investigates the execution of tree-shaped task graphs using multiple processors. Each edge of such a tree represents a large IO file. A task can only be executed if all input and output files fit into memory, and a file can only…

Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…

The Subtree Isomorphism problem asks whether a given tree is contained in another given tree. The problem is of fundamental importance and has been studied since the 1960s. For some variants, e.g., ordered trees, near-linear time algorithms…

We study the influence of the seed in random trees grown according to the uniform attachment model, also known as uniform random recursive trees. We show that different seeds lead to different distributions of limiting trees from a total…

In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…

We investigate the size of vertex confidence sets for including part of (or the entirety of) the seed in seeded uniform attachment trees, given knowledge of some of the seed's properties, and with a prescribed probability of failure. We…

Rooted phylogenetic networks allow biologists to represent evolutionary relationships between present-day species by revealing ancestral speciation and hybridization events. A convenient and well-studied class of such networks are…

Consider two networks on overlapping, non-identical vertex sets. Given vertices of interest in the first network, we seek to identify the corresponding vertices, if any exist, in the second network. While in moderately sized networks graph…

The kernel method is a potential approach to analyzing structured data such as sequences, trees, and graphs; however, unordered trees have not been investigated extensively. Kimura et al. (2011) proposed a kernel function for unordered…

Kondo et al. (DS 2014) proposed methods for computing distances between unordered rooted trees by transforming an instance of the distance computing problem into an instance of the integer programming problem. They showed that the tree edit…

LRM-Trees are an elegant way to partition a sequence of values into sorted consecutive blocks, and to express the relative position of the first element of each block within a previous block. They were used to encode ordinal trees and to…

Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…

Network alignment consists of finding a structure-preserving correspondence between the nodes of two correlated, but not necessarily identical, networks. This problem finds applications in a wide variety of fields, from the alignment of…

Tree kernels are fundamental tools that have been leveraged in many applications, particularly those based on machine learning for Natural Language Processing tasks. In this paper, we devise a parallel implementation of the sequential…

Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…

Balanced search trees are widely used in computer science to efficiently maintain dynamic ordered data. To support efficient set operations (e.g., union, intersection, difference) using trees, the join-based framework is widely studied.…