Related papers: Efficient chaining of seeds in ordered trees

One can often make inferences about a growing network from its current state alone. For example, it is generally possible to determine how a network changed over time or pick among plausible mechanisms explaining its growth. In practice,…

Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…

In this paper, we consider a coverage problem for uncertain points in a tree. Let T be a tree containing a set P of n (weighted) demand points, and the location of each demand point P_i\in P is uncertain but is known to appear in one of m_i…

Given a rooted tree and a ranking of its leaves, what is the minimum number of inversions of the leaves that can be attained by ordering the tree? This variation of the problem of counting inversions in arrays originated in mathematical…

Matching cells over time has long been the most difficult step in cell tracking. In this paper, we approach this problem by recasting it as a classification problem. We construct a feature set for each cell, and compute a feature difference…

Graphs are extremely versatile and ubiquitous mathematical structures with potential to model a wide range of domains. For this reason, graph problems have been of interest since the early days of computer science. Some of these problems…

We address the problem of summarizing embedded tree patterns extracted from large data trees. We do so by defining and mining closed and maximal embedded unordered tree patterns from a single large data tree. We design an embedded frequent…

We present a complete classification of the deterministic distributed time complexity for a family of graph problems: binary labeling problems in trees. These are locally checkable problems that can be encoded with an alphabet of size two…

Dynamic regression trees are an attractive option for automatic regression and classification with complicated response surfaces in on-line application settings. We create a sequential tree model whose state changes in time with the…

We provide decidability and undecidability results on the model-checking problem for infinite tree structures. These tree structures are built from sequences of elements of infinite relational structures. More precisely, we deal with the…

This work addresses the intrinsic relationship between trees and networks (i.e. graphs). A complete (invertible) mapping is presented which allows trees to be mapped into weighted graphs and then backmapped into the original tree without…

Given a graph where every vertex has exactly one labeled token, how can we most quickly execute a given permutation on the tokens? In (sequential) token swapping, the goal is to use the shortest possible sequence of swaps, each of which…

Given two point sets $R$ and $B$ in the plane, with cardinalities $m$ and $n$, respectively, and each set stored in a separate R-tree, we present an algorithm to decide whether $R$ and $B$ are linearly separable. Our algorithm exploits the…

Given a tree of weighted vertices, it is sometimes possible to break the tree into two equally-weighted subtrees within an allowable error. We give a fast algorithm that finds an edge which breaks the tree into equal-weight components or…

The rooted tree is an important data structure, and the subtree size, height, and depth are naturally defined attributes of every node. We consider the problem of the existence of a k-ary tree given a list of attribute sequences. We give…

In this paper, we introduce the Fixed Topology Minimum-Length Tree with Neighborhood Problem, which aims to embed a rooted tree-shaped graph into a $d$-dimensional metric space while minimizing its total length provided that the nodes must…

We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…

Phylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is…

Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…

In this paper, we are interested in the number of red nodes in red-black trees. We first present an $O(n^2\log n)$ time dynamic programming solution for computing $r(n)$, the largest number of red internal nodes in a red-black tree on $n$…