Related papers: Subtree Isomorphism Revisited

The tree edit distance problem is a natural generalization of the classic string edit distance problem. Given two ordered, edge-labeled trees $T_1$ and $T_2$, the edit distance between $T_1$ and $T_2$ is defined as the minimum total cost of…

Phylogenetic networks allow modeling reticulate evolution, capturing events such as hybridization and horizontal gene transfer. A fundamental computational problem in this context is the Tree Containment problem, which asks whether a given…

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…

Over the past decade, we witness an increasing amount of interest in the design of exact exponential-time and parameterized algorithms for problems in Graph Drawing. Unfortunately, we still lack knowledge of general methods to develop such…

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…

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…

In the context of tree-search stochastic planning algorithms where a generative model is available, we consider on-line planning algorithms building trees in order to recommend an action. We investigate the question of avoiding re-planning…

Thin spanning trees lie at the intersection of graph theory, approximation algorithms, and combinatorial optimization. They are central to the long-standing \emph{thin tree conjecture}, which asks whether every $k$-edge-connected graph…

This work considers a number of optimization problems and reductive relations between them. The two main problems we are interested in are the \emph{Optimal Decision Tree} and \emph{Set Cover}. We study these two fundamental tasks under…

In the first paper (part I) of this series of two, we introduce four novel definitions of the ODT problems: three for size-constrained trees and one for depth-constrained trees. These definitions are stated unambiguously through executable…

The subtree prune-and-regraft (SPR) distance metric is a fundamental way of comparing evolutionary trees. It has wide-ranging applications, such as to study lateral genetic transfer, viral recombination, and Markov chain Monte Carlo…

The problem of Subgraph Isomorphism is defined as follows: Given a pattern H and a host graph G on n vertices, does G contain a subgraph that is isomorphic to H? Eppstein [SODA 95, J'GAA 99] gives the first linear time algorithm for…

The dynamic trees problem is to maintain a forest subject to edge insertions and deletions while facilitating queries such as connectivity, path weights, and subtree weights. Dynamic trees are a fundamental building block of a large number…

We revisit the issue of low-distortion embedding of metric spaces into the line, and more generally, into the shortest path metric of trees, from the parameterized complexity perspective.Let $M=M(G)$ be the shortest path metric of an edge…

Dynamic tree data structures maintain a forest while supporting insertion and deletion of edges and a broad set of queries in $O(\log n)$ time per operation. Such data structures are at the core of many modern algorithms. Recent work has…

The \emph{Steiner tree} problem is one of the fundamental and classical problems in combinatorial optimization. In this paper, we study this problem in the $\mathcal{CONGESTED}$ $\mathcal{CLIQUE}$ model of distributed computing and present…

Self-nested trees present a systematic form of redundancy in their subtrees and thus achieve optimal compression rates by DAG compression. A method for quantifying the degree of self-similarity of plants through self-nested trees has been…

In this paper we propose and study a new complexity model for approximation algorithms. The main motivation are practical problems over large data sets that need to be solved many times for different scenarios, e.g., many multicast trees…

We give the first non-trivial fully dynamic probabilistic tree embedding algorithm for weighted graphs undergoing edge insertions and deletions. We obtain a trade-off between amortized update time and expected stretch against an oblivious…

We present approximation algorithms for the following NP-hard optimization problems related to bottleneck spanning trees in metric spaces. 1. The disjoint bottleneck spanning tree problem: Given $n$ pairs of points in a metric space, find…