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The quartet distance is a measure of similarity used to compare two unrooted phylogenetic trees on the same set of $n$ leaves, defined as the number of subsets of four leaves related by a different topology in both trees. After a series of…
The {\em edit distance} between two ordered trees with vertex labels is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling existing nodes, as well as…
While a lot of work in theoretical computer science has gone into optimizing the runtime and space usage of data structures, such work very often neglects a very important component of modern computers: the cache. In doing so, very often,…
Tree comparison metrics have proven to be an invaluable aide in the reconstruction and analysis of phylogenetic (evolutionary) trees. The path-length distance between trees is a particularly attractive measure as it reflects differences in…
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…
Edit distance between trees is a natural generalization of the classical edit distance between strings, in which the allowed elementary operations are contraction, uncontraction and relabeling of an edge. Demaine et al. [ACM Trans. on…
Tree edit distance is a well-studied measure of dissimilarity between rooted trees with node labels. It can be computed in $O(n^3)$ time [Demaine, Mozes, Rossman, and Weimann, ICALP 2007], and fine-grained hardness results suggest that the…
Labeling schemes seek to assign a short label to each node in a network, so that a function on two nodes can be computed by examining their labels alone. For the particular case of trees, optimal bounds (up to low order terms) were recently…
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,…
Computing the edit distance of two strings is one of the most basic problems in computer science and combinatorial optimization. Tree edit distance is a natural generalization of edit distance in which the task is to compute a measure of…
The (unweighted) tree edit distance problem for $n$ node trees asks to compute a measure of dissimilarity between two rooted trees with node labels. The current best algorithm from more than a decade ago runs in $O(n ^ 3)$ time [Demaine,…
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…
In the $k$-dispersion problem, we need to select $k$ nodes of a given graph so as to maximize the minimum distance between any two chosen nodes. This can be seen as a generalization of the independent set problem, where the goal is to…
We consider the problem of augmenting an $n$-vertex tree with one shortcut in order to minimize the diameter of the resulting graph. The tree is embedded in an unknown space and we have access to an oracle that, when queried on a pair of…
The tree edit distance is a natural dissimilarity measure between rooted ordered trees whose nodes are labeled over an alphabet $\Sigma$. It is defined as the minimum number of node edits (insertions, deletions, and relabelings) required to…
As secure processors such as Intel SGX (with hyperthreading) become widely adopted, there is a growing appetite for private analytics on big data. Most prior works on data-oblivious algorithms adopt the classical PRAM model to capture…
We consider distance labeling schemes for trees: given a tree with $n$ nodes, label the nodes with binary strings such that, given the labels of any two nodes, one can determine, by looking only at the labels, the distance in the tree…
In a recent paper Chan et al. [SODA '19] proposed a relaxation of the notion of (full) memory obliviousness, which was introduced by Goldreich and Ostrovsky [J. ACM '96] and extensively researched by cryptographers. The new notion,…
The edit distance between two rooted ordered trees with $n$ nodes labeled from an alphabet~$\Sigma$ is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling…
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…