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Rotation distance measures the difference in shape between binary trees of the same size by counting the minimum number of rotations needed to transform one tree to the other. We describe several types of rotation distance where…
We suggest a new non-recursive algorithm for constructing a binary search tree given an array of numbers. The algorithm has $O(N)$ time and $O(1)$ memory complexity if the given array of $N$ numbers is sorted. The resulting tree is of…
Comparing and computing distances between phylogenetic trees are important biological problems, especially for models where edge lengths play an important role. The geodesic distance measure between two phylogenetic trees with edge lengths…
We present a deterministic algorithm that given a tree T with n vertices, a starting vertex v and a slackness parameter epsilon > 0, estimates within an additive error of epsilon the cover and return time, namely, the expected time it takes…
An important problem in geometric computing is defining and computing similarity between two geometric shapes, e.g. point sets, curves and surfaces, etc. Important geometric and topological information of many shapes can be captured by…
Computing optimal transport (OT) distances such as the earth mover's distance is a fundamental problem in machine learning, statistics, and computer vision. In this paper, we study the problem of approximating the general OT distance…
The last decade brought a significant increase in the amount of data and a variety of new inference methods for reconstructing the detailed evolutionary history of various cancers. This brings the need of designing efficient procedures for…
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…
In the PATH COVER problem, one asks to cover the vertices of a graph using the smallest possible number of (not necessarily disjoint) paths. While the variant where the paths need to be pairwise vertex-disjoint, which we call PATH…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
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:…
Polytrees are a subclass of Bayesian networks that seek to capture the conditional dependencies between a set of $n$ variables as a directed forest and are motivated by their more efficient inference and improved interpretability. Since the…
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…
Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to measure the dissimilarity of the two trees.…
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…
We study the problem of computing the triplet distance between two rooted unordered trees with $n$ labeled leafs. Introduced by Dobson 1975, the triplet distance is the number of leaf triples that induce different topologies in the two…
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…
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,…
We give a 2-approximation algorithm for the Maximum Agreement Forest problem on two rooted binary trees. This NP-hard problem has been studied extensively in the past two decades, since it can be used to compute the Subtree…
We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem…