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Sorting is a foundational problem in computer science that is typically employed on sequences or total orders. More recently, a more general form of sorting on partially ordered sets (or posets), where some pairs of elements are…
In graph theory, a tree is one of the more popular families of graphs with a wide range of applications in computer science as well as many other related fields. While there are several distance measures over the set of all trees, we…
In distance query reconstruction, we wish to reconstruct the edge set of a hidden graph by asking as few distance queries as possible to an oracle. Given two vertices $u$ and $v$, the oracle returns the shortest path distance between $u$…
Given a set of $n$ points $S$ in the plane, a triangulation $T$ of $S$ is a maximal set of non-crossing segments with endpoints in $S$. We present an algorithm that computes the number of triangulations on a given set of $n$ points in time…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…
We study space and time efficient quantum algorithms for two graph problems -- deciding whether an $n$-vertex graph is a forest, and whether it is bipartite. Via a reduction to the s-t connectivity problem, we describe quantum algorithms…
Distance based algorithms are a common technique in the construction of phylogenetic trees from taxonomic sequence data. The first step in the implementation of these algorithms is the calculation of a pairwise distance matrix to give a…
In the \emph{$k$-Diameter-Optimally Augmenting Tree Problem} we are given a tree $T$ of $n$ vertices as input. The tree is embedded in an unknown \emph{metric} space and we have unlimited access to an oracle that, given two distinct…
For any two point sets $A,B \subset \mathbb{R}^d$ of size up to $n$, the Chamfer distance from $A$ to $B$ is defined as $\text{CH}(A,B)=\sum_{a \in A} \min_{b \in B} d_X(a,b)$, where $d_X$ is the underlying distance measure (e.g., the…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…
Reachability is the problem of deciding whether there is a path from one vertex to the other in the graph. Standard graph traversal algorithms such as DFS and BFS take linear time to decide reachability however their space complexity is…
For many algorithmic problems on graphs of treewidth $t$, a standard dynamic programming approach gives an algorithm with time and space complexity $2^{\mathcal{O}(t)}\cdot n^{\mathcal{O}(1)}$. It turns out that when one considers the more…
We present a near-linear time algorithm that approximates the edit distance between two strings within a polylogarithmic factor; specifically, for strings of length n and every fixed epsilon>0, it can compute a (log n)^O(1/epsilon)…
The similarity of two polygonal curves can be measured using the Fr\'echet distance. We introduce the notion of a more robust Fr\'echet distance, where one is allowed to shortcut between vertices of one of the curves. This is a natural…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two…
Tree rotations (left and right) are basic local deformations allowing to transform between two unlabeled binary trees of the same size. Hence, there is a natural problem of practically finding such transformation path with low number of…
Rotation distance between trees measures the number of simple operations it takes to transform one tree into another. There are no known polynomial-time algorithms for computing rotation distance. In the case of ordered rooted trees, we…
In recent years, spectral clustering has become one of the most popular clustering algorithms for image segmentation. However, it has restricted applicability to large-scale images due to its high computational complexity. In this paper, we…
We present the first truly subcubic, combinatorial algorithm for detecting an induced $4$-cycle in a graph. The running time is $O(n^{2.84})$ on $n$-node graphs, thus separating the task of detecting induced $4$-cycles from detecting…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…