Related papers: A Linear Time Algorithm for Constructing Hierarchi…
Given a set of finite words, the Overlap Graph (OG) is a complete weighted digraph where each word is a node and where the weight of an arc equals the length of the longest overlap of one word onto the other (Overlap is an asymmetric…
Genome assembly is a fundamental problem in Bioinformatics, where for a given set of overlapping substrings of a genome, the aim is to reconstruct the source genome. The classical approaches to solving this problem use assembly graphs, such…
Genome assembly is a prominent problem studied in bioinformatics, which computes the source string using a set of its overlapping substrings. Classically, genome assembly uses assembly graphs built using this set of substrings to compute…
The layer-ordered heap (LOH) is a simple, recently proposed data structure used in optimal selection on $X+Y$, thealgorithm with the best known runtime for selection on $X_1+X_2+\cdots+X_m$, and the fastest method in practice for computing…
We present algorithms that extend the path-based hierarchical drawing framework and give experimental results. Our algorithms run in $O(km)$ time, where $k$ is the number of paths and $m$ is the number of edges of the graph, and provide…
Dujmovi\'c et al (FOCS2019) recently proved that every planar graph $G$ is a subgraph of $H\boxtimes P$, where $\boxtimes$ denotes the strong graph product, $H$ is a graph of treewidth 8 and $P$ is a path. This result has found numerous…
We show how to construct an overlay network of constant degree and diameter $O(\log n)$ in time $O(\log n)$ starting from an arbitrary weakly connected graph. We assume a synchronous communication network in which nodes can send messages to…
A geometric graph is a graph whose vertices are points in general position in the plane and its edges are straight line segments joining these points. In this paper we give an $O(n^2 \log n)$ algorithm to compute the number of pairs of…
Given two convex polygons $P$ and $Q$ with $n$ and $m$ edges, the maximum overlap problem is to find a translation of $P$ that maximizes the area of its intersection with $Q$. We give the first randomized algorithm for this problem with…
We study the widely used hierarchical agglomerative clustering (HAC) algorithm on edge-weighted graphs. We define an algorithmic framework for hierarchical agglomerative graph clustering that provides the first efficient $\tilde{O}(m)$ time…
In this paper, we show that given a weighted, directed planar graph $G$, and any $\epsilon >0$, there exists a polynomial time and $O(n^{\frac{1}{2}+\epsilon})$ space algorithm that computes the shortest path between two fixed vertices in…
In this paper we define a construct called a time-graph. A complete time-graph of order n is the cartesian product of a complete graph with n vertices and a linear graph with n vertices. A time-graph of order n is given by a subset of the…
Higher-Order Hypergraph Learning (HOHL) was recently introduced as a principled alternative to classical hypergraph regularization, enforcing higher-order smoothness via powers of multiscale Laplacians induced by the hypergraph structure.…
This paper considers structures of systems beyond dyadic (pairwise) interactions and investigates mathematical modeling of multi-way interactions and connections as hypergraphs, where captured relationships among system entities are…
We shall present an algorithm for determining whether or not a given planar graph H can ever be a subgraph of a 4-regular planar graph. The algorithm has running time O(|H|^{2.5}) and can be used to find an explicit 4-regular planar graph G…
Chaining algorithms aim to form a semi-global alignment of two sequences based on a set of anchoring local alignments as input. Depending on the optimization criteria and the exact definition of a chain, there are several $O(n \log n)$ time…
In this paper we are interested in decomposing a dihypergraph $\mathcal{H} = (V, \mathcal{E})$ into simpler dihypergraphs, that can be handled more efficiently. We study the properties of dihypergraphs that can be hierarchically decomposed…
We consider the task of drawing a graph on multiple horizontal layers, where each node is assigned a layer, and each edge connects nodes of different layers. Known algorithms determine the orders of nodes on each layer to minimize crossings…
We use exponential start time clustering to design faster and more work-efficient parallel graph algorithms involving distances. Previous algorithms usually rely on graph decomposition routines with strict restrictions on the diameters of…
A fundamental problem in shape matching and geometric similarity is computing the maximum area overlap between two polygons under translation. For general simple polygons, the best-known algorithm runs in $O((nm)^2 \log(nm))$ time [Mount,…