Related papers: Optimal Construction of Hierarchical Overlap Graph…
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 hierarchical overlap graph (HOG) is a graph that encodes overlaps from a given set P of n strings, as the overlap graph does. A best known algorithm constructs HOG in O(||P|| log n) time and O(||P||) space, where ||P|| is the sum of…
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…
The first step in any genome assembly algorithm entails the conversion from the domain of strings and overlaps to the language of graphs and paths, typically using one of the two conventional methods: de Bruijn graphs or overlap graphs.…
Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories -- based on the data structures which…
Genome sequencing is essential to decode genetic information, identify organisms, understand diseases and advance personalized medicine. A critical step in any genome sequencing technique is genome assembly. However, de novo genome…
In earlier versions of the community discovering problem, the overlap between communities was restricted by a simple count upper-bound [17,5,11,8]. In this paper, we introduce the $\Pi$-Packing with $\alpha()$-Overlap problem to allow for…
We consider the group isomorphism problem: given two finite groups G and H specified by their multiplication tables, decide if G cong H. For several decades, the n^(log_p n + O(1)) generator-enumeration bound (where p is the smallest prime…
Genome assembly asks to reconstruct an unknown string from many shorter substrings of it. Even though it is one of the key problems in Bioinformatics, it is generally lacking major theoretical advances. Its hardness stems both from…
Given $n$ points in the plane, we propose algorithms to compile connected crossing-free geometric graphs into directed acyclic graphs (DAGs). The DAGs allow efficient counting, enumeration, random sampling, and optimization. Our algorithms…
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…
An exact-match overlap graph of $n$ given strings of length $\ell$ is an edge-weighted graph in which each vertex is associated with a string and there is an edge $(x,y)$ of weight $\omega = \ell - |ov_{max}(x,y)|$ if and only if $\omega…
We present ROBO (Riemannian Overlapping Block Optimization), a distributed and parallel approach to multi-robot pose graph optimization (PGO) based on the idea of overlapping domain decomposition. ROBO offers a middle ground between…
We consider the problem of sampling and approximately counting an arbitrary given motif $H$ in a graph $G$, where access to $G$ is given via queries: degree, neighbor, and pair, as well as uniform edge sample queries. Previous algorithms…
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,…
In real life, it is always an urge to reach our goal in minimum effort i.e., it should have a minimum constrained path. The path may be shortest route in practical life, either physical or electronic medium. The scenario is to represents…
De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a…
Randomized parallel algorithms for many fundamental problems achieve optimal linear work in expectation, but upgrading this guarantee to hold with high probability (whp) remains a recurring theoretical challenge. In this paper, we address…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
The Hierarchical Clustering (HC) problem consists of building a hierarchy of clusters to represent a given dataset. Motivated by the modern large-scale applications, we study the problem in the \streaming model, in which the memory is…