Related papers: Shotgun assembly of labeled graphs
Graph shotgun assembly refers to the problem of reconstructing a graph from a collection of local neighborhoods. In this paper, we consider shotgun assembly of \ER random graphs $G(n, p_n)$, where $p_n = n^{-\alpha}$ for $0 < \alpha < 1$.…
In the graph shotgun assembly problem, we are given the balls of radius $r$ around each vertex of a graph and asked to reconstruct the graph. We study the shotgun assembly of the Erd\H{o}s-R\'enyi random graph $\mathcal G(n,p)$ for a wide…
Mossel and Ross (2019) introduce the shotgun assembly problem for random graphs: what radius $R$ ensures that the random graph $G$ can be uniquely recovered from its list of rooted $R$-neighborhoods, with high probability? Here we consider…
In a recent work, Huang and Tikhomirov considered the shotgun assembly for Erd\H os-R\'enyi graphs $\mathcal G(n,p_n)$ with $p_n=n^{-\alpha}$, and showed that the graph is reconstructable if $0<\alpha < \frac{1}{2}$ and not reconstructable…
In a recent paper [6], J. Gaudio and E. Mossel studied the shotgun assembly of the Erd\H{o}s-R\'enyi graph $\mathcal G(n,p_n)$ with $p_n=n^{-\alpha}$, and showed that the graph is reconstructable form its $1$-neighbourhoods if $0<\alpha <…
The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to…
We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in…
In the shotgun assembly problem for a graph, we are given the empirical profile for rooted neighborhoods of depth $r$ (up to isomorphism) for some $r\geq 1$ and we wish to recover the underlying graph up to isomorphism. When the underlying…
Consider a collection of random variables attached to the vertices of a graph. The reconstruction problem requires to estimate one of them given `far away' observations. Several theoretical results (and simple algorithms) are available when…
We study the shotgun assembly problem for the lattice labeling model, where i.i.d. uniform labels are assigned to each vertex in a $d$-dimensional box of side length $n$. We wish to recover the labeling configuration on the whole box given…
This paper addresses the problem of reassembling images from disjointed fragments. More specifically, given an unordered set of fragments, we aim at reassembling one or several possibly incomplete images. The main contributions of this work…
In a recent work, Mossel and Ross considered the shotgun assembly problem for a random jigsaw puzzle. Their model consists of a puzzle - an $n\times n$ grid, where each vertex is viewed as a center of a piece. They assume that each of the…
Mossel and Ross raised the question of when a random colouring of a graph can be reconstructed from local information, namely the colourings (with multiplicity) of balls of given radius. In this paper, we are concerned with random…
DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…
We tackle the image reassembly problem with wide space between the fragments, in such a way that the patterns and colors continuity is mostly unusable. The spacing emulates the erosion of which the archaeological fragments suffer. We…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…
Given a positive integer $n$, an unlabeled graph $G$ on $n$ vertices, and a vertex $v$ of $G$, let $N_G(v)$ be the subgraph of $G$ induced by vertices of $G$ of distance at most one from $v$. We show that there are universal constants…
The labeled stochastic block model is a random graph model representing networks with community structure and interactions of multiple types. In its simplest form, it consists of two communities of approximately equal size, and the edges…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…
Reconstructing a complete object from its parts is a fundamental problem in many scientific domains. The purpose of this article is to provide a systematic survey on this topic. The reassembly problem requires understanding the attributes…