Searcharxiv⌕ Search
Home/Archive/arXiv

arXiv · 1204.3293

Efficiently decoding strings from their shingles

Aryeh Kontorovich·Ari Trachtenberg
View original source ↗Read source document ↗Export metadata ↓

Abstract

Determining whether an unordered collection of overlapping substrings (called shingles) can be uniquely decoded into a consistent string is a problem that lies within the foundation of a broad assortment of disciplines ranging from networking and information theory through cryptography and even genetic engineering and linguistics. We present three perspectives on this problem: a graph theoretic framework due to Pevzner, an automata theoretic approach from our previous work, and a new insight that yields a time-optimal streaming algorithm for determining whether a string of $n$ characters over the alphabet $\Sigma$ can be uniquely decoded from its two-character shingles. Our algorithm achieves an overall time complexity $\Theta(n)$ and space complexity $O(|\Sigma|)$. As an application, we demonstrate how this algorithm can be extended to larger shingles for efficient string reconciliation.

Explore related subjects

cs.DM

Keep this discovery

BibTeXRIS

Aryeh Kontorovich, Ari Trachtenberg. 2012-04-15. Efficiently decoding strings from their shingles. https://arxiv.org/abs/1204.3293

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

An FPTAS for Two-Machine Open-Shop Scheduling with a Single Unavailability Interval

We consider the two-machine open-shop scheduling problem in which one machine is unavailable during a fixed interval. We study the resumable setting: an operation interrupted by the unavailability interval may resume, without penalty, when the machine becomes available. The objective is to minimize the makespan. Although the problem is NP-hard and several approximation algorithms are known, whether it admits a fully polynomial-time approximation scheme (FPTAS) has remained open for two decades. We resolve this question affirmatively by giving the first FPTAS, thereby strengthening the previously known polynomial-time approximation scheme (PTAS). As an intermediate result, we develop a new pseudo-polynomial dynamic program with seven state dimensions, improving on the ten-dimensional formulation in the literature.

cs.DM↗
arXiv2026

Generalized Graph Search Trees

Graph search algorithms and their corresponding graph search trees are commonly used in algorithmic graph theory. In recent years, the recognition problem of these graph search trees has received significant attention. So far, the research has focused on two types of search trees: first-in trees that behave like BFS-trees and last-in trees that behave like DFS-trees. The search tree paradigms differ from each other by the parent a vertex is connected to. In first-in trees, it is the first visited neighbor, while in last-in trees it is the last neighbor visited before that vertex. Here, we will generalize these concepts of graph search trees by allowing every preceding neighbor of a vertex to be the parent. We study the complexity of the recognition problem of these generalized graph search trees. We present NP-completeness proofs for most searches. We also show that the problem is trivial for Generic Search and polynomial-time solvable for several searches on bipartite graphs and chordal graphs. We also study the question how fixing the start vertex influences the complexity of the problem.

cs.DM↗
arXiv2026

The exact asymptotic constant in the metric dimension of Jaccard space

Let $X$ be a finite set with $|X|=n$ and let $\mathrm{Jac}(a,b)=|a\,\triangle\, b|/|a\cup b|$ be the Jaccard distance on the power set $2^X$. Lladser and Paradise recently proved that the metric dimension of $(2^X,\mathrm{Jac})$ is $\Theta(n/\ln n)$, with the constant left open; their bounds are $(\ln 2)\,n/\ln n\lesssim \beta(2^X,\mathrm{Jac})\lesssim 2\ln(2e)\,n/\ln n$. We determine the constant: \[ \beta(2^X,\mathrm{Jac})=\frac{2n}{\log_2 n}\,(1+o(1))=(2\ln 2)\,\frac{n}{\ln n}\,(1+o(1)). \] The proof identifies the problem, on each ``slice'' of subsets of fixed cardinality, with the Erd\H{o}s--R\'enyi coin-weighing problem for a spring scale (the problem of \emph{detecting matrices}). The lower bound is the Erd\H{o}s--R\'enyi entropy argument applied to the middle slice; the upper bound follows from the explicit detecting families of Lindstr\"om and of Cantor and Mills, augmented by a single extra landmark that reveals cardinality.

cs.DM↗