Related papers: Exact Reconstruction from Insertions in Synchroniz…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…
We improve Levenshtein's upper bound for the cardinality of a code of length four that is capable of correcting single deletions over an alphabet of even size. We also illustrate that the new upper bound is sharp. Furthermore we construct…
The high repair cost of (n,k) Maximum Distance Separable (MDS) erasure codes has recently motivated a new class of codes, called Regenerating Codes, that optimally trade off storage cost for repair bandwidth. In this paper, we address…
This thesis makes several significant contributions to the theory of both Regenerating (RG) and Locally Recoverable (LR) codes. The two principal contributions are characterizing the optimal rate of an LR code designed to recover from $t$…
This paper studies the problem of encoding messages into sequences which can be uniquely recovered from some noisy observations about their substrings. The observed reads comprise consecutive substrings with some given minimum overlap. This…
The problem of string reconstruction from substring information has found many applications due to its relevance in DNA- and polymer-based data storage. One practically important and challenging paradigm requires reconstructing mixtures of…
Finding deletion-correcting codes of maximum size has been an open problem for over 70 years, even for a single deletion. In this paper, we propose a novel approach for constructing deletion-correcting codes. A code is a set of sequences…
Levenshtein introduced the problem of constructing $k$-deletion correcting codes in 1966, proved that the optimal redundancy of those codes is $O(k\log N)$, and proposed an optimal redundancy single-deletion correcting code (using the…
Insertion-deletion codes (insdel codes for short) play an important role in synchronization error correction. The higher the minimum insdel distance, the more insdel errors the code can correct. Haeupler and Shahrasbi established the…
Recent advances in DNA sequencing technology and DNA storage systems have rekindled the interest in deletion channels. Multiple recent works have looked at variants of sequence reconstruction over a single and over multiple deletion…
Nanopore sequencers are emerging as promising new platforms for high-throughput sequencing. As with other technologies, sequencer errors pose a major challenge for their effective use. In this paper, we present a novel information theoretic…
Erasure coding techniques are getting integrated in networked distributed storage systems as a way to provide fault-tolerance at the cost of less storage overhead than traditional replication. Redundancy is maintained over time through…
Let $\mathcal{B}(\cdot)$ be an error ball function. A set of $q$-ary sequences of length $n$ is referred to as an \emph{$(n,q,N;\mathcal{B})$-reconstruction code} if each sequence $\boldsymbol{x}$ within this set can be uniquely…
We study the exact and optimal repair of multiple failures in codes for distributed storage. More particularly, we examine the use of interference alignment to build exact scalar minimum storage coordinated regenerating codes (MSCR). We…
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…
Several recent works have considered the \emph{trace reconstruction problem}, in which an unknown source string $x\in\{0,1\}^n$ is transmitted through a probabilistic channel which may randomly delete coordinates or insert random bits,…
In this paper, we investigate the problem of recovering source information from an incomplete set of network coded data. We first study the theoretical performance of such systems under maximum a posteriori (MAP) decoding and derive the…
We introduce a general class of codes which includes several well-known classes of deletion/insertion correcting codes as special cases. For example, the Helberg code, the Levenshtein code, the Varshamov--Tenengolts code, and most variants…
This paper gives new results for synchronization strings, a powerful combinatorial object that allows to efficiently deal with insertions and deletions in various communication settings: $\bullet$ We give a deterministic, linear time…
This paper gives some theory and efficient design of binary block systematic codes capable of controlling the deletions of the symbol ``$0$'' (referred to as $0$-deletions) and/or the insertions of the symbol ``$0$'' (referred to as…