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The problem of correcting deletions has received significant attention, partly because of the prevalence of these errors in DNA data storage. In this paper, we study the problem of correcting a consecutive burst of at most $t$ deletions in…
In this paper we consider the problem of encoding data into \textit{repeat-free} sequences in which sequences are imposed to contain any $k$-tuple at most once (for predefined $k$). First, the capacity of the repeat-free constraint are…
We construct deletion error-correcting codes in the oblivious model, where errors are adversarial but oblivious to the encoder's randomness. Oblivious errors bridge the gap between the adversarial and random error models, and are motivated…
We study codes that can correct backtracking errors during nanopore sequencing. In this channel, a sequence of length $n$ over an alphabet of size $q$ is being read by a sliding window of length $\ell$, where from each window we obtain only…
One of the most common problems in statistical experimentation is computing D-optimal designs on large finite candidate sets. While optimal approximate (i.e., infinite-sample) designs can be efficiently computed using convex methods,…
An edit refers to a single insertion, deletion, or substitution. This paper aims to construct binary codes that can correct two edits. To do this, a necessary and sufficient condition for a code to be two-edit correctable is provided,…
Imperfect measurement can degrade a quantum error correction scheme. A solution that restores fault tolerance is to add redundancy to the process of syndrome extraction. In this work, we show how to optimize this process for an arbitrary…
The Damerau-Levenshtein distance between two sequences is the minimum number of operations (deletions, insertions, substitutions, and adjacent transpositions) required to convert one sequence into another. Notwithstanding a long history of…
In this work, we consider the problem of efficient decoding of codes from insertions and deletions. Most of the known efficient codes are codes with synchronization strings which allow one to reduce the problem of decoding insertions and…
Dynamic data race detectors are indispensable for flagging concurrency errors in software, but their high runtime overhead limits their adoption. This overhead stems primarily from pervasive instrumentation of memory accesses - a…
This work studies problems in data reconstruction, an important area with numerous applications. In particular, we examine the reconstruction of binary and non-binary sequences from synchronization (insertion/deletion-correcting) codes.…
Recently, codes for correcting a burst of errors have attracted significant attention. One of the most important reasons is that bursts of errors occur in certain emerging techniques, such as DNA storage. In this paper, we investigate a…
Reconstruction codes are generalizations of error-correcting codes that can correct errors by a given number of noisy reads. The study of such codes was initiated by Levenshtein in 2001 and developed recently due to applications in modern…
This paper presents new lower and upper bounds for the compression rate of binary prefix codes optimized over memoryless sources according to various nonlinear codeword length objectives. Like the most well-known redundancy bounds for…
In recent years, several integer programming (IP) approaches were developed for maximum-likelihood decoding and minimum distance computation for binary linear codes. Two aspects in particular have been demonstrated to improve the…
In this paper, we study the problem of reducing the delay of downloading data from cloud storage systems by leveraging multiple parallel threads, assuming that the data has been encoded and stored in the clouds using fixed rate forward…
The analysis of the decoding failure rate of the bit-flipping algorithm has received increasing attention. For a binary linear code we consider the minimum number of rows in a parity-check matrix such that the bit-flipping algorithm is able…
Tandem duplication in DNA 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 {\em et al.} (2016) proposed the study of codes that…
The substring edit error is the operation of replacing a substring $u$ of $x$ with another string $v$, where the lengths of $u$ and $v$ are bounded by a given constant $k$. It encompasses localized insertions, deletions, and substitutions…
In this work, we propose constructions that correct duplications of multiple consecutive symbols. These errors are known as tandem duplications, where a sequence of symbols is repeated; respectively as palindromic duplications, where a…