Related papers: Low-redundancy codes for correcting multiple short…
Motivated by DNA-based storage applications, we study the problem of reconstructing a coded sequence from multiple traces. We consider the model where the traces are outputs of independent deletion channels, where each channel deletes each…
We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…
The biggest challenge when using DNA as a storage medium is maintaining its stability. The relative occurrence of Guanine (G) and Cytosine (C) is essential for the longevity of DNA. In addition to that, reverse complementary base pairs…
In the field of automated program repair, the redundancy assumption claims large programs contain the seeds of their own repair. However, most redundancy-based program repair techniques do not reason about the repair ingredients---the code…
In order to achieve fault tolerance, highly reliable system often require the ability to detect errors as soon as they occur and prevent the speared of erroneous information throughout the system. Thus, the need for codes capable of…
Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…
We consider analog error-correcting codes (analog ECCs) that are designed to correct/detect outlying errors arising in analog implementations of vector-matrix multiplication. The error-correction/detection capability of an analog ECC can be…
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…
We consider the problem of constructing binary codes to recover from $k$-bit deletions with efficient encoding/decoding, for a fixed $k$. The single deletion case is well understood, with the Varshamov-Tenengolts-Levenshtein code from 1965…
Redundant code is a persistent challenge in software development that makes systems harder to maintain, scale, and update. It adds unnecessary complexity, hinders bug fixes, and increases technical debt. Despite their impact, removing…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
DNA has many valuable characteristics that make it suitable for a long-term storage medium, in particular its durability and high information density. DNA can be stored safely for hundreds of years with virtually no degradation, in contrast…
DNA-based storage is an emerging technology that enables digital information to be archived in DNA molecules. This method enjoys major advantages over magnetic and optical storage solutions such as exceptional information density, enhanced…
Distributed storage systems need to store data redundantly in order to provide some fault-tolerance and guarantee system reliability. Different coding techniques have been proposed to provide the required redundancy more efficiently than…
In this paper, we propose a novel iterative encoding algorithm for DNA storage to satisfy both the GC balance and run-length constraints using a greedy algorithm. DNA strands with run-length more than three and the GC balance ratio far from…
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…
Burst errors involving simultaneous insertions, deletions, and substitutions occur in practical scenarios, including DNA data storage and document synchronization, motivating developments of channel codes that can correct such errors. In…
Ever since deoxyribonucleic acid (DNA) was considered as a next-generation data-storage medium, lots of research efforts have been made to correct errors occurred during the synthesis, storage, and sequencing processes using error…
We study segmented burst-deletion channels motivated by the observation that synchronization errors commonly occur in a bursty manner in real-world settings. In this channel model, transmitted sequences are implicitly divided into…
DNA has been considered a promising medium for storing digital information. As an essential step in the DNA-based data storage workflow, coding algorithms are responsible to implement functions including bit-to-base transcoding, error…