Related papers: Low-redundancy codes for correcting multiple short…
The exponential increase in storage demand and low lifespan of data storage devices has resulted in long-term archival and preservation emerging as a critical bottlenecks in data storage. In order to meet this demand, researchers are now…
The efficiency of a code is estimated by its redundancy $R$, while the complexity of a code is estimated by its average delay $\bar N$. In this work we construct word-based codes, for which $R \lesssim \bar N^{-5/3}$. Therefore, word-based…
We consider error-correcting coding for DNA-based storage. We model the DNA storage channel as a multi-draw IDS channel where the input data is chunked into $M$ short DNA strands, which are copied a random number of times, and the channel…
During cancer progression, malignant cells accumulate somatic mutations that can lead to genetic aberrations. In particular, evolutionary events akin to segmental duplications or deletions can alter the copy-number profile (CNP) of a set of…
We consider the problem of constructing codes that can correct $\delta$ deletions occurring in an arbitrary binary string of length $n$ bits. Varshamov-Tenengolts (VT) codes can correct all possible single deletions $(\delta=1)$ with an…
This paper studies \emph{linear} and \emph{affine} error-correcting codes for correcting synchronization errors such as insertions and deletions. We call such codes linear/affine insdel codes. Linear codes that can correct even a single…
In this paper, we present an efficiently encodable and decodable code construction that is capable of correction a burst of deletions of length at most $k$. The redundancy of this code is $\log n + k(k+1)/2\log \log n+c_k$ for some constant…
DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on…
Erasure codes provide a storage efficient alternative to replication based redundancy in (networked) storage systems. They however entail high communication overhead for maintenance, when some of the encoded fragments are lost and need to…
Data storage systems are more reliable than their individual components. In order to build highly reliable systems out of less reliable parts, systems introduce redundancy. In replicated systems, objects are simply copied several times with…
DNA codes have many applications, such as in data storage, DNA computing, etc. Good DNA codes have large sizes and satisfy some certain constraints. In this paper, we present a new construction method for reversible DNA codes. We show that…
With the rapid increase of available digital data, DNA storage is identified as a storage media with high density and capability of long-term preservation, especially for archival storage systems. However, the encoding density (i.e., how…
Data synchronization is a fundamental problem with applications in diverse fields such as cloud storage, genomics, and distributed systems. This paper addresses the challenge of synchronizing two files, one of which is a subsequence of the…
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…
The efficient storage of digital data is becoming very challenging over the years due to the exponential increase in the generation of data which can't compete with the existing storage resources. Furthermore, the infrequently accessed data…
We study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect…
We study ensembles of codes on graphs (generalized low-density parity-check, or LDPC codes) constructed from random graphs and fixed local constrained codes, and their extension to codes on hypergraphs. It is known that the average minimum…
Data redundancy is ubiquitous in the inputs and intermediate results of Deep Neural Networks (DNN). It offers many significant opportunities for improving DNN performance and efficiency and has been explored in a large body of work. These…
This paper studies the problem of constructing codes correcting deletions in arrays. Under this model, it is assumed that an $n\times n$ array can experience deletions of rows and columns. These deletion errors are referred to as…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…