Related papers: Constrained Coding for Composite DNA: Channel Capa…
The short lifespan of traditional data storage media, coupled with an exponential increase in storage demand, has made long-term archival a fundamental problem in the data storage industry and beyond. Consequently, researchers are looking…
Compressed indexing is a powerful technique that enables efficient querying over data stored in compressed form, significantly reducing memory usage and often accelerating computation. While extensive progress has been made for…
Recent works have shown that modern machine learning techniques can provide an alternative approach to the long-standing joint source-channel coding (JSCC) problem. Very promising initial results, superior to popular digital schemes that…
We consider a molecular channel, in which messages are encoded to the frequency of objects (or concentration of molecules) in a pool, and whose output during reading time is a noisy version of the input frequencies, as obtained by sampling…
Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a…
Recently, DNA storage has surfaced as a promising alternative for data storage, presenting notable benefits in terms of storage capacity, cost-effectiveness in maintenance, and the capability for parallel replication. Mathematically, the…
In this paper, we propose a novel conservative chaotic standard map-driven dynamic DNA coding (encoding, addition, subtraction and decoding) for the image encryption. The proposed image encryption algorithm is a dynamic DNA coding algorithm…
In the recent years, DNA has emerged as a potentially viable storage technology. DNA synthesis, which refers to the task of writing the data into DNA, is perhaps the most costly part of existing storage systems. Accordingly, this high cost…
Two-dimensional constrained coding is a problem that is much more difficult than its one-dimensional counterpart. Indeed, in two dimensions, obtaining the answers to very natural questions becomes uncomputable. In particular, it is…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
We consider the problem of joint source and channel coding of structured data such as natural language over a noisy channel. The typical approach to this problem in both theory and practice involves performing source coding to first…
We examine an error-correcting coding framework in which each coded symbol is constrained to be a function of a fixed subset of the message symbols. With an eye toward distributed storage applications, we seek to design systematic codes…
This paper extends the foundational work of Dollma \emph{et al}. on codes for ordered composite DNA sequences. We consider the general setting with an alphabet of size $q$ and a resolution parameter $k$, moving beyond the binary ($q=2$)…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
Motivated by communication channels in which the transmitted sequences are subject to random permutations, as well as by certain DNA storage systems, we study the error control problem in settings where the information is stored/transmitted…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
DNA is an attractive candidate for data storage. Its millennial durability and nanometer scale offer exceptional data density and longevity. Its relevance to medical applications also drives advances in DNA-related biotechnology. To protect…
DNA is a promising storage medium, but its stability and occurrence of Indel errors pose a significant challenge. The relative occurrence of Guanine(G) and Cytosine(C) in DNA is crucial for its longevity, and reverse complementary base…
Constellation shaping is a practical and effective technique to improve the performance and the rate adaptivity of optical communication systems. In principle, it could also be used to mitigate the impact of nonlinear effects, possibly…
Motivation: Next Generation Sequencing technologies revolutionized many fields in biology by enabling the fast and cheap sequencing of large amounts of genomic data. The ever increasing sequencing capacities enabled by current sequencing…