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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…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (rarely accessed data), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
DNA storage has matured from concept to practical stage, yet its integration with neural compression pipelines remains inefficient. Early DNA encoders applied redundancy-heavy constraint layers atop raw binary data - workable but primitive.…
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…
Deoxyribonucleic acid (DNA) has shown great promise in enabling computational applications, most notably in the fields of DNA digital data storage and DNA computing. Information is encoded as DNA strands, which will naturally bind in…
The coverage depth problem in DNA data storage is about computing the expected number of reads needed to recover all encoded strands. Given a generator matrix of a linear code, this quantity equals the expected number of randomly drawn…
This work presents a theoretical analysis of the probability of successfully retrieving data encoded with MDS codes (e.g., Reed-Solomon codes) in DNA storage systems. We study this probability under independent and identically distributed…
A new family of codes, called clustering-correcting codes, is presented in this paper. This family of codes is motivated by the special structure of data that is stored in DNA-based storage systems. The data stored in these systems has the…
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…
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…
Current research on DNA storage usually focuses on the improvement of storage density by developing effective encoding and decoding schemes while lacking the consideration on the uncertainty in ultra-long-term data storage and retention.…
In this paper, we study error exponents for a concatataned coding based class of DNA storage codes in which the number of reads performed can be variable. That is, the decoder can sequentially perform reads and choose whether to output the…
In this paper, fundamental limits in sequencing of a set of closely related DNA molecules are addressed. This problem is called pooled-DNA sequencing which encompasses many interesting problems such as haplotype phasing, metageomics, and…
Exponential increase of data has motivated advances of data storage technologies. As a promising storage media, DeoxyriboNucleic Acid (DNA) storage provides a much higher data density and superior durability, compared with state-of-the-art…
DNA labeling is a powerful tool in molecular biology and biotechnology that allows for the visualization, detection, and study of DNA at the molecular level. Under this paradigm, a DNA molecule is being labeled by specific k patterns and is…
In the current era, DeoxyriboNucleic Acid (DNA) based data storage emerges as an intriguing approach, garnering substantial academic interest and investigation. This paper introduces a novel deep joint source-channel coding (DJSCC) scheme…
DNA has been discussed as a potential medium for data storage. Potentially it could be denser, could consume less energy, and could be more durable than conventional storage media such as hard drives, solid-state storage, and optical media.…
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…
The coverage depth problem in DNA data storage is about minimizing the expected number of reads until all data is recovered. When they exist, MDS codes offer the best performance in this context. This paper focuses on the scenario where the…
We propose a novel and flexible DNA-storage architecture, which divides the storage space into fixed-size units (blocks) that can be independently and efficiently accessed at random for both read and write operations, and further allows…