Related papers: Concatenated Code Design for Constrained DNA Data …
As the global need for large-scale data storage is rising exponentially, existing storage technologies are approaching their theoretical and functional limits in terms of density and energy consumption, making DNA based storage a potential…
Distributed storage systems suffer from significant repair traffic generated due to frequent storage node failures. This paper shows that properly designed low-density parity-check (LDPC) codes can substantially reduce the amount of…
Low-density parity-check (LDPC) coding for a multitude of equal-capacity channels is studied. First, based on numerous observations, a conjecture is stated that when the belief propagation decoder converges on a set of equal-capacity…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
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…
Most low-density parity-check (LDPC) code constructions are considered over finite fields. In this work, we focus on regular LDPC codes over integer residue rings and analyze their performance with respect to the Lee metric. Their…
Nanopore sequencing, superior to other sequencing technologies for DNA storage in multiple aspects, has recently attracted considerable attention. Its high error rates, however, demand thorough research on practical and efficient coding…
We obtain exact expressions for the asymptotic behaviour of the average probability of the block decoding error for ensembles of regular low density parity check error correcting codes, by employing diagrammatic techniques. Furthermore, we…
This paper studies achievable rates of nanopore-based DNA storage when nanopore signals are decoded using a tractable channel model that does not rely on a basecalling algorithm. Specifically, the noisy nanopore channel (NNC) with the…
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 paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
The base station-mobile device communication traffic has dramatically increased recently due to mobile data, which in turn heavily overloaded the underlying infrastructure. To decrease Base Station (BS) interaction, intra-cell communication…
In this review paper, we delve into the nascent field of molecular data storage, focusing on system implementations and code constructions. We start by providing an overview of basic concepts in synthetic and computational biology.…
We initiate the study of DNA-based distributed storage systems, where information is encoded across multiple DNA data storage containers to achieve robustness against container failures. In this setting, data are distributed over $M$…
A variety of low-density parity-check (LDPC) ensembles have now been observed to approach capacity with message-passing decoding. However, all of them use soft (i.e., non-binary) messages and a posteriori probability (APP) decoding of their…
This paper presents a novel hybrid tokenization strategy that enhances the performance of DNA Language Models (DLMs) by combining 6-mer tokenization with Byte Pair Encoding (BPE-600). Traditional k-mer tokenization is effective at capturing…
The biochemical processes underlying DNA data storage, including synthesis, amplification, and sequencing, are inherently noisy. Consequently, base-level insertion, deletion, and substitution (IDS) errors, as well as sequence-level…
DNA storage technology offers new possibilities for addressing massive data storage due to its high storage density, long-term preservation, low maintenance cost, and compact size. To improve the reliability of stored information, base…
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 present a new class of irregular low-density parity-check (LDPC) codes for moderate block lengths (up to a few thousand bits) that are well-suited for rate-compatible puncturing. The proposed codes show good performance under puncturing…