Related papers: Shift-Interleave Coding for DNA-Based Storage: Cor…
This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…
In the wake of the swift evolution of technologies such as the Internet of Things (IoT), the global data landscape undergoes an exponential surge, propelling DNA storage into the spotlight as a prospective medium for contemporary cloud…
Code-Switching refers to the phenomenon of switching languages within a sentence or discourse. However, limited code-switching , different language phoneme-sets and high rebuilding costs throw a challenge to make the specialized acoustic…
Digital information can be encoded in the building-block sequence of macro-molecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive.…
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…
The errors occurring in DNA-based storage are correlated in nature, which is a direct consequence of the synthesis and sequencing processes. In this paper, we consider the memory-$k$ nanopore channel model recently introduced by Hamoum et…
In this paper, we propose an efficient reliability based segmentation-discarding decoding (SDD) algorithm for short block-length codes. A novel segmentation-discarding technique is proposed along with the stopping rule to significantly…
Motivation: Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read…
We study the problem of compressing a source sequence in the presence of side-information that is related to the source via insertions, deletions and substitutions. We propose a simple algorithm to compress the source sequence when the…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (i.e. rarely accessed), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…
In this paper, we consider the decoding of fountain codes where the received symbols may have errors. It is motivated by the application of fountain codes in DNA-based data storage systems where the inner code decoding, which generally has…
The space-time bit-interleaved coded modulation (ST-BICM) is an efficient technique to obtain high diversity and coding gain on a block-fading MIMO channel. Its maximum-likelihood (ML) performance is computed under ideal interleaving…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
Motivation: Next generation methods of DNA sequencing produce relatively high rate of reading errors, which interfere with de novo genome assembly of newly sequenced organisms and particularly affect the quality of SNP detection important…
Constrained sequence codes have been widely used in modern communication and data storage systems. Sequences encoded with constrained sequence codes satisfy constraints imposed by the physical channel, hence enabling efficient and reliable…
In this paper we propose a matched encoding (ME) scheme for convolutionally encoded transmission over intersymbol interference (usually called ISI) channels. A novel trellis description enables to perform equalization and decoding jointly,…
Code-switching is a data augmentation scheme mixing words from multiple languages into source lingual text. It has achieved considerable generalization performance of cross-lingual transfer tasks by aligning cross-lingual contextual word…
We propose a DNA sequencing scheme based on silicene nanopores. Using first principles theory, we compute the electrical properties of such pores in the absence and presence of nucleobases. Within a two-terminal geometry, we analyze the…
Cochlear implants (CIs) play a vital role in restoring hearing for individuals with severe to profound sensorineural hearing loss by directly stimulating the auditory nerve with electrical signals. While traditional coding strategies, such…