Related papers: DNA Tails for Molecular Flash Memory
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,…
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…
We propose a novel coding scheme for DNA-based storage systems, called the shift-interleave (SI) coding, designed to correct insertion, deletion, and substitution (IDS) errors, as well as sequence losses. The SI coding scheme employs…
In this paper, we consider the outer channel for DNA-based data storage. When transmitting over the outer channel, each DNA string is treated as a unit/symbol that would be either correctly received, or erased, or corrupted by uniformly…
Biological data mainly comprises of Deoxyribonucleic acid (DNA) and protein sequences. These are the biomolecules which are present in all cells of human beings. Due to the self-replicating property of DNA, it is a key constitute of genetic…
Splice sites play a crucial role in gene expression, and accurate prediction of these sites in DNA sequences is essential for diagnosing and treating genetic disorders. We address the challenge of splice site prediction by introducing…
The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like…
Flash memory is a non-volatile computer memory comprised of blocks of cells, wherein each cell is implemented as either NAND or NOR floating gate. NAND flash is currently the most widely used type of flash memory. In a NAND flash memory,…
Flash memory devices are winning the competition for storage density against magnetic recording devices. This outcome results from advances in physics that allow storage of more than one bit per cell, coupled with advances in signal…
Deoxyribonucleic Acid (DNA) as a storage medium with high density and long-term preservation properties can satisfy the requirement of archival storage for rapidly increased digital volume. The read and write processes of DNA storage are…
Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of…
Enzymatic DNA labeling is a powerful tool with applications in biochemistry, molecular biology, biotechnology, medical science, and genomic research. This paper contributes to the evolving field of DNA-based data storage by presenting a…
Technologies for sequencing (reading) and synthesizing (writing) DNA have progressed on a Moore's law-like trajectory over the last three decades. This has motivated the idea of using DNA for data storage. Theoretically, DNA-based storage…
Tail-biting convolutional codes extend the classical zero-termination convolutional codes: Both encoding schemes force the equality of start and end states, but under the tail-biting each state is a valid termination. This paper proposes a…
In this work, we study a new model of defect memory cells, called partially stuck-at memory cells, which is motivated by the behavior of multi-level cells in non-volatile memories such as flash memories and phase change memories. If a cell…
Sequencing a DNA strand, as part of the read process in DNA storage, produces multiple noisy copies which can be combined to produce better estimates of the original strand; this is called trace reconstruction. One can reduce the error rate…
In this paper, we attempt to address the challenge of applying Neural Architecture Search (NAS) algorithms, specifically the Differentiable Architecture Search (DARTS), to long-tailed datasets where class distribution is highly imbalanced.…
Long-tailed data is prevalent in real-world classification tasks and heavily relies on supervised information, which makes the annotation process exceptionally labor-intensive and time-consuming. Unfortunately, despite being a common…
In this paper, we present a novel design strategy of DNA codes with length $3n$ over the non-chain ring $R=\mathbb{Z}_4+u\mathbb{Z}_4+u^2\mathbb{Z}_4$ with $64$ elements and $u^3=1$, where $n$ denotes the length of a code over $R$. We first…
DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have…