Related papers: Half-Marker Codes for Deletion Channels with Appli…
In this paper, we propose a novel iterative encoding algorithm for DNA storage to satisfy both the GC balance and run-length constraints using a greedy algorithm. DNA strands with run-length more than three and the GC balance ratio far from…
In this paper, we shed light on how an adaptive, efficient error coding in the transport layer helps ensure the application requirements. We recap the use of MDS codes and show that binary coding can significantly reduce the complexity and…
Motivated by the sequence reconstruction problem from traces in DNA-based storage, we consider the problem of designing codes for the deletion channel when multiple observations (or traces) are available to the decoder. We propose simple…
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 study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect…
The exponential growth in data generation and large-scale data analysis creates an unprecedented need for inexpensive, low-latency, and high-density information storage. This need has motivated significant research into multi-level memory…
DNA has emerged as a promising alternative for long-term data storage due to its high capacity, durability, and low-energy potential. However, storing data in DNA presents several challenges. First, it requires complex and costly…
Encoding digital information into DNA sequences offers an attractive potential solution for storing rapidly growing data under the information age and the rise of artificial intelligence. However, practical implementations of DNA storage…
DNA storage is a promising archival data storage solution to today's big data problem. A DNA storage system encodes and stores digital data with synthetic DNA sequences and decodes DNA sequences back to digital data via sequencing. For…
In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…
Digital information can be encoded in the building-block sequence of macromolecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive. In…
Data-driven fault detection has been regarded as a 3D image segmentation task. The models trained from synthetic data are difficult to generalize in some surveys. Recently, training 3D fault segmentation using sparse manual 2D slices is…
Using nuclear magnetic resonance techniques, we experimentally investigated the effects of applying a two bit phase error detection code to preserve quantum information in nuclear spin systems. Input states were stored with and without…
Distributed storage codes have important applications in the design of modern storage systems. In a distributed storage system, every storage node has a probability to fail and once an individual storage node fails, it must be reconstructed…
SD codes are erasure codes that address the mixed failure mode of current RAID systems. Rather than dedicate entire disks to erasure coding, as done in RAID-5, RAID-6 and Reed-Solomon coding, an SD code dedicates entire disks, plus…
This paper introduces a neural polar decoder (NPD) for deletion channels with a constant deletion rate. Existing polar decoders for deletion channels exhibit high computational complexity of $O(N^4)$, where $N$ is the block length. This…
Partial MDS (PMDS) and sector-disk (SD) codes are classes of erasure codes that combine locality with strong erasure correction capabilities. We construct PMDS and SD codes where each local code is a bandwidth-optimal regenerating MDS code.…
Recent experiments have demonstrated the feasibility of storing digital information in macromolecules such as DNA and protein. However, the DNA storage channel is prone to errors such as deletions, insertions, and substitutions. During the…
Racetrack memory is a new technology which utilizes magnetic domains along a nanoscopic wire in order to obtain extremely high storage density. In racetrack memory, each magnetic domain can store a single bit of information, which can be…
DNA code design aims to generate a set of DNA sequences (codewords) with minimum likelihood of undesired hybridizations among sequences and their reverse-complement (RC) pairs (cross-hybridization). Inspired by the distinct hybridization…