Related papers: Iterative Soft Decoding Algorithm for DNA Storage …
Quantum error-correcting codes (QECCs) can eliminate the negative effects of quantum noise, the major obstacle to the execution of quantum algorithms. However, realizing practical quantum error correction (QEC) requires resolving many…
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…
Reconstructing DNA sequences without a reference, known as de novo assembly, is a complex computational task involving the alignment of overlapping fragments. To address this problem, a usual strategy is to map the assembly to a Quadratic…
We introduce a novel algorithm for decoding binary linear codes by linear programming. We build on the LP decoding algorithm of Feldman et al. and introduce a post-processing step that solves a second linear program that reweights the…
Motivation: High-coverage sequencing data have significant, yet hard to exploit, redundancy. Most FASTQ compressors cannot efficiently compress the DNA stream of large datasets, since the redundancy between overlapping reads cannot be…
The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…
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…
Regenerating codes provide an efficient way to recover data at failed nodes in distributed storage systems. It has been shown that regenerating codes can be designed to minimize the per-node storage (called MSR) or minimize the…
In a digital communication system, information is sent from one place to another over a noisy communication channel. It may be possible to detect and correct errors that occur during the transmission if one encodes the original information…
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…
We consider the correction of errors from nucleotide sequences produced by next-generation targeted amplicon sequencing. The next-generation sequencing (NGS) platforms can provide a great deal of sequencing data thanks to their high…
Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences. However, rather than merely generating designs that are natural, we often aim to optimize downstream reward functions while…
Topological error correcting codes, and particularly the surface code, currently provide the most feasible roadmap towards large-scale fault-tolerant quantum computation. As such, obtaining fast and flexible decoding algorithms for these…
The performance of algebraic soft-decision decoding of Reed-Solomon codes using bit-level soft information is investigated. Optimal multiplicity assignment strategies of algebraic soft-decision decoding with infinite cost are first studied…
The general trace reconstruction problem seeks to recover an original sequence from its noisy copies independently corrupted by deletions, insertions, and substitutions. This problem arises in applications such as DNA data storage, a…
Recently, deep learning has shown to be effective for Electroencephalography (EEG) decoding tasks. Yet, its performance can be negatively influenced by two key factors: 1) the high variance and different types of corruption that are…
Nanopore sequencing technology remains highly error-prone, making efficient error correction essential in DNA-based data storage. Prior work addressed high error rates using convolutional codes with their decoder coupled with the…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
DNA storage systems face significant challenges, including insertion, deletion, and substitution (IDS) errors. Therefore, designing effective synchronization codes, i.e., codes capable of correcting IDS errors, is essential for DNA storage…
Deoxyribonucleic Acid (DNA), with its high density and long durability, is a promising storage medium for long-term archival storage and has attracted much attention. Several studies have verified the feasibility of using DNA for archival…