Related papers: Trellis BMA: Coded Trace Reconstruction on IDS Cha…
Variable length codes exhibit de-synchronization problems when transmitted over noisy channels. Trellis decoding techniques based on Maximum A Posteriori (MAP) estimators are often used to minimize the error rate on the estimated sequence.…
Recent advances in DNA sequencing technology and DNA storage systems have rekindled the interest in deletion channels. Multiple recent works have looked at variants of sequence reconstruction over a single and over multiple deletion…
Due to its higher data density, longevity, energy efficiency, and ease of generating copies, DNA is considered a promising storage technology for satisfying future needs. However, a diverse set of errors including deletions, insertions,…
This paper investigates the use of redundancy and self repairing against node failures in distributed storage systems, using various strategies. In replication method, access to one replication node is sufficient to reconstruct a lost node,…
Ever since deoxyribonucleic acid (DNA) was considered as a next-generation data-storage medium, lots of research efforts have been made to correct errors occurred during the synthesis, storage, and sequencing processes using error…
In the trace reconstruction problem our goal is to learn an unknown string $x\in \{0,1\}^n$ given independent traces of $x$. A trace is obtained by independently deleting each bit of $x$ with some probability $\delta$ and concatenating the…
The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication setting in which a sender transmits a codeword and the receiver observes K independent noisy versions of this codeword. In this work, we study…
This paper presents a stochastic algorithm for iterative error control decoding. We show that the stochastic decoding algorithm is an approximation of the sum-product algorithm. When the code's factor graph is a tree, as with trellises, the…
The goal of the trace reconstruction problem is to recover a string $x\in\{0,1\}^n$ given many independent {\em traces} of $x$, where a trace is a subsequence obtained from deleting bits of $x$ independently with some given probability…
With the emergence of new storage and communication methods, the insertion, deletion, and substitution (IDS) channel has attracted considerable attention. However, many topics on the IDS channel and the associated Levenshtein distance…
Register Transfer Level (RTL) code optimization is crucial for enhancing the efficiency and performance of digital circuits during early synthesis stages. Currently, optimization relies heavily on manual efforts by skilled engineers, often…
Maximum-distance-separable (MDS) codes are a class of erasure codes that are widely adopted to enhance the reliability of distributed storage systems (DSS). In (n, k) MDS coded DSS, the original data are stored into n distributed nodes in…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…
Error-correcting codes over sets, with applications to DNA storage, are studied. The DNA-storage channel receives a set of sequences, and produces a corrupted version of the set, including sequence loss, symbol substitution, symbol…
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…
The goal of trace reconstruction is to reconstruct an unknown $n$-bit string $x$ given only independent random traces of $x$, where a random trace of $x$ is obtained by passing $x$ through a deletion channel. A Statistical Query (SQ)…
DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…
Recent advances in high-throughput cDNA sequencing (RNA-Seq) technology have revolutionized transcriptome studies. A major motivation for RNA-Seq is to map the structure of expressed transcripts at nucleotide resolution. With accurate…
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…
In the current era, DeoxyriboNucleic Acid (DNA) based data storage emerges as an intriguing approach, garnering substantial academic interest and investigation. This paper introduces a novel deep joint source-channel coding (DJSCC) scheme…