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DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on…
High-throughput and quantitative experimental technologies are experiencing rapid advances in the biological sciences. One important recent technique is multiplexed fluorescence in situ hybridization (mFISH), which enables the…
Reverse engineering of binary executables is a critical problem in the computer security domain. On the one hand, malicious parties may recover interpretable source codes from the software products to gain commercial advantages. On the…
We propose a new class of efficient decoding algorithms for Reed-Muller (RM) codes over binary-input memoryless channels. The algorithms are based on projecting the code on its cosets, recursively decoding the projected codes (which are…
Sampling is classically performed by recording the amplitude of an input signal at given time instants; however, sampling and reconstructing a signal using multiple devices in parallel becomes a more difficult problem to solve when the…
In order to provide high data reliability, distributed storage systems disperse data with redundancy to multiple storage nodes. Regenerating codes is a new class of erasure codes to introduce redundancy for the purpose of improving the data…
Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in…
Monotone chain polar codes generalize classical polar codes to multivariate settings, offering a flexible approach for achieving the entire admissible rate region in the distributed lossless coding problem. However, this flexibility also…
In coding theory, handling errors that occur when symbols are inserted or deleted from a transmitted message is a long-standing challenge. Optimising redundancy for insertion and deletion channels remains a key open problem with significant…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
This paper considers the multiple-access relay channel in a setting where two source nodes transmit packets to a destination node, both directly and via a relay node, over packet erasure channels. Intra-session network coding is used at the…
In this paper, we introduce a model of a distributed storage system that is locally recoverable from any single server failure. Unlike the usual local recovery model of codes for distributed storage, this model accounts for the fact that…
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…
We consider recursive decoding techniques for RM codes, their subcodes, and newly designed codes. For moderate lengths up to 512, we obtain near-optimum decoding with feasible complexity.
The problem of designing codes for deletion-correction and synchronization has received renewed interest due to applications in DNA-based data storage systems that use nanopore sequencers as readout platforms. In almost all instances,…
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,…
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…
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…
Code search is vital in the maintenance and extension of software systems. Past works have used separate language models for the natural language and programming language artifacts on models with multiple encoders and different loss…
We investigate the problem of encoding data into an $(n, t)$-break-resilient code ($(n, t)$-BRC), i.e., a collections of sequences of length~$n$ from which the original data can be reconstructed even if they are adversarially broken at up…