Related papers: Capacity-Approaching Constrained Codes with Error …
In data storage and data transmission, certain patterns are more likely to be subject to error when written (transmitted) onto the media. In magnetic recording systems with binary data and bipolar non-return-to-zero signaling, patterns that…
DNA codes have many applications, such as in data storage, DNA computing, etc. Good DNA codes have large sizes and satisfy some certain constraints. In this paper, we present a new construction method for reversible DNA codes. We show that…
DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while…
We provide a general formulation for the code-based test compression problem with fixed-length input blocks and propose a solution approach based on Evolutionary Algorithms. In contrast to existing code-based methods, we allow unspecified…
In order to overcome the limitations imposed by DNA barcoding when multiplexing a large number of samples in the current generation of high-throughput sequencing instruments, we have recently proposed a new protocol that leverages advances…
Run-Length Encoding (RLE) is one of the most fundamental tools in data compression. However, its compression power drops significantly if there lacks consecutive elements in the sequence. In extreme cases, the output of the encoder may…
Biomolecular computation has emerged as an important area of computer science research due to its high information density, immense parallelism opportunity along with potential applications in cryptography, genetic engineering and…
The widespread use of Large Language Models (LLMs) in software engineering has intensified the need for improved model and resource efficiency. In particular, for neural code generation, LLMs are used to translate function/method signature…
In this paper, we consider quantum error correction over depolarizing channels with non-binary low-density parity-check codes defined over Galois field of size $2^p$ . The proposed quantum error correcting codes are based on the binary…
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…
This paper presents a novel auto-encoder based end-to-end channel encoding and decoding. It integrates deep reinforcement learning (DRL) and graph neural networks (GNN) in code design by modeling the generation of code parity-check matrices…
This paper introduces a new approach to proving that a sequence of deterministic linear codes achieves capacity on an erasure channel under maximum a posteriori decoding. Rather than relying on the precise structure of the codes, this…
One of the primary sequencing methods gaining prominence in DNA storage is nanopore sequencing, attributed to various factors. In this work, we consider a simplified model of the sequencer, characterized as a channel. This channel takes a…
Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being…
Motivated by communication channels in which the transmitted sequences are subject to random permutations, as well as by certain DNA storage systems, we study the error control problem in settings where the information is stored/transmitted…
Linear programming approaches have been applied to derive upper bounds on the size of classical codes and quantum codes. In this paper, we derive similar results for general quantum codes with entanglement assistance, including nonadditive…
Regenerating codes allow distributed storage systems to recover from the loss of a storage node while transmitting the minimum possible amount of data across the network. We present a systematic computer search for optimal systematic…
Nanopore sequencing is a promising technology for DNA sequencing. In this paper, we investigate a specific model of the nanopore sequencer, which takes a $q$-ary sequence of length $n$ as input and outputs a vector of length $n+\ell-1$…
In this thesis we present several results in coding theory, concerning error-correcting codes and the Shannon capacity. 1. We give a general symmetry reduction of matrices occuring in semidefinite programs in coding theory. 2. We apply the…
Error correcting codes play a central role in digital communication, ensuring that transmitted information can be accurately reconstructed despite channel impairments. Recently, autoencoder (AE) based approaches have gained attention for…