Related papers: Single-Error Detection and Correction for Duplicat…
Neural machine translation (NMT) generates the next target token given as input the previous ground truth target tokens during training while the previous generated target tokens during inference, which causes discrepancy between training…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
Long-distance optical quantum channels are necessarily lossy, leading to errors in transmitted quantum information, entanglement degradation and, ultimately, poor protocol performance. Quantum states carrying information in the channel can…
A number of methods have been proposed over the last decade for encoding information using deoxyribonucleic acid (DNA), giving rise to the emerging area of DNA data embedding. Since a DNA sequence is conceptually equivalent to a sequence of…
Genomic evolution can be viewed as string-editing processes driven by mutations. An understanding of the statistical properties resulting from these mutation processes is of value in a variety of tasks related to biological sequence data,…
Nanopore sequencing, superior to other sequencing technologies for DNA storage in multiple aspects, has recently attracted considerable attention. Its high error rates, however, demand thorough research on practical and efficient coding…
DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the…
Owing to its immense storage density and durability, DNA has emerged as a promising storage medium. However, due to technological constraints, data can only be written onto many short DNA molecules called data blocks that are stored in an…
We construct new families of multi-error-correcting quantum codes for the amplitude damping channel. Our key observation is that, with proper encoding, two uses of the amplitude damping channel simulate a quantum erasure channel. This…
Despite their growing capabilities, language models still frequently reproduce content from their training data, generate repetitive text, and favor common grammatical patterns and vocabulary. A possible cause is the decoding strategy: the…
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…
In network communication, the source often transmits messages at several different information rates within a session. How to deal with information transmission and network error correction simultaneously under different rates is introduced…
Mutation testing can be used to assess the fault-detection capabilities of a given test suite. To this aim, two characteristics of mutation testing frameworks are of paramount importance: (i) they should generate mutants that are…
Gene duplication is a fundamental evolutionary mechanism that contributes to biological complexity and diversity (Fortna et al., 2004). Traditionally, research has focused on the duplication of gene sequences (Zhang, 1914). However,…
We propose a novel coding scheme for DNA-based storage systems, called the shift-interleave (SI) coding, designed to correct insertion, deletion, and substitution (IDS) errors, as well as sequence losses. The SI coding scheme employs…
Short tandem repeats (STRs) are low-entropy regions in the genome, consisting of a short (1-6 bp) unit that is consecutively repeated multiple times. They are known for high mutational instability, due to so-called stutter-mutations, in…
Error-correction codes are central for fault-tolerant information processing. Here we develop a rigorous framework to describe various coding models based on quantum resource theory of superchannels. We find, by treating codings as…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
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 this paper, we study codes correcting $t$ duplications of $\ell$ consecutive symbols. These errors are known as tandem duplication errors, where a sequence of symbols is repeated and inserted directly after its original occurrence. Using…