Related papers: Error-Correcting Codes for Nanopore Sequencing
Quantum error correction and the use of quantum error correction codes is likely to be essential for the realisation of practical quantum computing. Because the error models of quantum devices vary widely, quantum codes which are tailored…
In this paper, we introduce a new channel model we term the q-ary multi-bit channel (QMBC). This channel models a memory device, where q-ary symbols (q=2^s) are stored in the form of current/voltage levels. The symbols are read in a…
Motivation: Detection of structural variants (SV) from the alignment of sample DNA reads to the reference genome is an important problem in understanding human diseases. Long reads that can span repeat regions, along with an accurate…
Recent work on approximate quantum error correction (QEC) has opened up the possibility of constructing subspace codes that protect information with high fidelity in scenarios where perfect error correction is impossible. Motivated by this,…
Despite Retrieval-Augmented Generation improving code completion, traditional retrieval methods struggle with information redundancy and a lack of diversity within limited context windows. To solve this, we propose a resource-optimized…
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…
Motivation: The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing error rate. In this paper, we…
Near term quantum computers suffer from the presence of different noise sources. In order to mitigate for this effect and acquire results with significantly better accuracy, there is the urge of designing efficient error correction or error…
Expanding genetic codes from natural standard nucleotides to artificial non-standard nucleotides marks a significant advancement in synthetic biology, with profound implications for biotechnology and medicine. Decoding the biological…
In this work, we present a new version of non-binary VT codes that are capable of correcting a single deletion or single insertion. Moreover, we provide the first known linear time algorithms that encode user messages into these codes of…
For $q$-ary $n$-sequences, we develop the concept of similarity functions that can be used (for $q=4$) to model a thermodynamic similarity on DNA sequences. A similarity function is identified by the length of a longest common subsequence…
Imperfect measurement can degrade a quantum error correction scheme. A solution that restores fault tolerance is to add redundancy to the process of syndrome extraction. In this work, we show how to optimize this process for an arbitrary…
We demonstrate that the performance of quantum error correction can be improved with noise-aware decoders that are calibrated to the likelihood of physical error configurations in a device. We show that noise-aware decoding increases the…
The scaling of high density NOR Flash memory devices with multi level cell (MLC) hits the reliability break wall because of relatively high intrinsic bit error rate (IBER). The chip maker companies offer two solutions to meet the output bit…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (i.e. rarely accessed), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
Let $\mathcal{B}(\cdot)$ be an error ball function. A set of $q$-ary sequences of length $n$ is referred to as an \emph{$(n,q,N;\mathcal{B})$-reconstruction code} if each sequence $\boldsymbol{x}$ within this set can be uniquely…
Quantum error-correcting codes protect fragile quantum information by encoding it redundantly, but identifying codes that perform well in practice with minimal overhead remains difficult due to the combinatorial search space and the high…
Developing ultra-low-energy superconducting computing and fault-tolerant quantum computing will require scalable superconducting memory. While conventional superconducting logic-based memory cells have facilitated early demonstrations,…