Related papers: Correcting a Single Deletion in Reads from a Nanop…
Solid-state nanopore DNA sequencers present mechanical and chemical stability, reusability, and large-scale integrability. However, their development is hindered by the absence of a protein-free mechanism for controlling DNA translocation,…
This study explores the self-synchronization problem in DNA coding, specifically addressing single-deletion errors without using delimiters between codewords. We aim to identify the beginning of each codeword without using delimiters,…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…
This work proves new results on the ability of binary Reed-Muller codes to decode from random errors and erasures. We obtain these results by proving improved bounds on the weight distribution of Reed-Muller codes of high degrees.…
The Oxford Nanopore Technologies's MinION is the first portable DNA sequencing device. It is capable of producing long reads, over 100 kBp were reported. However, it has significantly higher error rate than other methods. In this study, we…
Burst errors involving simultaneous insertions, deletions, and substitutions occur in practical scenarios, including DNA data storage and document synchronization, motivating developments of channel codes that can correct such errors. In…
In the recent years, DNA has emerged as a potentially viable storage technology. DNA synthesis, which refers to the task of writing the data into DNA, is perhaps the most costly part of existing storage systems. Accordingly, this high cost…
The Damerau-Levenshtein distance between two sequences is the minimum number of operations (deletions, insertions, substitutions, and adjacent transpositions) required to convert one sequence into another. Notwithstanding a long history of…
In this work, we investigate the problem of constructing codes capable of correcting two deletions. In particular, we construct a code that requires redundancy approximately 8 log n + O(log log n) bits of redundancy, where n is the length…
As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
Pairwise sequence comparison is one of the most fundamental problems in string processing. The most common metric to quantify the similarity between sequences S and T is edit distance, d(S,T), which corresponds to the number of characters…
Scaling of the behavior of a nanodevice means that the device function (selectivity) is a unique smooth and monotonic function of a scaling parameter that is an appropriate combination of the system's parameters. For the uniformly charged…
Recent work by Smagloy et al. (ISIT 2020) shows that the redundancy of a single-deletion $s$-substitution correcting code is asymptotically at least $(s+1)\log n+o(\log n)$, where $n$ is the length of the codes. They also provide a…
This paper summarizes our work on experimentally characterizing, mitigating, and recovering read disturb errors in multi-level cell (MLC) NAND flash memory, which was published in DSN 2015, and examines the work's significance and future…
We investigate adaptive single-trial error/erasure decoding of binary codes whose decoder is able to correct e errors and t erasures if le+t<=d-1. Thereby, d is the minimum Hamming distance of the code and 1<l<=2 is the tradeoff parameter…
This paper presents a new approach to the problem of correcting speech recognition errors by means of post-editing. It consists of using a neural sequence tagger that learns how to correct an ASR (Automatic Speech Recognition) hypothesis…
Neural networks (NNs) are capable of learning complex patterns and relationships in data to make predictions with high accuracy, making them useful for various tasks. However, NNs are both computation-intensive and memory-intensive methods,…
A growing need exists for efficient and accurate methods for detecting defects in semiconductor materials and devices. These defects can have a detrimental impact on the efficiency of the manufacturing process, because they cause critical…