An Improvement of Non-binary Code Correcting Single b-Burst of Insertions or Deletions

This paper constructs a non-binary code correcting a single $b$-burst of insertions or deletions with a large cardinality. This paper also proposes a decoding algorithm of this code and evaluates a lower bound of the cardinality of this code. Moreover, we evaluate an asymptotic upper bound on the cardinality of codes which correct a single burst of insertions or deletions.Comment: 7 pages, accepted to ISITA 201

Bit Flipping Moment Balancing Schemes for Insertion, Deletion and Substitution Error Correction

In this paper, two moment balancing schemes, namely a variable index scheme and a fixed index scheme, for either single insertion/deletion error correction or multiple substitution error correction are introduced for coded sequences originally developed for correcting substitution errors only. By judiciously flipping bits of the original substitution error correcting code word, the resulting word is able to correct either a reduced number of substitution errors or a single insertion/deletion error. The number of flips introduced by the two schemes can be kept small compared to the code length. It shows a practical value of applying the schemes to a long substitution error correcting code for a severe channel where substitution errors dominate but insertion/deletion errors can occur with a low probability. The new schemes can be more easily implemented in an existing coding system than any previously published moment balancing templates since no additional parity bits are required which also means the code rate remains same and the existing substitution error correcting decoder requires no changes. Moreover, the work extends the class of Levenshtein codes capable of correcting either single substitution or single insertion/deletion errors to codes capable of correcting either multiple substitution errors or single insertion/deletion error

Tutorial on algebraic deletion correction codes

The deletion channel is known to be a notoriously diffcult channel to design error-correction codes for. In spite of this difficulty, there are some beautiful code constructions which give some intuition about the channel and about what good deletion codes look like. In this tutorial we will take a look at some of them. This document is a transcript of my talk at the coding theory reading group on some interesting works on deletion channel. It is not intended to be an exhaustive survey of works on deletion channel, but more as a tutorial to some of the important and cute ideas in this area. For a comprehensive survey, we refer the reader to the cited sources and surveys. We also provide an implementation of VT codes that correct single insertion/deletion errors for general alphabets at https://github.com/shubhamchandak94/VT_codes/

Codes for Correcting Localized Deletions

We consider the problem of constructing binary codes for correcting deletions that are localized within certain parts of the codeword that are unknown a priori. The model that we study is when $\delta \leq w$ deletions are localized in a window of size $w$ bits. These $\delta$ deletions do not necessarily occur in consecutive positions, but are restricted to the window of size $w$. The localized deletions model is a generalization of the bursty model, in which all the deleted bits are consecutive. In this paper, we construct new explicit codes for the localized model, based on the family of Guess & Check codes which was previously introduced by the authors. The codes that we construct can correct, with high probability, $\delta \leq w$ deletions that are localized in a single window of size $w$, where $w$ grows with the block length. Moreover, these codes are systematic; have low redundancy; and have efficient deterministic encoding and decoding algorithms. We also generalize these codes to deletions that are localized within multiple windows in the codeword.Comment: arXiv admin note: text overlap with arXiv:1705.0956

Optimal Codes Correcting a Burst of Deletions of Variable Length

In this paper, we present an efficiently encodable and decodable code construction that is capable of correction a burst of deletions of length at most $k$. The redundancy of this code is $\log n + k(k+1)/2\log \log n+c_k$ for some constant $c_k$ that only depends on $k$ and thus is scaling-optimal. The code can be split into two main components. First, we impose a constraint that allows to locate the burst of deletions up to an interval of size roughly $\log n$. Then, with the knowledge of the approximate location of the burst, we use several {shifted Varshamov-Tenengolts} codes to correct the burst of deletions, which only requires a small amount of redundancy since the location is already known up to an interval of small size. Finally, we show how to efficiently encode and decode the code.Comment: 6 page

Construction and redundancy of codes for correcting deletable errors

Consider a binary word being transmitted through a communication channel that introduces deletable errors where each bit of the word is either retained, flipped, erased or deleted. The simplest code for correcting \emph{all} possible deletable error patterns of a fixed size is the repetition code whose redundancy grows linearly with the code length. In this paper, we relax this condition and construct codes capable of correcting \emph{nearly} all deletable error patterns of a fixed size, with redundancy growing as a logarithm of the word length

Duplication-Correcting Codes

In this work, we propose constructions that correct duplications of multiple consecutive symbols. These errors are known as tandem duplications, where a sequence of symbols is repeated; respectively as palindromic duplications, where a sequence is repeated in reversed order. We compare the redundancies of these constructions with code size upper bounds that are obtained from sphere packing arguments. Proving that an upper bound on the code cardinality for tandem deletions is also an upper bound for inserting tandem duplications, we derive the bounds based on this special tandem deletion error as this results in tighter bounds. Our upper bounds on the cardinality directly imply lower bounds on the redundancy which we compare with the redundancy of the best known construction correcting arbitrary burst insertions. Our results indicate that the correction of palindromic duplications requires more redundancy than the correction of tandem duplications and both significantly less than arbitrary burst insertions.Comment: 24 pages, 1 figure. arXiv admin note: text overlap with arXiv:1707.0005

Efficient and Explicit Balanced Primer Codes

To equip DNA-based data storage with random-access capabilities, Yazdi et al. (2018) prepended DNA strands with specially chosen address sequences called primers and provided certain design criteria for these primers. We provide explicit constructions of error-correcting codes that are suitable as primer addresses and equip these constructions with efficient encoding algorithms. Specifically, our constructions take cyclic or linear codes as inputs and produce sets of primers with similar error-correcting capabilities. Using certain classes of BCH codes, we obtain infinite families of primer sets of length $n$, minimum distance $d$ with $(d + 1) \log_4 n + O(1)$ redundant symbols. Our techniques involve reversible cyclic codes (1964), an encoding method of Tavares et al. (1971) and Knuth's balancing technique (1986). In our investigation, we also construct efficient and explicit binary balanced error-correcting codes and codes for DNA computing

Construction and Encoding Algorithm for Maximum Run-Length Limited Single Insertion/Deletion Correcting Code

Maximum run-length limited codes are constraint codes used in communication and data storage systems. Insertion/deletion correcting codes correct insertion or deletion errors caused in transmitted sequences and are used for combating synchronization errors. This paper investigates the maximum run-length limited single insertion/deletion correcting (RLL-SIDC) codes. More precisely, we construct efficiently encodable and decodable RLL-SIDC codes. Moreover, we present its encoding algorithm and show the redundancy of the code.Comment: 8 pages, 3 figures, 7 tables, submitted to IEICE transaction on Fundamental

Optimal Reconstruction Codes for Deletion Channels

The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication scenario where the sender transmits a codeword from some codebook and the receiver obtains multiple noisy reads of the codeword. Motivated by modern storage devices, we introduced a variant of the problem where the number of noisy reads $N$ is fixed (Kiah et al. 2020). Of significance, for the single-deletion channel, using $\log_2\log_2 n +O(1)$ redundant bits, we designed a reconstruction code of length $n$ that reconstructs codewords from two distinct noisy reads. In this work, we show that $\log_2\log_2 n -O(1)$ redundant bits are necessary for such reconstruction codes, thereby, demonstrating the optimality of our previous construction. Furthermore, we show that these reconstruction codes can be used in $t$-deletion channels (with $t\ge 2$) to uniquely reconstruct codewords from $n^{t-1}+O\left(n^{t-2}\right)$ distinct noisy reads