Codes for Correcting Asymmetric Adjacent Transpositions and Deletions

Codes in the Damerau--Levenshtein metric have been extensively studied recently owing to their applications in DNA-based data storage. In particular, Gabrys, Yaakobi, and Milenkovic (2017) designed a length-$n$ code correcting a single deletion and $s$ adjacent transpositions with at most $(1+2s)\log n$ bits of redundancy. In this work, we consider a new setting where both asymmetric adjacent transpositions (also known as right-shifts or left-shifts) and deletions may occur. We present several constructions of the codes correcting these errors in various cases. In particular, we design a code correcting a single deletion, $s^+$ right-shift, and $s^-$ left-shift errors with at most $(1+s)\log (n+s+1)+1$ bits of redundancy where $s=s^{+}+s^{-}$. In addition, we investigate codes correcting $t$ $0$-deletions, $s^+$ right-shift, and $s^-$ left-shift errors with both uniquely-decoding and list-decoding algorithms. Our main contribution here is the construction of a list-decodable code with list size $O(n^{\min\{s+1,t\}})$ and with at most $(\max \{t,s+1\}) \log n+O(1)$ bits of redundancy, where $s=s^{+}+s^{-}$. Finally, we construct both non-systematic and systematic codes for correcting blocks of $0$-deletions with $\ell$-limited-magnitude and $s$ adjacent transpositions

Codes Correcting All Patterns of Tandem-Duplication Errors of Maximum Length 3

The set of all $q$-ary strings that do not contain repeated substrings of length $\leq\ell$ forms a code correcting all patterns of tandem-duplication errors of length $\leq\ell$, when $\ell \in \{1, 2, 3\}$. For $\ell \in \{1, 2\}$, this code is also known to be optimal in terms of asymptotic rate. The purpose of this paper is to demonstrate asymptotic optimality for the case $\ell = 3$ as well, and to give the corresponding characterization of the zero-error capacity of the $(\leq 3)$-tandem-duplication channel. This settles the zero-error problem for $(\leq\ell)$-tandem-duplication channels in all cases where duplication roots of strings are unique.Comment: 5 pages (double-column format

Systematic Codes for Correcting Deletion/Insertion of One Zero in Each and Every Bucket of Zeros

In this thesis, we propose a systematic code for correcting t = 1 insertion/deletion errors of the character ”0” that can occur between any two consecutive 1’s in a binary string. The code requires balanced input strings, where each word of length n contains ⌈n/2⌉ 0’s and ⌊n/2⌋ 1’s. This error model is shown to be related to zero-error capacity-achieving codes for a limited-magnitude error channel. We prove that the inputs can be partitioned in to different subsets and the words in the same subset can be assigned a unique check for this error model. We deduce that the upper bound for the number of checks required is 2w, where w is the weight of the input. Efficient encoding and decoding algorithms are provided. Our algorithms return variable-length checks and may require up to r = 3w check bits. While the optimal rate for this error model is not known, we establish our rate to be between 0.4 and 0.666 and demonstrate potential avenues for improvement

Codes for Synchronization in Channels and Sources with Edits

Edit channels are a class of communication channels where the output of the channel is an edited version of the input. The edits are considered to be deletions and insertions. DNA-based data storage system is one of the motivations for this model. This thesis studies various problems related to edit channel and also edit synchronization problem. Varshamov-Tenengolts (VT) codes are first introduced. These codes can correct a single deletion or insertion and have a linear-time decoder. The problem of efficient encoding of the non-binary version of VT codes is addressed, where a simple linear-time encoding method to systematically map binary message sequences onto VT codewords is proposed. Another model that is studied is segmented edit channels, where we have the additional assumption that the channel input sequence is implicitly divided into segments such that at most one edit can occur within a segment. A code construction is proposed for this model based on subsets of VT codes chosen with pre-determined prefxes and/or sufxes. Also an upper bound is derived on the rate of any zero-error code for the segmented edit channel in terms of the segment length. This upper bound shows that the rate scaling of the proposed codes as the segment length increases is the same as that of the maximal code. Edit synchronization is another problem studied in this thesis. In this model, there are two remote nodes (encoder and decoder), each having a binary sequence. The sequence X, available at the encoder, is the updated sequence and differs from Y (available at the decoder) by a small number of edits. The goal is to construct a message M, to be sent via a one-way error-free link, such that the decoder can reconstruct X using M and Y. A coding scheme is devised for this one-way synchronization model. The scheme is based on multiple layers of VT codes combined with off-the-shelf linear error-correcting codes and uses a list decoder. Motivated by the sequence reconstruction problem from traces in DNA-based storage, the problem of designing codes for the deletion channel when multiple observations (or traces) are available to the decoder is considered. A simple binary and non-binary code is proposed that splits the codeword into blocks and employs a VT code in each block. The availability of multiple traces helps the decoder to identify deletion-free copies of a block, and to avoid mis-synchronization while decoding. The encoding complexity of the proposed scheme is linear in the codeword length; the decoding complexity is linear in the codeword length and quadratic in the number of deletions and the number of traces. The list decoding technique for the proposed code is also considered