Search

The de Bruijn graph, its sequences, and their various generalizations, have found many applications in information theory, including many new ones in the last decade. In this paper, motivated by a coding problem for emerging memory technologies, a set of sequences which generalize the window property of de Bruijn sequences, on its shorter subsequences, are defined. These sequences can be also defined and viewed as constrained sequences. Hence, they will be called locally-constrained de Bruijn sequences and a set of such sequences will be called a locally-constrained de Bruijn code. Several properties and alternative definitions for such codes are examined and they are analyzed as generalized sequences in the de Bruijn graph (and its generalization) and as constrained sequences. Various enumeration techniques are used to compute the total number of sequences for any given set of parameters. A construction method of such codes from the theory of shift-register sequences is proposed. Finally, we show how these locally-constrained de Bruijn sequences and codes can be applied in constructions of codes for correcting synchronization errors in the $\ell $ -symbol read channel and in the racetrack memory channel. For this purpose, these codes are superior in their size to previously known codes. [ABSTRACT FROM AUTHOR]

The sequence reconstruction problem corresponds to the model in which a sequence from some code is transmitted over several noisy channels that produce distinct outputs. Then, the channels’ outputs, received by the decoder, are used to recover the transmitted sequence, and the main problem under this paradigm is to calculate the minimum number of channels that enables unique reconstruction of the transmitted word. This problem is equivalent to finding the size of the largest intersection of channels’ outputs sets received after transmitting distinct codewords. Motivated by the error behavior observed in DNA storage systems, the present work extends the study of the reconstruction model to the case in which a binary word is transmitted over channels prone to substitutions, insertions, and deletions. Furthermore, we also study the size of the error balls generated by either one deletion and at most a fixed number of substitutions or one insertion and at most one substitution in a binary word. For the case of only substitutions, we present a decoder of optimal complexity, which improves upon a recent construction of such a decoder. Lastly, a simplification of that decoder is studied in case there are more channels than the minimum required number. [ABSTRACT FROM AUTHOR]

Mutually uncorrelated (MU) codes are a class of codes in which no proper prefix of one codeword is a suffix of another codeword. These codes were originally studied for synchronization purposes and recently, Yazdi et al. showed their applicability to enable random access in DNA storage. In this paper,we follow the research of Yazdi et al. and study MU codes along with their extensions to correct errors and balanced codes. We first review a well-known construction of MU codes and study the asymptotic behavior of its cardinality. This task is accomplished by studying a special class of run-length limited codes that impose the longest run of zeros to be at most some function of the codewords length. We also present an efficient algorithm for this class of constrained codes and show how to use this analysis for MU codes. Next, we extend the results on the run-length limited codes in order to study $(d_{h},d_{m})$ -MU codes that impose a minimum Hamming distance of $d_{h}$ between different codewords and $d_{m}$ between prefixes and suffixes. In particular, we show an efficient construction of these codes with nearly optimal redundancy. We also provide similar results for the edit distance and balanced MU codes. Last, we draw connections to the problems of comma-free and prefix synchronized codes. [ABSTRACT FROM AUTHOR]