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The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes for DNA storage channel, a new metric, termed the sequence-subset distance, is introduced, which generalizes the Hamming distance to a distance function defined between any two sets of unordered vectors and helps to establish a uniform framework to design error correcting codes for DNA storage channel. We further introduce a family of error correcting codes, referred to as sequence-subset codes, for DNA storage and show that the error-correcting ability of such codes is completely determined by their minimum distance. We derive some upper bounds on the size of the sequence-subset codes including a tight bound for a special case, a Singleton-like bound and a Plotkin-like bound. We also propose some constructions, including an optimal construction for that special case, which imply lower bounds on the size of such codes. [ABSTRACT FROM AUTHOR]

Limited magnitude asymmetric error model is well suited for flash memory. In this paper, we consider the construction of asymmetric codes correcting single error over $\mathbb {Z}_{2^{k}r}$ which is based on so called $B_{1}[{4}](2^{k}r)$ set. In fact, we reduce the construction of a maximal size $B_{1}[{4}](2^{k}r)$ set for $k\geq 3$ to the construction of a maximal size $B_{1}[{4}](2^{k-3}r)$ set. Finally, we give an explicit formula of a maximal size $B_{1}[{4}](4r)$ set and some lower bounds of a maximal size $B_{1}[{4}](2r)$ set. By computer searching up to $q\leq 106$ , we conjecture that those lower bounds are tight. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Because of their capacity-approaching performance and their complexity/latency advantages, spatially-coupled (SC) codes are among the most attractive error-correcting codes for use in modern dense data storage systems. SC codes are constructed by partitioning an underlying block code and coupling the partitioned components. Here, we focus on circulant-based SC codes. Recently, the optimal overlap (OO), circulant power optimizer (CPO) approach was introduced to construct high performance SC codes for additive white Gaussian noise (AWGN) and Flash channels. The OO stage operates on the protograph of the SC code to derive the optimal partitioning that minimizes the number of graphical objects that undermine the performance of SC codes under iterative decoding. Then, the CPO optimizes the circulant powers to further reduce this number. Since the nature of detrimental objects in the graph of a code critically depends on the characteristics of the channel of interest, extending the OO-CPO approach to construct SC codes for channels with intrinsic memory is not a straightforward task. In this paper, we tackle one relevant extension; we construct high performance SC codes for practical 1-D magnetic recording channels, i.e., partial-response (PR) channels. Via combinatorial techniques, we carefully build and solve the optimization problem of the OO partitioning, focusing on the objects of interest in the case of PR channels. Then, we customize the CPO to further reduce the number of these objects in the graph of the code. SC codes designed using the proposed OO-CPO approach for PR channels outperform prior state-of-the-art SC codes by up to around 3 orders of magnitude in frame error rate (FER) and 1.1 dB in signal-to-noise ratio (SNR). More intriguingly, our SC codes outperform structured block codes of the same length and rate by up to around 1.8 orders of magnitude in FER and 0.4 dB in SNR. The performance advantage of SC codes designed using the devised OO-CPO approach over block codes of the same parameters is not only pronounced in the error floor region, but also in the waterfall region. [ABSTRACT FROM AUTHOR]

We consider binary error correcting codes when errors are deletions. A basic challenge concerning deletion codes is determining ${p}_{0}^{(adv)}$ , the zero-rate threshold of adversarial deletions, defined to be the supremum of all $p$ for which there exists a code family with rate bounded away from 0 capable of correcting a fraction $p$ of adversarial deletions. A recent construction of deletion-correcting codes shows that ${p}_{0}^{(adv)} \ge \sqrt {2}-1$ , and the trivial upper bound, ${p}_{0}^{(adv)}\le {1}/{2}$ , is the best known. Perhaps surprisingly, we do not know whether or not ${p}_{0}^{(adv)} = 1/2$. In this work, to gain further insight into deletion codes, we explore two related error models: oblivious deletions and online deletions, which are in between random and adversarial deletions in power. In the oblivious model, the channel can inflict an arbitrary pattern of ${pn}$ deletions, picked without knowledge of the codeword. We prove the existence of binary codes of positive rate that can correct any fraction ${p} < 1$ of oblivious deletions, establishing that the associated zero-rate threshold ${p}_{0}^{(obliv)}$ equals 1. For online deletions, where the channel decides whether to delete bit ${x}_{{i}}$ based only on knowledge of bits ${x}_{1}{x}_{2} {\dots }{x}_{{i}}$ , define the deterministic zero-rate threshold for online deletions ${p}_{0}^{(on,{d})}$ to be the supremum of $p$ for which there exist deterministic codes against an online channel causing ${pn}$ deletions with low average probability of error. That is, the probability that a randomly chosen codeword is decoded incorrectly is small. We prove ${p}_{0}^{(adv)}={1}/{2}$ if and only if ${p}_{0}^{(on,{d})}={1}/{2}$. [ABSTRACT FROM AUTHOR]

We consider the decoding of linear and array codes from errors when we are only allowed to download a part of the codeword. More specifically, suppose that we have encoded $k$ data symbols using an $(n,k)$ code with code length $n$ and dimension $k$. During storage, some of the codeword coordinates might be corrupted by errors. We aim to recover the original data by reading the corrupted codeword with a limit on the transmission bandwidth, namely, we can only download an $\alpha $ proportion of the corrupted codeword. For a given $\alpha $ , our objective is to design a code and a decoding scheme such that we can recover the original data from the largest possible number of errors. A naive scheme is to read $\alpha n$ coordinates of the codeword. This method used in conjunction with MDS codes guarantees recovery from any $\lfloor (\alpha n-k)/2\rfloor $ errors. In this paper we show that we can instead download an $\alpha $ proportion from each of the codeword’s coordinates. For a well-designed MDS code, this method can guarantee recovery from $\lfloor (n-k/\alpha)/2 \rfloor $ errors, which is $1/\alpha $ times more than the naive method, and is also the maximum number of errors that an $(n,k)$ code can correct by downloading only an $\alpha $ proportion of the codeword. We present two families of such optimal constructions and decoding schemes of which one is based on Interleaved Reed-Solomon codes and the other on Folded Reed-Solomon codes. We further show that both code constructions attain asymptotically optimal list decoding radius when downloading only a part of the corrupted codeword. We also construct an ensemble of random codes that with high probability approaches the upper bound on the number of correctable errors when the decoder downloads an $\alpha $ proportion of the corrupted codeword. [ABSTRACT FROM AUTHOR]

We construct error-correcting write-once memory (WOM) codes that guarantee correction of any specified number of errors in $q$ -level memories. The constructions use suitably designed short $q$ -ary WOM codes and concatenate them with outer error-correcting codes over different alphabets using suitably designed mappings. With a new storage-efficiency measure, we call EC-rate and show that for common error types the codes save redundancy and implementation complexity over straightforward concatenation. In addition to constructions for guaranteed error correction, we extend the error-correcting WOM scheme to binary multi-level coding for random errors, and toward soft-decision decoding provide an efficient way to extract reliability information without using higher-precision readout. [ABSTRACT FROM AUTHOR]

Motivated by communication channels in which the transmitted sequences are subjected to random permutations, as well as by certain DNA storage systems, we study the error control problem in settings where the information is stored/transmitted in the form of multisets of symbols from a given finite alphabet. A general channel model is assumed in which the transmitted multisets are potentially impaired by insertions, deletions, substitutions, and erasures of symbols. Several constructions of error-correcting codes for this channel are described, and bounds on the size of optimal codes correcting any given number of errors are derived. The construction based on the notion of Sidon sets in finite Abelian groups is shown to be optimal, in the sense of the asymptotic scaling of code redundancy, for any error radius and alphabet size. It is also shown to be optimal in the stronger sense of maximal code cardinality in various cases. [ABSTRACT FROM AUTHOR]

In this paper, new index coding problems are studied, where each receiver has erroneous side information. Although side information is a crucial part of index coding, the existence of erroneous side information has not been considered yet. We study an index code with receivers that have erroneous side information symbols in the error-free broadcast channel, which is called an index code with side information errors (ICSIE). The encoding and decoding procedures of the ICSIE are proposed, based on the syndrome decoding. Then, we derive the bounds on the optimal codelength of the proposed index code with erroneous side information. Furthermore, we introduce a special graph for the proposed index coding problem, called a \delta s -cycle whose properties are similar to those of the cycle in the conventional index coding problem. Properties of the ICSIE are also discussed in the \delta s -cycle and clique. Finally, the proposed ICSIE is generalized to an index code for the scenario having both additive channel errors and side information errors, called a generalized error correcting index code. [ABSTRACT FROM AUTHOR]

We construct error-correcting codes over permutations under the infinity-metric, which are also Gray codes in the context of rank modulation, i.e., are generated as simple circuits in the rotator graph. These errors model limited-magnitude or spike errors, for which only single-error-detecting Gray codes are currently known. Surprisingly, the error-correcting codes we construct achieve a better asymptotic rate than that of presently known constructions not having the Gray property, and exceed the Gilbert-Varshamov bound. Additionally, we present efficient ranking and unranking procedures, as well as a decoding procedure that runs in linear time. Finally, we also apply our methods to solve an outstanding issue with error-detecting rank-modulation Gray codes (also known in this context as snake-in-the-box codes) under a different metric, the Kendall $\tau $ -metric, in the group of permutations over an even number of elements S_{2n} , where we provide asymptotically optimal codes. [ABSTRACT FROM AUTHOR]

We consider the problem of computing a binary linear transformation when all circuit components are unreliable. Two models of unreliable components are considered: probabilistic errors and permanent errors. We introduce the “ENCODED” technique that ensures that the error probability of the computation of the linear transformation is kept bounded below a small constant independent of the size of the linear transformation even when all logic gates in the computation are noisy. By deriving a lower bound, we show that in some cases, the computational complexity of the ENCODED technique achieves the optimal scaling in error probability. Further, we examine the gain in energy-efficiency from the use of a “voltage-scaling” scheme, where gate-energy is reduced by lowering the supply voltage. We use a gate energy-reliability model to show that tuning gate-energy appropriately at different stages of the computation (“dynamic” voltage scaling), in conjunction with ENCODED, can lead to orders of magnitude energy-savings over the classical “uncoded” approach. Finally, we also examine the problem of computing a linear transformation when noiseless decoders can be used, providing upper and lower bounds to the problem. [ABSTRACT FROM AUTHOR]

We describe a general method for turning quantum circuits into sparse quantum subsystem codes. The idea is to turn each circuit element into a set of low-weight gauge generators that enforce the input–output relations of that circuit element. Using this prescription, we can map an arbitrary stabilizer code into a new subsystem code with the same distance and number of encoded qubits but where all the generators have constant weight, at the cost of adding some ancilla qubits. With an additional overhead of ancilla qubits, the new code can also be made spatially local. Applying our construction to certain concatenated stabilizer codes yields families of subsystem codes with constant-weight generators and with minimum distance d = n^1- \epsilon , where \epsilon = O(1/\sqrt \log n) . For spatially local codes in D dimensions, we nearly saturate a bound due to Bravyi and Terhal and achieve d = n^{1- \epsilon -1/D} . Previously the best code distance achievable with constant-weight generators in any dimension, due to Freedman, Meyer, and Luo, was O(\sqrt {n\log n})$ for a stabilizer code. [ABSTRACT FROM PUBLISHER]

We give an infinite family of maximum rank distance (MRD) codes, which covers properly the largest known linear MRD code family. Our family contains infinite families of non-linear MRD codes, which are the first non-linear examples for most of the parameters. We also give explicit examples and a table that demonstrates the proportion of linear and non-linear families for some small parameters. [ABSTRACT FROM PUBLISHER]

In this paper, list decoding of crisscross errors in arrays over finite fields is considered. For this purpose, the so-called cover metric is used, where the cover of a matrix is a set of rows and columns which contains all non-zero elements of the matrix. A Johnson-like upper bound on the maximum list size in the cover metric is derived, showing that the list of codewords has polynomial size up to a certain radius. Furthermore, a simple list decoding algorithm for a known optimal code construction is presented, which decodes errors in the cover metric up to our upper bound. These results reveal significant differences between the cover metric and the rank metric and show that the cover metric is more suitable for correcting crisscross errors. [ABSTRACT FROM PUBLISHER]

We consider codes over fixed alphabets against worst case symbol deletions. For any fixed k \ge 2 , we construct a family of codes over alphabet of size k with positive rate, which allow efficient recovery from a worst case deletion fraction approaching 1-(2/(k+\sqrt k)) . In particular, for binary codes, we are able to recover a fraction of deletions approaching 1/(\sqrt 2 +1)=\sqrt 2-1 \approx 0.414 . Previously, even non-constructively, the largest deletion fraction known to be correctable with positive rate was 1-\Theta (1/\sqrt k) , and around 0.17 for the binary case. Our result pins down the largest fraction of correctable deletions for $k$ -ary codes as 1-\Theta (1/k)$ , since 1-1/k$ is an upper bound even for the simpler model of erasures where the locations of the missing symbols are known. Closing the gap between and 1/2 for the limit of worst case deletions correctable by binary codes remains a tantalizing open question. [ABSTRACT FROM PUBLISHER]

We study error correction codes for multimedia streaming applications where a stream of source packets must be transmitted in real-time, with in-order decoding, and strict delay constraints. In our setup, the encoder observes a stream of source packets in a sequential fashion, and $M$ channel packets must be transmitted between the arrival of successive source packets. Each channel packet can depend on all the source packets observed up to and including that time, but not on any future source packets. The decoder must reconstruct the source stream with a delay of $T$ packets. We consider a class of packet erasure channels with burst and isolated erasures, where the erasure patterns are locally constrained. Our proposed model provides a tractable approximation to statistical models, such as the Gilbert–Elliott channel, for capacity analysis. When $M=1$ , i.e., when the source-packet arrival and channel-packet transmission rates are equal, we establish upper and lower bounds on the capacity, that are within one unit of the decoding delay $T$ . We also establish necessary and sufficient conditions on the column distance and column span of a convolutional code to be feasible, and in turn establish a fundamental tradeoff between these. Our proposed codes—maximum distance and span codes—achieve a near-optimal tradeoff between the column distance and column span, and involve a layered construction. When $M>1$ , we establish the capacity for the burst-erasure channel and an achievable rate in the general case. Extensive numerical simulations over Gilbert–Elliott and Fritchman channel models suggest that our codes also achieve significant gains in the residual loss probability over statistical channel models. [ABSTRACT FROM PUBLISHER]

Improved lower and upper bounds on the size and the rate of grain-correcting codes are presented. The lower bound is Gilbert–Varshamov-like combined with a construction by Gabrys et al., and it improves on the previously best known lower bounds on the asymptotic rate of \lceil \tau n \rceil -grain-correcting codes of length n on the interval [0,0.0668] . One of the two newly presented upper bounds improves on the best known upper bounds on the asymptotic rate of \lceil \tau n \rceil -grain-correcting codes of length n on the interval \tau \in (0,{1}/{8}] and meets the lower bound of {1}/{2} for \tau \geq 1/8 . Moreover, in a nonasymptotic regime, both upper bounds improve on the previously best known results on the largest size of t -grain-correcting codes of length $n$ , for certain values of n$ and t$ . Constructions of 1-grain-correcting codes based on a partitioning technique are presented for lengths up to 18. Finally, a lower bound of on the minimum redundancy of $\infty $ -grain-detecting codes of length $n$ is presented. [ABSTRACT FROM PUBLISHER]

Random network coding recently attracts attention as a technique to disseminate information in a network. This paper considers a noncoherent multishot network, where the unknown and time-variant network is used several times. In order to create dependence between the different shots, particular convolutional codes in rank metric are used. These codes are so-called (partial) unit memory ((P)UM) codes, i.e., convolutional codes with memory one. First, distance measures for convolutional codes in rank metric are shown and two constructions of (P)UM codes in rank metric based on the generator matrices of maximum rank distance codes are presented. Second, an efficient error-erasure decoding algorithm for these codes is presented. Its guaranteed decoding radius is derived and its complexity is bounded. Finally, it is shown how to apply these codes for error correction in random linear and affine network coding. [ABSTRACT FROM AUTHOR]

We present new constructions of codes for asymmetric channels for both binary and nonbinary alphabets, based on methods of generalized code concatenation. For the binary asymmetric channel, our methods construct nonlinear single-error-correcting codes from ternary outer codes. We show that some of the Varshamov–Tenengol’ts–Constantin–Rao codes, a class of binary nonlinear codes for this channel, have a nice structure when viewed as ternary codes. In many cases, our ternary construction yields even better codes. For the nonbinary asymmetric channel, our methods construct linear codes for many lengths and distances which are superior to the linear codes of the same length capable of correcting the same number of symmetric errors. [ABSTRACT FROM AUTHOR]

Quantum synchronizable error-correcting codes are special quantum error-correcting codes that are designed to correct both the effect of quantum noise on qubits and misalignment in block synchronization. It is known that, in principle, such a code can be constructed through a combination of a classical linear code and its subcode if the two are both cyclic and dual-containing. However, finding such classical codes that lead to promising quantum synchronizable error-correcting codes is not a trivial task. In fact, although there are two families of classical codes that are proved to produce quantum synchronizable codes with good minimum distances and highest possible tolerance against misalignment, their code lengths have been restricted to primes and Mersenne numbers. In this paper, examining the incidence vectors of projective spaces over the finite fields of characteristic 2, we give quantum synchronizable codes from cyclic codes whose lengths are not primes or Mersenne numbers. These projective geometric codes achieve good performance in quantum error correction and possess the best possible ability to recover synchronization, thereby enriching the variety of good quantum synchronizable codes. We also extend the current knowledge of cyclic codes in classical coding theory by explicitly giving generator polynomials of the finite geometric codes and completely characterizing the minimum weight nonzero codewords. In addition to the codes based on projective spaces, we carry out a similar analysis on the well-known cyclic codes from Euclidean spaces that are known to be majority logic decodable and determine their exact minimum distances. [ABSTRACT FROM PUBLISHER]

In this paper, a new class of (N,K) near-optimal partial Hadamard codebooks is proposed. The construction of the proposed codebooks from Hadamard matrices is based on binary row selection sequences, which are generated by quadratic residue mapping of p -ary m -sequences. The proposed codebooks have parameters and K=({p-1}/{2p})(N+\sqrt{N})+1 for an odd prime p$ and an even positive integer $n$ . We prove that the maximum magnitude of inner products between the code vectors of the proposed codebooks asymptotically achieves the Welch bound equality for sufficiently large $p$ and derive their inner product distribution. [ABSTRACT FROM PUBLISHER]

Pulse position modulation (PPM) is a popular signal modulation technique which converts signals into M-ary data by means of the position of a pulse within a time interval. While PPM and its variations have great advantages in many contexts, this type of modulation is vulnerable to loss of synchronization, potentially causing a severe error floor or throughput penalty even when little or no noise is assumed. Another disadvantage is that this type of modulation typically offers no error correction mechanism on its own, making them sensitive to intersymbol interference and environmental noise. In this paper, we propose a coding theoretic variation of PPM that allows for significantly more efficient symbol and frame synchronization as well as strong error correction. The proposed scheme can be divided into a synchronization layer and a modulation layer. This makes our technique compatible with major existing techniques such as standard PPM, multipulse PPM, and expurgated PPM as well in that the scheme can be realized by adding a simple synchronization layer to one of these standard techniques. We also develop a generalization of expurgated PPM suited for the modulation layer of the proposed self-synchronizing modulation scheme. This generalized PPM can also be used as stand-alone error-correcting PPM with a larger number of available symbols. [ABSTRACT FROM AUTHOR]