In modern age, the increasing complexity of computation and communication technology is leading us towards the necessity of new paradigm. As a result, unconventional approach like DNA coding theory is gaining considerable attention. The storage capacity, information processing and transmission properties of DNA molecules stimulate the notion of DNA coding theory as well as DNA cryptography. In this paper we generate DNA codeword using DNA linear block codes which ensures the secure transmission of information. In the proposed code design strategy DNA-based XOR operation (DNAX) is applied for effective construction of DNA codewords which are quadruples generated over the set of alphabets consisting of four DNA bases adenine, thymine, guanine, and cytosine. By worked out examples we explain the use of generator matrix and parity check matrix in encryption and decryption of coded data in the form of short single stranded DNA sequences. The newly developed technique can detect as well as correcting error in transmission of DNA codewords through biological channels from sender to the intended receiver. Through DNA coding theory we are expanding the paths towards data compression and error correction in the form of DNA strands. This leads us towards a broader domain of DNA cryptography.
We propose coding techniques that limit the length of homopolymers runs, ensure the GC-content constraint, and are capable of correcting a single edit error in strands of nucleotides in DNA-based data storage systems. In particular, for given $\ell, ε > 0$, we propose simple and efficient encoders/decoders that transform binary sequences into DNA base sequences (codewords), namely sequences of the symbols A, T, C and G, that satisfy the following properties: (i) Runlength constraint: the maximum homopolymer run in each codeword is at most $\ell$, (ii) GC-content constraint: the GC-content of e…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a special constraint. Each codeword of the DNA code has a specific property that any two consecutive sub-strings of the DNA codeword will not be the same (a generalization of homo-polymers constraint). This is in addition to the usual constraints such as Hamming, reverse, reverse-complement and $GC$-content. We believe that the new constraint will help further i…
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 work 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…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding scheme is considered, in which the $m$th molecule of the codeword is restricted to a subset of all possible molecules (an inner code), which is unique for each $m$. The decoder has low-complexity, and is based on first decoding each molecule separately (the inner code), and then decoding the sequence of molecules (an outer code). Only mild assumptions are made o…
In this paper, we consider the problem of designing DNA sequences (codewords) for DNA storage systems and DNA computing that are unlikely to fold back onto themselves to form undesirable secondary structures. The paper addresses both the issue of enumerating the sequences with such properties and the problem of practical code construction.
In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short, secondary structure refers to the tendency of a single-stranded DNA sequence to fold back upon itself, thus becoming inactive in the computation process. While some design criteria that reduces the possibility of secondary structure formation has been proposed by Milenkovic and Kashyap (2006), the main contribution of this work is to provide an explicit const…
DNA code design aims to generate a set of DNA sequences (codewords) with minimum likelihood of undesired hybridizations among sequences and their reverse-complement (RC) pairs (cross-hybridization). Inspired by the distinct hybridization affinities (or stabilities) of perfect double helix constructed by individual single-stranded DNA (ssDNA) and its RC pair, we propose a novel similarity significance (SS) model to measure the similarity between DNA sequences. Particularly, instead of directly measuring the similarity of two sequences by any metric/approach, the proposed SS works in a way to ev…
In this work, we study the DNA codes from the ring R = Z4 + wZ4, where w^2 = 2+2w with 16 elements. We establish a one to one correspondence between the elements of the ring R and all the DNA codewords of length 2 by defining a distance-preserving Gau map phi. Using this map, we give several new classes of the DNA codes which satisfies reverse and reverse complement constraints. Some of the constructed DNA codes are optimal.
In large scale distributed storage systems (DSS) deployed in cloud computing, correlated failures resulting in simultaneous failure (or, unavailability) of blocks of nodes are common. In such scenarios, the stored data or a content of a failed node can only be reconstructed from the available live nodes belonging to available blocks. To analyze the resilience of the system against such block failures, this work introduces the framework of Block Failure Resilient (BFR) codes, wherein the data (e.g., file in DSS) can be decoded by reading out from a same number of codeword symbols (nodes) from e…
An indel refers to a single insertion or deletion, while an edit refers to a single insertion, deletion or substitution. In this paper, we investigate codes that combat either a single indel or a single edit and provide linear-time algorithms that encode binary messages into these codes of length n. Over the quaternary alphabet, we provide two linear-time encoders. One corrects a single edit with log n + O(log log n) redundancy bits, while the other corrects a single indel with log n + 2 redundant bits. These two encoders are order-optimal. The former encoder is the first known order-optimal e…
We study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect information stored in DNA molecules using the rank-modulation scheme, and read using the shotgun sequencing technique. We construct systematic codes with an efficient encoding algorithm, and show that they are optimal in size. The length of the DNA sequences that correspond to the codewords is shown to be polynomial in the code parameters. Non-systematic with large…
We consider a new family of codes, termed asymmetric Lee distance codes, that arise in the design and implementation of DNA-based storage systems and systems with parallel string transmission protocols. The codewords are defined over a quaternary alphabet, although the results carry over to other alphabet sizes; furthermore, symbol confusability is dictated by their underlying binary representation. Our contributions are two-fold. First, we demonstrate that the new distance represents a linear combination of the Lee and Hamming distance and derive upper bounds on the size of the codes under th…
Message-passing iterative decoders for low-density parity-check (LDPC) block codes are known to be subject to decoding failures due to so-called pseudo-codewords. These failures can cause the large signal-to-noise ratio performance of message-passing iterative decoding to be worse than that predicted by the maximum-likelihood decoding union bound. In this paper we address the pseudo-codeword problem from the convolutional-code perspective. In particular, we compare the performance of LDPC convolutional codes with that of their ``wrapped'' quasi-cyclic block versions and we show that the minimu…
DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the prohibitive cost of reads and writes, the high frequency and the peculiar nature of errors occurring in DNA storage pose a significant challenge to its adoption. In this work we make a novel observation that the probability of successful recovery of a given bit from any type of a DNA-based storage system highly depends on its physical location within the DNA molecu…
In this paper, we consider the problem of distinguishing the noisy codewords of a known binary linear block code from a random bit sequence. We propose to use the generalized likelihood ratio test (GLRT) to solve this problem. We also give a formula to find approximate number of codewords required and compare our results with an existing method.
Given a classical error-correcting block code, the task of quantum list decoding is to produce from any quantumly corrupted codeword a short list containing all messages whose codewords exhibit high "presence" in the quantumly corrupted codeword. Efficient quantum list decoders have been used to prove a quantum hardcore property of classical codes. However, the code rates of all known families of efficiently quantum list-decodable codes are, unfortunately, too small for other practical applications. To improve those known code rates, we prove that a specific code family of polynomially small c…
In large scale distributed storage systems (DSS) deployed in cloud computing, correlated failures resulting in simultaneous failure (or, unavailability) of blocks of nodes are common. In such scenarios, the stored data or a content of a failed node can only be reconstructed from the available live nodes belonging to the available blocks. To analyze the resilience of the system against such block failures, this work introduces the framework of Block Failure Resilient (BFR) codes, wherein the data (e.g., a file in DSS) can be decoded by reading out from a same number of codeword symbols (nodes) …
The evaluation of the minimum distance of linear block codes remains an open problem in coding theory, and it is not easy to determine its true value by classical methods, for this reason the problem has been solved in the literature with heuristic techniques such as genetic algorithms and local search algorithms. In this paper we propose two approaches to attack the hardness of this problem. The first approach is based on genetic algorithms and it yield to good results comparing to another work based also on genetic algorithms. The second approach is based on a new randomized algorithm which …
This paper studies the effect of optimal power allocation on the performance of communication systems utilizing automatic repeat request (ARQ). Considering Type-I ARQ, the problem is cast as the minimization of the outage probability subject to an average power constraint. The analysis is based on some recent results on the achievable rates of finite-length codes and we investigate the effect of codewords length on the performance of ARQ-based systems. We show that the performance of ARQ protocols is (almost) insensitive to the length of the codewords, for codewords of length $\ge 50$ channel …
The DNA storage channel is considered, in which the $M$ Deoxyribonucleic acid (DNA) molecules comprising each codeword are stored without order, sampled $N$ times with replacement, and then sequenced over a discrete memoryless channel. For a constant coverage depth $M/N$ and molecule length scaling $Θ(\log M)$, lower (achievability) and upper (converse) bounds on the capacity of the channel, as well as a lower (achievability) bound on the reliability function of the channel are provided. Both the lower and upper bounds on the capacity generalize a bound which was previously known to hold only …
Ultra-Reliable Low-Latency Communications have stringent delay constraints, and hence use codes with small block length (short codewords). In these cases, classical models that provide good approximations to systems with infinitely long codewords become imprecise. To remedy this, in this paper, an average coding rate expression is derived for a large scale network with short codewords using stochastic geometry and the theory of coding in the finite blocklength regime. The average coding rate and upper and lower bounds on the outage probability of the large-scale network are derived, and a tigh…
Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a concatenated coding scheme with an outer low-density parity-check code and either an inner convolutional code or a block code. We propose two new decoding algorithms for inference from multiple received sequences, both combining the inner code and channel to a joint hidden Markov model to infer symbolwise a posteriori probabilities (APPs). The first decoder…
This paper applies error-exponent and dispersion-style analyses to derive finite-blocklength achievability bounds for low-density parity-check (LDPC) codes over the point-to-point channel (PPC) and multiple access channel (MAC). The error-exponent analysis applies Gallager's error exponent to bound achievable symmetrical and asymmetrical rates in the MAC. The dispersion-style analysis begins with a generalization of the random coding union (RCU) bound from random code ensembles with i.i.d. codewords to random code ensembles in which codewords may be statistically dependent; this generalization…
Motivated by the sequence reconstruction problem from traces in DNA-based storage, we consider the problem of designing codes for the deletion channel when multiple observations (or traces) are available to the decoder. We propose simple binary and non-binary codes based on Varshamov-Tenengolts (VT) codes. The proposed codes split the codeword in blocks and employ 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 …
A distribution matcher (DM) encodes a binary input data sequence into a sequence of symbols (codeword) with desired target probability distribution. The set of the output codewords constitutes a codebook (or code) of a DM. Constant-composition DM (CCDM) uses arithmetic coding to efficiently encode data into codewords from a constant-composition (CC) codebook. The CC constraint limits the size of the codebook, and hence the coding rate of the CCDM. The performance of CCDM degrades with decreasing output length. To improve the performance for short transmission blocks we present a class of multi…
We consider universal variable-to-fixed length compression of memoryless sources with a fidelity criterion. We design a dictionary codebook over the reproduction alphabet which is used to parse the source stream. Once a source subsequence is within a specified distortion of a dictionary codeword, the index of the codeword is emitted as the reproduced string. Our proposed dictionary consists of coverings of type classes in the boundary of transition from low to high empirical lossy rate. We derive the asymptotics of the ε-coding rate (up to the third-order term) of our coding scheme for large e…
This paper considers the achievability and converse bounds on the maximal channel coding rate at a given blocklength and error probability over AWGN channels. The problem stems from covert communication with Gaussian codewords. By re-visiting [18], we first present new and more general achievability bounds for random coding schemes under maximal or average probability of error requirements. Such general bounds are then applied to covert communication in AWGN channels where codewords are generated from Gaussian distribution while meeting the maximal power constraint. Further comparison is made …
We consider a peak-power-limited single-antenna block-stationary Gaussian fading channel where neither the transmitter nor the receiver knows the channel state information, but both know the channel statistics. This model subsumes most previously studied Gaussian fading models. We first compute the asymptotic channel capacity in the high SNR regime and show that the behavior of channel capacity depends critically on the channel model. For the special case where the fading process is symbol-by-symbol stationary, we also reveal a fundamental interplay between the codeword length, communication r…
This paper studies the outage probability and the throughput of amplify-and-forward relay networks with wireless information and energy transfer. We use some recent results on finite block-length codes to analyze the system performance in the cases with short codewords. Specifically, the time switching relaying and the power splitting relaying protocols are considered for energy and information transfer. We derive tight approximations for the outage probability/throughput. Then, we analyze the outage probability in asymptotically high signal-to-noise ratios. Finally, we use numerical results t…
Motivated by applications in DNA-based storage, we introduce the new problem of code design in the Damerau metric. The Damerau metric is a generalization of the Levenshtein distance which, in addition to deletions, insertions and substitution errors also accounts for adjacent transposition edits. We first provide constructions for codes that may correct either a single deletion or a single adjacent transposition and then proceed to extend these results to codes that can simultaneously correct a single deletion and multiple adjacent transpositions. We conclude with constructions for joint block…
Tel Aviv University（特拉维夫大学）；Facebook AI Research（Facebook AI研究院）
We revisit recent methods that employ graph neural networks for decoding error correcting codes and employ messages that are computed in an autoregressive manner. The outgoing messages of the variable nodes are conditioned not only on the incoming messages, but also on an estimation of the SNR and on the inferred codeword and on two downstream computations: (i) an extended vector of parity check outcomes, (ii) the mismatch between the inferred codeword and the re-encoding of the information bits of this codeword. Unlike most learned methods in the field, our method violates the symmetry condit…
We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing read-only methods that require decoding the whole file in order to read one data fragment. Our system is based on new constrained coding techniques and accompanying DNA editing methods that ensure data reliability, specificity and sensitivity of access, and at the same time provide exceptionally high data storage capacity. As a proof of concept, we encoded par…
In this work, we present the first local-decoding algorithm for expander codes. This yields a new family of constant-rate codes that can recover from a constant fraction of errors in the codeword symbols, and where any symbol of the codeword can be recovered with high probability by reading $N^ε$ symbols from the corrupted codeword, where $N$ is the block-length of the code. Expander codes, introduced by Sipser and Spielman, are formed from an expander graph $G = (V,E)$ of degree $d$, and an inner code of block-length $d$ over an alphabet $Σ$. Each edge of the expander graph is associated with…
Convolutional codes are error-correcting linear codes that utilize shift registers to encode. These codes have an arbitrary block size and they can incorporate both past and current information bits. DNA codes represent DNA sequences and are defined as sets of words comprised of the alphabet A, C, T, G satisfying certain mathematical bounds and constraints. The application of convolutional code models to DNA codes is a growing field of biocomputation. As opposed to block codes, convolutional codes factor in nearby information bits, which makes them an optimal model for representing biological …
Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a concatenated coding scheme with an outer nonbinary low-density parity-check code or a polar code and either an inner convolutional code or a time-varying block code. We propose two novel decoding algorithms for inference from multiple received sequences, both combining the inner code and channel to a joint hidden Markov model to infer symbolwise a posterior…
This letter studies the power-limited throughput of a communication system utilizing incremental redundancy (INR) hybrid automatic repeat request (HARQ). We use some recent results on the achievable rates of finite-length codes to analyze the system performance. With codewords of finite length, we derive closed-form expressions for the outage probabilities of INR HARQ and study the throughput in the cases with variable-length coding. Moreover, we evaluate the effect of feedback delay on the throughput and derive sufficient conditions for the usefulness of the HARQ protocols, in terms of power-…
We study the tradeoff between the sum rate and the error probability in downlink of wireless networks. Using the recent results on the achievable rates of finite-length codewords, the problem is cast as a joint optimization of the network sum rate and the per-user error probability. Moreover, we develop an efficient algorithm based on the divide-and-conquer technique to simultaneously maximize the network sum rate and minimize the maximum users' error probability and to evaluate the effect of the codewords length on the system performance. The results show that, in delay-constrained scenarios,…
This paper presents a new class of sparse superposition codes for low-rates and short-packet communications over the additive white Gaussian noise channel. The new code is orthogonal sparse superposition (OSS) code. A codeword of OSS codes is represented as a superposition of sparse sub-codewords whose support sets are mutually non-overlapping. To construct such codewords in a computationally efficient manner, a successive encoding method is presented. Harnessing the orthogonal property among sub-codewords, a simple yet near-optimal decoding method is proposed, which performs element-wise maxi…
A reduced complexity sequential decoding algorithm for polar (sub)codes is described. The proposed approach relies on a decomposition of the polar (sub)code being decoded into a number of outer codes, and on-demand construction of codewords of these codes in the descending order of their probability. Construction of such codewords is implemented by fast decoding algorithms, which are available for many codes arising in the decomposition of polar codes. Further complexity reduction is achieved by taking hard decisions of the intermediate LLRs, and avoiding decoding of some outer codes. Data str…
We establish a general formula for the maximum size of finite length block codes with minimum pairwise distance no less than $d$. The achievability argument involves an iterative construction of a set of radius-$d$ balls, each centered at a codeword. We demonstrate that the number of such balls that cover the entire code alphabet cannot exceed this maximum size. Our approach can be applied to codes $i)$ with elements over arbitrary code alphabets, and $ii)$ under a broad class of distance measures, thereby ensuring the generality of our formula. Our formula indicates that the maximum code size…
