Motivated by applications in DNA-based storage and communication systems, we study deletion and insertion errors simultaneously in a burst. In particular, we study a type of error named $t$-deletion-$s$-insertion-burst ($(t,s)$-burst for short) which is a generalization of the $(2,1)$-burst error proposed by Schoeny {\it et. al}. Such an error deletes $t$ consecutive symbols and inserts an arbitrary sequence of length $s$ at the same coordinate. We provide a sphere-packing upper bound on the size of binary codes that can correct a $(t,s)$-burst error, showing that the redundancy of such codes is at least $\log n+t-1$. For $t\geq 2s$, an explicit construction of binary $(t,s)$-burst correcting codes with redundancy $\log n+(t-s-1)\log\log n+O(1)$ is given. In particular, we construct a binary $(3,1)$-burst correcting code with redundancy at most $\log n+9$, which is optimal up to a constant.
We generalize Helberg's number-theoretic construction of multiple insertion-deletion correcting binary codes to non-binary alphabets and describe a linear decoding algorithm for correcting multiple deletions.
We first give a construction of binary $t_1$-deletion-$t_2$-insertion-burst correcting codes with redundancy at most $\log(n)+(t_1-t_2-1)\log\log(n)+O(1)$, where $t_1\ge 2t_2$. Then we give an improved construction of binary codes capable of correcting a burst of $4$ non-consecutive deletions, whose redundancy is reduced from $7\log(n)+2\log\log(n)+O(1)$ to $4\log(n)+6\log\log(n)+O(1)$. Lastly, by connecting non-binary $b$-burst-deletion correcting codes with binary $2b$-deletion-$b$-insertion-burst correcting codes, we give a new construction of non-binary $b$-burst-deletion correcting codes …
In this paper, we construct systematic $q$-ary two-deletion correcting codes and burst-deletion correcting codes, where $q\geq 2$ is an even integer. For two-deletion codes, our construction has redundancy $5\log n+O(\log q\log\log n)$ and has encoding complexity near-linear in $n$, where $n$ is the length of the message sequences. For burst-deletion codes, we first present a construction of binary codes with redundancy $\log n+9\log\log n+γ_t+o(\log\log n)$ bits $(γ_t$ is a constant that depends only on $t)$ and capable of correcting a burst of at most $t$ deletions, which improves the Lenz-P…
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.
A Decoding Algorithm for Composite Errors Consisting of Deletions and Insertions in Quantum Deletion-Correcting Codes Based on Quantum Reed-Solomon Codes
This paper investigates the problem of correcting multiple criss-cross insertions and deletions in arrays. More precisely, we study the unique recovery of $n \times n$ arrays affected by $t$-criss-cross deletions defined as any combination of $t_r$ row and $t_c$ column deletions such that $t_r + t_c = t$ for a given $t$. We show an equivalence between correcting $t$-criss-cross deletions and $t$-criss-cross insertions and show that a code correcting $t$-criss-cross insertions/deletions has redundancy at least $tn + t \log n - \log(t!)$. Then, we present an existential construction of $t$-criss…
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.
We study codes that can detect the exact number of deletions and insertions in concatenated binary strings. We construct optimal codes for the case of detecting up to $\del$ deletions. We prove the optimality of these codes by deriving a converse result which shows that the redundancy of our codes is asymptotically optimal in $\del$ among all families of deletion detecting codes, and particularly optimal among all block-by-block decodable codes. For the case of insertions, we construct codes that can detect up to $2$ insertions in each concatenated binary string.
Levenshtein introduced the problem of constructing $k$-deletion correcting codes in 1966, proved that the optimal redundancy of those codes is $O(k\log N)$, and proposed an optimal redundancy single-deletion correcting code (using the so-called VT construction). However, the problem of constructing optimal redundancy $k$-deletion correcting codes remained open. Our key contribution is a solution to this longstanding open problem. We present a $k$-deletion correcting code that has redundancy $8k\log n +o(\log n)$ and encoding/decoding algorithms of complexity $O(n^{2k+1})$ for constant $k$.
New bounds for covering codes under insertions or deletions
Institute of Mathematics and Interdisciplinary Sciences, Xidian University（西安电子科技大学数学与交叉科学研究院）；School of Mathematical Sciences, Capital Normal University（首都师范大学数学科学学院）
List decoding of insertions and deletions in the Levenshtein metric is considered. The Levenshtein distance between two sequences is the minimum number of insertions and deletions needed to turn one of the sequences into the other. In this paper, a Johnson-like upper bound on the maximum list size when list decoding in the Levenshtein metric is derived. This bound depends only on the length and minimum Levenshtein distance of the code, the length of the received word, and the alphabet size. It shows that polynomial-time list decoding beyond half the Levenshtein distance is possible for many pa…
In this work, we investigate the problem of constructing codes capable of correcting two deletions. In particular, we construct a code that requires redundancy approximately 8 log n + O(log log n) bits of redundancy, where n is the length of the code. To the best of the author's knowledge, this represents the best known construction in that it requires the lowest number of redundant bits for a code correcting two deletions.
We consider the problem of correcting insertion and deletion errors in the $d$-dimensional space. This problem is well understood for vectors (one-dimensional space) and was recently studied for arrays (two-dimensional space). For vectors and arrays, the problem is motivated by several practical applications such as DNA-based storage and racetrack memories. From a theoretical perspective, it is interesting to know whether the same properties of insertion/deletion correcting codes generalize to the $d$-dimensional space. In this work, we show that the equivalence between insertion and deletion …
We develop several analytical lower bounds on the capacity of binary insertion and deletion channels by considering independent uniformly distributed (i.u.d.) inputs and computing lower bounds on the mutual information between the input and output sequences. For the deletion channel, we consider two different models: independent and identically distributed (i.i.d.) deletion-substitution channel and i.i.d. deletion channel with additive white Gaussian noise (AWGN). These two models are considered to incorporate effects of the channel noise along with the synchronization errors. For the insertio…
In this paper, we prove the equivalence of inserting separable quantum states and deletions. Hence any quantum code that corrects deletions automatically corrects separable insertions. First, we describe the quantum insertion/deletion error using the Kraus operators. Next, we develop an algebra for commuting Kraus operators corresponding to insertions and deletions. Using this algebra, we prove the equivalence between quantum insertion codes and quantum deletion codes using the Knill-Laflamme conditions.
In this work, we study the problem of list decoding of insertions and deletions. We present a Johnson-type upper bound on the maximum list size. The bound is meaningful only when insertions occur. Our bound implies that there are binary codes of rate $Ω(1)$ that are list-decodable from a $0.707$-fraction of insertions. For any $τ_\mathsf{I} \geq 0$ and $τ_\mathsf{D} \in [0,1)$, there exist $q$-ary codes of rate $Ω(1)$ that are list-decodable from a $τ_\mathsf{I}$-fraction of insertions and $τ_\mathsf{D}$-fraction of deletions, where $q$ depends only on $τ_\mathsf{I}$ and $τ_\mathsf{D}$. We als…
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.…
Correcting insertions/deletions as well as substitution errors simultaneously plays an important role in DNA-based storage systems as well as in classical communications. This paper deals with the fundamental task of constructing codes that can correct a single insertion or deletion along with a single substitution. A non-asymptotic upper bound on the size of single-deletion single-substitution correcting codes is derived, showing that the redundancy of such a code of length $n$ has to be at least $2 \log n$. The bound is presented both for binary and non-binary codes while an extension to sin…
In this paper, we study how often unique decoding from $t$ insertions or $t$ deletions occurs for error correcting codes. Insertions and deletions frequently occur in synchronization problems and DNA, a medium which is beginning to be used for long term data storage. We define natural probabilistic channels that make $t$ insertions or $t$ deletions, and study the probability of unique decoding. Our most substantial contribution is the derivation of tight upper bounds on the probability of unique decoding for messages passed though these channels. We also consider other aspects of the problem, …
We consider the problem of constructing codes that can correct $δ$ deletions occurring in an arbitrary binary string of length $n$ bits. Varshamov-Tenengolts (VT) codes, dating back to 1965, are zero-error single deletion $(δ=1)$ correcting codes, and have an asymptotically optimal redundancy. Finding similar codes for $δ\geq 2$ deletions remains an open problem. In this work, we relax the standard zero-error (i.e., worst-case) decoding requirement by assuming that the positions of the $δ$ deletions (or insertions) are independent of the codeword. Our contribution is a new family of explicit c…
This paper studies codes that correct bursts of deletions. Namely, a code will be called a $b$-burst-deletion-correcting code if it can correct a deletion of any $b$ consecutive bits. While the lower bound on the redundancy of such codes was shown by Levenshtein to be asymptotically $\log(n)+b-1$, the redundancy of the best code construction by Cheng et al. is $b(\log (n/b+1))$. In this paper we close on this gap and provide codes with redundancy at most $\log(n) + (b-1)\log(\log(n)) +b -\log(b)$. We also derive a non-asymptotic upper bound on the size of $b$-burst-deletion-correcting codes an…
We improve Levenshtein's upper bound for the cardinality of a code of length four that is capable of correcting single deletions over an alphabet of even size. We also illustrate that the new upper bound is sharp. Furthermore we construct an optimal perfect code that is capable of correcting single deletions for the same parameters.
Insdel errors occur in communication systems caused by the loss of positional information of the message. Since the work by Guruswami and Wang, there have been some further investigations on the list decoding of insertion codes, deletion codes and insdel codes. However, unlike classical Hamming metric or even rank-metric, there are still many unsolved problems on list decoding of insdel codes. The contributions of this paper mainly consist of two parts. Firstly, we analyze the list decodability of random insdel codes. We show that list decoding of random insdel codes surpasses the Singleton bo…
Recent work by Smagloy et al. (ISIT 2020) shows that the redundancy of a single-deletion $s$-substitution correcting code is asymptotically at least $(s+1)\log n+o(\log n)$, where $n$ is the length of the codes. They also provide a construction of single-deletion and single-substitution codes with redundancy $6\log n+8$. In this paper, we propose a family of systematic single-deletion $s$-substitution correcting codes of length $n$ with asymptotical redundancy at most $(3s+4)\log n+o(\log n)$ and polynomial encoding/decoding complexity, where $s\geq 2$ is a constant. Specifically, the encoding…
The insertion-deletion codes were motivated to correct the synchronization errors. In this paper we prove several coordinate-ordering-free upper bounds on the insdel distances of linear codes, which are based on the generalized Hamming weights and the formation of minimum Hamming weight codewords. Our bounds are stronger than some previous known bounds. We apply these upper bounds to some cyclic codes and one algebraic-geometric code with any rearrangement of coordinate positions. Some strong upper bounds on the insdel distances of Reed-Muller codes with special coordinate-ordering are also gi…
This paper presents a coding scheme for an insertion deletion substitution channel. We extend a previous scheme for the deletion channel where polar codes are modified by adding "guard bands" between segments. In the new scheme, each guard band is comprised of a middle segment of '1' symbols, and left and right segments of '0' symbols. Our coding scheme allows for a regular hidden-Markov input distribution, and achieves the information rate between the input and corresponding output of such a distribution. Thus, we prove that our scheme can be used to efficiently achieve the capacity of the ch…
The problem of correcting deletions has received significant attention, partly because of the prevalence of these errors in DNA data storage. In this paper, we study the problem of correcting a consecutive burst of at most $t$ deletions in non-binary sequences. We first propose a non-binary code correcting a burst of at most 2 deletions for $q$-ary alphabets. Afterwards, we extend this result to the case where the length of the burst can be at most $t$ where $t$ is a constant. Finally, we consider the setup where the sequences that are transmitted are permutations. The proposed codes are the l…
This paper studies the problem of constructing codes correcting deletions in arrays. Under this model, it is assumed that an $n\times n$ array can experience deletions of rows and columns. These deletion errors are referred to as $(t_r,t_c)$-criss-cross deletions if $t_r$ rows and $t_c$ columns are deleted, while a code correcting these deletion patterns is called a $(t_r,t_c)$-criss-cross deletion correction code. The definitions for criss-cross insertions are similar. It is first shown that when $t_r=t_c$ the problems of correcting criss-cross deletions and criss-cross insertions are equival…
In this paper, we show that the single deletion correcting Varshamov-Tenengolts code, with minor modifications, can also correct an ordered deletion-erasure pattern where one deletion and at most one erasure occur and the deletion always occurs before the erasure. For large code lengths, the constructed code has the same logarithmic redundancy as optimal codes.
Permutation codes and multi-permutation codes have been widely considered due to their various applications, especially in flash memory. In this paper, we consider permutation codes and multi-permutation codes against a burst of stable deletions. In particular, we propose a construction of permutation codes correcting a burst stable deletion of length $s$, with redundancy $\log n+ 2\log \log n+O(1)$. Compared to the previous known results, our improvement relies on a different strategy to retrieve the missing symbol on the first row of the array representation of a permutation. We also general…
The channel output entropy of a transmitted word is the entropy of the possible channel outputs and similarly, the input entropy of a received word is the entropy of all possible transmitted words. The goal of this work is to study these entropy values for the k-deletion, k-insertion channel, where exactly k symbols are deleted, and inserted in the transmitted word, respectively. If all possible words are transmitted with the same probability then studying the input and output entropies is equivalent. For both the 1-insertion and 1-deletion channels, it is proved that among all words with a fi…
This paper presents general bounds on the highest achievable rate for list-decodable insertion-deletion codes. In particular, we give novel outer and inner bounds for the highest achievable communication rate of any insertion-deletion code that can be list-decoded from any $γ$ fraction of insertions and any $δ$ fraction of deletions. Our bounds simultaneously generalize the known bounds for the previously studied special cases of insertion-only, deletion-only, and zero-rate and correct other bounds that had been reported for the general case.
Racetrack memory is a non-volatile memory engineered to provide both high density and low latency, that is subject to synchronization or shift errors. This paper describes a fast coding solution, in which delimiter bits assist in identifying the type of shift error, and easily implementable graph-based codes are used to correct the error, once identified. A code that is able to detect and correct double shift errors is described in detail.
We consider the problem of reliable communication over non-binary insertion/deletion channels where symbols are randomly deleted from or inserted in the transmitted sequence and all symbols are corrupted by additive white Gaussian noise. To this end, we utilize the inherent redundancy achievable in non-binary symbol sets by first expanding the symbol set and then allocating part of the bits associated with each symbol to watermark symbols. The watermark sequence, known at the receiver, is then used by a forward-backward algorithm to provide soft information for an outer code which decodes the …
This work constructs codes that are efficiently decodable from a constant fraction of \emph{worst-case} insertion and deletion errors in three parameter settings: (i) Binary codes with rate approaching 1; (ii) Codes with constant rate for error fraction approaching 1 over fixed alphabet size; and (iii) Constant rate codes over an alphabet of size $k$ for error fraction approaching $(k-1)/(k+1)$. When errors are constrained to deletions alone, efficiently decodable codes in each of these regimes were constructed recently. We complete the picture by constructing similar codes that are efficientl…
Codes for correcting sticky insertions/deletions and limited-magnitude errors have attracted significant attention due to their applications of flash memories, racetrack memories, and DNA data storage systems. In this paper, we first consider the error type of $t$-sticky deletions with $\ell$-limited-magnitude and propose a non-systematic code for correcting this type of error with redundancy $2t(1-1/p)\cdot\log(n+1)+O(1)$, where $p$ is the smallest prime larger than $\ell+1$. Next, we present a systematic code construction with an efficient encoding and decoding algorithm with redundancy $\fr…
We consider the problem of constructing codes that can correct deletions that are localized within a certain part of the codeword that is unknown a priori. Namely, the model that we study is when at most $k$ deletions occur in a window of size $k$, where the positions of the deletions within this window are not necessarily consecutive. Localized deletions are thus a generalization of burst deletions that occur in consecutive positions. We present novel explicit codes that are efficiently encodable and decodable and can correct up to $k$ localized deletions. Furthermore, these codes have $\log …
Construction of capacity achieving deletion correcting codes has been a baffling challenge for decades. A recent breakthrough by Brakensiek $et~al$., alongside novel applications in DNA storage, have reignited the interest in this longstanding open problem. In spite of recent advances, the amount of redundancy in existing codes is still orders of magnitude away from being optimal. In this paper, a novel approach for constructing binary two-deletion correcting codes is proposed. By this approach, parity symbols are computed from indicator vectors (i.e., vectors that indicate the positions of ce…
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 $δ\leq w$ deletions are localized in a window of size $w$ bits. These $δ$ 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…
Deletion-Correcting Codes for the $\ell$-Symbol Read Channel
Institute of Mathematics and Interdisciplinary Sciences, Xidian University（西安电子科技大学数学与交叉科学研究院）；School of Mathematical Sciences, Capital Normal University（首都师范大学数学科学学院）
In this paper, we discuss a construction method of quantum deletion error-correcting codes. First of all, we define deletion errors for quantum states, an encoder, a decoder, and two conditions which is expressed by only the combinatorial language. Then, we prove that quantum deletion error-correcting codes can be constructed by two sets that satisfy the conditions. In other words, problems that correct the deletion errors for quantum states are reduced to problems that find the sets satisfying the condition by this paper. Also, we performed experiment of the codes over IBM Quantum Experience.
A client/encoder edits a file, as modeled by an insertion-deletion (InDel) process. An old copy of the file is stored remotely at a data-centre/decoder, and is also available to the client. We consider the problem of throughput- and computationally-efficient communication from the client to the data-centre, to enable the server to update its copy to the newly edited file. We study two models for the source files/edit patterns: the random pre-edit sequence left-to-right random InDel (RPES-LtRRID) process, and the arbitrary pre-edit sequence arbitrary InDel (APES-AID) process. In both models, we…
We propose two systematic constructions of deletion-correcting codes for protecting quantum information. The first one works with qudits of any dimension, but only one deletion is corrected and the constructed codes are asymptotically bad. The second one corrects multiple deletions and can construct asymptotically good codes. The second one also allows conversion of stabilizer-based quantum codes to deletion-correcting codes, and entanglement assistance.
