Synthetic polymer-based storage seems to be a particularly promising candidate that could help to cope with the ever-increasing demand for archival storage requirements. It involves designing molecules of distinct masses to represent the respective bits $\{0,1\}$, followed by the synthesis of a polymer of molecular units that reflects the order of bits in the information string. Reading out the stored data requires the use of a tandem mass spectrometer, that fragments the polymer into shorter substrings and provides their corresponding masses, from which the \emph{composition}, i.e. the number of $1$s and $0$s in the concerned substring can be inferred. Prior works have dealt with the problem of unique string reconstruction from the set of all possible compositions, called \emph{composition multiset}. This was accomplished either by determining which string lengths always allow unique reconstruction, or by formulating coding constraints to facilitate the same for all string lengths. Additionally, error-correcting schemes to deal with substitution errors caused by imprecise fragmentation during the readout process, have also been suggested. This work builds on this research by generalizing previously considered error models, mainly confined to substitution of compositions. To this end, we define new error models that consider insertions of spurious compositions and deletions of existing ones, thereby corrupting the composition multiset. We analyze if the reconstruction codebook proposed by Pattabiraman \emph{et al.} is indeed robust to such errors, and if not, propose new coding constraints to remedy this.
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.
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.
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）
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 …
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…
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.…
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…
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…
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 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…
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…
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…
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…
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…
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 …
One of the main challenges in developing racetrack memory systems is the limited precision in controlling the track shifts, that in turn affects the reliability of reading and writing the data. A current proposal for combating deletions in racetrack memories is to use redundant heads per-track resulting in multiple copies (potentially erroneous) and recovering the data by solving a specialized version of a sequence reconstruction problem. Using this approach, $k$-deletion correcting codes of length $n$, with $d \ge 2$ heads per-track, with redundancy $\log \log n + 4$ were constructed. However…
Recent efforts in coding theory have focused on building codes for insertions and deletions, called insdel codes, with optimal trade-offs between their redundancy and their error-correction capabilities, as well as efficient encoding and decoding algorithms. In many applications, polynomial running time may still be prohibitively expensive, which has motivated the study of codes with super-efficient decoding algorithms. These have led to the well-studied notions of Locally Decodable Codes (LDCs) and Locally Correctable Codes (LCCs). Inspired by these notions, Ostrovsky and Paskin-Cherniavsky (…
In this paper, a new problem of transmitting information over the adversarial insertion-deletion channel with feedback is introduced. Suppose that the encoder transmits $n$ binary symbols one-by-one over a channel, in which some symbols can be deleted and some additional symbols can be inserted. After each transmission, the encoder is notified about the insertions or deletions that have occurred within the previous transmission and the encoding strategy can be adapted accordingly. The goal is to design an encoder that is able to transmit error-free as much information as possible under the ass…
In this work, we study the performance of Reed--Solomon codes against adversarial insertion-deletion (insdel) errors. We prove that over fields of size $n^{O(k)}$ there are $[n,k]$ Reed-Solomon codes that can decode from $n-2k+1$ insdel errors and hence attain the half-Singleton bound. We also give a deterministic construction of such codes over much larger fields (of size $n^{k^{O(k)}}$). Nevertheless, for $k=O(\log n /\log\log n)$ our construction runs in polynomial time. For the special case $k=2$, which received a lot of attention in the literature, we construct an $[n,2]$ Reed-Solomon cod…
We propose a new coding scheme, called the delayed coding (DC) scheme, for channels with insertion, deletion, and substitution (IDS) errors. The proposed scheme employs delayed encoding and non-iterative detection and decoding strategies to manage the transmission of multiple codewords in a linear code. In the DC scheme, a channel input sequence consists of subblocks of multiple codewords from the previous to current time instances. At the receiver side, the maximum a posteriori detection applies to the received sequences that contain information of the codeword at the current time instance, w…
We present a construction of subspace codes along with an efficient algorithm for list decoding from both insertions and deletions, handling an information-theoretically maximum fraction of these with polynomially small rate. Our construction is based on a variant of the folded Reed-Solomon codes in the world of linearized polynomials, and the algorithm is inspired by the recent linear-algebraic approach to list decoding. Ours is the first list decoding algorithm for subspace codes that can handle deletions; even one deletion can totally distort the structure of the basis of a subspace and is …
Insertion and deletion (insdel for short) errors are synchronization errors in communication systems caused by the loss of positional information in the message. Reed-Solomon codes have gained a lot of interest due to its encoding simplicity, well structuredness and list-decoding capability in the classical setting. This interest also translates to the insdel metric setting, as the Guruswami-Sudan decoding algorithm can be utilized to provide a deletion correcting algorithm in the insdel metric. Nevertheless, there have been few studies on the insdel error-correcting capability of Reed-Solomon…
This paper considers a binary channel with deletions and insertions, where each input bit is transformed in one of the following ways: it is deleted with probability d, or an extra bit is added after it with probability i, or it is transmitted unmodified with probability 1-d-i. A computable lower bound on the capacity of this channel is derived. The transformation of the input sequence by the channel may be viewed in terms of runs as follows: some runs of the input sequence get shorter/longer, some runs get deleted, and some new runs are added. It is difficult for the decoder to synchronize th…
Consider two remote nodes (encoder and decoder), each with a binary sequence. The encoder's sequence $X$ differs from the decoder's sequence $Y$ by a small number of edits (deletions and insertions). 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 $Y$. In this paper, we devise a coding scheme for this one-way synchronization model. The scheme is based on multiple layers of Varshamov-Tenengolts (VT) codes combined with off-the-shelf linear error-correcting codes, and uses a list decoder. We bound the expec…
This paper gives some theory and efficient design of binary block systematic codes capable of controlling the deletions of the symbol ``$0$'' (referred to as $0$-deletions) and/or the insertions of the symbol ``$0$'' (referred to as $0$-insertions). The problem of controlling $0$-deletions and/or $0$-insertions (referred to as $0$-errors) is known to be equivalent to the efficient design of $L_{1}$ metric asymmetric error control codes over the natural alphabet, $\mathbb{N}$. So, $t$ $0$-insertion correcting codes can actually correct $t$ $0$-errors, detect $(t+1)$ $0$-errors and, simultaneous…
This work studies problems in data reconstruction, an important area with numerous applications. In particular, we examine the reconstruction of binary and non-binary sequences from synchronization (insertion/deletion-correcting) codes. These sequences have been corrupted by a fixed number of symbol insertions (larger than the minimum edit distance of the code), yielding a number of distinct traces to be used for reconstruction. We wish to know the minimum number of traces needed for exact reconstruction. This is a general version of a problem tackled by Levenshtein for uncoded sequences. We i…
We present many new results related to reliable (interactive) communication over insertion-deletion channels. Synchronization errors, such as insertions and deletions, strictly generalize the usual symbol corruption errors and are much harder to protect against. We show how to hide the complications of synchronization errors in many applications by introducing very general channel simulations which efficiently transform an insertion-deletion channel into a regular symbol corruption channel with an error rate larger by a constant factor and a slightly smaller alphabet. We generalize synchroniza…
We improve the upper bound of Levenshtein for the cardinality of a code of length 4 capable of correcting single deletions over an alphabet of even size. We also illustrate that the new upper bound is sharp. Furthermore we will construct an optimal perfect code capable of correcting single deletions for the same parameters.
