This paper tackles two problems that fall under the study of coding for insertions and deletions. These problems are motivated by several applications, among them is reconstructing strands in DNA-based storage systems. Under this paradigm, a word is transmitted over some fixed number of identical independent channels and the goal of the decoder is to output the transmitted word or some close approximation of it. The first part of the paper studies optimal decoding for a special case of the deletion channel, referred by the $k$-deletion channel, which deletes exactly $k$ symbols of the transmitted word uniformly at random. In this part, the goal is to understand how an optimal decoder operates in order to minimize the expected normalized distance. A full characterization of an efficient optimal decoder for this setup, referred to as the maximum likelihood* (ML*) decoder, is given for a channel that deletes one or two symbols. The second part of this paper studies the deletion channel that deletes a symbol with some fixed probability $p$, while focusing on two instances of this channel. Since operating the maximum likelihood (ML) decoder, in this case, is computationally unfeasible, we study a slightly degraded version of this decoder for two channels and study its expected normalized distance. We observe that the dominant error patterns are deletions in the same run or errors resulting from alternating sequences. Based on these observations, we derive lower bounds on the expected normalized distance of the degraded ML decoder for any transmitted $q$-ary sequence of length $n$ and any deletion probability $p$. We further show that as the word length approaches infinity and the channel's deletion probability $p$ approaches zero, these bounds converge to approximately $\frac{3q - 1}{q - 1} p^2$. These theoretical results are verified by corresponding simulations.
A Decoding Algorithm for Composite Errors Consisting of Deletions and Insertions in Quantum Deletion-Correcting Codes Based on Quantum Reed-Solomon 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…
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, …
Guess & Check (GC) codes are systematic binary codes that can correct multiple deletions, with high probability. GC codes have logarithmic redundancy in the length of the message $k$, and the encoding and decoding algorithms of these codes are deterministic and run in polynomial time for a constant number of deletions $δ$. The unique decoding properties of GC codes were examined in a previous work by the authors. In this paper, we investigate the list decoding performance of these codes. Namely, we study the average size and the maximum size of the list obtained by a GC decoder for a constant …
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…
This paper investigates linear-time decoding algorithms for two classes of error-correcting codes. One of the classes is monotone codes which are known as single deletion codes. The other is azinv codes which are known as single balanced adjacent deletion codes. As results, this paper proposes generalizations of Levenshtein's decoding algorithm for Levenshtein's single deletion codes. This paper points out that it is possible to unify our new two decoding algorithms.
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 …
This paper studies the problem of reconstructing a word given several of its noisy copies. This setup is motivated by several applications, among them is reconstructing strands in DNA-based storage systems. Under this paradigm, a word is transmitted over some fixed number of identical independent channels and the goal of the decoder is to output the transmitted word or some close approximation. The main focus of this paper is the case of two deletion channels and studying the error probability of the maximum-likelihood (ML) decoder under this setup. First, it is discussed how the ML decoder op…
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…
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 …
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 study the application of polar codes in deletion channels by analyzing the cascade of a binary erasure channel (BEC) and a deletion channel. We show how polar codes can be used effectively on a BEC with a single deletion, and propose a list decoding algorithm with a cyclic redundancy check for this case. The decoding complexity is $O(N^2\log N)$, where $N$ is the blocklength of the code. An important contribution is an optimization of the amount of redundancy added to minimize the overall error probability. Our theoretical results are corroborated by numerical simulations which show that th…
We study codes that are list-decodable under insertions and deletions. Specifically, we consider the setting where a codeword over some finite alphabet of size $q$ may suffer from $δ$ fraction of adversarial deletions and $γ$ fraction of adversarial insertions. A code is said to be $L$-list-decodable if there is an (efficient) algorithm that, given a received word, reports a list of $L$ codewords that include the original codeword. Using the concept of synchronization strings, introduced by the first two authors [STOC 2017], we show some surprising results. We show that for every $0\leqδ<1$, e…
We give a complete answer to the following basic question: "What is the maximal fraction of deletions or insertions tolerable by $q$-ary list-decodable codes with non-vanishing information rate?" This question has been open even for binary codes, including the restriction to the binary insertion-only setting, where the best-known result was that a $γ\leq 0.707$ fraction of insertions is tolerable by some binary code family. For any desired $ε> 0$, we construct a family of binary codes of positive rate which can be efficiently list-decoded from any combination of $γ$ fraction of insertions and …
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…
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…
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…
This paper presents the first proof of polarization for the deletion channel with a constant deletion rate and a regular hidden-Markov input distribution. A key part of this work involves representing the deletion channel using a trellis and describing the plus and minus polar-decoding operations on that trellis. In particular, the plus and minus operations can be seen as combining adjacent trellis stages to yield a new trellis with half as many stages. Using this viewpoint, we prove a weak polarization theorem for standard polar codes on the deletion channel. To achieve strong polarization, w…
We introduce a general class of codes which includes several well-known classes of deletion/insertion correcting codes as special cases. For example, the Helberg code, the Levenshtein code, the Varshamov--Tenengolts code, and most variants of these codes including most of those which have been recently used in studying DNA-based data storage systems are all special cases of our code. Then, using a number theoretic method, we give an explicit formula for the weight enumerator of our code which in turn gives explicit formulas for the weight enumerators and so the sizes of all the aforementioned …
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…
Quantum deletions, which are harder to correct than erasure errors, occur in many realistic settings. It is therefore pertinent to develop quantum coding schemes for quantum deletion channels. To date, not much is known about which explicit quantum error correction codes can combat quantum deletions. We note that {\em any} permutation-invariant quantum code that has a distance of $t+1$ can correct $t$ quantum deletions for any positive integer $t$ in both the qubit and the qudit setting. Leveraging on coding properties of permutation-invariant quantum codes under erasure errors, we derive corr…
Two of the most common models for channels with synchronisation errors are the Binary Deletion Channel with parameter $p$ ($\text{BDC}_p$) -- a channel where every bit of the codeword is deleted i.i.d with probability $p$, and the Poisson Repeat Channel with parameter $λ$ ($\text{PRC}_λ$) -- a channel where every bit of the codeword is repeated $\text{Poisson}(λ)$ times. Previous constructions based on synchronisation strings yielded codes with rates far lower than the capacities of these channels [CS19, GL18], and the only efficient construction to achieve capacity on the BDC at the time of w…
We consider the problem of constructing deletion correcting codes over a binary alphabet and take a graph theoretic view. An $n$-bit $s$-deletion correcting code is an independent set in a particular graph. We propose constructing such a code by taking the union of many constant Hamming weight codes. This results in codes that have additional structure. Searching for codes in constant Hamming weight induced subgraphs is computationally easier than searching the original graph. We prove a lower bound on size of a codebook constructed this way for any number of deletions and show that it is only…
This work gives an explicit construction of a family of error correcting codes for the binary deletion channel and for the Poisson repeat channel. In the binary deletion channel with parameter $p$ (BDC$_p$) every bit is deleted independently with probability $p$. A lower bound of $(1-p)/9$ is known on the capacity of the BDC$_p$ \cite{mitzenmacher2006simple}, yet no explicit construction is known to achieve this rate. We give an explicit family of codes of rate $(1-p)/16$, for every $p$. This improves upon the work of Guruswami and Li \cite{guruswami2017efficiently} that gave a construction of…
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…
In this paper, we derive the exact weight distributions that emerge during each stage of successive cancellation decoding of polar codes. Though we do not compute the distance spectrum of polar codes, the results allow us to get an estimate of the decoding error probability and to show a link between the first nonzero components of the weight distribution and the partial order between the synthetic channels. Also, we establish the minimal distance between two cosets associated with two paths that differ in two positions. This can be regarded as a first step toward analyzing the weight distribu…
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…
We analyze Linear Programming (LP) decoding of graphical binary codes operating over soft-output, symmetric and log-concave channels. We show that the error-surface, separating domain of the correct decoding from domain of the erroneous decoding, is a polytope. We formulate the problem of finding the lowest-weight pseudo-codeword as a non-convex optimization (maximization of a convex function) over a polytope, with the cost function defined by the channel and the polytope defined by the structure of the code. This formulation suggests new provably convergent heuristics for finding the lowest w…
Reed-Muller (RM) codes exhibit good performance under maximum-likelihood (ML) decoding due to their highly-symmetric structure. In this paper, we explore the question of whether the code symmetry of RM codes can also be exploited to achieve near-ML performance in practice. The main idea is to apply iterative decoding to a highly-redundant parity-check (PC) matrix that contains only the minimum-weight dual codewords as rows. As examples, we consider the peeling decoder for the binary erasure channel, linear-programming and belief propagation (BP) decoding for the binary-input additive white Gau…
Memoryless channels with deletion errors as defined by a stochastic channel matrix allowing for bit drop outs are considered in which transmitted bits are either independently deleted with probability $d$ or unchanged with probability $1-d$. Such channels are information stable, hence their Shannon capacity exists. However, computation of the channel capacity is formidable, and only some upper and lower bounds on the capacity exist. In this paper, we first show a simple result that the parallel concatenation of two different independent deletion channels with deletion probabilities $d_1$ and $…
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 revisits the ordered statistics decoding (OSD). It provides a comprehensive analysis of the OSD algorithm by characterizing the statistical properties, evolution and the distribution of the Hamming distance and weighted Hamming distance from codeword estimates to the received sequence in the reprocessing stages of the OSD algorithm. We prove that the Hamming distance and weighted Hamming distance distributions can be characterized as mixture models capturing the decoding error probability and code weight enumerator. Simulation and numerical results show that our proposed statistical…
