A binary string transmitted via a memoryless i.i.d. deletion channel is received as a subsequence of the original input. From this, one obtains a posterior distribution on the channel input, corresponding to a set of candidate supersequences weighted by the number of times the received subsequence can be embedded in them. In a previous work it is conjectured on the basis of experimental data that the entropy of the posterior is minimized and maximized by the constant and the alternating strings, respectively. In this work, we present an algorithm for counting the number of subsequence embeddings using a run-length encoding of strings. We then describe two different ways of clustering the space of supersequences and prove that their cardinality depends only on the length of the received subsequence and its Hamming weight, but not its exact form. Then, we consider supersequences that contain a single embedding of a fixed subsequence, referred to as singletons, and provide a closed form expression for enumerating them using the same run-length encoding. We prove an analogous result for the minimization and maximization of the number of singletons, by the alternating and the uniform strings, respectively. Next, we prove the original minimal entropy conjecture for the special cases of single and double deletions using similar clustering techniques and the same run-length encoding, which allow us to characterize the distribution of the number of subsequence embeddings in the space of compatible supersequences to demonstrate the effect of an entropy decreasing operation.
In coding theory, and more specifically in the context of insertion and deletions channels, similar long-standing problems have been studied extensively, and yet many problems still remain elusive. This includes designing optimal coding schemes and determining the capacity of deletion channels, both of which incorporate the same underlying combinatorial problem addressed in the present work. Considering a finite number of insertions and deletions for designing correcting codes for synchronization errors @cite_16 @cite_1 @cite_17 and reconstructing the original string from a fixed subsequence @cite_8 represent two specific and related research areas. More recent work on the characterization of the number of subsequences obtained via the deletion channel @cite_2 @cite_18 @cite_10 , e.g., in terms of the number of runs in a string, shows great overlap with our work. A graph-theoretic approach for deletion correcting codes, closely related to our clustering analysis, including an alternative proof for the Hamming weight clustering given in Theorem based on a different approach, is given in @cite_14 .
@cite_18 @cite_14 @cite_8 @cite_1 @cite_2 @cite_16 @cite_10 @cite_17
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This paper studies problems in data reconstruction, an important area with numerous applications. In particular, we examine the reconstruction of binary and nonbinary 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 introduce an exact formula for the maximum number of common supersequences shared by sequences at a certain edit distance, yielding an upper bound on the number of distinct traces necessary to guarantee exact reconstruction. Without specific knowledge of the code words, this upper bound is tight. We apply our results to the famous single deletion insertion-correcting Varshamov–Tenengolts (VT) codes and show that a significant number of VT code word pairs achieve the worst case number of outputs needed for exact reconstruction. We also consider extensions to other channels, such as adversarial deletion and insertion deletion channels and probabilistic channels. We study the problem of synchronization of two remotely located data sources, which are mis-synchronized due to deletions and insertions. This is an important problem since a small number of synchronization errors can induce a large Hamming distance between the two sources. The goal is to effect synchronization with the rate-efficient use of lossless bidirectional links between the two sources. In this work, we focus on the following model. A binary sequence X of length n is edited to generate the sequence at the remote end, say Y, where the editing involves random deletions and insertions, possibly in small bursts. The problem is to synchronize Y with X with minimal exchange of information (in terms of both the average communication rate and the average number of interactive rounds of communication). We focus here on the case where the number of edits is much smaller than n, and propose an interactive algorithm which is computationally simple and has near-optimal communication complexity. Our algorithm works by efficiently splitting the source sequence into pieces containing either just a single deletion insertion or a single burst deletion insertion. Each of these pieces is then synchronized using an optimal one-way synchronization code, based on the single-deletion correcting channel codes of Varshamov and Tenengolts (VT codes). We study memoryless channels with synchronization errors as defined by a stochastic channel matrix allowing for symbol drop-outs or symbol insertions with particular emphasis on the binary and non-binary deletion channels. We offer a different look at these channels by considering equivalent models by fragmenting the input sequence where different subsequences travel through different channels. The resulting output symbols are combined appropriately to come up with an equivalent input-output representation of the original channel which allows for derivation of new upper bounds on the channel capacity. We consider both random and deterministic types of fragmentation processes applied to binary and nonbinary deletion channels. With two specific applications of this idea, a random fragmentation applied to a binary deletion channel and a deterministic fragmentation process applied to a nonbinary deletion channel, we prove certain inequality relations among the capacities of the original channels and those of the introduced subchannels. The resulting inequalities prove useful in deriving tighter capacity upper bounds for: 1) independent identically distributed (i.i.d.) deletion channels when the deletion probability exceeds 0.65 and 2) nonbinary deletion channels. Some extensions of these results, for instance, to the case of deletion substitution channels are also explored. We introduce and solve some new problems of efficient reconstruction of an unknown sequence from its versions distorted by errors of a certain type. These erroneous versions are considered as outputs of repeated transmissions over a channel, either a combinatorial channel defined by the maximum number of permissible errors of a given type, or a discrete memoryless channel. We are interested in the smallest N such that N erroneous versions always suffice to reconstruct a sequence of length n, either exactly or with a preset accuracy and or with a given probability. We are also interested in simple reconstruction algorithms. Complete solutions for combinatorial channels with some types of errors of interest in coding theory, namely, substitutions, transpositions, deletions, and insertions of symbols are given. For these cases, simple reconstruction algorithms based on majority and threshold principles and their nontrivial combination are found. In general, for combinatorial channels the considered problem is reduced to a new problem of reconstructing a vertex of an arbitrary graph with the help of the minimum number of vertices in its metrical ball of a given radius. A certain sufficient condition for solution of this problem is presented. For a discrete memoryless channel, the asymptotic behavior of the minimum number of repeated transmissions which are sufficient to reconstruct any sequence of length n within Hamming distance d with error probability spl epsiv is found when d n and spl epsiv tend to 0 as n spl rarr spl infin . A similar result for the continuous channel with discrete time and additive Gaussian noise is also obtained. 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 the channel output sequence to the transmitted codeword mainly due to deleted runs and new inserted runs. The main idea is a mutual information decomposition in terms of the rate achieved by a suboptimal decoder that determines the positions of the deleted and inserted runs in addition to decoding the transmitted codeword. The mutual information between the channel input and output sequences is expressed as the sum of the rate achieved by this decoder and the rate loss due to its suboptimality. Obtaining computable lower bounds on each of these quantities yields a lower bound on the capacity. The bounds proposed in this paper provide the first characterization of achievable rates for channels with general insertions, and for channels with both deletions and insertions. For the special case of the deletion channel, the proposed bound improves on the previous best lower bound for deletion probabilities up to 0.3. The sequence reconstruction problem , first proposed by Levenshtein, models the setup in which a sequence from some set is transmitted over several channels, and the decoder receives the outputs from every channel. The channels are almost independent as it is only required that all outputs are different from each other. The main problem of interest is to determine the minimum number of channels required to reconstruct the transmitted sequence. In the combinatorial context, the problem is equivalent to finding the maximum intersection between two balls of radius @math , where the distance between their centers is at least @math . The setup of this problem was studied before for several error metrics such as the Hamming metric, the Kendall-tau metric, and the Johnson metric. In this paper, we extend the study initiated by Levenshtein for reconstructing sequences over the deletion channel. While he solved the case where the transmitted sequence can be arbitrary, we study the setup, where the transmitted sequence belongs to a single-deletion-correcting code and there are @math deletions in every channel. Under this paradigm, we study the minimum number of different channel outputs in order to construct a successful decoder. We consider deletion correcting codes over a (q ) -ary alphabet. It is well known that any code capable of correcting (s ) deletions can also correct any combination of (s ) total insertions and deletions. To obtain asymptotic upper bounds on code size, we apply a packing argument to channels that perform different mixtures of insertions and deletions. Even though the set of codes is identical for all of these channels, the bounds that we obtain vary. Prior to this paper, only the bounds corresponding to the all-insertion case and the all-deletion case were known. We recover these as special cases. The bound from the all-deletion case, due to Levenshtein, has been the best known for more than 45 years. Our generalized bound is better than Levenshtein's bound whenever the number of deletions to be corrected is larger than the alphabet size. We take a graph theoretic view of deletion correcting codes. The problem of finding an n-bit s-deletion correcting code is equivalent to finding an independent set in a particular graph. We discuss the relationship between codes and colorings and demonstrate that the VT codes are optimal in a coloring sense. We describe a method of partitioning the set of bit strings by Hamming weight and finding codes within each partition. In the single deletion case, we find an optimal coloring of the constant Hamming weight induced subgraphs. We show that the resulting code is asymptotically optimal. We also prove a lower bound on size of codes constructed using these partitions for any number of deletions. 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: 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 insertion channel case, we consider Gallager's model in which the transmitted bits are replaced with two random bits and uniform over the four possibilities independently of any other insertion events. The general approach taken is similar in all cases, however the specific computations differ. Furthermore, the approach yields a useful lower bound on the capacity for a wide range of deletion probabilities of the deletion channels, while it provides a beneficial bound only for small insertion probabilities (less than 0.25) of the insertion model adopted. We emphasize the importance of these results by noting that: 1) our results are the first analytical bounds on the capacity of deletion-AWGN channels, 2) the results developed are the best available analytical lower bounds on the deletion-substitution case, 3) for the Gallager insertion channel model, the new lower bound improves the existing results for small insertion probabilities. The binary deletion channel is the simplest point-to-point communication channel that models lack of synchronization. Input bits are deleted independently with probability d, and when they are not deleted, they are not affected by the channel. Despite significant effort, little is known about the capacity of this channel and even less about optimal coding schemes. In this paper, we develop a new systematic approach to this problem, by demonstrating that capacity can be computed in a series expansion for small deletion probability. We compute three leading terms of this expansion, and find an input distribution that achieves capacity up to this order. This constitutes the first optimal random coding result for the deletion channel. The key idea employed is the following: We understand perfectly the deletion channel with deletion probability d=0. It has capacity 1 and the optimal input distribution is iid Bernoulli (1 2). It is natural to expect that the channel with small deletion probabilities has a capacity that varies smoothly with d, and that the optimal input distribution is obtained by smoothly perturbing the iid Bernoulli (1 2) process. Our results show that this is indeed the case. We develop a systematic approach, based on convex programming and real analysis, for obtaining upper bounds on the capacity of the binary deletion channel and, more generally, channels with i.i.d. insertions and deletions. Other than the classical deletion channel, we give a special attention to the Poisson-repeat channel introduced by Mitzenmacher and Drinea (IEEE Transactions on Information Theory, 2006). Our framework can be applied to obtain capacity upper bounds for any repetition distribution (the deletion and Poisson-repeat channels corresponding to the special cases of Bernoulli and Poisson distributions). Our techniques essentially reduce the task of proving capacity upper bounds to maximizing a univariate, real-valued, and often concave function over a bounded interval. The corresponding univariate function is carefully designed according to the underlying distribution of repetitions and the choices vary depending on the desired strength of the upper bounds as well as the desired simplicity of the function (e.g., being only efficiently computable versus having an explicit closed-form expression in terms of elementary, or common special, functions). Among our results, we show that the capacity of the binary deletion channel with deletion probability d is at most (1−d) logϕ for d ≥ 1 2, and, assuming the capacity function is convex, is at most 1−d log(4 ϕ) for d Furthermore, we derive the first set of capacity upper bounds for the Poisson-repeat channel. Our results uncover further striking connections between this channel and the deletion channel, and suggest, somewhat counter-intuitively, that the Poisson-repeat channel is actually analytically simpler than the deletion channel and may be of key importance to a complete understanding of the deletion channel. Finally, we derive several novel upper bounds on the capacity of the deletion channel. All upper bounds are maximums of efficiently computable, and concave, univariate real functions over a bounded domain. In turn, we upper bound these functions in terms of explicit elementary and standard special functions, whose maximums can be found even more efficiently (and sometimes, analytically, for example for d=1 2). Along the way, we develop several new techniques of potentially independent interest. For example, we develop systematic techniques to study channels with mean constraints over the reals. Furthermore, we motivate the study of novel probability distributions over non-negative integers, as well as novel special functions which could be of interest to mathematical analysis. Synchronization channels, which can remove codeword symbols or introduce extraneous symbols, pose additional difficulties when compared to the commonly-studied substitution channel. A traditional problem in this area is to count the number of sequences formed when deleting a fixed number of symbols from a sequence. This work contains our first effort towards solving a similar, yet previously unexplored, problem: deriving bounds on the number of sequences obtained by deleting and inserting a fixed number of symbols. Motivated by the error behavior in the DNA storage channel, in this paper, we extend the previously studied sequence reconstruction problem by Levenshtein. The reconstruction problem studies the model in which the information is read through multiple noisy channels, and the decoder, which receives all channel estimations, is required to decode the information. For the combinatorial setup, the assumption is that all the channels cause at most some @math errors. Levenshtein considered the case in which all the channels have the same behavior, and we generalize this model and assume that the channels are not identical. Thus, different channels may cause different maximum numbers of errors. For example, we assume that there are @math channels, which cause at most @math or @math errors, where @math t_ 1 @math pN @math 0 . If the information codeword belongs to a code with minimum distance @math , the problem is then to find the minimum number of channels that guarantees successful decoding in the worst case. A different problem we study in this paper is where the number of channels is fixed, and the question is finding the minimum distance @math that provides exact reconstruction. We study these problems and show how to apply them for the cases of substitutions and transpositions. A problem of index coding with side information was first considered by Birk and Kol in 1998. In this study, a generalization of index coding scheme, where transmitted symbols are subject to errors, is studied. Error-correcting methods for such a scheme, and their parameters, are investigated. In particular, the following question is discussed: given the side information hypergraph of index coding scheme and the maximal number of erroneous symbols δ , what is the shortest length of a linear index code, such that every receiver is able to recover the required information? This question turns out to be a generalization of the problem of finding a shortest length error-correcting code with a prescribed error-correcting capability in the classical coding theory. The Singleton bound and two other bounds, referred to as the α-bound and the κ -bound, for the optimal length of a linear error-correcting index code (ECIC) are established. For large alphabets, a construction based on concatenation of an optimal index code with a maximum distance separable classical code is shown to attain the Singleton bound. For smaller alphabets, however, this construction may not be optimal. A random construction is also analyzed. It yields another inexplicit bound on the length of an optimal linear ECIC. Further, the problem of error-correcting decoding by a linear ECIC is studied. It is shown that in order to decode correctly the desired symbol, the decoder is required to find one of the vectors, belonging to an affine space containing the actual error vector. The syndrome decoding is shown to produce the correct output if the weight of the error pattern is less or equal to the error-correcting capability of the corresponding ECIC. Finally, the notion of static ECIC, which is suitable for use with a family of instances of an index coding problem, is introduced. Several bounds on the length of static ECICs are derived, and constructions for static ECICs are discussed. Connections of these codes to weakly resilient Boolean functions are established. We present simple, polynomial time encodable and decodable codes which are asymptotically good for channels allowing insertions, deletions, and transpositions. As a corollary, they achieve exponential error probability in a stochastic model of insertion-deletion. We consider coding schemes for computationally bounded channels, which can introduce an arbitrary set of errors as long as (a) the fraction of errors is bounded with high probability by a parameter p and (b) the process that adds the errors can be described by a sufficiently “simple” circuit. Codes for such channel models are attractive since, like codes for standard adversarial errors, they can handle channels whose true behavior is unknown or varying over time. For two classes of channels, we provide explicit, efficiently encodable decodable codes of optimal rate where only inefficiently decodable codes were previously known. In each case, we provide one encoder decoder that works for every channel in the class. The encoders are randomized, and probabilities are taken over the (local, unknown to the decoder) coins of the encoder and those of the channel. Unique decoding for additive errors: We give the first construction of a polynomial-time encodable decodable code for additive (a.k.a. oblivious) channels that achieve the Shannon capacity 1 − H(p). These are channels that add an arbitrary error vector e ∈ 0, 1 N of weight at most pN to the transmitted word; the vector e can depend on the code but not on the randomness of the encoder or the particular transmitted word. Such channels capture binary symmetric errors and burst errors as special cases. List decoding for polynomial-time channels: For every constant c > 0, we construct codes with optimal rate (arbitrarily close to 1 − H(p)) that efficiently recover a short list containing the correct message with high probability for channels describable by circuits of size at most Nc. Our construction is not fully explicit but rather Monte Carlo (we give an algorithm that, with high probability, produces an encoder decoder pair that works for all time Nc channels). We are not aware of any channel models considered in the information theory literature other than purely adversarial channels, which require more than linear-size circuits to implement. We justify the relaxation to list decoding with an impossibility result showing that, in a large range of parameters (p > 1 4), codes that are uniquely decodable for a modest class of channels (online, memoryless, nonuniform channels) cannot have positive rate. A (tandem) duplication of length @math is an insertion of an exact copy of a substring of length @math next to its original position. This and related types of impairments are of relevance in modeling communication in the presence of synchronization errors, as well as in several information storage applications. We demonstrate that Levenshtein’s construction of binary codes correcting insertions of zeros is, with minor modifications, applicable also to channels with arbitrary alphabets and with duplication errors of arbitrary (but fixed) length @math . Furthermore, we derive bounds on the cardinality of optimal @math -ary codes correcting up to @math duplications of length @math and establish the following corollaries in the asymptotic regime of growing block length: 1) the presented family of codes is optimal for every @math , in the sense of the asymptotic scaling of code redundancy; 2) the upper bound, when specialized to @math , @math , improves upon Levenshtein’s bound for every @math ; and 3) the bounds coincide for @math , thus yielding the exact asymptotic behavior of the size of optimal single-duplication-correcting codes. We study the binary deletion channel where each input bit is independently deleted according to a fixed probability. We relate the conditional probability distribution of the output of the deletion channel given the input to the hidden pattern matching problem. This yields a new characterization of the mutual information between the input and output of the deletion channel. Through this characterization we are able to comment on the the deletion channel capacity, in particular for deletion probabilities approaching 0 and 1. We initiate the probabilistic analysis of linear programming (LP) decoding of low-density parity-check (LDPC) codes. Specifically, we show that for a random LDPC code ensemble, the linear programming decoder of Feldman succeeds in correcting a constant fraction of errors with high probability. The fraction of correctable errors guaranteed by our analysis surpasses previous nonasymptotic results for LDPC codes, and in particular, exceeds the best previous finite-length result on LP decoding by a factor greater than ten. This improvement stems in part from our analysis of probabilistic bit-flipping channels, as opposed to adversarial channels. At the core of our analysis is a novel combinatorial characterization of LP decoding success, based on the notion of a flow on the Tanner graph of the code. An interesting by-product of our analysis is to establish the existence of ldquoprobabilistic expansionrdquo in random bipartite graphs, in which one requires only that almost every (as opposed to every) set of a certain size expands, for sets much larger than in the classical worst case setting. A new class of exact-repair regenerating codes is constructed by stitching together shorter erasure correction codes, where the stitching pattern can be viewed as block designs. The proposed codes have the help-by-transfer property where the helper nodes simply transfer part of the stored data directly, without performing any computation. This embedded error correction structure makes the decoding process straightforward, and in some cases the complexity is very low. We show that this construction is able to achieve performance better than space-sharing between the minimum storage regenerating codes and the minimum repair-bandwidth regenerating codes, and it is the first class of codes to achieve this performance. In fact, it is shown that the proposed construction can achieve a nontrivial point on the optimal functional-repair tradeoff, and it is asymptotically optimal at high rate, i.e., it asymptotically approaches the minimum storage and the minimum repair-bandwidth simultaneously.