This paper is motivated by the problem of error-free communication through the i.i.d. duplication channel which acts on the transmitted sequence by inserting a random number of duplicates of each symbol next to the original symbol. A construction of optimal codes correcting all patterns of errors of this type is described, and the zero-error capacity of the duplication channel is determined. A generalization of these results to channel models in which blocks of @math consecutive symbols are being duplicated, and which are inspired by DNA-based data storage systems where the stored molecules are subject to tandem-duplication mutations, is also given.
The binary @math - @math -insertion channel was first studied in @cite_16 , where a construction of codes correcting @math such errors was given, and asymptotic bounds on the cardinality of optimal codes derived for any fixed @math and @math . Another construction for same model was later given in @cite_9 . Generalizations of the constructions from @cite_16 and @cite_9 for the @math -duplication channel were given in @cite_22 and @cite_5 , respectively. The best known asymptotic bounds for the @math -duplication channel in the regime of fixed @math and @math , were reported in @cite_22 , where the upper bound from @cite_16 (for @math ) was improved for every @math , and the bounds were also generalized to the case @math .
@cite_5 @cite_9 @cite_16 @cite_22
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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. In this paper, we study codes correcting @math duplications of @math consecutive symbols. These errors are known as tandem duplication errors, where a sequence of symbols is repeated and inserted directly after its original occurrence. Using sphere packing arguments, we derive non-asymptotic upper bounds on the cardinality of codes that correct such errors for any choice of parameters. Based on the fact that a code correcting insertions of @math zero-blocks can be used to correct @math tandem duplications, we construct codes for tandem duplication errors. We compare the cardinalities of these codes with their sphere packing upper bounds. Finally, we discuss the asymptotic behavior of the derived codes and bounds, which yields insights about the tandem duplication channel. We study a noiseless broadcast link serving @math users whose requests arise from a library of @math files. Every user is equipped with a cache of size @math files each. It has been shown that by splitting all the files into packets and placing individual packets in a random independent manner across all the caches prior to any transmission, at most @math file transmissions are required for any set of demands from the library. The achievable delivery scheme involves linearly combining packets of different files following a greedy clique cover solution to the underlying index coding problem. This remarkable multiplicative gain of random placement and coded delivery has been established in the asymptotic regime when the number of packets per file @math scales to infinity. The asymptotic coding gain obtained is roughly @math . In this paper, we initiate the finite-length analysis of random caching schemes when the number of packets @math is a function of the system parameters @math , and @math . Specifically, we show that the existing random placement and clique cover delivery schemes that achieve optimality in the asymptotic regime can have at most a multiplicative gain of 2 even if the number of packets is exponential in the asymptotic gain @math . Furthermore, for any clique cover-based coded delivery and a large class of random placement schemes that include the existing ones, we show that the number of packets required to get a multiplicative gain of @math is at least @math . We design a new random placement and an efficient clique cover-based delivery scheme that achieves this lower bound approximately. We also provide tight concentration results that show that the average (over the random placement involved) number of transmissions concentrates very well requiring only a polynomial number of packets in the rest of the system parameters. 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.