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Permutation codes have recently garnered substantial research interest due to their potential in various applications including cloud storage systems, genome resequencing and flash memories. In this paper, we study the theoretical bounds and constructions of permutation codes in the generalized Cayley metric. The generalized Cayley metric captures the number of generalized transposition errors in a permutation, and subsumes previously studied error types, including transpositions and translocations, without imposing restrictions on the lengths and positions of the translocated segments. Relying on the breakpoint analysis proposed by Chee and Vu, we first propose a coding scheme that is order-optimal albeit not constructive based on this method. We then develop another construction of permutation codes in the generalized Cayley distance. This scheme is both explicit and systematic. We also prove the existence of order-optimal systematic codes and offer a concrete construction based on this method. For the generalized Cayley metric, we prove that our coding schemes have less redundancy than the existing codes based on interleaving when the codelength is sufficiently large and the number of errors is relatively small., Comment: 18 pages; 0 figures; published on IEEE Transactions on Information Theory

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 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 codewords, 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 codeword 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., Comment: 18 pages, 3 figures. Accepted to IEEE Transactions on Information Theory

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 and extend the burst deletion model to two more cases: 1) A deletion burst of at most $b$ consecutive bits and 2) A deletion burst of size at most $b$ (not necessarily consecutive). We extend our code construction for the first case and study the second case for $b=3,4$. The equivalent models for insertions are also studied and are shown to be equivalent to correcting the corresponding burst of deletions.