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Motivated by applications to DNA storage, we study reconstruction and list-reconstruction schemes for integer vectors that suffer from limited-magnitude errors. We characterize the asymptotic size of the intersection of error balls in relation to the code’s minimum distance. We also devise efficient reconstruction algorithms for various limited-magnitude error parameter ranges. We then extend these algorithms to the list-reconstruction scheme, and show the trade-off between the asymptotic list size and the number of required channel outputs. These results apply to all codes, without any assumptions on the code structure. Finally, we also study linear reconstruction codes with small intersection, as well as show a connection to list-reconstruction codes for the tandem-duplication channel. [ABSTRACT FROM AUTHOR]

We study generalized covering radii, a fundamental property of linear codes that characterizes the trade-off between storage, latency, and access in linear data-query protocols such as PIR. We prove lower and upper bounds on the generalized covering radii of Reed-Muller codes, as well as finding their exact value in certain extreme cases. With the application to linear data-query protocols in mind, we also construct a covering algorithm that gets as input a set of points in space, and find a corresponding set of codewords from the Reed-Muller code that are jointly not farther away from the input than the upper bound on the generalized covering radius of the code. We prove that the algorithm runs in time that is polynomial in the code parameters. [ABSTRACT FROM AUTHOR]

Error-correcting codes over sets, with applications to DNA storage, are studied. The DNA-storage channel receives a set of sequences, and produces a corrupted version of the set, including sequence loss, symbol substitution, symbol insertion/deletion, and limited-magnitude errors in symbols. Various parameter regimes are studied. New bounds on code parameters are provided, which improve upon known bounds. New codes are constructed, at times matching the bounds up to lower-order terms or small constant factors. [ABSTRACT FROM AUTHOR]