Asymptotic bounds for spherical codes

The set of all error-correcting codes C over a fixed finite alphabet F of cardinality q determines the set of code points in the unit square with coordinates (R(C), delta (C)):= (relative transmission rate, relative minimal distance). The central problem of the theory of such codes consists in maximizing simultaneously the transmission rate of the code and the relative minimum Hamming distance between two different code words. The classical approach to this problem explored in vast literature consists in the inventing explicit constructions of "good codes" and comparing new classes of codes with earlier ones. Less classical approach studies the geometry of the whole set of code points (R,delta) (with q fixed), at first independently of its computability properties, and only afterwords turning to the problems of computability, analogies with statistical physics etc. The main purpose of this article consists in extending this latter strategy to domain of spherical codes.Comment: 34 pages amstex, 3 figure

Non-asymptotic Upper Bounds for Deletion Correcting Codes

Explicit non-asymptotic upper bounds on the sizes of multiple-deletion correcting codes are presented. In particular, the largest single-deletion correcting code for $q$-ary alphabet and string length $n$ is shown to be of size at most $\frac{q^n-q}{(q-1)(n-1)}$. An improved bound on the asymptotic rate function is obtained as a corollary. Upper bounds are also derived on sizes of codes for a constrained source that does not necessarily comprise of all strings of a particular length, and this idea is demonstrated by application to sets of run-length limited strings. The problem of finding the largest deletion correcting code is modeled as a matching problem on a hypergraph. This problem is formulated as an integer linear program. The upper bound is obtained by the construction of a feasible point for the dual of the linear programming relaxation of this integer linear program. The non-asymptotic bounds derived imply the known asymptotic bounds of Levenshtein and Tenengolts and improve on known non-asymptotic bounds. Numerical results support the conjecture that in the binary case, the Varshamov-Tenengolts codes are the largest single-deletion correcting codes.Comment: 18 pages, 4 figure

Mutually Uncorrelated Primers for DNA-Based Data Storage

We introduce the notion of weakly mutually uncorrelated (WMU) sequences, motivated by applications in DNA-based data storage systems and for synchronization of communication devices. WMU sequences are characterized by the property that no sufficiently long suffix of one sequence is the prefix of the same or another sequence. WMU sequences used for primer design in DNA-based data storage systems are also required to be at large mutual Hamming distance from each other, have balanced compositions of symbols, and avoid primer-dimer byproducts. We derive bounds on the size of WMU and various constrained WMU codes and present a number of constructions for balanced, error-correcting, primer-dimer free WMU codes using Dyck paths, prefix-synchronized and cyclic codes.Comment: 14 pages, 3 figures, 1 Table. arXiv admin note: text overlap with arXiv:1601.0817

Constructions and bounds for codes with restricted overlaps

Non-overlapping codes have been studied for almost 60 years. In such a code, no proper, non-empty prefix of any codeword is a suffix of any codeword. In this paper, we study codes in which overlaps of certain specified sizes are forbidden. We prove some general bounds and we give several constructions in the case of binary codes. Our techniques also allow us to provide an alternative, elementary proof of a lower bound on non-overlapping codes due to Levenshtein in 1964.Comment: 25 pages. Extra citations, typos corrected and explanations expande

Constructions and bounds for codes with restricted overlaps

Non-overlapping codes have been studied for almost 60 years. In such a code, no proper, non-empty prefix of any codeword is a suffix of any codeword. In this paper, we study codes in which over-laps of certain specified sizes are forbidden. We prove some general bounds and we give several constructions in the case of binary codes. Our techniques also allow us to provide an alternative, elementary proof of a lower bound on non-overlapping codes due to Levenshtein [9] in 1964