Asymmetric Lee Distance Codes for DNA-Based Storage

We consider a new family of codes, termed asymmetric Lee distance codes, that arise in the design and implementation of DNA-based storage systems and systems with parallel string transmission protocols. The codewords are defined over a quaternary alphabet, although the results carry over to other alphabet sizes; furthermore, symbol confusability is dictated by their underlying binary representation. Our contributions are two-fold. First, we demonstrate that the new distance represents a linear combination of the Lee and Hamming distance and derive upper bounds on the size of the codes under this metric based on linear programming techniques. Second, we propose a number of code constructions which imply lower bounds

Semidefinite programming bounds for Lee codes

For $q,n,d \in \mathbb{N}$, let $A_q^L(n,d)$ denote the maximum cardinality of a code $C \subseteq \mathbb{Z}_q^n$ with minimum Lee distance at least $d$, where $\mathbb{Z}_q$ denotes the cyclic group of order $q$. We consider a semidefinite programming bound based on triples of codewords, which bound can be computed efficiently using symmetry reductions, resulting in several new upper bounds on $A_q^L(n,d)$. The technique also yields an upper bound on the independent set number of the $n$-th strong product power of the circular graph $C_{d,q}$, which number is related to the Shannon capacity of $C_{d,q}$. Here $C_{d,q}$ is the graph with vertex set $\mathbb{Z}_q$, in which two vertices are adjacent if and only if their distance (mod $q$) is strictly less than $d$. The new bound does not seem to improve significantly over the bound obtained from Lov\'asz theta-function, except for very small $n$.Comment: 14 pages. arXiv admin note: text overlap with arXiv:1703.0517

Correcting Charge-Constrained Errors in the Rank-Modulation Scheme

We investigate error-correcting codes for a the rank-modulation scheme with an application to flash memory devices. In this scheme, a set of n cells stores information in the permutation induced by the different charge levels of the individual cells. The resulting scheme eliminates the need for discrete cell levels, overcomes overshoot errors when programming cells (a serious problem that reduces the writing speed), and mitigates the problem of asymmetric errors. In this paper, we study the properties of error-correcting codes for charge-constrained errors in the rank-modulation scheme. In this error model the number of errors corresponds to the minimal number of adjacent transpositions required to change a given stored permutation to another erroneous one—a distance measure known as Kendall’s τ-distance.We show bounds on the size of such codes, and use metric-embedding techniques to give constructions which translate a wealth of knowledge of codes in the Lee metric to codes over permutations in Kendall’s τ-metric. Specifically, the one-error-correcting codes we construct are at least half the ball-packing upper bound