Reconstruction and Error-Correction Codes for Polymer-Based Data Storage

Abstract

Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for unique string reconstruction and correction of one mass error. Our approach is based on introducing redundancy that scales logarithmically with the length of the string and allows for the string to be uniquely reconstructed based only on its erroneous substring composition multiset. The key idea behind our unique reconstruction approach is to interleave Catalan-type paths with arbitrary binary strings and "reflect" them so as to allow prefixes and suffixes of the same length to have different weights. For error correction, we add a constant number of bits that provides information about the weights of reflected pairs of bits and hence enable recovery from a single mass error. The asymptotic code rate of the scheme is one, and decoding is accomplished via a simplified version of the backtracking algorithm used for the Turnpike problem.

Insertion and Deletion Correction in Polymer-based Data Storage

“…(2) The number of redundant bits can thus be upper-bounded in terms of n as 1/2 log(n) + 5 [11]. Alternatively, we obtain the following statement from [12].…”

“…For values of n where it is not possible to achieve the aforementioned bound, it is necessary to formulate a code, as done in [11], [12].…”

“…The first major coding-theoretic problem concerning polymer-based storage involved designing constraints in order to guarantee unique reconstruction for codewords of a fixed length, i.e., to formulate a composition-reconstructable code. To this end, [12] introduced the following compositionreconstructable code for even codeword lengths.…”

“…Construction 2 [11], [12]: A single (asymmetric or symmetric) composition code for odd values of n is stated below.…”

“…Since the errors introduced during an MS/MS readout are often context-dependent, we devote this work to the generalization of the error model considered in [11], [12]. Specifically, we investigate the impact of inserting and deleting one or more compositions on the reconstructability of the encoded strings.…”