R&D: Finite Blocklength Performance Bound for DNA Storage Channel

arxiv.org has published an article written by Issam Maarouf, Simula UiB, N-5006 Bergen, Norway, Gianluigi Liva, nstitute of Communications and Navigation, German Aerospace Center, 82234 Weßling, Germany, Eirik Rosnes, Simula UiB, N-5006 Bergen, Norway, and Alexandre Graell i Amat, Department of Electrical Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.

Abstract: “We present a finite blocklength performance bound for a DNA storage channel with insertions, deletions, and substitutions. The considered bound — the dependency testing (DT) bound, introduced by Polyanskiy et al. in 2010 — provides an upper bound on the achievable frame error probability and can be used to benchmark coding schemes in the practical short-to-medium blocklength regime. In particular, we consider a concatenated coding scheme where an inner synchronization code deals with insertions and deletions and the outer code corrects remaining (mostly substitution) errors. The bound depends on the inner synchronization code. Thus, it allows to guide its choice. We then consider low-density parity-check codes for the outer code, which we optimize based on extrinsic information transfer charts. Our optimized coding schemes achieve a normalized rate of 88% to 96% with respect to the DT bound for code lengths up to 2000 DNA symbols for a frame error probability of 10⁻³ and code rate 1/2.“