Concatenated Codes for Multiple Reads of a DNA Sequence

• Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a concatenated coding scheme with an outer nonbinary low-density parity-check code or a polar code and either an inner convolutional code or a time-varying block code. We propose two novel decoding algorithms for inference from multiple received sequences, both combining the inner code and channel to a joint hidden Markov model to infer symbolwise a posteriori probabilities (APPs). The first decoder computes the exact APPs by jointly decoding the received sequences, whereas the second decoder approximates the APPs by combining the results of separately decoded received sequences and has a complexity that is linear with the number of sequences. Using the proposed algorithms, we evaluate the performance of decoding multiple received sequences by means of achievable information rates and Monte-Carlo simulations. We show significant performance gains compared to a single received sequence. In addition, we succeed in improving the performance of the aforementioned coding scheme by optimizing both the inner and outer codes.

Ämnesord

TEKNIK OCH TEKNOLOGIER  -- Elektroteknik och elektronik -- Telekommunikation (hsv//swe)

ENGINEERING AND TECHNOLOGY  -- Electrical Engineering, Electronic Engineering, Information Engineering -- Telecommunications (hsv//eng)

TEKNIK OCH TEKNOLOGIER  -- Elektroteknik och elektronik -- Kommunikationssystem (hsv//swe)

ENGINEERING AND TECHNOLOGY  -- Electrical Engineering, Electronic Engineering, Information Engineering -- Communication Systems (hsv//eng)

TEKNIK OCH TEKNOLOGIER  -- Elektroteknik och elektronik -- Signalbehandling (hsv//swe)

ENGINEERING AND TECHNOLOGY  -- Electrical Engineering, Electronic Engineering, Information Engineering -- Signal Processing (hsv//eng)

Nyckelord

concatenated codes

DNA storage

polar code

low-density parity-check (LDPC) code

Achievable information rates

synchronization codes

insertion/deletion/substitution (IDS) channel

Publikations- och innehållstyp

art (ämneskategori)

ref (ämneskategori)