Optimized code design for constrained DNA data storage with asymmetric errors

With ultra-high density and preservation longevity, deoxyribonucleic acid (DNA)-based data storage is becoming an emerging storage technology. Limited by the current biochemical techniques, data might be corrupted during the processes of DNA data storage. A hybrid coding architecture consisting of modified variable-length run-length limited (VL-RLL) codes and optimized protograph low-density parity-check (LDPC) codes is proposed in order to suppress error occurrence and correct asymmetric substitution errors. Based on the analyses of the different asymmetric DNA sequencer channel models, a series of the protograph LDPC codes are optimized using a modified extrinsic information transfer algorithm (EXIT). The simulation results show the better error performance of the proposed protograph LDPC codes over the conventional good codes and the codes used in the existing DNA data storage system. In addition, the theoretical analysis shows that the proposed hybrid coding scheme stores ~1.98 bits per nucleotide (bits/nt) with only 1% gap from the upper boundary (2 bits/nt)

Low-Density Parity-Check Coded High-order Modulation Schemes

In this thesis, we investigate how to support reliable data transmissions at high speeds in future communication systems, such as 5G/6G, WiFi, satellite, and optical communications. One of the most fundamental problems in these communication systems is how to reliably transmit information with a limited number of resources, such as power and spectral. To obtain high spectral efficiency, we use coded modulation (CM), such as bit-interleaved coded modulation (BICM) and delayed BICM (DBICM). To be specific, BICM is a pragmatic implementation of CM which has been largely adopted in both industry and academia. While BICM approaches CM capacity at high rates, the capacity gap between BICM and CM is still noticeable at lower code rates. To tackle this problem, DBICM, as a variation of BICM, introduces a delay module to create a dependency between multiple codewords, which enables us to exploit extrinsic information from the decoded delayed sub-blocks to improve the detection of the undelayed sub-blocks. Recent work shows that DBICM improves capacity over BICM. In addition, BICM and DBICM schemes protect each bit-channel differently, which is often referred to as the unequal error protection (UEP) property. Therefore, bit mapping designs are important for constructing pragmatic BICM and DBICM. To provide reliable communication, we have jointly designed bit mappings in DBICM and irregular low-density parity-check (LDPC) codes. For practical considerations, spatially coupled LDPC (SC-LDPC) codes have been considered as well. Specifically, we have investigated the joint design of the multi-chain SC-LDPC and the BICM bit mapper. In addition, the design of SC-LDPC codes with improved decoding threshold performance and reduced rate loss has been investigated in this thesis as well. The main body of this thesis consists of three parts. In the first part, considering Gray-labeled square M-ary quadrature amplitude modulation (QAM) constellations, we investigate the optimal delay scheme with the largest spectrum efficiency of DBICM for a fixed maximum number of delayed time slots and a given signal-to-noise ratio. Furthermore, we jointly optimize degree distributions and channel assignments of LDPC codes using protograph-based extrinsic information transfer charts. In addition, we proposed a constrained progressive edge growth-like algorithm to jointly construct LDPC codes and bit mappings for DBICM, taking the capacity of each bit-channel into account. Simulation results demonstrate that the designed LDPC-coded DBICM systems significantly outperform LDPC-coded BICM systems. In the second part, we proposed a windowed decoding algorithm for DBICM, which uses the extrinsic information of both the decoded delayed and undelayed sub-blocks, to improve the detection for all sub-blocks. We show that the proposed windowed decoding significantly outperforms the original decoding, demonstrating the effectiveness of the proposed decoding algorithm. In the third part, we apply multi-chain SC-LDPC to BICM. We investigate various connections for multi-chain SC-LDPC codes and bit mapping designs and analyze the performance of the multi-chain SC-LDPC codes over the equivalent binary erasure channels via density evolution. Numerical results demonstrate the superiority of the proposed design over existing connected-chain ensembles and over single-chain ensembles with the existing bit mapping design

A STUDY OF LINEAR ERROR CORRECTING CODES

Since Shannon's ground-breaking work in 1948, there have been two main development streams of channel coding in approaching the limit of communication channels, namely classical coding theory which aims at designing codes with large minimum Hamming distance and probabilistic coding which places the emphasis on low complexity probabilistic decoding using long codes built from simple constituent codes. This work presents some further investigations in these two channel coding development streams. Low-density parity-check (LDPC) codes form a class of capacity-approaching codes with sparse parity-check matrix and low-complexity decoder Two novel methods of constructing algebraic binary LDPC codes are presented. These methods are based on the theory of cyclotomic cosets, idempotents and Mattson-Solomon polynomials, and are complementary to each other. The two methods generate in addition to some new cyclic iteratively decodable codes, the well-known Euclidean and projective geometry codes. Their extension to non binary fields is shown to be straightforward. These algebraic cyclic LDPC codes, for short block lengths, converge considerably well under iterative decoding. It is also shown that for some of these codes, maximum likelihood performance may be achieved by a modified belief propagation decoder which uses a different subset of 7^ codewords of the dual code for each iteration. Following a property of the revolving-door combination generator, multi-threaded minimum Hamming distance computation algorithms are developed. Using these algorithms, the previously unknown, minimum Hamming distance of the quadratic residue code for prime 199 has been evaluated. In addition, the highest minimum Hamming distance attainable by all binary cyclic codes of odd lengths from 129 to 189 has been determined, and as many as 901 new binary linear codes which have higher minimum Hamming distance than the previously considered best known linear code have been found. It is shown that by exploiting the structure of circulant matrices, the number of codewords required, to compute the minimum Hamming distance and the number of codewords of a given Hamming weight of binary double-circulant codes based on primes, may be reduced. A means of independently verifying the exhaustively computed number of codewords of a given Hamming weight of these double-circulant codes is developed and in coiyunction with this, it is proved that some published results are incorrect and the correct weight spectra are presented. Moreover, it is shown that it is possible to estimate the minimum Hamming distance of this family of prime-based double-circulant codes. It is shown that linear codes may be efficiently decoded using the incremental correlation Dorsch algorithm. By extending this algorithm, a list decoder is derived and a novel, CRC-less error detection mechanism that offers much better throughput and performance than the conventional ORG scheme is described. Using the same method it is shown that the performance of conventional CRC scheme may be considerably enhanced. Error detection is an integral part of an incremental redundancy communications system and it is shown that sequences of good error correction codes, suitable for use in incremental redundancy communications systems may be obtained using the Constructions X and XX. Examples are given and their performances presented in comparison to conventional CRC schemes