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Register a new userConcatenated Codes for Recovery From Multiple Reads of DNA Sequences
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Added by
Andreas Lenz
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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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 low-density parity-check code and either an inner convolutional code or a block code. We propose two new 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. 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.
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Multiple reads of the same Flash memory cell with distinct word-line voltages provide enhanced precision for LDPC decoding. In this paper, the word-line voltages are optimized by maximizing the mutual information (MI) of the quantized channel. The enhanced precision from a few additional reads allows FER performance to approach that of full-precision soft information and enables an LDPC code to significantly outperform a BCH code. A constant-ratio constraint provides a significant simplification in the optimization with no noticeable loss in performance. For a well-designed LDPC code, the quantization that maximizes the mutual information also minimizes the frame error rate in our simulations. However, for an example LDPC code with a high error floor caused by small absorbing sets, the MMI quantization does not provide the lowest frame error rate. The best quantization in this case introduces more erasures than would be optimal for the channel MI in order to mitigate the absorbing sets of the poorly designed code. The paper also identifies a trade-off in LDPC code design when decoding is performed with multiple precision levels; the best code at one level of precision will typically not be the best code at a different level of precision.
Two concatenated coding schemes incorporating algebraic Reed-Solomon (RS) codes and polarization-adjusted convolutional (PAC) codes are proposed. Simulation results show that at a bit error rate of $10^{-5}$, a concatenated scheme using RS and PAC codes has more than $0.25$ dB coding gain over the NASA standard concatenation scheme, which uses RS and convolutional codes.
A locally recoverable code is an error-correcting code such that any erasure in a single coordinate of a codeword can be recovered from a small subset of other coordinates. In this article we develop an algorithm that computes a recovery structure as concise posible for an arbitrary linear code $mathcal{C}$ and a recovery method that realizes it. This algorithm also provides the locality and the dual distance of $mathcal{C}$. Complexity issues are studied as well. Several examples are included.
Streaming codes are a class of packet-level erasure codes that are designed with the goal of ensuring recovery in low-latency fashion, of erased packets over a communication network. It is well-known in the streaming code literature, that diagonally embedding codewords of a $[tau+1,tau+1-a]$ Maximum Distance Separable (MDS) code within the packet stream, leads to rate-optimal streaming codes capable of recovering from $a$ arbitrary packet erasures, under a strict decoding delay constraint $tau$. Thus MDS codes are geared towards the efficient handling of the worst-case scenario corresponding to the occurrence of $a$ erasures. In the present paper, we have an increased focus on the efficient handling of the most-frequent erasure patterns. We study streaming codes which in addition to recovering from $a>1$ arbitrary packet erasures under a decoding delay $tau$, have the ability to handle the more common occurrence of a single-packet erasure, while incurring smaller delay $r<tau$. We term these codes as $(a,tau,r)$ locally recoverable streaming codes (LRSCs), since our single-erasure recovery requirement is similar to the requirement of locality in a coded distributed storage system. We characterize the maximum possible rate of an LRSC by presenting rate-optimal constructions for all possible parameters ${a,tau,r}$. Although the rate-optimal LRSC construction provided in this paper requires large field size, the construction is explicit. It is also shown that our $(a,tau=a(r+1)-1,r)$ LRSC construction provides the additional guarantee of recovery from the erasure of $h, 1 leq h leq a$, packets, with delay $h(r+1)-1$. The construction thus offers graceful degradation in decoding delay with increasing number of erasures.
In this paper, we present a new construction of asymmetric quantum codes (AQCs) by combining classical concatenated codes (CCs) with tensor product codes (TPCs), called asymmetric quantum concatenated and tensor product codes (AQCTPCs) which have the following three advantages. First, only the outer codes in AQCTPCs need to satisfy the orthogonal constraint in quantum codes, and any classical linear code can be used for the inner, which makes AQCTPCs very easy to construct. Second, most AQCTPCs are highly degenerate, which means they can correct many more errors than their classical TPC counterparts. Consequently, we construct several families of AQCs with better parameters than known results in the literature. Third, AQCTPCs can be efficiently decoded although they are degenerate, provided that the inner and outer codes are efficiently decodable. In particular, we significantly reduce the inner decoding complexity of TPCs from $Omega(n_2a^{n_1})(a>1)$ to $O(n_2)$ by considering error degeneracy, where $n_1$ and $n_2$ are the block length of the inner code and the outer code, respectively. Furthermore, we generalize our concatenation scheme by using the generalized CCs and TPCs correspondingly.
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