2,190 research outputs found
Achievable Information Rates and Concatenated Codes for the DNA Nanopore Sequencing Channel
The errors occurring in DNA-based storage are correlated in nature, which is
a direct consequence of the synthesis and sequencing processes. In this paper,
we consider the memory- nanopore channel model recently introduced by Hamoum
et al., which models the inherent memory of the channel. We derive the maximum
a posteriori (MAP) decoder for this channel model. The derived MAP decoder
allows us to compute achievable information rates for the true DNA storage
channel assuming a mismatched decoder matched to the memory- nanopore
channel model, and quantify the loss in performance assuming a small memory
length--and hence limited decoding complexity. Furthermore, the derived MAP
decoder can be used to design error-correcting codes tailored to the DNA
storage channel. We show that a concatenated coding scheme with an outer
low-density parity-check code and an inner convolutional code yields excellent
performance.Comment: This paper has been accepted and awaiting publication in informatio
theory workshop (ITW) 202
Simplification Resilient LDPC-Coded Sparse-QIM Watermarking for 3D-Meshes
We propose a blind watermarking scheme for 3-D meshes which combines sparse
quantization index modulation (QIM) with deletion correction codes. The QIM
operates on the vertices in rough concave regions of the surface thus ensuring
impeccability, while the deletion correction code recovers the data hidden in
the vertices which is removed by mesh optimization and/or simplification. The
proposed scheme offers two orders of magnitude better performance in terms of
recovered watermark bit error rate compared to the existing schemes of similar
payloads and fidelity constraints.Comment: Submitted, revised and Copyright transfered to IEEE Transactions on
Multimedia, October 9th 201
A Tutorial on Coding Methods for DNA-based Molecular Communications and Storage
Exponential increase of data has motivated advances of data storage
technologies. As a promising storage media, DeoxyriboNucleic Acid (DNA) storage
provides a much higher data density and superior durability, compared with
state-of-the-art media. In this paper, we provide a tutorial on DNA storage and
its role in molecular communications. Firstly, we introduce fundamentals of
DNA-based molecular communications and storage (MCS), discussing the basic
process of performing DNA storage in MCS. Furthermore, we provide tutorials on
how conventional coding schemes that are used in wireless communications can be
applied to DNA-based MCS, along with numerical results. Finally, promising
research directions on DNA-based data storage in molecular communications are
introduced and discussed in this paper
Beyond Single-Deletion Correcting Codes: Substitutions and Transpositions
We consider the problem of designing low-redundancy codes in settings where one must correct deletions in conjunction with substitutions or adjacent transpositions; a combination of errors that is usually observed in DNA-based data storage. One of the most basic versions of this problem was settled more than 50 years ago by Levenshtein, who proved that binary Varshamov-Tenengolts codes correct one arbitrary edit error, i.e., one deletion or one substitution, with nearly optimal redundancy. However, this approach fails to extend to many simple and natural variations of the binary single-edit error setting. In this work, we make progress on the code design problem above in three such variations:
- We construct linear-time encodable and decodable length-n non-binary codes correcting a single edit error with nearly optimal redundancy log n+O(log log n), providing an alternative simpler proof of a result by Cai, Chee, Gabrys, Kiah, and Nguyen (IEEE Trans. Inf. Theory 2021). This is achieved by employing what we call weighted VT sketches, a new notion that may be of independent interest.
- We show the existence of a binary code correcting one deletion or one adjacent transposition with nearly optimal redundancy log n+O(log log n).
- We construct linear-time encodable and list-decodable binary codes with list-size 2 for one deletion and one substitution with redundancy 4log n+O(log log n). This matches the existential bound up to an O(log log n) additive term
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