Kees Schouhamer Immink

Dr. Kees Schouhamer Immink

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Academic Career Length

26Years (2001-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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17 March 2021 in IEEE Transactions on Information Theory
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Tuan Thanh NguyenTuan Thanh Nguyen
Tuan Thanh Nguyen
KCKui Cai
Kui Cai
KIKees Schouhamer Immink
Kees Schouhamer Immink
HKHan Mao Kiah
Han Mao Kiah
We propose coding techniques that simultaneously limit the length of homopolymers runs, ensure the GC-content constraint, and are capable of correcting a single edit error in strands of nucleotides in DNA-based data storage systems. In particular, for given l , ∈ > 0, we propose simple and efficient encoders/decoders that transform binary sequences into DNA base sequences (codewords), namely sequences of the symbols A, T, C and G, that satisfy all of the following properties: 1) runlength constraint: the maximum homopolymer run in each codeword is at most l ; 2) GC-content constraint: the GC-content of each codeword is within [0.5-∈,0.5+∈]; 3) error-correction: each codeword is capable of correcting a single deletion, or single insertion, or single substitution error. While various combinations of these properties have been considered in the literature, this work provides generalizations of codes constructions that satisfy all the properties with arbitrary parameters of l and ∈. Furthermore, for practical values of l and ∈, we show that our encoders achieve higher rates than existing results in the literature and approach capacity. Our methods have low encoding/decoding complexity and limited error propagation.
20 November 2017 in IEEE Communications Letters
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Journal Article
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KIKees Schouhamer Immink
Kees Schouhamer Immink
KCKui Cai
Kui Cai
We consider coding techniques that limit the lengths of homopolymer runs in strands of nucleotides used in DNAbased mass data storage systems. We compute the maximum number of user bits that can be stored per nucleotide when a maximum homopolymer runlength constraint is imposed. We describe simple and efficient implementations of coding techniques that avoid the occurrence of long homopolymers, and the rates of the constructed codes are close to the theoretical maximum. The proposed sequence replacement method for k- constrained q-ary data yields a significant improvement in coding redundancy than the prior art sequence replacement method for the k-constrained binary data. Using a simple transformation, standard binary maximum runlength limited sequences can be transformed into maximum runlength limited q-ary sequences, which opens the door to applying the vast prior art binary code constructions to DNA-based storage.
11 March 2020 in IEEE Access
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KIKees Schouhamer Immink
Kees Schouhamer Immink
KCKui Cai
Kui Cai
We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. Generating functions and approximations are presented for computing the number of sequences with maximum repetition length and AT/GC balance constraint. We describe routines for translating binary runlength limited and/or balanced strings into DNA strands, and compute the efficiency of such routines. Expressions for the redundancy of codes that account for both the maximum repetition length and AT/GC balance are derived.
30 July 2014 in IEEE Transactions on Information Theory
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KIKees Schouhamer Immink
Kees Schouhamer Immink
JWJos H. Weber
Jos H. Weber
The performance of certain transmission and storage channels, such as optical data storage and nonvolatile memory (flash), is seriously hampered by the phenomena of unknown offset (drift) or gain. We will show that minimum Pearson distance (MPD) detection, unlike conventional minimum Euclidean distance detection, is immune to offset and/or gain mismatch. MPD detection is used in conjunction with T-constrained codes that consist of q-ary codewords, where in each codeword T reference symbols appear at least once. We will analyze the redundancy of the new q-ary coding technique and compute the error performance of MPD detection in the presence of additive noise. Implementation issues of MPD detection will be discussed, and results of simulations will be given.
15 June 2020 in IEEE Transactions on Information Theory
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WSWentu Song
Wentu Song
KCKui Cai
Kui Cai
KIKees Schouhamer Immink
Kees Schouhamer Immink
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes for DNA storage channel, a new metric, termed the sequence-subset distance, is introduced, which generalizes the Hamming distance to a distance function defined between any two sets of unordered vectors and helps to establish a uniform framework to design error correcting codes for DNA storage channel. We further introduce a family of error correcting codes, referred to as sequence-subset codes, for DNA storage and show that the error-correcting ability of such codes is completely determined by their minimum distance. We derive some upper bounds on the size of the sequence-subset codes including a tight bound for a special case, a Singleton-like bound and a Plotkinlike bound. We also propose some constructions, including an optimal construction for that special case, which imply lower bounds on the size of such codes.
25 July 2019 in IEEE Communications Letters
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Journal Article
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KIKees Schouhamer Immink
Kees Schouhamer Immink
KCKui Cai
Kui Cai
We analyze codes for DNA-based data storage which accounts for the maximum homopolymer repetition length and GC-AT balance. We present a new precoding method for translating words with a maximum run of k zeros into words with a maximum homopolymer run m = k + 1, which is atractive for securing GC-AT balance. Generating functions are presented for enumerating the number of n-symbol k-constrained codewords of given GC-AT balance Various efficient constructions are presented of block codes that satisfy a combined balance and maximum homopolymer run.