Han Mao Kiah

DNA-Based Storage: Trends and Methods

We provide an overview of current approaches to DNA-based storage system design and of accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random access DNA storage channels. The analytic contribution of our work is the construction and design of sequences over discrete alphabets that avoid pre-specified address patterns, have balanced base content, and exhibit other relevant substring constraints. These schemes adapt the stored signals to the DNA medium and thereby reduce the inherent error-rate of the system.

Cross-Bifix-Free Codes Within a Constant Factor of Optimality

A cross-bifix-free code is a set of words in which no prefix of any length of any word is the suffix of any word in the set. Cross-bifix-free codes arise in the study of distributed sequences for frame synchronization. We provide a new construction of cross-bifix-free codes which generalizes the construction by Bajic to longer code lengths and to any alphabet size. The codes are shown to be nearly optimal in size. We also establish new results on Fibonacci sequences, which are used in estimating the size of the cross-bifix-free codes.

PURE ASYMMETRIC QUANTUM MDS CODES FROM CSS CONSTRUCTION: A COMPLETE CHARACTERIZATION

Using the Calderbank–Shor–Steane (CSS) construction, pure q-ary asymmetric quantum error-correcting codes attaining the quantum Singleton bound are constructed. Such codes are called pure CSS asymmetric quantum maximum distance separable (AQMDS) codes. Assuming the validity of the classical maximum distance separable (MDS) Conjecture, pure CSS AQMDS codes of all possible parameters are accounted for.

Maximum Distance Separable Codes for Symbol-Pair Read Channels

We study (symbol-pair) codes for symbol-pair read channels introduced recently by Cassuto and Blaum (2010). A Singleton-type bound on symbol-pair codes is established and infinite families of optimal symbol-pair codes are constructed. These codes are maximum distance separable (MDS) in the sense that they meet the Singleton-type bound. In contrast to classical codes, where all known q-ary MDS codes have length O(q), we show that q-ary MDS symbol-pair codes can have length Ω(q2). In addition, we completely determine the existence of MDS symbol-pair codes for certain parameters.

Multiply Constant-Weight Codes and the Reliability of Loop Physically Unclonable Functions

We introduce the class of multiply constant-weight codes to improve the reliability of certain physically unclonable function response, and extend classical coding methods to construct multiply constant-weight codes from known \(q\) -ary and constant-weight codes. We derive analogs of Johnson bounds and give constructions showing these bounds to be asymptotically tight up to a constant factor under certain conditions. We also examine the rates of multiply constant-weight codes and demonstrate that these rates are the same as those of constant-weight codes of corresponding parameters.

Optimal binary switch codes with small query size

In this paper, we study a construction of binary switch codes. A switch code is a code such that a multi-set request of information symbols can be simultaneously recovered from disjoint sets of codeword symbols. Our construction is optimal in the sense that it has the smallest codeword length given its average encoding degree, which is logarithmic in the code dimension. Moreover, the number of queries needed to recover any information symbol in the request is at most 2. As a result, our construction is the first family of switch codes with low encoding and decoding complexity.

Maximum distance separable symbol-pair codes

We study (symbol-pair) codes for symbol-pair read channels introduced recently by Cassuto and Blaum (2010). A Singleton-type bound on symbol-pair codes is established and infinite families of optimal symbol-pair codes are constructed. These codes are maximum distance separable (MDS) in the sense that they meet the Singleton-type bound. In contrast to classical codes, where all known q-ary MDS codes have length O(q), we show that q-ary MDS symbol-pair codes can have length Ω(q2). We also construct equidistant cyclic MDS symbol-pair codes from Mendelsohn designs.

Importance of symbol equity in coded modulation for power line communications

The use of multiple frequency shift keying modulation with permutation codes addresses the problem of permanent narrowband noise disturbance in a power line communications system. In this paper, we extend this coded modulation scheme based on permutation codes to general codes and introduce an additional new parameter that more precisely captures a codes performance against permanent narrowband noise. As a result, we define a new class of codes, namely, equitable symbol weight codes, which are optimal with respect to this measure.

Synchronizing edits in distributed storage networks

We consider the problem of synchronizing data in distributed storage networks under edits that include deletions and insertions. We present modifications of codes on distributed storage systems that allow updates in the parity-check values to be performed with one round of communication at low bit rates and a small storage overhead. Our main contributions are novel protocols for synchronizing both frequently updated and semi-static data, and protocols for data deduplication applications, based on intermediary coding using permutation and Vandermonde matrices.

Codes for DNA sequence profiles

We consider the problem of storing and retrieving information from synthetic DNA media. We introduce the DNA storage channel and model the read process through the use of profile vectors. We provide an asymptotic analysis of the number of profile vectors and propose new asymmetric coding techniques to combat the effects of synthesis and sequencing noise. Furthermore, we construct two families of codes for this new channel model.