arXiv subjects

Tuan Thanh Nguyen

Publications and source records attributed to Tuan Thanh Nguyen.

16 recordsLinked to original sources

arXiv2025

From One-Dimensional Codes to Two-Dimensional Codes: A Universal Framework for the Bounded-Weight Constraint

Recent developments in storage -- especially in the area of resistive random access memory (ReRAM) -- are attempting to scale the storage density by regarding the information data as two-dimensional (2D), instead of one-dimensional (1D). Correspondingly, new types of 2D constraints are introduced into the input information data to improve the system reliability. While 1D constraints have been extensively investigated in the literature, the study for 2D constraints is much less profound. Particularly, given a constraint $\mathcal{F}$ and a design of 1D codes whose codewords satisfy $\mathcal{F}$, the problem of constructing efficient 2D codes, such that every row and every column in every codeword satisfy $\mathcal{F}$, has been a challenge. This work provides an efficient solution to the challenging coding problem above for the binary bounded-weight constrained codes that restrict the maximum number of $1$'s (called {\em weight}). Formally, we propose a universal framework to design 2D codes that guarantee the weight of every row and every column of length $n$ to be at most $f(n)$ for any given function $f(n)$. We show that if there exists a design of capacity-approaching 1D codes, then our method also provides capacity-approaching 2D codes for all $f=ω(\log n)$.

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arXiv2025

Constrained Coding for Composite DNA: Channel Capacity and Efficient Constructions

Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture of the four nucleotides in a predetermined ratio. By using different mixtures and ratios, the alphabet can be extended to have much more than four symbols in the naive approach. While this method enables higher data content per synthesis cycle, potentially reducing the DNA synthesis cost, it also imposes significant challenges for accurate DNA sequencing since the base-level errors can easily change the mixture of bases and their ratio, resulting in changes to the composite symbols. With this motivation, we propose efficient constrained coding techniques to enforce the biological constraints, including the runlength-limited constraint and the GC-content constraint, into every DNA synthesized oligo, regardless of the mixture of bases in each composite letter and their corresponding ratio. Our goals include computing the capacity of the constrained channel, constructing efficient encoders/decoders, and providing the best options for the composite letters to obtain capacity-approaching codes. For certain codes' parameters, our methods incur only one redundant symbol.

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arXiv2024

High Information Density and Low Coverage Data Storage in DNA with Efficient Channel Coding Schemes

DNA-based data storage has been attracting significant attention due to its extremely high data storage density, low power consumption, and long duration compared to conventional data storage media. Despite the recent advancements in DNA data storage technology, significant challenges remain. In particular, various types of errors can occur during the processes of DNA synthesis, storage, and sequencing, including substitution errors, insertion errors, and deletion errors. Furthermore, the entire oligo may be lost. In this work, we report a DNA-based data storage architecture that incorporates efficient channel coding schemes, including different types of error-correcting codes (ECCs) and constrained codes, for both the inner coding and outer coding for the DNA data storage channel. We also carried out large scale experiments to validate our proposed DNA-based data storage architecture. Specifically, 1.61 and 1.69 MB data were encoded into 30,000 oligos each, with information densities of 1.731 and 1.815, respectively. It has been found that the stored information can be fully recovered without any error at average coverages of 4.5 and 6.0, respectively. This experiment achieved the highest net information density and lowest coverage among existing DNA-based data storage experiments (with standard DNA), with data recovery rates and coverage approaching theoretical optima.

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arXiv2023

A New Version of q-ary Varshamov-Tenengolts Codes with More Efficient Encoders: The Differential VT Codes and The Differential Shifted VT Codes

The problem of correcting deletions and insertions has recently received significantly increased attention due to the DNA-based data storage technology, which suffers from deletions and insertions with extremely high probability. In this work, we study the problem of constructing non-binary burst-deletion/insertion correcting codes. Particularly, for the quaternary alphabet, our designed codes are suited for correcting a burst of deletions/insertions in DNA storage. Non-binary codes correcting a single deletion or insertion were introduced by Tenengolts [1984], and the results were extended to correct a fixed-length burst of deletions or insertions by Schoeny et al. [2017]. Recently, Wang et al. [2021] proposed constructions of non-binary codes of length n, correcting a burst of length at most two for q-ary alphabets with redundancy log n+O(log q log log n) bits, for arbitrary even q. The common idea in those constructions is to convert non-binary sequences into binary sequences, and the error decoding algorithms for the q-ary sequences are mainly based on the success of recovering the corresponding binary sequences, respectively. In this work, we look at a natural solution in which the error detection and correction algorithms are performed directly over q-ary sequences, and for certain cases, our codes provide a more efficient encoder with lower redundancy than the best-known encoder in the literature.

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arXiv2023

DiffSpectralNet : Unveiling the Potential of Diffusion Models for Hyperspectral Image Classification

Hyperspectral images (HSI) have become popular for analysing remotely sensed images in multiple domain like agriculture, medical. However, existing models struggle with complex relationships and characteristics of spectral-spatial data due to the multi-band nature and data redundancy of hyperspectral data. To address this limitation, we propose a new network called DiffSpectralNet, which combines diffusion and transformer techniques. Our approach involves a two-step process. First, we use an unsupervised learning framework based on the diffusion model to extract both high-level and low-level spectral-spatial features. The diffusion method is capable of extracting diverse and meaningful spectral-spatial features, leading to improvement in HSI classification. Then, we employ a pretrained denoising U-Net to extract intermediate hierarchical features for classification. Finally, we use a supervised transformer-based classifier to perform the HSI classification. Through comprehensive experiments on HSI datasets, we evaluate the classification performance of DiffSpectralNet. The results demonstrate that our framework significantly outperforms existing approaches, achieving state-of-the-art performance.

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arXiv2023

Average Redundancy of Variable-Length Balancing Schemes à la Knuth

We study and propose schemes that map messages onto constant-weight codewords using variable-length prefixes. We provide polynomial-time computable formulas that estimate the average number of redundant bits incurred by our schemes. In addition to the exact formulas, we also perform an asymptotic analysis and demonstrate that our scheme uses $\frac12 \log n+O(1)$ redundant bits to encode messages into length-$n$ words with weight $(n/2)+{\sf q}$ for constant ${\sf q}$. We also propose schemes that map messages into balanced codebooks with error-correcting capabilities. For such schemes, we provide methods to enumerate the average number of redundant bits.

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arXiv2023

On the Design of Codes for DNA Computing: Secondary Structure Avoidance Codes

In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short, secondary structure refers to the tendency of a single-stranded DNA sequence to fold back upon itself, thus becoming inactive in the computation process. While some design criteria that reduces the possibility of secondary structure formation has been proposed by Milenkovic and Kashyap (2006), the main contribution of this work is to provide an explicit construction of DNA codes that completely avoid secondary structure of arbitrary stem length. Formally, given codeword length n and arbitrary integer m>=2, we provide efficient methods to construct DNA codes of length n that avoid secondary structure of any stem length more than or equal to m. Particularly, when m = 3, our constructions yield a family of DNA codes of rate 1.3031 bits/nt, while the highest rate found in the prior art was 1.1609 bits/nt. In addition, for m>=3log n + 4, we provide an efficient encoder that incurs only one redundant symbol.

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arXiv2022

Every Bit Counts: A New Version of Non-binary VT Codes with More Efficient Encoder

In this work, we present a new version of non-binary VT codes that are capable of correcting a single deletion or single insertion. Moreover, we provide the first known linear time algorithms that encode user messages into these codes of length n over the $q$-ary alphabet for $q\ge 2$ with at most $\ceil{\log_q n} + 1$ redundant symbols, while the optimal redundancy required is at least $\log_q n + \log_q (q - 1)$ symbols. Our designed encoder reduces the redundancy of the best-known encoder of Tenengolts (1984) by at least $2+\log_q(3)$ redundant symbols, or equivalently $2\log_2 q+3$ redundant bits.

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arXiv2022

Two dimensional RC/Subarray Constrained Codes: Bounded Weight and Almost Balanced Weight

In this work, we study two types of constraints on two-dimensional binary arrays. In particular, given $p,ε>0$, we study (i) The $p$-bounded constraint: a binary vector of size $m$ is said to be $p$-bounded if its weight is at most $pm$, and (ii) The $ε$-balanced constraint: a binary vector of size $m$ is said to be $ε$-balanced if its weight is within $[(0.5-ε)*m,(0.5+ε)*m]$. Such constraints are crucial in several data storage systems, those regard the information data as two-dimensional (2D) instead of one-dimensional (1D), such as the crossbar resistive memory arrays and the holographic data storage. In this work, efficient encoding/decoding algorithms are presented for binary arrays so that the weight constraint (either $p$-bounded constraint or $ε$-balanced constraint) is enforced over every row and every column, regarded as 2D row-column (RC) constrained codes; or over every subarray, regarded as 2D subarray constrained codes. While low-complexity designs have been proposed in the literature, mostly focusing on 2D RC constrained codes where $p = 1/2$ and $ε= 0$, this work provides efficient coding methods that work for both 2D RC constrained codes and 2D subarray constrained codes, and more importantly, the methods are applicable for arbitrary values of $p$ and $ε$. Furthermore, for certain values of $p$ and $ε$, we show that, for sufficiently large array size, there exists linear-time encoding/decoding algorithm that incurs at most one redundant bit.

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arXiv2022

List-decodable Codes for Single-deletion Single-substitution with List-size Two

In this paper, we present an explicit construction of list-decodable codes for single-deletion and single-substitution with list size two and redundancy 3log n+4, where n is the block length of the code. Our construction has lower redundancy than the best known explicit construction by Gabrys et al. (arXiv 2021), whose redundancy is 4log n+O(1).

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arXiv2020

Efficient Design of Subblock Energy-Constrained Codes and Sliding Window-Constrained Codes

The subblock energy-constrained codes (SECCs) and sliding window-constrained codes (SWCCs) have recently attracted attention due to various applications in communcation systems such as simultaneous energy and information transfer. In a SECC, each codewod is divided into smaller non-overlapping windows, called subblocks, and every subblock is constrained to carry sufficient energy. In a SWCC, the energy constraint is enforced over every window. In this work, we focus on the binary channel, where sufficient energy is achieved theoretically by using relatively high weight codes, and study SECCs and SWCCs under more general constraints, namely bounded SECCs and bounded SWCCs. We propose two methods to construct such codes with low redundancy and linear-time complexity, based on Knuth's balancing technique and sequence replacement technique. For certain codes parameters, our methods incur only one redundant bit. We also impose the minimum distance constraint for error correction capability of the designed codes, which helps to reduce the error propagation during decoding as well.

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arXiv2020

Coding for Sequence Reconstruction for Single Edits

The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication scenario where the sender transmits a codeword from some codebook and the receiver obtains multiple noisy reads of the codeword. The common setup assumes the codebook to be the entire space and the problem is to determine the minimum number of distinct reads that is required to reconstruct the transmitted codeword. Motivated by modern storage devices, we study a variant of the problem where the number of noisy reads $N$ is fixed. Specifically, we design reconstruction codes that reconstruct a codeword from $N$ distinct noisy reads. We focus on channels that introduce single edit error (i.e. a single substitution, insertion, or deletion) and their variants, and design reconstruction codes for all values of $N$. In particular, for the case of a single edit, we show that as the number of noisy reads increases, the number of redundant bits required can be gracefully reduced from $\log n+O(1)$ to $\log \log n+O(1)$, and then to $O(1)$, where $n$ denotes the length of a codeword. We also show that the redundancy of certain reconstruction codes is within one bit of optimality.

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arXiv2020

Capacity-Approaching Constrained Codes with Error Correction for DNA-Based Data Storage

We propose coding techniques that 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 $\ell, ε > 0$, 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 the following properties: (i) Runlength constraint: the maximum homopolymer run in each codeword is at most $\ell$, (ii) GC-content constraint: the GC-content of each codeword is within $[0.5-ε, 0.5+ε]$, (iii) Error-correction: each codeword is capable of correcting a single deletion, or single insertion, or single substitution error. For practical values of $\ell$ and $ε$, we show that our encoders achieve much higher rates than existing results in the literature and approach the capacity. Our methods have low encoding/decoding complexity and limited error propagation.

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arXiv2019

Optimal Codes Correcting a Single Indel / Edit for DNA-Based Data Storage

An indel refers to a single insertion or deletion, while an edit refers to a single insertion, deletion or substitution. In this paper, we investigate codes that combat either a single indel or a single edit and provide linear-time algorithms that encode binary messages into these codes of length n. Over the quaternary alphabet, we provide two linear-time encoders. One corrects a single edit with log n + O(log log n) redundancy bits, while the other corrects a single indel with log n + 2 redundant bits. These two encoders are order-optimal. The former encoder is the first known order-optimal encoder that corrects a single edit, while the latter encoder (that corrects a single indel) reduces the redundancy of the best known encoder of Tenengolts (1984) by at least four bits. Over the DNA alphabet, we impose an additional constraint: the GC-balanced constraint and require that exactly half of the symbols of any DNA codeword to be either C or G. In particular, via a modification of Knuth's balancing technique, we provide a linear-time map that translates binary messages into GC-balanced codewords and the resulting codebook is able to correct a single indel or a single edit. These are the first known constructions of GC-balanced codes that correct a single indel or a single edit.

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arXiv2018

Efficient Encoding/Decoding of Irreducible Words for Codes Correcting Tandem Duplications

Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem duplications. Known code constructions are based on {\em irreducible words}. We study efficient encoding/decoding methods for irreducible words. First, we describe an $(\ell,m)$-finite state encoder and show that when $m=Θ(1/ε)$ and $\ell=Θ(1/ε)$, the encoder achieves rate that is $ε$ away from the optimal. Next, we provide ranking/unranking algorithms for irreducible words and modify the algorithms to reduce the space requirements for the finite state encoder.

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arXiv2017

Deciding the Confusability of Words under Tandem Repeats

Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that correct tandem duplications to improve the reliability of data storage. We investigate algorithms associated with the study of these codes. Two words are said to be ${\le}k$-confusable if there exists two sequences of tandem duplications of lengths at most $k$ such that the resulting words are equal. We demonstrate that the problem of deciding whether two words is ${\le}k$-confusable is linear-time solvable through a characterisation that can be checked efficiently for $k=3$. Combining with previous results, the decision problem is linear-time solvable for $k\le 3$. We conjecture that this problem is undecidable for $k>3$. Using insights gained from the algorithm, we study the size of tandem-duplication codes. We improve the previous known upper bound and then construct codes with larger sizes as compared to the previous constructions. We determine the sizes of optimal tandem-duplication codes for lengths up to twenty, develop recursive methods to construct tandem-duplication codes for all word lengths, and compute explicit lower bounds for the size of optimal tandem-duplication codes for lengths from 21 to 30.

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