Related papers: Improved Lower Bounds for Constant GC-Content DNA …
DNA, with remarkable properties of high density, durability, and replicability, is one of the most appealing storage media. Emerging DNA storage technologies use composite DNA letters, where information is represented by probability…
The family of codeword stabilized codes encompasses the stabilizer codes as well as many of the best known nonadditive codes. However, constructing optimal $n$-qubit codeword stabilized codes is made difficult by two main factors. The first…
This research paper presents a novel approach to enhance optimization performance through the hybridization of Gaussian Crunching Search (GCS) and Powell's Method for derivative-free optimization. While GCS has shown promise in overcoming…
We study the amount of reliable information that can be stored in a DNA-based storage system with noisy sequencing, where each codeword is composed of short DNA molecules. We analyze a concatenated coding scheme, where the outer code is…
A constant weight binary code consists of $n$-bit binary codewords, each with exactly $w$ bits equal to 1, such that any two codewords are at least Hamming distance $d$ apart. $A(n,d,w)$ is the maximum size of a constant weight binary code…
Future beyond-5G and 6G systems demand ultra-reliable, low-latency communication with short blocklengths, motivating the development of universal decoding algorithms. Guessing decoding, which infers the noise or codeword candidate in order…
As a medium for cold data storage, DNA stands out as it promises significant gains in storage capacity and lifetime. However, it comes with its own data processing challenges to overcome. Constrained codes over the DNA alphabet…
Constrained codes are used to prevent errors from occurring in various data storage and data transmission systems. They can help in increasing the storage density of magnetic storage devices, in managing the lifetime of electronic storage…
Oligo pools are array-synthesized, user-defined mixtures of single-stranded oligonucleotides that can be used as a source of synthetic DNA for library cloning. While currently offering the most affordable source of synthetic DNA, oligo…
The huge amount of data acquired by high-throughput sequencing requires data reduction for effective analysis. Here we give a clustering algorithm for genome-wide open chromatin data using a new data reduction method. This method regards…
We present new upper and lower bounds on the minimum distance of certain generalized bicycle (GB) codes beyond the reach of techniques for classical codes capable of even capturing the true minimum distance for some cases. These bounds are…
Protein variant libraries produced by site-directed mutagenesis are a useful tool utilized by protein engineers to explore variants with potentially improved properties, such as activity and stability. These libraries are commonly built by…
In this paper, we propose a novel iterative encoding algorithm for DNA storage to satisfy both the GC balance and run-length constraints using a greedy algorithm. DNA strands with run-length more than three and the GC balance ratio far from…
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…
We introduce a framework for proving lower bounds on computational problems over distributions against algorithms that can be implemented using access to a statistical query oracle. For such algorithms, access to the input distribution is…
DNA is an attractive medium for digital data storage. When data is stored on DNA, errors occur, which makes error-correcting coding techniques critical for reliable DNA data storage. To reduce the errors, a common technique is to include…
Product quantization-based approaches are effective to encode high-dimensional data points for approximate nearest neighbor search. The space is decomposed into a Cartesian product of low-dimensional subspaces, each of which generates a sub…
This paper is concerned with the ordered statistic decoding with local constraints (LC-OSD) of binary linear block codes, which is a near maximum-likelihood decoding algorithm. Compared with the conventional OSD, the LC-OSD significantly…
Recently, DNA storage has surfaced as a promising alternative for data storage, presenting notable benefits in terms of storage capacity, cost-effectiveness in maintenance, and the capability for parallel replication. Mathematically, the…
This paper is concerned with a guessing codeword decoding (GCD) of linear block codes. Compared with the guessing noise decoding (GND), which is only efficient for high-rate codes, the GCD is efficient for not only high-rate codes but also…