Related papers: Improved Lower Bounds for Constant GC-Content DNA …
Nonsmooth composite optimization with orthogonality constraints has a wide range of applications in statistical learning and data science. However, this problem is challenging due to its nonsmooth objective and computationally expensive…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…
DNA storage is now being considered as a new archival storage method for its durability and high information density, but still facing some challenges like high costs and low throughput. By reducing sequencing sample size for decoding…
In the current era, DeoxyriboNucleic Acid (DNA) based data storage emerges as an intriguing approach, garnering substantial academic interest and investigation. This paper introduces a novel deep joint source-channel coding (DJSCC) scheme…
Weighted Hamming distance, as a similarity measure between binary codes and binary queries, provides superior accuracy in search tasks than Hamming distance. However, how to efficiently and accurately find $K$ binary codes that have the…
Spatially-coupled (SC) codes, known for their threshold saturation phenomenon and low-latency windowed decoding algorithms, are ideal for streaming applications. They also find application in various data storage systems because of their…
We present a base-pairing model of oligonuleotide duplex formation and show in detail its equivalence to the Nearest-Neighbour dimer methods from fits to free energy of duplex formation data for short DNA-DNA and DNA-RNA hybrids containing…
Computer-aided molecular design (CAMD) studies quantitative structure-property relationships and discovers desired molecules using optimization algorithms. With the emergence of machine learning models, CAMD score functions may be replaced…
Guessing Codeword Decoding (GCD) is a recently proposed soft-input forward error correction decoder for arbitrary binary linear codes. Inspired by recent proposals that leverage binary linear codebook structure to reduce the number of…
We introduce the Genetic-Gated Networks (G2Ns), simple neural networks that combine a gate vector composed of binary genetic genes in the hidden layer(s) of networks. Our method can take both advantages of gradient-free optimization and…
The evaluation of the minimum distance of linear block codes remains an open problem in coding theory, and it is not easy to determine its true value by classical methods, for this reason the problem has been solved in the literature with…
To better understand the wireless network design with a large number of hops, we investigate a line network formed by general discrete memoryless channels (DMCs), which may not be identical. Our focus lies on Generalized Batched Network…
We describe a general technique that yields the first {\em Statistical Query lower bounds} for a range of fundamental high-dimensional learning problems involving Gaussian distributions. Our main results are for the problems of (1) learning…
DNA-based storage is an emerging technology that enables digital information to be archived in DNA molecules. This method enjoys major advantages over magnetic and optical storage solutions such as exceptional information density, enhanced…
Hybrid Bayesian Networks (HBNs), which contain both discrete and continuous variables, arise naturally in many application areas (e.g., image understanding, data fusion, medical diagnosis, fraud detection). This paper concerns inference in…
Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence…
Effective and reliable data retrieval is critical for the feasibility of DNA storage, and the development of random access efficiency plays a key role in its practicality and reliability. In this paper, we study the Random Access Problem,…
The Local Search problem, which finds a local minimum of a black-box function on a given graph, is of both practical and theoretical importance to many areas in computer science and natural sciences. In this paper, we show that for the…
Content delivery networks often employ caching to reduce transmission rates from the central server to the end users. Recently, the technique of coded caching was introduced whereby coding in the caches and coded transmission signals from…
We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…