Related papers: Complex DNA Synthesis Sequences
We investigate the fundamental limits of the recently proposed random access coverage depth problem for DNA data storage. Under this paradigm, it is assumed that the user information consists of $k$ information strands, which are encoded…
The modeling of genomic sequences presents unique challenges due to their length and structural complexity. Traditional sequence models struggle to capture long-range dependencies and biological features inherent in DNA. In this work, we…
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…
The goal of Feature Selection - comprising filter, wrapper, and embedded approaches - is to find the optimal feature subset for designated downstream tasks. Nevertheless, current feature selection methods are limited by: 1) the selection…
As the global need for large-scale data storage is rising exponentially, existing storage technologies are approaching their theoretical and functional limits in terms of density and energy consumption, making DNA based storage a potential…
As deep learning models grow in complexity and the volume of training data increases, reducing storage and computational costs becomes increasingly important. Dataset distillation addresses this challenge by synthesizing a compact set of…
DNA is not only the genetic material of life, but also a favorable material for a new computing model. Various research works based on DNA computing have been carried out in recent years. DNA sequence design is the foundation of such…
We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…
Kernel segmentation aims at partitioning a data sequence into several non-overlapping segments that may have nonlinear and complex structures. In general, it is formulated as a discrete optimization problem with combinatorial constraints. A…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (i.e. rarely accessed), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like…
We present an assignment for a full Parallel Computing course. Since 2017/2018, we have proposed a different problem each academic year to illustrate various methodologies for approaching the same computational problem using different…
The recently proposed multi-layer sparse model has raised insightful connections between sparse representations and convolutional neural networks (CNN). In its original conception, this model was restricted to a cascade of convolutional…
Convolutional Neural Networks (CNNs) have achieved significant breakthroughs in various fields. However, these advancements have led to a substantial increase in the complexity and size of these networks. This poses a challenge when…
The short lifespan of traditional data storage media, coupled with an exponential increase in storage demand, has made long-term archival a fundamental problem in the data storage industry and beyond. Consequently, researchers are looking…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
Rapid analysis of DNA sequences is important in preventing the evolution of different viruses and bacteria during an early phase, early diagnosis of genetic predispositions to certain diseases (cancer, cardiovascular diseases), and in DNA…
Program synthesis aims to automatically construct human-readable programs that satisfy given task specifications, such as input/output pairs or demonstrations. Recent works have demonstrated encouraging results in a variety of domains, such…
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and tradeoffs of DNA-based storage systems under a simple model, motivated by current…
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many…