Related papers: Complex DNA Synthesis Sequences
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
Because of its high data density and longevity, DNA is emerging as a promising candidate for satisfying increasing data storage needs. Compared to conventional storage media, however, data stored in DNA is subject to a wider range of errors…
This work presents a hybrid approach to solve the maximum stable set problem, using constraint and semidefinite programming. The approach consists of two steps: subproblem generation and subproblem solution. First we rank the variable…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…
DNA sequencing is revolutionising the field of medicine. DNA sequencers, the machines which perform DNA sequencing, have evolved from the size of a fridge to that of a mobile phone over the last two decades. The cost of sequencing a human…
Massively parallel hardware (GPUs) and long sequence data have made parallel algorithms essential for machine learning at scale. Yet dynamical systems, like recurrent neural networks and Markov chain Monte Carlo, were thought to suffer from…
Accurate segmentation and classification of nuclei in histology images is critical but challenging due to nuclei heterogeneity, staining variations, and tissue complexity. Existing methods often struggle with limited dataset variability,…
In this paper, we study the Random Access Problem in DNA storage, which addresses the challenge of retrieving a specific information strand from a DNA-based storage system. In this framework, the data is represented by $k$ information…
With the proliferation of increasingly complicated Deep Learning architectures, data synthesis is a highly promising technique to address the demand of data-hungry models. However, reliably assessing the quality of a 'synthesiser' model's…
Computational cost of training state-of-the-art deep models in many learning problems is rapidly increasing due to more sophisticated models and larger datasets. A recent promising direction for reducing training cost is dataset…
DNA has many valuable characteristics that make it suitable for a long-term storage medium, in particular its durability and high information density. DNA can be stored safely for hundreds of years with virtually no degradation, in contrast…
Encoding information in combinations of pre-synthesised deoxyribonucleic acid (DNA) strands (referred to as motifs) is an interesting approach to DNA storage that could potentially circumvent the prohibitive costs of…
Inspired by the principle of deliberate practice in human learning, we propose Deliberate Practice for Synthetic Data Generation (DP), a novel framework that improves sample efficiency through dynamic synthetic data generation. Prior work…
We present scalable hybrid-parallel algorithms for training large-scale 3D convolutional neural networks. Deep learning-based emerging scientific workflows often require model training with large, high-dimensional samples, which can make…
Motivation: Low-complexity (LC) DNA sequences are compositionally repetitive sequences that are often associated with spurious homologous matches and variant calling artifacts. While algorithms for identifying LC sequences exist, they…
Convolutional Neural Networks (CNN) based image reconstruction methods have been intensely used for X-ray computed tomography (CT) reconstruction applications. Despite great success, good performance of this data-based approach critically…
DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the…
We consider the problem of synthesizing programs with numerical constants that optimize a quantitative objective, such as accuracy, over a set of input-output examples. We propose a general framework for optimal synthesis of such programs…
DNA-coated colloids can crystallize into a multitude of lattices, ranging from face-centered cubic to diamond and thereby contribute to our understanding of crystallization and open avenues to producing structures with useful photonic…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…