Related papers: Enabling Fast, Accurate, and Efficient Real-Time G…
Deep learning-based histopathology image classification is a key technique to help physicians in improving the accuracy and promptness of cancer diagnosis. However, the noisy labels are often inevitable in the complex manual annotation…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
Nanopore based sequencing has demonstrated significant potential for the development of fast, accurate, and cost-efficient fingerprinting techniques for next generation molecular detection and sequencing. We propose a specific multi-layered…
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…
Noise is a part of data whether the data is from measurement, experiment or ... A few techniques are suggested for noise reduction to improve the data quality in recent years some of which are based on wavelet, orthogonalization and neural…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
DNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted in exponential growth in genomic datasets over the past…
Integrating deep neural networks with the Hawkes process has significantly improved predictive capabilities in finance, health informatics, and information technology. Nevertheless, these models often face challenges in real-world settings,…
In any knowledge discovery process the value of extracted knowledge is directly related to the quality of the data used. Big Data problems, generated by massive growth in the scale of data observed in recent years, also follow the same…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
Advances in third-generation sequencing have enabled portable and real-time genomic sequencing, but real-time data processing remains a bottleneck, hampering on-site genomic analysis due to prohibitive time and energy costs. These…
In this paper we describe a new technique for the comparison of populations of DNA strands. Comparison is vital to the study of ecological systems, at both the micro and macro scales. Existing methods make use of DNA sequencing and cloning,…
Nanopore sequencing is a widely-used high-throughput genome sequencing technology that can sequence long fragments of a genome into raw electrical signals at low cost. Nanopore sequencing requires two computationally-costly processing steps…
Neural Architecture Search (NAS) has recently become a topic of great interest. However, there is a potentially impactful issue within NAS that remains largely unrecognized: noise. Due to stochastic factors in neural network initialization,…
In this paper, fundamental limits in sequencing of a set of closely related DNA molecules are addressed. This problem is called pooled-DNA sequencing which encompasses many interesting problems such as haplotype phasing, metageomics, and…
Genetic analysis methods are foundational to advancing personalized and preventative medicine, accelerating disease diagnostics, and monitoring the health of organisms and ecosystems. Current nucleic acid technologies such as polymerase…
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,…
Recently, sparsity-based algorithms are proposed for super-resolution spectrum estimation. However, to achieve adequately high resolution in real-world signal analysis, the dictionary atoms have to be close to each other in frequency,…
While measurement advances now allow extensive surveys of gene activity (large numbers of genes across many samples), interpretation of these data is often confounded by noise -- expression counts can differ strongly across samples due to…
Next-generation sequencing (NGS) is a pivotal technique in genome sequencing due to its high throughput, rapid results, cost-effectiveness, and enhanced accuracy. Its significance extends across various domains, playing a crucial role in…