Related papers: LISA: Towards Learned DNA Sequence Search
High throughput technologies have become the practice of choice for comparative studies in biomedical applications. Limited number of sample points due to sequencing cost or access to organisms of interest necessitates the development of…
LISA is a planned space-based gravitational-wave (GW) detector that would be sensitive to waves from low-frequency sources, in the band of roughly $(0.03 - 0.1) {\rm mHz} \lesssim f \lesssim 0.1 {\rm Hz}$. This is expected to be an…
The incessant advent of online services demands high speed and efficient recommender systems (ReS) that can maintain real-time performance along with processing very complex user-item interactions. The present study, therefore, considers…
Neural Architecture Search (NAS) methods are widely used in various industries to obtain high quality taskspecific solutions with minimal human intervention. Event Sequences find widespread use in various industrial applications including…
Metagenomic studies have increasingly utilized sequencing technologies in order to analyze DNA fragments found in environmental samples.One important step in this analysis is the taxonomic classification of the DNA fragments. Conventional…
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…
Motivation: The comparison of diverse genomic datasets is fundamental to understanding genome biology. Researchers must explore many large datasets of genome intervals (e.g., genes, sequence alignments) to place their experimental results…
Convolutional neural networks (CNNs) have been successful in representing the fully-connected inferencing ability perceived to be seen in the human brain: they take full advantage of the hierarchy-style patterns commonly seen in complex…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
The Third-Generation in DNA sequencing has emerged in the last few years using new technologies that allow the production of long-read sequences. Applications of the Third-Generation sequencing enable real-time and on-site data production,…
The cost of DNA sequencing has dropped exponentially over the past decade, making genomic data accessible to a growing number of scientists. In bioinformatics, localization of short DNA sequences (reads) within large genomic sequences is…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
Bidirectional Long Short-Term Memory (LSTM) is a special kind of Recurrent Neural Network (RNN) architecture which is designed to model sequences and their long-range dependencies more precisely than RNNs. This paper proposes to use deep…
Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…
Graphs are foundational across domains but remain hard to use without deep expertise. LLMs promise accessible natural language (NL) graph analytics, yet they fail to process industry-scale property graphs effectively and efficiently: such…
Cheap high-throughput DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food…
Strong Lensing is a powerful probe of the matter distribution in galaxies and clusters and a relevant tool for cosmography. Analyses of strong gravitational lenses with Deep Learning have become a popular approach due to these astronomical…
Linear mixed models (LMM) are widely adopted in genome-wide association studies (GWAS) to account for population stratification and cryptic relatedness. However, the parameter estimation of LMMs imposes substantial computational burdens due…
Although the expenses associated with DNA sequencing have been rapidly decreasing, the current cost of sequencing information stands at roughly $120/GB, which is dramatically more expensive than reading from existing archival storage…
Genome and metagenome comparisons based on large amounts of next-generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads.…