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There are currently plenty of programs available for mapping short sequences (reads) to a genome. Most of them, however, including such popular and actively developed programs as Bowtie, BWA, TopHat and many others, are based on…
Multi-omic datasets offer opportunities for improved biomarker discovery in cancer research, but their high dimensionality and limited sample sizes make identifying compact and effective biomarker panels challenging. Feature selection in…
A major hindrance to studies of microbial diversity has been that the vast majority of microbes cannot be cultured in the laboratory and thus are not amenable to traditional methods of characterization. Environmental shotgun sequencing…
We present a novel approach to detecting over and under translations (OT/UT) as part of adequacy error checks in translation evaluation. We do not restrict ourselves to machine translation (MT) outputs and specifically target applications…
Genome analysis has revolutionized fields such as personalized medicine and forensics. Modern sequencing machines generate vast amounts of fragmented strings of genome data called reads. The alignment of these reads into a complete DNA…
In this paper, we propose a sequence-to-set method that can transform any sequence generative model based on maximum likelihood to a set generative model where we can evaluate the utility/probability of any set. An efficient importance…
Artificial intelligence may assist healthcare systems in meeting increasing demand for pathology services while maintaining diagnostic quality and reducing turnaround time and costs. We aimed to investigate the performance of an…
Several of the next generation sequencers are limited in their sample preparation process by the need to make an absolute measurement of the number of template molecules in the library to be sequenced. As currently practiced, the practical…
Many modern sequence alignment tools implement fast string matching using the space efficient data structure called FM-index. The succinct nature of this data structure presents unique challenges for the algorithm designers. In this paper,…
Deep learning has been successfully applied to OCT segmentation. However, for data from different manufacturers and imaging protocols, and for different regions of interest (ROIs), it requires laborious and time-consuming data annotation…
Utility mining has emerged as an important and interesting topic owing to its wide application and considerable popularity. However, conventional utility mining methods have a bias toward items that have longer on-shelf time as they have a…
Motivation: Illumina Sequencing data can provide high coverage of a genome by relatively short (100 bp150 bp) reads at a low cost. Our goal is to produce trimmed and error-corrected reads to improve genome assemblies. Our error correction…
In contemporary age, Computational Intelligence (CI) performs an essential role in the interpretation of big biological data considering that it could provide all of the molecular biology and DNA sequencing computations. For this purpose,…
Recent studies revealed an important interplay between the detailed structure of fibration symmetric circuits and the functionality of biological and non-biological networks within which they have be identified. The presence of these…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
The high throughput and cost-effectiveness afforded by short-read sequencing technologies, in principle, enable researchers to perform 16S rRNA profiling of complex microbial communities at unprecedented depth and resolution. Existing…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
Molecular docking is a central method in the computer-based screening of compound libraries as a part of the rational approach to drug design. Although the method has proved its competence in predicting binding modes correctly, its inherent…
The research community continues to seek increasingly more advanced synthetic data generators to reliably evaluate the strengths and limitations of machine learning methods. This work aims to increase the availability of datasets…
In the Click-Through Rate (CTR) prediction scenario, user's sequential behaviors are well utilized to capture the user interest in the recent literature. However, despite being extensively studied, these sequential methods still suffer from…