Related papers: Statistical Linear Models in Virus Genomic Alignme…
The typical process for classifying and submitting a newly sequenced virus to the NCBI database involves two steps. First, a BLAST search is performed to determine likely family candidates. That is followed by checking the candidate…
The ICTV develops, refines and maintains a universal virus taxonomy; Order is the highest taxon in the branching hierarchy of recognised viral taxa. Historically, ICTV (sub)committees have classified viruses on the basis of morphological…
Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed…
Set classification problems arise when classification tasks are based on sets of observations as opposed to individual observations. In set classification, a classification rule is trained with $N$ sets of observations, where each set is…
The recent development of metagenomic sequencing makes it possible to sequence microbial genomes including viruses in an environmental sample. Identifying viral sequences from metagenomic data is critical for downstream virus analyses. The…
Viruses are submicroscopic agents that can infect all kinds of lifeforms and use their hosts' living cells to replicate themselves. Despite having some of the simplest genetic structures among all living beings, viruses are highly…
The aim of the study is to analyze viruses using parameters obtained from distributions of nucleotide sequences in the viral RNA. Seeking for the input data homogeneity, we analyze single-stranded RNA viruses only. Two approaches are used…
In 2022, a group of basic and clinical virologists, bioinformaticians, and evolutionary and structural biologists met in Oxford, UK, to develop a consensus on methodologies used to classify viruses. They concluded that virus taxonomy, which…
Hepatitis C virus (HCV) is a widely spread disease all over the world. HCV has very high mutation rate that makes it resistant to antibodies. Modeling HCV to identify the virus mutation process is essential to its detection and predicting…
Histogram-valued variables are a particular kind of variables studied in Symbolic Data Analysis where to each entity under analysis corresponds a distribution that may be represented by a histogram or by a quantile function. Linear…
HIV RNA viral load (VL) is an important outcome variable in studies of HIV infected persons. There exists only a handful of methods which classify patients by viral load patterns. Most methods place limits on the use of viral load…
Motivation: Array-based comparative genomic hybridization (arrayCGH) has recently become a popular tool to identify DNA copy number variations along the genome. These profiles are starting to be used as markers to improve prognosis or…
In this paper we present a methodology of classifying hepatic (liver) lesions using multidimensional persistent homology, the matching metric (also called the bottleneck distance), and a support vector machine. We present our classification…
Motivated by observations in sequence data of herpesviruses, we introduce a multi-locus model for the joint evolution of different genotypes in a virus population that is distributed across a population of hosts. In the model, virus…
Class distribution plays an important role in learning deep classifiers. When the proportion of each class in the test set differs from the training set, the performance of classification nets usually degrades. Such a label distribution…
Set classification aims to classify a set of observations as a whole, as opposed to classifying individual observations separately. To formally understand the unfamiliar concept of binary set classification, we first investigate the optimal…
Motivated by the challenge of using DNA-seq data to identify viruses in human blood samples, we propose a novel classification algorithm called "Radial Distance Weighted Discrimination" (or Radial DWD). This classifier is designed for…
Hepatitis C is a viral infection that appears as a result of the Hepatitis C Virus (HCV), and it has been recognized as the main reason for liver diseases. HCV incidence is growing as an important issue in the epidemiology of infectious…
In this paper, a mathematical analysis of the global dynamics of a partial differential equation viral infection cellular model is carried out. We study the dynamics of a hepatitis C virus (HCV) model, under therapy, that considers both…
Classification is one of the main areas of pattern recognition research, and within it, Support Vector Machine (SVM) is one of the most popular methods outside of field of deep learning -- and a de-facto reference for many Machine Learning…