Statistical Linear Models in Virus Genomic Alignment-free Classification: Application to Hepatitis C Viruses Machine Learning

Viral sequence classification is an important task in pathogen detection, epidemiological surveys and evolutionary studies. Statistical learning methods are widely used to classify and identify viral sequences in samples from environments. These methods face several challenges associated with the nature and properties of viral genomes such as recombination, mutation rate and diversity. Also, new generations of sequencing technologies rise other difficulties by generating massive amounts of fragmented sequences. While linear classifiers are often used to classify viruses, there is a lack of exploration of the accuracy space of existing models in the context of alignment free approaches. In this study, we present an exhaustive assessment procedure exploring the power of linear classifiers in genotyping and subtyping partial and complete genomes. It is applied to the Hepatitis C viruses (HCV). Several variables are considered in this investigation such as classifier types (generative and discriminative) and their hyper-parameters (smoothing value and penalty function), the classification task (genotyping and subtyping), the length of the tested sequences (partial and complete) and the length of k-mer words. Overall, several classifiers perform well given a set of precise combination of the experimental variables mentioned above. Finally, we provide the procedure and benchmark data to allow for more robust assessment of classification from virus genomes.

Fast Classification Rates for High-dimensional Gaussian Generative Models

Neural Information Processing Systems

We consider the problem of binary classification when the covariates conditioned on the each of the response values follow multivariate Gaussian distributions. We focus on the setting where the covariance matrices for the two conditional distributions are the same. The corresponding generative model classifier, derived via the Bayes rule, also called Linear Discriminant Analysis, has been shown to behave poorly in high-dimensional settings. We present a novel analysis of the classification error of any linear discriminant approach given conditional Gaussian models. This allows us to compare the generative model classifier, other recently proposed discriminative approaches that directly learn the discriminant function, and then finally logistic regression which is another classical discriminative model classifier.

Partial AUC Maximization via Nonlinear Scoring Functions Machine Learning

We propose a method for maximizing a partial area under a receiver operating characteristic (ROC) curve (pAUC) for binary classification tasks. In binary classification tasks, accuracy is the most commonly used as a measure of classifier performance. In some applications such as anomaly detection and diagnostic testing, accuracy is not an appropriate measure since prior probabilties are often greatly biased. Although in such cases the pAUC has been utilized as a performance measure, few methods have been proposed for directly maximizing the pAUC. This optimization is achieved by using a scoring function. The conventional approach utilizes a linear function as the scoring function. In contrast we newly introduce nonlinear scoring functions for this purpose. Specifically, we present two types of nonlinear scoring functions based on generative models and deep neural networks. We show experimentally that nonlinear scoring fucntions improve the conventional methods through the application of a binary classification of real and bogus objects obtained with the Hyper Suprime-Cam on the Subaru telescope.

Data Science Simplified Part 10: An Introduction to Classification Models


The world around is full of classifiers. Classifiers help in preventing spam e-mails. Classifiers help in identifying customers who may churn. Classifiers help in predicting whether it will rain or not. This supervised learning method is ubiquitous in business applications.

Using Transfer Learning for NLP with Small Data


Text classification has numerous applications, from tweet sentiment, product reviews, toxic comments, and more. It's a popular project topic among Insight Fellows, however a lot of time is spent collecting labeled datasets, cleaning data, and deciding which classification method to use. Services like Clarifai, and Google AutoML have made it very easy to create image classification models with less labeled data, but it's not as easy to create such models for text classification. For image classification tasks, transfer learning has proven to be very effective in providing good accuracy with fewer labeled datasets. Transfer learning is a technique that enables the transfer of knowledge learned from one dataset to another.