Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is assigned to a taxonomic clade. Due to the large volume of metagenomics datasets, binning methods need fast and accurate algorithms that can operate with reasonable computing requirements. While standard alignment-based methods provide state-of-the-art performance, compositional approaches that assign a taxonomic class to a DNA read based on the k-mers it contains have the potential to provide faster solutions. In this work, we investigate the potential of modern, large-scale machine learning implementations for taxonomic affectation of next-generation sequencing reads based on their k-mers profile. We show that machine learning-based compositional approaches benefit from increasing the number of fragments sampled from reference genome to tune their parameters, up to a coverage of about 10, and from increasing the k-mer size to about 12. Tuning these models involves training a machine learning model on about 10 8 samples in 10 7 dimensions, which is out of reach of standard soft-wares but can be done efficiently with modern implementations for large-scale machine learning. The resulting models are competitive in terms of accuracy with well-established alignment tools for problems involving a small to moderate number of candidate species, and for reasonable amounts of sequencing errors. We show, however, that compositional approaches are still limited in their ability to deal with problems involving a greater number of species, and more sensitive to sequencing errors. We finally confirm that compositional approach achieve faster prediction times, with a gain of 3 to 15 times with respect to the BWA-MEM short read mapper, depending on the number of candidate species and the level of sequencing noise.
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.
We develop a novel approach for supervised learning based on adaptively partitioning the feature space into different regions and learning local region-specific classifiers. We formulate an empirical risk minimization problem that incorporates both partitioning and classification in to a single global objective. We show that space partitioning can be equivalently reformulated as a supervised learning problem and consequently any discriminative learning method can be utilized in conjunction with our approach. Nevertheless, we consider locally linear schemes by learning linear partitions and linear region classifiers. Locally linear schemes can not only approximate complex decision boundaries and ensure low training error but also provide tight control on over-fitting and generalization error. We train locally linear classifiers by using LDA, logistic regression and perceptrons, and so our scheme is scalable to large data sizes and high-dimensions. We present experimental results demonstrating improved performance over state of the art classification techniques on benchmark datasets. We also show improved robustness to label noise.
An inductive probabilistic classification rule must generally obey the principles of Bayesian predictive inference, such that all observed and unobserved stochastic quantities are jointly modeled and the parameter uncertainty is fully acknowledged through the posterior predictive distribution. Several such rules have been recently considered and their asymptotic behavior has been characterized under the assumption that the observed features or variables used for building a classifier are conditionally independent given a simultaneous labeling of both the training samples and those from an unknown origin. Here we extend the theoretical results to predictive classifiers acknowledging feature dependencies either through graphical models or sparser alternatives defined as stratified graphical models. We also show through experimentation with both synthetic and real data that the predictive classifiers based on stratified graphical models have consistently best accuracy compared with the predictive classifiers based on either conditionally independent features or on ordinary graphical models.
Paul Graham popularized the term "Bayesian Classification" (or more accurately "Naïve Bayesian Classification") after his "A Plan for Spam" article was published (http://www.paulgraham.com/spam.html). In fact, text classifiers based on naïve Bayesian and other techniques have been around for many years. Companies such as Autonomy and Interwoven incorporate machine-learning techniques to automatically classify documents of all kinds; one such machine-learning technique is naïve Bayesian text classification. Naïve Bayesian text classifiers are fast, accurate, simple, and easy to implement. In this article, I present a complete naïve Bayesian text classifier written in 100 lines of commented, nonobfuscated Perl.