Resource saving taxonomy classification with k-mer distributions and machine learning

Abstract: Modern high throughput sequencing technologies like metagenomic sequencing generate millions of sequences which have to be classified based on their taxonomic rank. Modern approaches either apply local alignment and comparison to existing data sets like MMseqs2 or use deep neural networks as it is done in DeepMicrobes and BERTax. Alignment-based approaches are costly in terms of runtime, especially since databases get larger and larger. For the deep learning-based approaches, specialized hardware is necessary for a computation, which consumes large amounts of energy. In this paper, we propose to use $k$-mer distributions obtained from DNA as features to classify its taxonomic origin using machine learning approaches like the subspace $k$-nearest neighbors algorithm, neural networks or bagged decision trees. In addition, we propose a feature space data set balancing approach, which allows reducing the data set for training and improves the performance of the classifiers. By comparing performance, time, and memory consumption of our approach to those of state-of-the-art algorithms (BERTax and MMseqs2) using several datasets, we show that our approach improves the classification on the genus level and achieves comparable results for the superkingdom and phylum level. Link: https://es-cloud.cs.uni-tuebingen.de/d/8e2ab8c3fdd444e1a135/?p=%2FTaxonomyClassification&mode=list