We present an approach to discriminate SARS-CoV-2 virus types based on their RNA sequence descriptions avoiding a sequence alignment. For that purpose, sequences are preprocessed by feature extraction and the resulting feature vectors are analyzed by prototype-based classification to remain interpretable. In particular, we propose to use variants of learning vector quantization (LVQ) based on dissimilarity measures for RNA sequence data. The respective matrix LVQ provides additional knowledge about the classification decisions like discriminant feature correlations and, additionally, can be equipped with easy to realize reject options for uncertain data. Those options provide self-controlled evidence, i.e., the model refuses to make a classification decision if the model evidence for the presented data is not sufficient. This model is first trained using a GISAID dataset with given virus types detected according to the molecular differences in coronavirus populations by phylogenetic tree clustering. In a second step, we apply the trained model to another but unlabeled SARS-CoV-2 virus dataset. For these data, we can either assign a virus type to the sequences or reject atypical samples. Those rejected sequences allow to speculate about new virus types with respect to nucleotide base mutations in the viral sequences. Moreover, this rejection analysis improves model robustness. Last but not least, the presented approach has lower computational complexity compared to methods based on (multiple) sequence alignment.

Motivation Viruses are the most abundant biological entities and constitute a large reservoir of genetic diversity. In recent years, knowledge about them has increased significantly as a result of dynamic development in life sciences and rapid technological progress. This knowledge is scattered across various data repositories, making a comprehensive analysis of viral data difficult. Results In response to the need for gathering a comprehensive knowledge of viruses and viral sequences, we developed Virxicon, a lexicon of all experimentally-acquired sequences for RNA and DNA viruses. The ability to quickly obtain data for entire viral groups, searching sequences by levels of taxonomic hierarchy—according to the Baltimore classification and ICTV taxonomy—and tracking the distribution of viral data and its growth over time are unique features of our database compared to the other tools. Availability Virxicon is a publicly available resource, updated weekly. It has an intuitive web interface and can be freely accessed at http://virxicon.cs.put.poznan.pl/. Supplementary information Supplementary data are available at Bioinformatics online.

We present an approach to investigate SARS-CoV-2 virus sequences based on alignment-free methods for RNA sequence comparison. In particular, we verify a given clustering result for the GISAID data set, which was obtained analyzing the molecular differences in coronavirus populations by phylogenetic trees. For this purpose, we use alignment-free dissimilarity measures for sequences and combine them with learning vector quantization classifiers for virus type discriminant analysis and classification. Those vector quantizers belong to the class of interpretable machine learning methods, which, on the one hand side provide additional knowledge about the classification decisions like discriminant feature correlations, and on the other hand can be equipped with a reject option. This option gives the model the property of self controlled evidence if applied to new data, i.e. the models refuses to make a classification decision, if the model evidence for the presented data is not given. After training such a classifier for the GISAID data set, we apply the obtained classifier model to another but unlabeled SARS-CoV-2 virus data set. On the one hand side, this allows us to assign new sequences to already known virus types and, on the other hand, the rejected sequences allow speculations about new virus types with respect to nucleotide base mutations in the viral sequences. Author summaryThe currently emerging global disease COVID-19 caused by novel SARS-CoV-2 viruses requires all scientific effort to investigate the development of the viral epidemy, the 1/24 properties of the virus and its types. Investigations of the virus sequence are of special interest. Frequently, those are based on mathematical/statistical analysis. However, machine learning methods represent a promising alternative, if one focuses on interpretable models, i.e. those that do not act as black-boxes. Doing so, we apply variants of Learning Vector Quantizers to analyze the SARS-CoV-2 sequences. We encoded the sequences and compared them in their numerical representations to avoid the computationally costly comparison based on sequence alignments. Our resulting model is interpretable, robust, efficient, and has a self-controlling mechanism regarding the applicability to data. This framework was applied to two data sets concerning SARS-CoV-2. We were able to verify previously published virus type findings for one of the data sets by training our model to accurately identify the virus type of sequences. For sequences without virus type information (second data set), our trained model can predict them. Thereby, we observe a new scattered spreading of the sequences in the data space which probably is caused by mutations in the viral sequences. 25Frequent mutations in SARS-CoV-2 genomes are in the genes encoding the S-protein 26 and RNA polymerase, RNA primase, and nucleoprotein. Applying a sequence alignment 27 and similarity comparison using the Jaccard index, a method for monitoring and tracing 28 SARS-CoV-2 mutations was established in [17]. However, a g...

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In the present article we propose the application of variants of the mutual information function as characteristic fingerprints of biomolecular sequences for classification analysis. In particular, we consider the resolved mutual information functions based on Shannon-, Rényi-, and Tsallis-entropy. In combination with interpretable machine learning classifier models based on generalized learning vector quantization, a powerful methodology for sequence classification is achieved which allows substantial knowledge extraction in addition to the high classification ability due to the model-inherent robustness. Any potential (slightly) inferior performance of the used classifier is compensated by the additional knowledge provided by interpretable models. This knowledge may assist the user in the analysis and understanding of the used data and considered task. After theoretical justification of the concepts, we demonstrate the approach for various example data sets covering different areas in biomolecular sequence analysis.