Abstract
Multidrug resistant bacteria represent an increasing challenge for medicine. In bacteria, most antibiotic resistances are transmitted by plasmids. Therefore, it is important to study the spread of plasmids in detail in order to initiate possible countermeasures. The classification of plasmids can provide insights into the epidemiology and transmission of plasmid-mediated antibiotic resistance. The previous methods to classify plasmids are replicon typing and MOB typing. Both methods are time consuming and labor-intensive. Therefore, a new approach to plasmid typing was developed, which uses word embeddings and support vector machines (SVM) to simplify plasmid typing. Visualizing the word embeddings with t-distributed stochastic neighbor embedding (t-SNE) shows that the word embeddings finds distinct structure in the plasmid sequences. The SVM assigned the plasmids in the testing dataset with an average accuracy of 85.9% to the correct MOB type.
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Kaufmann, M., Schüle, M., Smits, T.H.M., Pothier, J.F. (2020). Typing Plasmids with Distributed Sequence Representation. In: Schilling, FP., Stadelmann, T. (eds) Artificial Neural Networks in Pattern Recognition. ANNPR 2020. Lecture Notes in Computer Science(), vol 12294. Springer, Cham. https://doi.org/10.1007/978-3-030-58309-5_16
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DOI: https://doi.org/10.1007/978-3-030-58309-5_16
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