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Application of the Architecture Transformer for Problem of Recognition of DNA Secondary Structures

Student: Daria Nichvidiuk

Supervisor: Maria Poptsova

Faculty: Faculty of Computer Science

Educational Programme: Applied Mathematics and Information Science (Bachelor)

Year of Graduation: 2021

The DNA secondary structure is a form of interaction between the nucleotides of the primary structure of DNA. This paper is a study of the use of various models of the Transformer architecture, trained on natural language corpora, as well as nucleotide chains, to solve the problem of recognizing DNA secondary structure, namely, the lefthanded Z-DNA helix in the genome of the Mus musculus (House mouse) in the mm10 assembly. Applications of the BERT, distilBERT, RoBERTa, XMLRoBERTa, CamemBERT, and ESM-1 models were trained. The paper is aimed at studying and comparing the use of methods that are designed to increase the speed of prediction without losing the accuracy of recognition.

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