Исследовательская группа

Лаборатория языковых инструментов

Анализатор вторичной структуры цепочек

Руководитель проекта: Семён Григорьев
Статус: Активный

The composition of formal grammars and artificial neural networks for secondary structure analysis.



  • Semyon Grigorev and Polina Lunina
    BMC Bioinformatics,
  • Semyon Grigorev and Polina Lunina

    We propose a way to combine formal grammars and artificial neural networks for biological sequences processing. Formal grammars encode the secondary structure of the sequence and neural networks deal with mutations and noise. In contrast to the classical way, when probabilistic grammars are used for secondary structure modeling, we propose to use arbitrary (not probabilistic) grammars which simplifies grammar creation. Instead of modeling the structure of the whole sequence, we create a grammar which only describes features of the secondary structure. Then we use matrix-based parsing to extract features: the fact that some substring can be derived from some nonterminal is a feature. After that, we use a dense neural network to process features.

    Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - BIOINFORMATICS,