Результаты исследований: Публикации в книгах, отчётах, сборниках, трудах конференций › статья в сборнике материалов конференции › научная › Рецензирование
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 undirected 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. In this paper, we describe in details all the parts of our receipt: a grammar, parsing algorithm, and network architecture. We discuss possible improvements and future work. Finally, we provide the results of tRNA and 16s rRNA processing which shows the applicability of our idea to real problems.
Язык оригинала | английский |
---|---|
Название основной публикации | BIOINFORMATICS 2019 - 10th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019 |
Редакторы | Elisabetta De Maria, Hugo Gamboa, Ana Fred |
Издатель | SciTePress |
Страницы | 234-241 |
Число страниц | 8 |
ISBN (электронное издание) | 9789897583537 |
Состояние | Опубликовано - 1 янв 2019 |
Событие | 10th International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2019 - Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019 - Prague, Чехия Продолжительность: 22 фев 2019 → 24 фев 2019 |
конференция | 10th International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2019 - Part of 12th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2019 |
---|---|
Страна/Tерритория | Чехия |
Город | Prague |
Период | 22/02/19 → 24/02/19 |
ID: 48534701