Zhang, Ying; Liu, Yan; Xu, Jian; Wang, Xiaoyu; Peng, Xinxin; Song, Jiangning; Yu, Dong-Jun published an article in 2021, the title of the article was Leveraging the attention mechanism to improve the identification of DNA N6-methyladenine sites.Formula: C6H7N5 And the article contains the following content:
DNA N6-methyladenine is an important type of DNA modification that plays important roles in multiple biol. processes. Despite the recent progress in developing DNA 6mA site prediction methods, several challenges remain to be addressed. For example, although the hand-crafted features are interpretable, they contain redundant information that may bias the model training and have a neg. impact on the trained model. Furthermore, although deep learning (DL)-based models can perform feature extraction and classification automatically, they lack the interpretability of the crucial features learned by those models. As such, considerable research efforts have been focused on achieving the trade-off between the interpretability and straight forwardness of DL neural networks. In this study, we develop two new DL-based models for improving the prediction of N6-methyladenine sites, termed LA6mA and AL6mA, which use bidirectional long short-term memory to resp. capture the long-range information and self-attention mechanism to extract the key position information from DNA sequences. The performance of the two proposed methods is benchmarked and evaluated on the two model organisms Arabidopsis thaliana and Drosophila melanogaster. On the two benchmark datasets, LA6mA achieves an area under the receiver operating characteristic curve (AUROC) value of 0.962 and 0.966, whereas AL6mA achieves an AUROC value of 0.945 and 0.941, resp. Moreover, an in-depth anal. of the attention matrix is conducted to interpret the important information, which is hidden in the sequence and relevant for 6mA site prediction. The two novel pipelines developed for DNA 6mA site prediction in this work will facilitate a better understanding of the underlying principle of DL-based DNA methylation site prediction and its future applications. The experimental process involved the reaction of N-Methyl-7H-purin-6-amine(cas: 443-72-1).Formula: C6H7N5
The Article related to arabidopsis drosophila dna n6 methyladenine, 6ma, dna modification, lstm, attention interpretation, deep learning, self-attention mechanism, Biochemical Methods: Biological and other aspects.Formula: C6H7N5
Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem