SDBA: Score Domain-Based Attention for DNA N4-Methylcytosine Site Prediction from Multiperspectives

In tasks related to DNA sequence classification, choosing the appropriate encoding methods is challenging. Some of the methods encode sequences based on prior knowledge that limits the ability of the model to obtain multiperspective information from the sequences. We introduced a new trainable ensem...

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Bibliographic Details
Published in:Journal of chemical information and modeling 2024-04, Vol.64 (7), p.2839-2853
Main Authors: Xin, Ruihao, Zhang, Fan, Zheng, Jiaxin, Zhang, Yangyi, Yu, Cuinan, Feng, Xin
Format: Article
Language:English
Subjects:
Bioinformatics
Cytosine - analogs & derivatives
DNA - chemistry
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Summary:In tasks related to DNA sequence classification, choosing the appropriate encoding methods is challenging. Some of the methods encode sequences based on prior knowledge that limits the ability of the model to obtain multiperspective information from the sequences. We introduced a new trainable ensemble method based on the attention mechanism SDBA, which stands for Score Domain-Based Attention. Unlike other methods, we fed the task-independent encoding results into the models and dynamically ensembled features from different perspectives using the SDBA mechanism. This approach allows the model to acquire and weight sequence features voluntarily. SDBA is conceptually general and empirically powerful. It has achieved new state-of-the-art results on the benchmark data sets associated with DNA N4-methylcytosine site prediction.
ISSN:1549-9596
1549-960X
1549-960X
DOI:10.1021/acs.jcim.3c00688