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作者:

Zhang, Jidong (Zhang, Jidong.) | Liu, Bo (Liu, Bo.) | Wu, Jiahui (Wu, Jiahui.) | Wang, Zhihan (Wang, Zhihan.) | Li, Jianqiang (Li, Jianqiang.)

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EI Scopus SCIE

摘要:

Understanding gene expression processes necessitates the accurate classification and identification of transcription factors, which is supported by high-throughput sequencing technologies. However, these techniques suffer from inherent limitations such as time consumption and high costs. To address these challenges, the field of bioinformatics has increasingly turned to deep learning technologies for analyzing gene sequences. Nevertheless, the pursuit of improved experimental results has led to the inclusion of numerous complex analysis function modules, resulting in models with a growing number of parameters. To overcome these limitations, it is proposed a novel approach for analyzing DNA transcription factor sequences, which is named as DeepCAC. This method leverages deep convolutional neural networks with a multi-head self-attention mechanism. By employing convolutional neural networks, it can effectively capture local hidden features in the sequences. Simultaneously, the multi-head self-attention mechanism enhances the identification of hidden features with long-distant dependencies. This approach reduces the overall number of parameters in the model while harnessing the computational power of sequence data from multi-head self-attention. Through training with labeled data, experiments demonstrate that this approach significantly improves performance while requiring fewer parameters compared to existing methods. Additionally, the effectiveness of our approach is validated in accurately predicting DNA transcription factor sequences.

关键词:

DNA transcription factors sequence Bioinformatics Convolutional neural networks Attention mechanism

作者机构:

  • [ 1 ] [Zhang, Jidong]Beijing Univ Technol, Fac Informat Technol, Beijing 100124, Peoples R China
  • [ 2 ] [Wu, Jiahui]Beijing Univ Technol, Fac Informat Technol, Beijing 100124, Peoples R China
  • [ 3 ] [Wang, Zhihan]Beijing Univ Technol, Fac Informat Technol, Beijing 100124, Peoples R China
  • [ 4 ] [Li, Jianqiang]Beijing Univ Technol, Fac Informat Technol, Beijing 100124, Peoples R China
  • [ 5 ] [Liu, Bo]Massey Univ, Sch Math & Computat Sci, Auckland 0745, New Zealand

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来源 :

BMC BIOINFORMATICS

ISSN: 1471-2105

年份: 2023

期: 1

卷: 24

3 . 0 0 0

JCR@2022

ESI学科: COMPUTER SCIENCE;

ESI高被引阀值:19

被引次数:

WoS核心集被引频次: 7

SCOPUS被引频次: 8

ESI高被引论文在榜: 0 展开所有

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