DTC-m6Am:基于DenseNet和注意力机制的不平衡分类模式中n6,2 '- o -二甲基腺苷位点识别框架。

IF 3.3 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY
Hui Huang, Fenglin Zhou, Jianhua Jia, Huachun Zhang
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引用次数: 0

摘要

背景:m6Am是一种特异性RNA修饰,在调节mRNA稳定性、翻译效率和细胞应激反应中起重要作用。m6Am的精确鉴定对于深入了解其转录和转录后水平的功能机制至关重要。由于实验分析的局限性,开发高效的计算工具来预测m6Am位点已成为研究的主要焦点,为RNA表观遗传学提供了潜在的突破。在这项研究中,我们提出了一个强大而可靠的深度学习模型,DTC-m6Am,用于识别转录组中的m6Am位点。方法:我们提出的DTC-m6Am模型首先通过One-Hot编码表示RNA序列,以捕获基于碱基的特征,并为后续深度学习模型提供结构化输入。然后,该模型结合了密集连接卷积网络(DenseNet)和时间卷积网络(TCN)。DenseNet模块利用其密集连接特性有效地提取局部特征并增强信息流,而TCN模块侧重于捕获全局时间序列依赖关系以增强长序列特征的建模能力。为了进一步优化特征提取,利用卷积块注意模块(CBAM)通过空间和通道注意机制对关键区域进行聚焦。最后,利用全连通层进行分类任务,实现对m6Am站点的准确预测。对于数据不平衡问题,我们使用焦点损失函数来平衡正负样本的学习效果,提高模型在不平衡数据上的性能。结果:基于深度学习的DTC-m6Am模型在所有评价指标上都表现良好,在独立测试集上,敏感性(Sn)、特异性(Sp)、准确性(ACC)、马修相关系数(MCC)和曲线下面积(AUC)分别达到87.8%、50.3%、69.1%、41.1%和76.5%。结论:我们使用10倍交叉验证和独立测试对DTC-m6Am的性能进行了批判性评估,并将其与现有方法进行了比较。使用独立测试时,MCC值达到41.1%,比目前最先进的预测方法m6Aminer高出19.7%。结果表明,DTC-m6Am模型具有较高的精度和稳定性,是预测m6Am位点的有效工具。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
DTC-m6Am: A Framework for Recognizing N6,2'-O-dimethyladenosine Sites in Unbalanced Classification Patterns Based on DenseNet and Attention Mechanisms.

Background: m6Am is a specific RNA modification that plays an important role in regulating mRNA stability, translational efficiency, and cellular stress response. m6Am's precise identification is essential to gain insight into its functional mechanisms at transcriptional and post-transcriptional levels. Due to the limitations of experimental assays, the development of efficient computational tools to predict m6Am sites has become a major focus of research, offering potential breakthroughs in RNA epigenetics. In this study, we present a robust and reliable deep learning model, DTC-m6Am, for identifying m6Am sites across the transcriptome.

Methods: Our proposed DTC-m6Am model first represents RNA sequences by One-Hot coding to capture base-based features and provide structured inputs for subsequent deep learning models. The model then combines densely connected convolutional networks (DenseNet) and temporal convolutional network (TCN). The DenseNet module leverages its dense connectivity property to effectively extract local features and enhance information flow, whereas the TCN module focuses on capturing global time series dependencies to enhance the modeling capability for long sequence features. To further optimize feature extraction, the Convolutional Block Attention Module (CBAM) is used to focus on key regions through spatial and channel attention mechanisms. Finally, a fully connected layer is used for the classification task to achieve accurate prediction of the m6Am site. For the data imbalance problem, we use the focal loss function to balance the learning effect of positive and negative samples and improve the performance of the model on imbalanced data.

Results: The deep learning-based DTC-m6Am model performs well on all evaluation metrics, achieving 87.8%, 50.3%, 69.1%, 41.1%, and 76.5% for sensitivity (Sn), specificity (Sp), accuracy (ACC), Mathew's correlation coefficient (MCC), and area under the curve (AUC), respectively, on the independent test set.

Conclusions: We critically evaluated the performance of DTC-m6Am using 10-fold cross-validation and independent testing and compared it to existing methods. The MCC value of 41.1% was achieved when using the independent test, which is 19.7% higher than the current state-of-the-art prediction method, m6Aminer. The results indicate that the DTC-m6Am model has high accuracy and stability and is an effective tool for predicting m6Am sites.

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