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-...
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IMR Press
2025-04-01
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| Series: | Frontiers in Bioscience-Landmark |
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| Online Access: | https://www.imrpress.com/journal/FBL/30/4/10.31083/FBL36603 |
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| author | Hui Huang Fenglin Zhou Jianhua Jia Huachun Zhang |
| author_facet | Hui Huang Fenglin Zhou Jianhua Jia Huachun Zhang |
| author_sort | Hui Huang |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-f4e95722d4b54a26aa9631bc4c8ec487 |
| institution | OA Journals |
| issn | 2768-6701 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | IMR Press |
| record_format | Article |
| series | Frontiers in Bioscience-Landmark |
| spelling | doaj-art-f4e95722d4b54a26aa9631bc4c8ec4872025-08-20T02:28:55ZengIMR PressFrontiers in Bioscience-Landmark2768-67012025-04-013043660310.31083/FBL36603S2768-6701(25)01700-9DTC-m6Am: A Framework for Recognizing N6,2′-O-dimethyladenosine Sites in Unbalanced Classification Patterns Based on DenseNet and Attention MechanismsHui Huang0Fenglin Zhou1Jianhua Jia2Huachun Zhang3School of Information Engineering, Jingdezhen Ceramic University, 333403 Jingdezhen, Jiangxi, ChinaSchool of Information Engineering, Jingdezhen Ceramic University, 333403 Jingdezhen, Jiangxi, ChinaSchool of Information Engineering, Jingdezhen Ceramic University, 333403 Jingdezhen, Jiangxi, ChinaSchool of Information Engineering, Jingdezhen Ceramic University, 333403 Jingdezhen, Jiangxi, ChinaBackground: 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.https://www.imrpress.com/journal/FBL/30/4/10.31083/FBL36603m6am site identificationdeep learningdensenettcncbamclass imbalance |
| spellingShingle | Hui Huang Fenglin Zhou Jianhua Jia Huachun Zhang DTC-m6Am: A Framework for Recognizing N6,2′-O-dimethyladenosine Sites in Unbalanced Classification Patterns Based on DenseNet and Attention Mechanisms Frontiers in Bioscience-Landmark m6am site identification deep learning densenet tcn cbam class imbalance |
| title | DTC-m6Am: A Framework for Recognizing N6,2′-O-dimethyladenosine Sites in Unbalanced Classification Patterns Based on DenseNet and Attention Mechanisms |
| title_full | DTC-m6Am: A Framework for Recognizing N6,2′-O-dimethyladenosine Sites in Unbalanced Classification Patterns Based on DenseNet and Attention Mechanisms |
| title_fullStr | DTC-m6Am: A Framework for Recognizing N6,2′-O-dimethyladenosine Sites in Unbalanced Classification Patterns Based on DenseNet and Attention Mechanisms |
| title_full_unstemmed | DTC-m6Am: A Framework for Recognizing N6,2′-O-dimethyladenosine Sites in Unbalanced Classification Patterns Based on DenseNet and Attention Mechanisms |
| title_short | DTC-m6Am: A Framework for Recognizing N6,2′-O-dimethyladenosine Sites in Unbalanced Classification Patterns Based on DenseNet and Attention Mechanisms |
| title_sort | dtc m6am a framework for recognizing n6 2 o dimethyladenosine sites in unbalanced classification patterns based on densenet and attention mechanisms |
| topic | m6am site identification deep learning densenet tcn cbam class imbalance |
| url | https://www.imrpress.com/journal/FBL/30/4/10.31083/FBL36603 |
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