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Background <p>Reliable identification of cancer subtypes is crucial for devising personalized treatment strategies. Integrating multi-omics data has proven to be an effective method for analyzing cancer subtypes. By combining molecular information across various layers, a more comprehensive understanding of biological characteristics and disease mechanisms can be achieved.</p> Results <p>We propose DEGCN, a novel deep learning model that integrates a three-channel Variational Autoencoder (VAE) for multi-omics dimensionality reduction and a densely connected Graph Convolutional Network (GCN) for effective subtype classification. DEGCN leverages the complementary strengths of non-linear feature extraction and graph-based relational learning, enabling accurate and robust classification of renal cancer subtypes. Experimental results demonstrate that DEGCN achieves a cross-validated classification accuracy of 97.06% ± 2.04% on renal cancer data, outperforming conventional machine learning algorithms and state-of-the-art deep learning models. Moreover, its generalization ability is validated on breast and gastric cancer datasets from TCGA, with cross-validated classification accuracies of 89.82% ± 2.29% and 88.64% ± 5.24%, respectively, indicating strong cross-cancer predictive performance.</p> Conclusion <p>The study highlights the outstanding performance of DEGCN in heterogeneous data integration and classification accuracy, demonstrating the model’s potential in cancer subtype prediction and its application in guiding clinical treatment.</p>

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A densely connected framework for cancer subtype classification

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年7月18日

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  • Yu Li,
  • Denggao Zheng,
  • Kaijie Sun,
  • Chi Qin,
  • Yuchen Duan,
  • Qingqing Zhou,
  • Yunxia Yin,
  • Hongxing Kan,
  • Jili Hu

摘要

Background

Reliable identification of cancer subtypes is crucial for devising personalized treatment strategies. Integrating multi-omics data has proven to be an effective method for analyzing cancer subtypes. By combining molecular information across various layers, a more comprehensive understanding of biological characteristics and disease mechanisms can be achieved.

Results

We propose DEGCN, a novel deep learning model that integrates a three-channel Variational Autoencoder (VAE) for multi-omics dimensionality reduction and a densely connected Graph Convolutional Network (GCN) for effective subtype classification. DEGCN leverages the complementary strengths of non-linear feature extraction and graph-based relational learning, enabling accurate and robust classification of renal cancer subtypes. Experimental results demonstrate that DEGCN achieves a cross-validated classification accuracy of 97.06% ± 2.04% on renal cancer data, outperforming conventional machine learning algorithms and state-of-the-art deep learning models. Moreover, its generalization ability is validated on breast and gastric cancer datasets from TCGA, with cross-validated classification accuracies of 89.82% ± 2.29% and 88.64% ± 5.24%, respectively, indicating strong cross-cancer predictive performance.

Conclusion

The study highlights the outstanding performance of DEGCN in heterogeneous data integration and classification accuracy, demonstrating the model’s potential in cancer subtype prediction and its application in guiding clinical treatment.