ProgCAE: a deep learning-based method that integrates multi-omics data to predict cancer subtypes

Abstract Determining cancer subtypes and estimating patient prognosis are crucial for cancer research. The massive amount of multi-omics data generated by high-throughput sequencing technology is an important resource for cancer prognosis. Deep learning methods can integrate such data to accurately identify more cancer subtypes. We propose a prognostic model based on a convolutional autoencoder (ProgCAE) that can predict cancer subtypes associated with survival using multi-omics data. We demonstrated that ProgCAE predicted subtypes of 12 cancer types with significant survival differences and outperformed traditional statistical methods for predicting the survival of most patients with cancer. Supervised classifiers can be constructed based on subtypes predicted by robust ProgCAE.