Pancancer survival prediction using a deep learning architecture with multimodal representation and integration

MOTIVATION: Use of multi-omics data carrying comprehensive signals about the disease is strongly desirable for understanding and predicting disease progression, cancer particularly as a serious disease with a high mortality rate. However, recent methods currently fail to effectively utilize the multi-omics data for cancer survival prediction and thus significantly limiting the accuracy of survival prediction using omics data. RESULTS: In this work, we constructed a deep learning model with multimodal representation and integration to predict the survival of patients using multi-omics data. We first developed an unsupervised learning part to extract high-level feature representations from omics data of different modalities. Then, we used an attention-based method to integrate feature representations, produced by the unsupervised learning part, into a single compact vector and finally we fed the vector into fully connected layers for survival prediction. We used multimodal data to train the model and predict pancancer survival, and the results show that using multimodal data can lead to higher prediction accuracy compared to using single modal data. Furthermore, we used the concordance index and the 5-fold cross-validation method for comparing our proposed method with current state-of-the-art methods and our results show that our model achieves better performance on the majority of cancer types in our testing datasets. AVAILABILITY AND IMPLEMENTATION: https://github.com/ZhangqiJiang07/MultimodalSurvivalPrediction. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.