Autosurv: interpretable deep learning framework for cancer survival analysis incorporating clinical and multi-omics data

Accurate prognosis for cancer patients can provide critical information for optimizing treatment plans and improving life quality. Combining omics data and demographic/clinical information can offer a more comprehensive view of cancer prognosis than using omics or clinical data alone and can also reveal the underlying disease mechanisms at the molecular level. In this study, we developed and validated a deep learning framework to extract information from high-dimensional gene expression and miRNA expression data and conduct prognosis prediction for breast cancer and ovarian-cancer patients using multiple independent multi-omics datasets. Our model achieved significantly better prognosis prediction than the current machine learning and deep learning approaches in various settings. Moreover, an interpretation method was applied to tackle the “black-box” nature of deep neural networks and we identified features (i.e., genes, miRNA, demographic/clinical variables) that were important to distinguish predicted high- and low-risk patients. The significance of the identified features was partially supported by previous studies.