Utilizing Graph Neural Networks for Breast Cancer Prognosis Prediction with High-dimensional Genomic Data

An accurate prediction of breast cancer is essential to help physicians make appropriate treatment recommendations to reduce the chance of excessive treatment, avoiding unnecessary anxiety for patients. Cancer prognosis is highly related to patients' genomic features, which are high-dimensional in nature. In this study, we utilize a systems biology feature selector for dimension reduction to select 20 prognostic biomarkers that are considered closely related to breast cancer prognosis from the high dimensional RNA Sequencing (RNA-Seq) data. Furthermore, we establish a graph neural network (GNN) and a multi-layer perception (MLP) graph-level readout method to better extract the underlying gene interactions from the corresponding gene interaction network (GIN). With the help of GINs, the model performs the best among all baseline models, especially in the area under the precision-recall curve (AUPRC) by as large as 23%. The results demonstrate that our approach using GNNs can successfully extract high-dimensional and complicated interactions within genomic data.