RA-GCN: Graph convolutional network for disease prediction problems with imbalanced data

•Study the class imbalance issue in the context of disease pre- diction problem modeled as a node classification task.•Propose a model to learn weight for each training sample and use it in the loss function to update the classifier.•Utilize an adversarial approach for training the classifier and weighing networks simultaneously.•Evaluation on 3 publicly available and a set of generated synthetic datasets with quantitative and qualitative experiments.•Enhance the performance on real and synthetic datasets. [Display omitted] Disease prediction is a well-known classification problem in medical applications. Graph Convolutional Networks (GCNs) provide a powerful tool for analyzing the patients’ features relative to each other. This can be achieved by modeling the problem as a graph node classification task, where each node is a patient. Due to the nature of such medical datasets, class imbalance is a prevalent issue in the field of disease prediction, where the distribution of classes is skewed. When the class imbalance is present in the data, the existing graph-based classifiers tend to be biased towards the major class(es) and neglect the samples in the minor class(es). On the other hand, the correct diagnosis of the rare positive cases (true-positives) among all the patients is vital in a healthcare system. In conventional methods, such imbalance is tackled by assigning appropriate weights to classes in the loss function which is still dependent on the relative values of weights, sensitive to outliers, and in some cases biased towards the minor class(es). In this paper, we propose a Re-weighted Adversarial Graph Convolutional Network (RA-GCN) to prevent the graph-based classifier from emphasizing the samples of any particular class. This is accomplished by associating a graph-based neural network to each class, which is responsible for weighting the class samples and changing the importance of each sample for the classifier. Therefore, the classifier adjusts itself and determines the boundary between classes with more attention to the important samples. The parameters of the classifier and weighting networks are trained by an adversarial approach. We show experiments on synthetic and three publicly available medical datasets. Our results demonstrate the superiority of RA-GCN compared to recent methods in identifying the patient’s status on all three datasets. The detailed analysis of our method is provided as quantitative and qualitative experiments on syn