An omics data analysis method based on feature linear relationship and graph convolutional network

Abstract

Biological networks are known to be highly modular, and the dysfunction of network modules may cause diseases. Defining the key modules from the omics data and establishing the classification model is helpful in promoting the research of disease diagnosis and prognosis. However, for applying modules in downstream analysis such as disease states discrimination, most methods only utilize the node information, and ignore the node interactions or topological information, which may lead to false positives and limit the model performance. In this study, we propose an omics data analysis method based on feature linear relationship and graph convolutional network (LCNet). In LCNet, we adopt a way of applying the difference of feature linear relationships during disease development to characterize physiological and pathological changes and construct the differential linear relation network, which is simple and interpretable from the perspective of feature linear relationship. A greedy strategy is developed for searching the highly interactive modules with a strong discrimination ability. To fully utilize the information of the detected modules, the personalized sub-graphs for each sample based on the modules are defined, and the graph convolutional network (GCN) classifiers are trained to predict the sample labels. The experimental results on public datasets show the superiority of LCNet in classification performance. For Breast Cancer metabolic data, the identified metabolites by LCNet involve important pathways. Thus, LCNet can identify the module biomarkers by feature linear relationship and a greedy strategy, and label samples by personalized sub-graphs and GCN. It provides a new manner of utilizing node (molecule) information and topological information in the defined modules for better disease classification.