Gated graph attention network for cancer prediction

Abstract

With its increasing incidence, cancer has become one of the main causes of worldwide mortality. In this work, we mainly propose a novel attention-based neural network model named Gated Graph ATtention network (GGAT) for cancer prediction, where a gating mechanism (GM) is introduced to work with the attention mechanism (AM), to break through the previous work’s limitation of 1-hop neighbourhood reasoning. In this way, our GGAT is capable of fully mining the potential correlation between related samples, helping for improving the cancer prediction accuracy. Additionally, to simplify the datasets, we propose a hybrid feature selection algorithm to strictly select gene features, which significantly reduces training time without affecting prediction accuracy. To the best of our knowledge, our proposed GGAT achieves the state-of-the-art results in cancer prediction task on LIHC, LUAD, KIRC compared to other traditional machine learning methods and neural network models, and improves the accuracy by 1% to 2% on Cora dataset, compared to the state-of-the-art graph neural network methods.