Deep-LC: A Novel Deep Learning Method of Identifying Non-Small Cell Lung Cancer-Related Genes

Abstract

According to statistics, lung cancer kills 1.8 million people each year and is the main cause of cancer mortality worldwide. Non-small cell lung cancer (NSCLC) accounts for over 85% of all lung cancers. Lung cancer has a strong genetic predisposition, demonstrating that the susceptibility and survival of lung cancer are related to specific genes. Genome-wide association studies (GWASs) and next-generation sequencing have been used to discover genes related to NSCLC. However, many studies ignored the intricate interaction information between gene pairs. In the paper, we proposed a novel deep learning method named Deep-LC for predicting NSCLC-related genes. First, we built a gene interaction network and used graph convolutional networks (GCNs) to extract features of genes and interactions between gene pairs. Then a simple convolutional neural network (CNN) module is used as the decoder to decide whether the gene is related to the disease. Deep-LC is an end-to-end method, and from the evaluation results, we can conclude that Deep-LC performs well in mining potential NSCLC-related genes and performs better than existing state-of-the-art methods.

Keywords: Deep-LC; convolutional neural network (CNN) accelerator; genome-wide association analysis; graph convolutional networks; non-small cell lung cancer.

Figure 1

The structure of Deep-LC.

Figure 2

The comparison results of Deep-LC and other four methods.