Multiclass Cancer Prediction Based on Copy Number Variation Using Deep Learning

Abstract

DNA copy number variation (CNV) is the type of DNA variation which is associated with various human diseases. CNV ranges in size from 1 kilobase to several megabases on a chromosome. Most of the computational research for cancer classification is traditional machine learning based, which relies on handcrafted extraction and selection of features. To the best of our knowledge, the deep learning-based research also uses the step of feature extraction and selection. To understand the difference between multiple human cancers, we developed three end-to-end deep learning models, i.e., DNN (fully connected), CNN (convolution neural network), and RNN (recurrent neural network), to classify six cancer types using the CNV data of 24,174 genes. The strength of an end-to-end deep learning model lies in representation learning (automatic feature extraction). The purpose of proposing more than one model is to find which architecture among them performs better for CNV data. Our best model achieved 92% accuracy with an ROC of 0.99, and we compared the performances of our proposed models with state-of-the-art techniques. Our models have outperformed the state-of-the-art techniques in terms of accuracy, precision, and ROC. In the future, we aim to work on other types of cancers as well.