Prediction of Cancer in DNA Sequences Using Unsupervised Learning Methods

Abstract

Today, with the development of technology, the decision-making capabilities of machines have also increased. With their high analytical skills, computers can easily catch points and relationships that may escape the human eye. Thanks to these capabilities, machines are also widely used in the field of health. For example, many machine learning techniques developed on cancer prediction have been successfully applied. Early detection of cancer is crucial to survival. In the early diagnosis of cancer, the rates of drug treatment, chemotherapy or radiotherapy that the person will be exposed to are significantly reduced and the patient gets through this process with the least amount of wear and tear. Gene Expression Cancer RNA-Seq Dataset was used in this study. This data set includes gene expression values of 5 cancer types (BRCA, KIRC, LUAD, LUSC, UCEC). DNA sequences in the dataset were analyzed using k-means and hierarchical clustering algorithms, which are unsupervised machine learning methods. The aim of the study is to develop a usable machine learning model for early detection of cancer at the gene level. Adjusted Rand Index (ARI), Silhouette Score, and Accuracy metrics were used to evaluate the analysis results. The rand index calculates similarity between clusters by counting the binaries assigned to clusters. The adjusted Rand Index is a randomly adjusted version of the Rand Index. The silhouette score indicates how well a data point fits within its own set among separated datasets. The accuracy metric is obtained as a percentage of correctly clustered data points divided by all predictions. Different connection methods are used in the hierarchical clustering algorithm. These are 'complete', 'ward', 'average' and 'single'. As a result of the study, the accuracy in the k-means algorithm was 0.990, the Adjusted Rand Index was 0.79, and the Silhouette Score was 0.14. Looking at the hierarchical clustering, ward performed the best of the four linkage methods, with an ARI score of 0.76 and a silhouette score of 0.13. As a result of the study, the accuracy of in the hierarchical clustering algorithm was 0.999.