Predicting tumour stages of lung cancer adenocarcinoma tumours from pooled microarray data using machine learning methods

Background: Microarray experiments can simultaneously determine the expression of thousands of genes. Identification of potential genes from microarray data for diagnosis of cancer is important. This study aimed to identify genes for the diagnosis of acute myeloid and lymphoblastic leukemia using a sparse feature selection method. Materials and Methods: In this descriptive study, the expression of 7129 genes of 25 patients with acute myeloid leukemia (AML), and 47 patients with lymphoblastic leukemia (ALL) achieved by the microarray technology were used in this study. Then, the important genes were identified using a sparse feature selection method to diagnose AML and ALL tissues based on the machine learning methods such as support vector machine (SVM), Gaussian kernel density estimation based classifier (GKDEC), k-nearest neighbor (KNN), and linear discriminant classifier (LDC). Results: Diagnosis of ALL and AML was done with the accuracy of 100% using 8 genes of microarray data selected by the sparse feature selection method, GKDEC, and LDC. Moreover, the KNN classifier using 6 genes and the SVM classifier using 7 genes diagnosed AML and ALL with the accuracy of 91.18% and 94.12%, respectively. The gene with the description “Paired-box protein PAX2 (PAX2) gene, exon 11 and complete CDs” was determined as the most important gene in the diagnosis of ALL and AML. Conclusion: The experimental results of the current study showed that AML and ALL can be diagnosed with high accuracy using sparse feature selection and machine learning methods. It seems that the investigation of the expression of selected genes in this study can be helpful in the diagnosis of ALL and AML.

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Classification of Pulmonary CT Images by Using Hybrid 3D-Deep Convolutional Neural Network Architecture

Applied Sciences ◽

10.3390/app9050940 ◽

2019 ◽

Vol 9 (5) ◽

pp. 940 ◽

Cited By ~ 20

Author(s):

Huseyin Polat ◽

Homay Danaei Mehr

Keyword(s):

Neural Network ◽

Machine Learning ◽

Lung Cancer ◽

Feature Extraction ◽

Extraction Methods ◽

Ct Images ◽

Learning Methods ◽

Machine Learning Methods ◽

Diagnosis Of Lung Cancer ◽

3D Cnn

Lung cancer is the most common cause of cancer-related deaths worldwide. Hence, the survival rate of patients can be increased by early diagnosis. Recently, machine learning methods on Computed Tomography (CT) images have been used in the diagnosis of lung cancer to accelerate the diagnosis process and assist physicians. However, in conventional machine learning techniques, using handcrafted feature extraction methods on CT images are complicated processes. Hence, deep learning as an effective area of machine learning methods by using automatic feature extraction methods could minimize the process of feature extraction. In this study, two Convolutional Neural Network (CNN)-based models were proposed as deep learning methods to diagnose lung cancer on lung CT images. To investigate the performance of the two proposed models (Straight 3D-CNN with conventional softmax and hybrid 3D-CNN with Radial Basis Function (RBF)-based SVM), the altered models of two-well known CNN architectures (3D-AlexNet and 3D-GoogleNet) were considered. Experimental results showed that the performance of the two proposed models surpassed 3D-AlexNet and 3D-GoogleNet. Furthermore, the proposed hybrid 3D-CNN with SVM achieved more satisfying results (91.81%, 88.53% and 91.91% for accuracy rate, sensitivity and precision respectively) compared to straight 3D-CNN with softmax in the diagnosis of lung cancer.

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