Leveraging hybrid 1D-CNN and RNN approach for classification of brain cancer gene expression

• Published in: Complex & intelligent systems 2024-12, Vol.10 (6), p.7605-7617
• Main Authors: Afify, Heba M., Mohammed, Kamel K., Hassanien, Aboul Ella
• Format: Article
• Language: English
• Subjects: Accessibility; Algorithms; Artificial neural networks; Bayesian optimization (BO); Bioinformatics; Brain; Brain cancer; Cancer; Classification; Classification of brain cancer genes; Complexity; Computational Intelligence; Curated microarray database (CuMiDa); Data Structures and Information Theory; Engineering; Gene expression; Machine learning; Neural networks; One dimensional-convolutional neural network (1D-CNN); Original Article; Recurrent neural network (RNN); Recurrent neural networks
• ISSN: 2199-4536; 2198-6053
• DOI: 10.1007/s40747-024-01555-4

Leveraging deep learning (DL) approaches in genomics data has led to significant advances in cancer prediction. The continuous availability of gene expression datasets over the preceding years has made them one of the most accessible sources of genome-wide data, advancing cancer bioinformatics research and advanced prediction of cancer genomic data. To contribute to this topic, the proposed work is based on DL prediction in both convolutional neural network (CNN) and recurrent neural network (RNN) for five classes in brain cancer using gene expression data obtained from Curated Microarray Database (CuMiDa). This database is used for cancer classification and is publicly accessible on the official CuMiDa website. This paper implemented DL approaches using a One Dimensional-Convolutional Neural Network (1D-CNN) followed by an RNN classifier with and without Bayesian hyperparameter optimization (BO). The accuracy of this hybrid model combination of (BO + 1D-CNN + RNN) produced the highest classification accuracy of 100% instead of the 95% for the ML model in prior work and 90% for the (1D-CNN + RNN) algorithm considered in the paper. Therefore, the classification of brain cancer gene expression according to the hybrid model (BO + 1D-CNN + RNN) provides more accurate and useful assessments for patients with different types of brain cancers. Thus, gene expression data are used to create a DL classification-based- hybrid model that will hold senior promise in the treatment of brain cancer.