Transfer Learning for Classification of Alzheimer's Disease Based on Genome Wide Data

• Published in: IEEE/ACM transactions on computational biology and bioinformatics 2023-09, Vol.20 (5), p.2700-2711
• Main Authors: Alatrany, Abbas Saad, Khan, Wasiq, Hussain, Abir J., Mustafina, Jamila, Al-Jumeily, Dhiya
• Format: Article
• Language: English
• Subjects: Alzheimer's disease; Alzheminer's disease; Artificial neural networks; Bioinformatics; Biomarkers; Classification; Data models; Datasets; Diseases; Feature extraction; genome wide data; Genome-wide association studies; Genomes; GWAS; Learning; machine learning; Medical imaging; Neural networks; Neurodegenerative diseases; Neuroimaging; Nucleotides; Predictive models; Signs and symptoms; Single-nucleotide polymorphism; SNPs; Support vector machines; Transfer learning
• ISSN: 1545-5963; 1557-9964
• DOI: 10.1109/TCBB.2022.3233869

Alzheimer's disease (AD) is a type of brain disorder that is regarded as a degenerative disease because the corresponding symptoms aggravate with the time progression. Single nucleotide polymorphisms (SNPs) have been identified as relevant biomarkers for this condition. This study aims to identify SNPs biomarkers associated with the AD in order to perform a reliable classification of AD. In contrast to existing related works, we utilize deep transfer learning with varying experimental analysis for reliable classification of AD. For this purpose, the convolutional neural networks (CNN) are firstly trained over the genome-wide association studies (GWAS) dataset requested from the AD neuroimaging initiative. We then employ the deep transfer learning for further training of our CNN (as base model) over a different AD GWAS dataset, to extract the final set of features. The extracted features are then fed into Support Vector Machine for classification of AD. Detailed experiments are performed using multiple datasets and varying experimental configurations. The statistical outcomes indicate an accuracy of 89% which is a significant improvement when benchmarked with existing related works.