Advance Genome Disorder Prediction Model Empowered With Deep Learning

被引:9
作者
Nasir, Muhammad Umar [2 ]
Gollapalli, Mohammed [3 ]
Zubair, Muhammad [4 ]
Saleem, Muhammad Aamer [5 ]
Mehmood, Shahid [2 ]
Khan, Muhammad Adnan [6 ]
Mosavi, Amir [7 ,8 ,9 ,10 ]
Atta-Ur-Rahman [1 ]
机构
[1] Imam Abdulrahman Bin Faisal Univ, Coll Comp Sci & Informat Technol, Dept Comp Sci, Dammam 31441, Saudi Arabia
[2] Riphah Int Univ, Fac Comp, Riphah Sch Comp & Innovat, Lahore Campus, Lahore 54000, Pakistan
[3] Imam Abdulrahman Bin Faisal Univ, Coll Comp Sci & Informat Technol, Dept Comp Informat Syst, Dammam 31441, Saudi Arabia
[4] Riphah Int Univ, Fac Comp, Islamabad 45000, Pakistan
[5] Hamdard Univ, Hamdard Inst Engn & Technol, Islamabad Campus, Islamabad 45000, Pakistan
[6] Gachon Univ, Dept Software, Pattern Recognit & Machine Learning Lab, Seongnam 13120, Gyeonggido, South Korea
[7] Tech Univ Dresden, Fac Civil Engn, D-01067 Dresden, Germany
[8] Obuda Univ, John von Neumann Fac Informat, H-1034 Budapest, Hungary
[9] Slovak Univ Technol Bratislava, Inst Informat Engn Automat & Math, Bratislava 81107, Slovakia
[10] Univ Publ Serv, Inst Informat Soc, H-1083 Budapest, Hungary
关键词
Genetics; Diseases; Genomics; Bioinformatics; Deep learning; Predictive models; Prediction algorithms; Genome disorder; AlexNet; deep learning; machine learning; artificial intelligence; data science; information systems; convolutional neural network;
D O I
10.1109/ACCESS.2022.3186998
中图分类号
TP [自动化技术、计算机技术];
学科分类号
0812 ;
摘要
A major and essential issue in biomedical research is to predict genome disorder. Genome disorders cause multivariate diseases like cancer, dementia, diabetes, cystic fibrosis, leigh syndrome, etc. which are causes of high mortality rates around the world. In past, theoretical and explanatory-based approaches were introduced to predict genome disorder. With the development of technology, genetic data were improved to cover almost genome and protein then machine and deep learning-based approaches were introduced to predict genome disorder. Parallel machine and deep learning approaches were introduced. In past, many types of research were conducted on genome disorder prediction using supervised, unsupervised, and semi-supervised learning techniques, most of the approaches using binary problem prediction using genetic sequence data. The prediction results of these approaches were uncertain because of their lower accuracy rate and binary class prediction techniques using genome sequence data but not genome disorder patients' data with his/her history. Most of the techniques used Ribonucleic acid (RNA) gene sequence and were not often capable of handling bid data effectively. Consequently, in this study, the AlexNet as an effective convolutional neural network architecture proposed to develop an advance genome disorder prediction model (AGDPM) for predicting genome multi classes disorder using a large amount of data. AGDPM tested and compare with the pre-trained AlexNet neural network model and AGDPM gives the best results with 89.89% & 81.25% accuracy of training and testing respectively. So, the advance genome disorder prediction model shows the ability to efficiently predict genome disorder and can process a large amount of patients' genome disorder data with a multi-class prediction method. AGDPM has proved that it is capable to predict single gene inheritance disorder, mitochondrial gene inheritance disorder, and multifactorial gene inheritance disorder with respect to various statistical performance parameters. So, with the help of AGDPM biomedical research will be improved in terms to predict genetic disorders and put control on high mortality rates.
引用
收藏
页码:70317 / 70328
页数:12
相关论文
共 31 条
[1]   Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes [J].
Alshahrani, Mona ;
Hoehndorf, Robert .
BIOINFORMATICS, 2018, 34 (17) :901-907
[2]  
[Anonymous], Rectifier (neural networks)
[3]  
[Anonymous], Softmax activation function with python
[4]  
[Anonymous], STAT 03 STANDARD DEV
[5]   Network medicine: a network-based approach to human disease [J].
Barabasi, Albert-Laszlo ;
Gulbahce, Natali ;
Loscalzo, Joseph .
NATURE REVIEWS GENETICS, 2011, 12 (01) :56-68
[6]   GCN-MF: Disease-Gene Association Identification By Graph Convolutional Networks and Matrix Factorization [J].
Han, Peng ;
Yang, Peng ;
Zhao, Peilin ;
Shang, Shuo ;
Liu, Yong ;
Zhou, Jiayu ;
Gao, Xin ;
Kalnis, Panos .
KDD'19: PROCEEDINGS OF THE 25TH ACM SIGKDD INTERNATIONAL CONFERENCCE ON KNOWLEDGE DISCOVERY AND DATA MINING, 2019, :705-713
[7]  
Irom B, 2020, GENET MOL BIOL RES, V4, P30
[8]   ImageNet Classification with Deep Convolutional Neural Networks [J].
Krizhevsky, Alex ;
Sutskever, Ilya ;
Hinton, Geoffrey E. .
COMMUNICATIONS OF THE ACM, 2017, 60 (06) :84-90
[9]  
Li Y., 2019, bioRxiv, DOI [10.1101/532226, DOI 10.1101/532226]
[10]   Application of deep learning algorithm on whole genome sequencing data uncovers structural variants associated with multiple mental disorders in African American patients [J].
Liu, Yichuan ;
Qu, Hui-Qi ;
Mentch, Frank D. ;
Qu, Jingchun ;
Chang, Xiao ;
Nguyen, Kenny ;
Tian, Lifeng ;
Glessner, Joseph ;
Sleiman, Patrick M. A. ;
Hakonarson, Hakon .
MOLECULAR PSYCHIATRY, 2022, 27 (03) :1469-1478