Deep learning techniques for cancer classification using microarray gene expression data

被引:28
作者
Gupta, Surbhi [1 ,2 ,3 ]
Gupta, Manoj K. [1 ,2 ]
Shabaz, Mohammad [3 ]
Sharma, Ashutosh [4 ]
机构
[1] SMVDU, Dept Comp Sci, Jammu, India
[2] SMVDU, Engn Dept, Jammu, India
[3] Model Inst Engn & Technol, Jammu, India
[4] Univ Petr & Energy Studies, Sch Comp Sci, Dehra Dun, India
关键词
artificial intelligence; cancer; deep learning; gene expression; Rna-sequences;
D O I
10.3389/fphys.2022.952709
中图分类号
Q4 [生理学];
学科分类号
071003 ;
摘要
Cancer is one of the top causes of death globally. Recently, microarray gene expression data has been used to aid in cancer's effective and early detection. The use of DNA microarray technology to uncover information from the expression levels of thousands of genes has enormous promise. The DNA microarray technique can determine the levels of thousands of genes simultaneously in a single experiment. The analysis of gene expression is critical in many disciplines of biological study to obtain the necessary information. This study analyses all the research studies focused on optimizing gene selection for cancer detection using artificial intelligence. One of the most challenging issues is figuring out how to extract meaningful information from massive databases. Deep Learning architectures have performed efficiently in numerous sectors and are used to diagnose many other chronic diseases and to assist physicians in making medical decisions. In this study, we have evaluated the results of different optimizers on a RNA sequence dataset. The Deep learning algorithm proposed in the study classifies five different forms of cancer, including kidney renal clear cell carcinoma (KIRC), Breast Invasive Carcinoma (BRCA), lung adenocarcinoma (LUAD), Prostate Adenocarcinoma (PRAD) and Colon Adenocarcinoma (COAD). The performance of different optimizers like Stochastic gradient descent (SGD), Root Mean Squared Propagation (RMSProp), Adaptive Gradient Optimizer (AdaGrad), and Adaptive Momentum (AdaM). The experimental results gathered on the dataset affirm that AdaGrad and Adam. Also, the performance analysis has been done using different learning rates and decay rates. This study discusses current advancements in deep learning-based gene expression data analysis using optimized feature selection methods.
引用
收藏
页数:14
相关论文
共 59 条
  • [1] Abdollahi J., 2021, arXiv
  • [2] Ahn T, 2018, IEEE INT C BIOINFORM, P1748, DOI 10.1109/BIBM.2018.8621108
  • [3] Deep Learning for Brain MRI Segmentation: State of the Art and Future Directions
    Akkus, Zeynettin
    Galimzianova, Alfiia
    Hoogi, Assaf
    Rubin, Daniel L.
    Erickson, Bradley J.
    [J]. JOURNAL OF DIGITAL IMAGING, 2017, 30 (04) : 449 - 459
  • [4] A novel gene selection method using modified MRMR and hybrid bat-inspired algorithm with β-hill climbing
    Alomari, Osama Ahmad
    Khader, Ahamad Tajudin
    Al-Betar, Mohammed Azmi
    Awadallah, Mohammed A.
    [J]. APPLIED INTELLIGENCE, 2018, 48 (11) : 4429 - 4447
  • [5] A novel approach for dimension reduction of microarray
    Aziz, Rabia
    Verma, C. K.
    Srivastava, Namita
    [J]. COMPUTATIONAL BIOLOGY AND CHEMISTRY, 2017, 71 : 161 - 169
  • [6] Deep learning approach for microarray cancer data classification
    Basavegowda, Hema Shekar
    Dagnew, Guesh
    [J]. CAAI TRANSACTIONS ON INTELLIGENCE TECHNOLOGY, 2020, 5 (01) : 22 - 33
  • [7] Human papillomavirus and cervical cancer
    Burd, EM
    [J]. CLINICAL MICROBIOLOGY REVIEWS, 2003, 16 (01) : 1 - +
  • [8] Deep learning classification of lung cancer histology using CT images
    Chaunzwa, Tafadzwa L.
    Hosny, Ahmed
    Xu, Yiwen
    Shafer, Andrea
    Diao, Nancy
    Lanuti, Michael
    Christiani, David C.
    Mak, Raymond H.
    Aerts, Hugo J. W. L.
    [J]. SCIENTIFIC REPORTS, 2021, 11 (01)
  • [9] Chen X, 2018, Arxiv, DOI arXiv:1812.08674
  • [10] Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data
    Ching, Travers
    Zhu, Xun
    Garmire, Lana X.
    [J]. PLOS COMPUTATIONAL BIOLOGY, 2018, 14 (04)