Deep learning-based cancer disease classification using Gene Expression Data
Abstract
Cancer disease caused a major death in worldwide. To prevent this, various cancer classification approaches are employed, which are mostly relied on clinical characteristics and histopathological characteristics. Deep learning-based classification models are very effective and accurate. As a result, this research established the Adam-based Deep Quantum Neural Network, which is the optimal deep learning-based cancer classification method. The information on gene expression is used to classify cancer. Using the Box-Cox transformation, which converts the data into a legible format, the data transformation procedure is carried out. Utilizing information gain, the features are chosen in order to choose the proper gene expression. Additionally, Deep QNN is used to classify cancer, and for better classification, which is trained via Adam optimization. The experimental result shows the developed model provide better classification result with respect to accuracy, true positive rate and true negative rate of 94.91%, 95.59% and 95.4%.
Keywords
Full Text:
PDFReferences
1. Sevakula RK, Singh V, Verma NK, et al. Transfer learning for molecular cancer classification using deep neural networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2019; 16(6): 2089–2100. doi: 10.1109/TCBB.2018.2822803
2. Joseph M, Devaraj M, Leung CK. DeepGx: Deep learning using gene expression for cancer classification. In: Proceedings of 2019 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM); 27–30 August 2019; Vancouver, Canada.
3. Guo Y, Liu S, Li Z, Shang X. Towards the classification of cancer subtypes by using cascade deep forest model in gene expression data. In: proceedings of 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM); 13–16 November 2017; Kansas City, USA.
4. Mohsen H, El-Dahshan ESA, El-Horbaty ESM, et al. Classification using deep learning neural networks for brain tumors. Future Computing and Informatics Journal 2018; 3(1): 68–71. doi: 10.1016/j.fcij.2017.12.001
5. Golub TR, Slonim DK, Tamayo P, et al. Molecular classiþcation of cancer: class discovery and class prediction by gene expression monitoring. Science 1999; 286(5439): 531–537. doi: 10.1126/science.286.5439.531
6. Lu Y, Han J. Cancer classification using gene expression data. Information Systems 2003; 28(4): 243–268. doi: 10.1016/S0306-4379(02)00072-8
7. Zhang Q, Zhang M, Chen T, et al. Recent advances in convolutional neural network acceleration. Neurocomputing 2019; 323: 37–51. doi: 10.1016/j.neucom.2018.09.038
8. Vinolin V. Breast cancer detection by optimal classification using GWO algorithm. Multimedia Research 2019; 2(2): 10–18.
9. Gao F, Wang W, Tan M, et al. DeepCC: A novel deep learning-based framework for cancer molecular subtype classification. Oncogenesis 2019; 8(9): 44. doi: 10.1038/s41389-019-0157-8
10. Rubin M, Stein O, Turko NA, et al. TOP-GAN: Stain-free cancer cell classification using deep learning with a small training set. Medical Image Analysis 2019; 57: 176–185. doi: 10.1016/j.media.2019.06.014
11. Gupta S, Gupta MK, Shabaz M, Sharma A. Deep learning techniques for cancer classification using microarray gene expression data. Frontiers in Physiology 2022; 13: 952709. doi: 10.3389/fphys.2022.952709
12. Alharbi F, Vakanski A. Machine learning methods for cancer classification using gene expression data: A review. Bioengineering 2023; 10(2): 173. doi: 10.3390/bioengineering10020173
13. Liu JJ, Cai WS, Shao XG. Cancer classification based on microarray gene expression data using a principal component accumulation method. Science China Chemistry 2011; 54(5): 802–811. doi: 10.1007/s11426-011-4263-5
14. Vijayakumar K, Mohan Kumar KP, Jesline D. Implementation of software agents and advanced AOA for disease data analysis. Journal of Medical Systems 2019; 43: 1–6. doi: 10.1007/s10916-019-1411-5
15. Nguyen T, Nahavandi S. Modified AHP for gene selection and cancer classification using type-2 fuzzy logic. IEEE Transactions on Fuzzy Systems 2016; 24(2): 273–287. doi: 10.1109/TFUZZ.2015.2453153
16. Zhao W, Wang L, Zhang Z. Atom search optimization and its application to solve a hydrogeologic parameter estimation problem. Knowledge-Based Systems 2019; 163: 283–304. doi: 10.1016/j.knosys.2018.08.030
17. Kadam VJ, Jadhav SM, Vijayakumar K. Breast cancer diagnosis using feature ensemble learning based on stacked sparse autoencoders and softmax regression. Journal of Medical Systems 2019; 43(8): 263. doi: 10.1007/s10916-019-1397-z
18. Vijayakumar K, Arun C. Integrated cloud-based risk assessment model for continuous integration. International Journal of Reasoning-based Intelligent Systems 2018; 10(3–4): 316–321. doi: 10.1504/IJRIS.2018.096227
19. Uğuz H. A two-stage feature selection method for text categorization by using information gain, principal component analysis and genetic algorithm. Knowledge-Based Systems 2011; 24(7): 1024–1032. doi: 10.1016/j.knosys.2011.04.014
20. Maciejewski R, Pattath A, Ko S, et al. Automated box-cox transformations for improved visual encoding. IEEE Transactions on Visualization and Computer Graphics 2012; 19(1): 130–140. doi: 10.1109/TVCG.2012.64
21. Beer K, Bondarenko D, Farrelly T, et al. Training deep quantum neural networks. Nature Communications 2020; 11(1): 808. doi: 10.1038/s41467-020-14454-2
22. Kingma DP, Ba J. Adam: A method for stochastic optimization. arXiv 2014; arXiv:1412.6980. doi: 10.48550/arXiv.1412.6980
23. Alon U, Barkai N, Notterman DA, et al. Broad patterns of gene expression revealed by clustering of tumor and normal colon tissues probed by oligonucleotide arrays. Proceedings of the National Academy of Sciences 1999; 96(12): 6745–6750. doi: 10.1073/pnas.96.12.6745
24. Leukemia data. Available online: https://hastie.su.domains/CASI_files/DATA/leukemia.html (accessed on 19 September 2023).
25. Yue T, Wang H. Deep learning for genomics: A concise overview. arXiv 2018; arXiv:1802.00810. doi: 10.48550/arXiv.1802.00810
26. Tipping ME, Bishop CM. Probabilistic principal component analysis. Journal of the Royal Statistical Society 1999; 61(3): 611–622. doi: 10.1111/1467-9868.00196
27. Inoue M, Inoue S, Nishida T. Deep recurrent neural network for mobile human activity recognition with high throughput. Artificial Life and Robotic 2018; 23(2): 173–185. doi: 10.1007/s10015-017-0422-x
DOI: https://doi.org/10.32629/jai.v7i1.734
Refbacks
- There are currently no refbacks.
Copyright (c) 2023 J. Dafni Rose, K. Vijayakumar, D. Menaga
License URL: https://creativecommons.org/licenses/by-nc/4.0/