DNA Microarray for Cancer Classification Using Deep Learning Based on RESNET-50 Convolutional Neural Network Technique

Authors

  • B. Shyamala Gowri, S. Anu H. Nair, K. P. Sanal Kumar, S. Kamalakkannan

Keywords:

DNA, Microarray, cancer classification, Image processing, ResNet-50 CNN, and Enhanced Canny Contour Detection

Abstract

In today's world, microarray data structures are significant in the diagnosis and classification of various malignant tissues and diseases. Therefore, to effectively address the difficulties of gene expression and classification, it offers high dimensionality and a limited number of genetic samples. Gene expression datasets are frequently utilized in disease prediction and diagnosis, particularly in cancer treatment. Medical diagnostics is one of the most important fields in which image-processing techniques are utilized effectively. Moreover, image processing is vital for enhancing diagnostic and surgical precision. However, accurately characterizing cancer biologically and identifying disease-causing gene expression can be challenging and time-consuming. To address this issue, we introduce the ResNet-50 Convolutional Neural Network (ResNet-50 CNN) method to increase the accuracy of DNA microarray cancer classification. Furthermore, we pre-process the image using the Adaptive Median Filter (AMF) method to remove background noise and enhance a smooth image. Additionally, the pixel-based color contrast, texture, and local contrast of blood cell cancer images are all enhanced using the Contrast-Limited Adaptive Histogram Equalization (CLAHE) technique. After that, we employ the Enhanced Canny Edge Detection (ECDD) algorithm to improve edge detection and reduce the error rate in image segmentation. Finally, we propose a ResNet-50 CNN method using a Deep Learning (DL) algorithm to improve the accuracy of classifying DNA microarrays as either cancerous or non-cancerous. Furthermore, the introduced algorithm can be used to classify microarray cancers through performance evaluations such as precision, recall, precision, time complexity, and F1 score. The results of the proposed model indicate an efficiency rating of 96.8% when assessed using various performance measures.

Downloads

Download data is not yet available.

References

Alharbi, F.; Vakanski, A. Machine Learning Methods for Cancer Classification Using Gene Expression Data: A Review. Bioengineering 2023, 10, 173. https://doi.org/10.3390/bioengineering10020173.

Thakur, Tanima, et al. "[Retracted] Gene Expression‐Assisted Cancer Prediction Techniques." Journal of Healthcare Engineering 2021.1 (2021): 4242646.

Haznedar, Bulent, Mustafa Turan Arslan, and Adem Kalinli. "Optimizing ANFIS using simulated annealing algorithm for classification of microarray gene expression cancer data." Medical & Biological Engineering & Computing 59 (2021): 497-509.

Devi, T. G., Patil, N., Rai, S., & Philipose, C. S. (2023). Gaussian Blurring Technique for Detecting and Classifying Acute Lymphoblastic Leukemia Cancer Cells from Microscopic Biopsy Images. Life, 13(2), 348. https://doi.org/10.3390/life13020348.

Danaee P, Ghaeini R, Hendrix DA. A Deep Learning Approach for Cancer Detection and Relevant Gene Identification. Pac Symp Biocomput. 2017; 22:219-229. doi: 10.1142/9789813207813_0022. PMID: 27896977; PMCID: PMC5177447.

Begum, S., Sarkar, R., Chakraborty, D., Sen, S., & Maulik, U. (2021). Application of active learning in DNA microarray data for cancerous gene identification. Expert Systems with Applications, 177, 114914. https://doi.org/10.1016/j.eswa.2021.114914

Hambali, M. A., Oladele, T. O., & Adewole, K. S. (2020). Microarray cancer feature selection: Review, challenges, and research directions. International Journal of Cognitive Computing in Engineering, 1, 78-97. https://doi.org/10.1016/j.ijcce.2020.11.001.

H. Almazrua and H. Alshamlan, "A Comprehensive Survey of Recent Hybrid Feature Selection Methods in Cancer Microarray Gene Expression Data," in IEEE Access, vol. 10, pp. 71427-71449, 2022, doi: 10.1109/ACCESS.2022.3185226.

Gupta, S., Gupta, M. K., Shabaz, M., & Sharma, A. (2022). Deep learning techniques for cancer classification using microarray gene expression data. Frontiers in Physiology, 13, 952709. https://doi.org/10.3389/fphys.2022.952709

Rupapara, V., Rustam, F., Aljedaani, W., Shahzad, H. F., Lee, E., & Ashraf, I. (2022). Blood cancer prediction using leukemia microarray gene data and hybrid logistic vector trees model. Scientific Reports, 12(1), 1-15. https://doi.org/10.1038/s41598-022-04835-6

E. H. Houssein, D. S. Abdelminaam, H. N. Hassan, M. M. Al-Sayed and E. Nabil, "A Hybrid Barnacles Mating Optimizer Algorithm with Support Vector Machines for Gene Selection of Microarray Cancer Classification," in IEEE Access, vol. 9, pp. 64895-64905, 2021, doi: 10.1109/ACCESS.2021.3075942.

Y. Ren, Z. -Y. Yang, H. Zhang, Y. Liang, H. -H. Huang and H. Chai, "A Genotype-Based Ensemble Classifier System for Non-Small-Cell Lung Cancer," in IEEE Access, vol. 8, pp. 128509-128518, 2020, doi: 10.1109/ACCESS.2020.3008750.

N. Bharanidharan et al., "Local Entropy Based Remora Optimization and Sparse Autoencoders for Cancer Diagnosis Through Microarray Gene Expression Analysis," in IEEE Access, vol. 12, pp. 39285-39299, 2024, doi: 10.1109/ACCESS.2024.3371887.

S. K. Prabhakar and S. -W. Lee, "An Integrated Approach for Ovarian Cancer Classification with the Application of Stochastic Optimization," in IEEE Access, vol. 8, pp. 127866-127882, 2020, doi: 10.1109/ACCESS.2020.3006154.

Ravindran U, Gunavathi C. A survey on gene expression data analysis using deep learning methods for cancer diagnosis. Prog Biophys Mol Biol. 2023 Jan; 177:1-13. doi: 10.1016/j.pbiomolbio.2022.08.004. Epub 2022 Aug 19. PMID: 35988771.

Mohamed, T. I., Ezugwu, A. E., Vincent, J., Ikotun, A. M., & Mohammed, M. (2023). A bio-inspired convolution neural network architecture for automatic breast cancer detection and classification using RNA-Seq gene expression data. Scientific Reports, 13(1), 1-19. https://doi.org/10.1038/s41598-023-41731-z.

M S, K.; Rajaguru, H.; Nair, A.R. Evaluation and Exploration of Machine Learning and Convolutional Neural Network Classifiers in Detection of Lung Cancer from Microarray Gene—A Paradigm Shift. Bioengineering 2023, 10, 933. https://doi.org/10.3390/bioengineering10080933

Nogueira, A.; Ferreira, A.; Figueiredo, M. A Machine Learning Pipeline for Cancer Detection on Microarray Data: The Role of Feature Discretization and Feature Selection. BioMedInformatics 2023, 3, 585-604. https://doi.org/10.3390/biomedinformatics3030040

Basavegowda, H. S., & Dagnew, G. (2020). Deep learning approach for microarray cancer data classification. CAAI Transactions on Intelligence Technology, 5(1), 22-33. https://doi.org/10.1049/trit.2019.0028

Xie, Weidong, et al. "Improved multi-layer binary firefly algorithm for optimizing feature selection and classification of microarray data." Biomedical Signal Processing and Control 79 (2023): 104080.

Ke, L., Li, M., Wang, L. et al. Improved swarm-optimization-based filter-wrapper gene selection from microarray data for gene expression tumor classification. Pattern Anal Applic 26, 455–472 (2023). https://doi.org/10.1007/s10044-022-01117-9

Alromema, N.; Syed, A.H.; Khan, T. A Hybrid Machine Learning Approach to Screen Optimal Predictors for the Classification of Primary Breast Tumors from Gene Expression Microarray Data. Diagnostics 2023, 13, 708. https://doi.org/10.3390/diagnostics13040708

Razzaque, Abdul, and Abhishek Badholia. "PCA based feature extraction and MPSO based feature selection for gene expression microarray medical data classification." Measurement: Sensors 31 (2024): 100945.

Hajieskandar, AliReza, et al. "Molecular cancer classification method on microarrays gene expression data using hybrid deep neural network and grey wolf algorithm." Journal of ambient intelligence and humanized computing (2023): 1-11.

Alisha Prasad, Syed Mohammad Abid Hasan, "DNA microarray analysis using a smartphone to detect the BRCA-1 gene", DOI: https://doi.org/10.1039/C8AN01020J, Issue 1, 2019.

Downloads

Published

06.08.2024

How to Cite

B. Shyamala Gowri. (2024). DNA Microarray for Cancer Classification Using Deep Learning Based on RESNET-50 Convolutional Neural Network Technique. International Journal of Intelligent Systems and Applications in Engineering, 12(23s), 1801–1815. Retrieved from https://ijisae.org/index.php/IJISAE/article/view/7126

Issue

Section

Research Article