×
Home Current Archive Editorial board
Instructions for papers
For Authors Aim & Scope Contact
Original scientific article

DEEP LEARNING-GUIDED GENOMIC PROFILING FOR BRAIN TUMOR SUBTYPING USING HYBRID FEATURE SELECTION AND ENSEMBLE CLASSIFICATION

By
M. Yuvaraja Orcid logo ,
M. Yuvaraja

Professor, Department of Electronics and Communication Engineering, P. A. College of Engineering and Technology , Pollachi , India

S. Sureshkumar Orcid logo ,
S. Sureshkumar

Assistant Professor, Department of Artificial Intelligence and Data Science,P. A. College of Engineering and Technology , Pollachi , India

J. Dhanasekar Orcid logo ,
J. Dhanasekar

Assistant Professor, Department of ECE ,Sri Eshwar College of Engineering , Coimbatore , India

Vilas Namdeo Nitnaware Orcid logo ,
Vilas Namdeo Nitnaware

Professor, MAEER’S MIT , Mumbai , India

M. Sowmya Orcid logo ,
M. Sowmya

Assistant Professor, Department of Computer Science and Applications (MCA), SRM Institute of Science and Technology (FSH) , Chennai , India

D. Kumar Orcid logo
D. Kumar

Associate Professor, Department of ECE, P.A. College of Engineering and Technology , Pollachi , India

Abstract

The problem of brain tumors is a range of different subtypes, which have a variety of clinical forms, and the diagnosis and treatment of tumors is a challenging task. This paper introduces a hybrid deep learning system that combines genomic profiling with MRI image analysis to provide an effective brain tumor subtyping. The framework is initiated by the preprocessing of MRI images, which is followed by grayscale conversion and noise reduction as done by Fast Non-Local Means (FNLM) filtering. This will aid in ensuring that important structural data is retained with minimal irrelevant noise. To conduct segmentation, the UNet++ framework is used, which is the best-performing architecture in medical image analysis. UNet++ enhances the conventional UNet by adding embedded skip routes, which allows a more productive information exchange between encoder and decoder networks, improving the accuracy of segmentation. The extraction of features is conducted by a local binary pattern (LBP), Gray-Level Co-occurrence Matrix (GLCM), and Discrete Wavelet Transform (DWT). These methods are able to reproduce both the frequency domain and textural characteristics of the tumor areas. The variables are further narrowed down to the most relevant ones by the Minimum Redundancy Maximum Relevance (mRMR) algorithm, thus only the most relevant features are taken in the classifier. The classification is done by an improved variant of the AlexNet that is optimized with the addition of batch normalization, global average pooling, and local response normalization parameters to minimize overfitting and maximize learning effectiveness. The model postulated in this study has a high performance of 99.79 %accuracy, 96.82 %sensitivity, 98.32 %specificity, and 98.61 %precision. These findings indicate the effectiveness of the hybrid approach, combining handcrafted characteristics and deep learning in early and confident brain tumor subtyping, which has considerable potential to enhance the level of diagnostic accuracy and individual treatment approaches in neuro-oncology.

References

1.
Solanki S, Singh UP, Chouhan SS, Jain S. Brain tumor detection and classification using intelligence  techniques: an overview. IEEE Access. 2023 Feb 6;11:12870-86.
2.
Esposito S, Ruggiero E, Di Castelnuovo A, Costanzo S, Bonaccio M, Bracone F, Esposito V, Innocenzi G,  Paolini S, Cerletti C, Donati MB. Identifying brain tumor patients’ subtypes based on pre-diagnostic history  and clinical characteristics: a pilot hierarchical clustering and association analysis. Frontiers in Oncology.  2023 Nov 29; 13:1276253.
3.
Park JH, de Lomana AL, Marzese DM, Juarez T, Feroze A, Hothi P, Cobbs C, Patel AP, Kesari S, Huang S,  Baliga NS. A systems approach to brain tumor treatment. Cancers. 2021 Jun 24;13(13):3152.
4.
Aggarwal M, Tiwari AK, Sarathi MP, Bijalwan A. An early detection and segmentation of Brain Tumor  using Deep Neural Network. BMC Medical Informatics and Decision Making. 2023 Apr 26;23(1):78.
5.
Shafana NJ, SenthilSelvi A. Analysis of AI based brain tumor detection and diagnosis. In2021 4th  international conference on computing and communications technologies (ICCCT) 2021 Dec 16 (pp. 627 633). IEEE.
6.
Abdusalomov AB, Mukhiddinov M, Whangbo TK. Brain tumor detection based on deep learning approaches  and magnetic resonance imaging. Cancers. 2023 Aug 18;15(16):4172.
7.
Jena B, Saxena S, Nayak GK, Balestrieri A, Gupta N, Khanna NN, Laird JR, Kalra MK, Fouda MM, Saba  L, Suri JS. Brain tumor characterization using radiogenomics in artificial intelligence framework. Cancers.  2022 Aug 22;14(16):4052.
8.
Mohan P, Veerappampalayam Easwaramoorthy S, Subramani N, Subramanian M, Meckanzi S. Handcrafted  deep-feature-based brain tumor detection and classification using mri images. Electronics. 2022 Dec  14;11(24):4178.
9.
Ramkissoon LA, Pegram W, Haberberger J, Danziger N, Lesser G, Strowd R, Dahiya S, Cummings TJ, Bi  WL, Abedalthagafi M, Sathyan P. Genomic profiling of circulating tumor DNA from cerebrospinal fluid to  guide clinical decision making for patients with primary and metastatic brain tumors. Frontiers in Neurology.  2020 Oct 19; 11:544680.
10.
Khalighi S, Reddy K, Midya A, Pandav KB, Madabhushi A, Abedalthagafi M. Artificial intelligence in  neuro-oncology: advances and challenges in brain tumor diagnosis, prognosis, and precision treatment. NPJ  precision oncology. 2024 Mar 29;8(1):80.
11.
Rasool M, Ismail NA, Boulila W, Ammar A, Samma H, Yafooz WM, Emara AH. A hybrid deep learning  model for brain tumour classification. Entropy. 2022 Jun 8;24(6):799.
12.
Raza A, Ayub H, Khan JA, Ahmad I, S. Salama A, Daradkeh YI, Javeed D, Ur Rehman A, Hamam H. A  hybrid deep learning-based approach for brain tumor classification. Electronics. 2022 Apr 5;11(7):1146.
13.
Díaz-Pernas FJ, Martínez-Zarzuela M, Antón-Rodríguez M, González-Ortega D. A deep learning approach  for brain tumor classification and segmentation using a multiscale convolutional neural network.  InHealthcare 2021 Feb 2 (Vol. 9, No. 2, p. 153). MDPI.
14.
Sadad T, Rehman A, Munir A, Saba T, Tariq U, Ayesha N, Abbasi R. Brain tumor detection and multi classification using advanced deep learning techniques. Microscopy research and technique. 2021  Jun;84(6):1296-308.
15.
Biswas A, Islam MS. Brain tumor types classification using K-means clustering and ANN approach. In2021  2nd International Conference on Robotics, Electrical and Signal Processing Techniques (ICREST) 2021 Jan  5 (pp. 654-658). IEEE.
16.
Renugadevi M, Narasimhan K, Ravikumar CV, Anbazhagan R, Pau G, Ramkumar K, Abbas M, Raju N,  Sathish K, Sevugan P. Machine learning empowered brain tumor segmentation and grading model for  lifetime prediction. IEEE Access. 2023 Oct 23; 11:120868-80.
17.
Thakur T, Batra I, Malik A, Ghimire D, Kim SH, Hosen AS. RNN-CNN based cancer prediction model for  gene expression. IEEE access. 2023 Nov 13; 11:131024-44.
18.
Dixon J, Akinniyi O, Abdelhamid A, Saleh GA, Rahman MM, Khalifa F. A hybrid learning-architecture for  improved brain tumor recognition. Algorithms. 2024 May 21;17(6):221.
19.
Gu C, Ren S. Enhancing brain cancer type prediction through machine learning algorithms and feature  selection techniques. Journal of Physics A: Mathematical and Theoretical. 2024 Oct 1;57(42):425601.
20.
Arora S, Lamba M. 3D brain image based tumor classification using ensemble of reinforcement transfer based belief neural networks. Multimedia Tools and Applications. 2025 Apr;84(14):14001-28.
21.
Menze BH, Jakab A, Bauer S, Kalpathy-Cramer J, Farahani K, Kirby J, Burren Y, Porz N, Slotboom J, Wiest  R, Lanczi L. The multimodal brain tumor image segmentation benchmark (BRATS). IEEE transactions on  medical imaging. 2014 Dec 4;34(10):1993-2024.
22.
Villani F, Civico R, Pucci S, Pizzimenti L, Nappi R, De Martini PM. A database of the coseismic effects  following the 30 October 2016 Norcia earthquake in Central Italy. Scientific data. 2018 Mar 27;5(1):1-1.
23.
Kim H, Lim S, Park M, Kim K, Kang SH, Lee Y. Optimization of fast non-local means noise reduction  algorithm parameter in computed tomographic phantom images using 3D printing technology. Diagnostics.  2024 Jul 23;14(15):1589. (1).
24.
Bhattacharyya S, Dutta P, Samanta D, Mukherjee A, Pan I, editors. Recent trends in computational  intelligence enabled research: theoretical foundations and applications. Academic Press; 2021 Jul 31.
25.
Madugalla AK, Perera M. Innovative uses of medical embedded systems in healthcare. Progress in  Electronics and Communication Engineering. 2024;2(1):48-59.

Citation

This is an open access article distributed under the  Creative Commons Attribution Non-Commercial License (CC BY-NC) License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 

Article metrics

Google scholar: See link

The statements, opinions and data contained in the journal are solely those of the individual authors and contributors and not of the publisher and the editor(s). We stay neutral with regard to jurisdictional claims in published maps and institutional affiliations.