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Scientific Reports

Hybrid classical and quantum computing for enhanced glioma tumor classification using TCGA data

Emine Akpinar, Murat Oduncuoğlu

Published Jul 17, 2025• 11 citations
Publisher

Abstract

Abstract Gliomas, which are the most common malignant primary brain tumors, present significant challenges in terms of varying survival rates, treatment modalities, and prognostic processes between patients with low-grade gliomas (LGGs) and high-grade gliomas (HGGs). Accurate classification and grading of LGGs and HGGs are crucial for appropriate treatment planning and assessment of overall prognosis. The classification and grading of gliomas have undergone evolution over time, and the inclusion of molecular markers in the classification of glioma tumors by the WHO Central Nervous System (CNS) Tumors Classification in 2016 and the incorporation of advanced molecular diagnostics in 2021 have improved glioma tumor characterization. However, the high cost and limited accessibility of molecular genetic tests, coupled with the time-consuming nature of obtaining results, can lead to delays in critical treatment decisions. To address these challenges, various classical artificial intelligence methods, such as machine learning and deep learning, have been applied to problems in this field, yielding a certain level of success. Nevertheless, the continuous expansion of medical data dimensions, the inherent noise level in the data, and the limitations of the classical vector space pose significant challenges that classical artificial intelligence methods struggle to overcome. Recent studies have demonstrated that the use of quantum computing and quantum artificial intelligence technologies in healthcare not only addresses these problems but also accelerates complex data analyses and processes large datasets more efficiently. This paper presents a novel hybrid quantum (or classical-quantum) computing model aimed at differentiating between LGGs and HGGs using data from The Cancer Genome Atlas (TCGA). To the best of our knowledge, this study is the first to investigate the classification of LGGs and HGGs using a hybrid classical-quantum framework within the TCGA dataset. In the classical part of the study, an ensemble feature selection method was used to identify the most important molecular markers and clinical features within the TCGA glioma dataset. In the quantum section, six variational quantum classifier (VQC) models with different hyperparameters are proposed. These classifiers are subsequently used to differentiate between LGGs and HGGs using the features obtained from the ensemble model. The computational results show that among the six VQC models, the VQC-1 model, which incorporates Rx and CX gates in the feature map and Ry, Rz and CY gates in the parameterized quantum circuit and utilizes the AQCD optimization method, achieves the highest classification accuracy of 0.74. This study provides a novel perspective on the classification of glioma tumors by combining classical and quantum computing methods.

DOI
10.1038/s41598-025-97067-3

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Brain tumor classification remains a challenging task due to the complex heterogeneity of glioma characteristics and the limitations of conventional machine learning approaches in effectively integrating multimodal biomedical data. Recent advances in quantum machine learning have demonstrated promising capabilities for handling high-dimensional data; however, existing models often suffer from limited feature representation, insufficient multimodal integration, and optimization challenges. This paper proposes an Enhanced Hybrid Quantum–Classical Architecture (EHQCA) for glioma classification by combining MRI imaging features and TCGA molecular biomarkers within a unified learning framework. The proposed methodology employs ResNet-50 for imaging feature extraction, ensemble feature selection for molecular biomarkers, attention-based multimodal fusion, adaptive amplitude encoding, and a Multi-Layer Variational Quantum Classifier (ML-VQC). A hybrid Adam-SPSA optimization strategy is introduced to improve convergence speed and training stability. Experimental analysis demonstrates that the proposed EHQCA framework achieves superior classification performance, attaining 91.2% accuracy while reducing training epochs compared with existing quantum and classical models. The results highlight the effectiveness of multimodal fusion and quantum-enhanced learning for improving brain tumor diagnosis and supporting precision medicine applications
Accurate classification of glioma grades from magnetic resonance imaging (MRI) is essential for clinical decision-making in neuro-oncology. Although deep learning performance has been impressive with classical models, they struggle with high-dimensional medical imaging data and generalise poorly beyond their training data, especially in time- and resource-constrained settings. In light of the aforementioned challenges, we propose QuantumMedDx, a hybrid quantum–classical learning framework for classifying gliomas using MRI. The framework combines quantum feature encoding and variational quantum circuits with classical neural inference to improve diagnostic performance. The base model, QImageNet, uses amplitude-based quantum encoding for writing, entanglement-enabled parameterised quantum circuits (EPQCs) as feature extractors, and classical dense layers for classifying HGG and LGG from multimodal MRI slices. We demonstrate the effectiveness of the proposed approach on the BraTS 2021 benchmark dataset using a patient-aware 5-fold cross-validation protocol. Experimental results show that QuantumMedDx achieves accuracies of 94.12%, 93.30%, and 96.42%; F1-scores of 93.30% and 96.42%; and AUCs of 96.42% and 96.42%, respectively, outperforming conventional CNN, DNN, and SVM baselines. Ablation studies provide additional evidence of the performance improvements enabled by quantum Fourier transform and entanglement layers. Such results suggest that quantum–classical learning can efficiently improve feature extraction and discrimination in medical imaging, thus providing a modular and scalable route towards quantum–inspired clinical decision–support systems of the future.
DNA microarray technology enables the simultaneous measurement of expression levels of thousands of genes, thereby facilitating the understanding of the molecular mechanisms underlying complex diseases such as brain tumors and the identification of diagnostic genetic signatures. To derive meaningful biological insights from the high-dimensional and complex gene features obtained through this technology and to analyze gene properties in detail, classical artificial intelligence (AI)-based approaches such as machine learning (ML) and deep learning (DL) are widely employed. However, these methods face various limitations in managing high-dimensional vector spaces and modeling the intricate relationships among genes. In particular, challenges such as hyperparameter tuning, computational costs, and high processing power requirements can hinder their efficiency. To overcome these limitations, quantum computing and quantum computing-based AI approaches are gaining increasing attention. Leveraging quantum properties such as superposition and entanglement, quantum methods enable more efficient parallel processing of high-dimensional data and offer faster and more effective solutions to problems that are computationally demanding for classical methods. In this study, a novel model called “Deep VQC” is proposed, based on the Variational Quantum Classifier (VQC) approach. Developed using microarray data containing 54,676 gene features, the model successfully classified four different types of brain tumors-ependymoma, glioblastoma, medulloblastoma, and pilocytic astrocytoma-alongside healthy samples with high accuracy. Furthermore, compared to classical ML algorithms, the Deep VQC model demonstrated either superior or comparable classification performance. These results highlight the potential of quantum AI methods as an effective and promising approach for the analysis and classification of complex structures such as brain tumors based on gene expression features.
Early and correct diagnosis plays a key role in enhancing the outcome in brain tumor and lung cancer patients. Traditional Artificial Intelligence (AI) and Deep Learning (DL) models are handicapped by expensive computational costs and challenges in handling high-dimensional medical data. This research article presents a Quantum AI based Diagnostics System employing a hybrid quantum-classical computing model. The framework combines traditional feature preprocessing with the exponential power of quantum computing. For classification in brain tumors (e.g., LGGs/HGGs), the quantum core uses a Hybrid Quantum-Classical Integrated Neural Network (HQCINN) or Variational Quantum Classifier (VQC). For lung cancer prediction, the framework might employ quantum-enhanced clustering such as Quantum-Enhanced K-Medoids or optimization models such as Quantum --Genetic Binary Grey Wolf Optimizer (Q-GBGWO) with Extreme Learning Machines (ELM). This hybrid methodology is intended to achieve superior diagnostic efficacy and speed across both MRI and CT modalities, laying the groundwork for faster and more individualized clinical diagnostics.
Accurate and computationally efficient classification of brain tumors from MRI scans is critical for deployment in resource-constrained clinical settings, where conventional deep CNN architectures-despite achieving strong accuracy-often require large parameter counts that limit scalability. This work proposes a hybrid quantum-classical deep learning framework that combines a classical convolutional feature extractor with a variational quantum circuit (VQC) for multi-class tumor classification. Spatial features extracted by the CNN backbone will be dimensionality-reduced and encoded into quantum states using angle encoding; a parameterized quantum circuit will then process these features in a higher-dimensional Hilbert space, leveraging superposition and entanglement to capture non-linear feature correlations. Measurement outputs from the quantum layer will be passed to a classical fully connected layer for classification into glioma, meningioma, pituitary tumor, and no-tumor categories. The proposed framework will be evaluated on a publicly available benchmark MRI dataset and benchmarked against state-of-the-art classical CNN architectures in terms of accuracy, precision, recall, F1-score, and parameter efficiency. This study aims to demonstrate that quantum-enhanced layers can achieve competitive classification performance while substantially reducing trainable parameters, offering a practical direction for efficient, quantum-assisted medical image analysis.
Brain tumor image classification is an essential pre-processing task for tumor diagnosis and treatment planning. In medical imaging, quantum computing analyse medical imaging data, offering potential speedups and new representations compared to classical methods. The brain images are transformed through resizing and normalization to a uniform 32 × 32 × 3 resolution. Subsequently, these processed images are converted into vectors to enable encoding into quantum states. The feature set is reduced using Principal Component Analysis (PCA) to ensure compatibility with the restricted qubit count in the quantum circuits. Through amplitude encoding, these vectors are mapped to quantum states, allowing for a compact and efficient data representation within the quantum domain. A parameterized Variational Quantum Circuit(VQC), consisting of entangling gates and trainable rotations, processes the encoded quantum states to learn features that can effectively discriminate between classes. The loss is calculated from the measured expectation values of Pauli-Z observables and optimized using classical gradient descent, where the objective function is the mean squared error. The trained quantum model is designed for multi-class classification, specifically distinguishing between meningioma, glioma tumors, pituitary tumors, and the absence of a tumor. The outcome of this proposed work demonstrates the VQC’s advantage over classical baselines, including Random Forest, and Support Vector Machine (SVM) and Multi-Layer Perceptron (MLP). The VQC achieved the highest accuracy of 95% and the best robustness (Specificity 0.983). Crucially, the VQC accomplished this using only 24 trainable parameters, showcasing a significant increase in parameter efficiency compared to the classical models. The novelty of this work is the quantitative demonstration that a custom-designed, resource-efficient quantum model can outperform established classical deep learning methods in both performance and efficiency for complex medical image classification. The VQC provides a 3.5-fold gain in parameter efficiency, achieving the highest accuracy of 95% using only 24 trainable parameters. This efficiency is enabled by the novel application of amplitude encoding to the medical images, which compresses 16 features into just 4 qubits. The VQC demonstrates robustness vital for medical diagnostics, achieving a Specificity of 0.983. Its shallow architecture is also NISQ-friendly and remains stable by avoiding the Barren Plateau issue (Gradient Norm: 0.11), validating the path toward quantum advantage in diagnostic tools. The results of this approach highlight the potential amplitude encoding in quantum machine learning, as a feasible and effective method for classifying real-world medical images. This work also opens avenues for future hybrid quantum-classical diagnostic systems that could utilize richer quantum state encodings for significant gains in computational efficiency and accuracy.