Abstract Quantum machine learning algorithms using the power of quantum computing provide fast- developing approaches for solving complicated problems and speeding-up calculations for big data. As such, they could effectively operate better than the classical algorithms. Herein, we demonstrate for the first time the classification of eleven cancers based on the gene expression values with 4495 samples using quantum machine learning. In addition, we compare the obtained quantum classification results with the classical outcomes. By implementing a dimensional reduction method, we introduce significant biomarkers for each cancer. In this research, we express that some of the identified gene biomarkers are consistent with DNA promotor methylation, and some other ones can be applied for the survival determination of patients.
Abstract Quantum machine learning algorithms using the power of quantum computing provide fast- developing approaches for solving complicated problems and speeding-up calculations for big data. As such, they could effectively operate better than the classical algorithms. Herein, we demonstrate for the first time the classification of eleven cancers based on the gene expression values with 4495 samples using quantum machine learning. In addition, we compare the obtained quantum classification results with the classical outcomes. By implementing a dimensional reduction method, we introduce significant biomarkers for each cancer. In this research, we express that some of the identified gene biomarkers are consistent with DNA promotor methylation, and some other ones can be applied for the survival determination of patients.
Quantum machine learning (QML) algorithms have demonstrated the power of quantum computing for solving complex problems and big data in certain tasks. In this study, we explore the capabilities of QML for the classification of real-world biological large datasets including ten different cancer types based on gene expression values. By comparing the classification results obtained from the quantum algorithm with those from classical approaches, we disclose that the QML algorithm overall achieves comparable and reliable results. Moreover, we identify novel biomarkers that can contribute to the understanding of cancer biology. Some of these biomarkers are consistent with DNA promoter methylation. Our findings highlight the potential of QML in cancer classification and biomarker discovery, paving the way for future advancements in other disease research and clinical applications.
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.
Quantum computing is a promising new approach to tackle the complex real-world computational problems by harnessing the power of quantum mechanics principles. The inherent parallelism and exponential computational power of quantum systems hold the potential to outpace classical counterparts in solving complex optimization problems, which are pervasive in machine learning. Quantum Support Vector Machine (QSVM) is a quantum machine learning algorithm inspired by classical Support Vector Machine (SVM) that exploits quantum parallelism to efficiently classify data points in high-dimensional feature spaces. We provide a comprehensive overview of the underlying principles of QSVM, elucidating how different quantum feature maps and quantum kernels enable the manipulation of quantum states to perform classification tasks. Through a comparative analysis, we reveal the quantum advantage achieved by these algorithms in terms of speedup and solution quality. As a case study, we explored the potential of quantum paradigms in the context of a real-world problem: classifying pancreatic cancer biomarker data. The Support Vector Classifier (SVC) algorithm was employed for the classical approach while the QSVM algorithm was executed on a quantum simulator provided by the Qiskit quantum computing framework. The classical approach as well as the quantum-based techniques reported similar accuracy. This uniformity suggests that these methods effectively captured similar underlying patterns in the dataset. Remarkably, quantum implementations exhibited substantially reduced execution times demonstrating the potential of quantum approaches in enhancing classification efficiency. This affirms the growing significance of quantum computing as a transformative tool for augmenting machine learning paradigms and also underscores the potency of quantum execution for computational acceleration.
Quantum machine learning offers a promising new paradigm for computational biology by leveraging quantum mechanical principles to enhance cancer classification, biomarker discovery, and bioinformatics diagnostics. In this study, we apply QML to identify subtype specific biomarkers for lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), the two predominant forms of non-small cell lung cancer. Our methodology involves a two-phase process: in Phase 1, differential expression analysis and methylation analysis between tumor and normal samples allows us to identify LUAD-specific and LUSC-specific genes, revealing potential prognostic biomarkers for cancer subtypes. Phase 2 focuses on developing a quantum classifier capable of distinguishing between LUAD and LUSC tumors, as well as between tumor and normal samples. This classifier not only enhances diagnostic precision but also demonstrates the quantum advantage in processing large-scale multiomic datasets. Our results consistently demonstrated that Sample3, representing the combined gene set, achieved the highest overall predictive performance in all metrics. These results demonstrate that QML provides an effective and scalable approach for biomarker discovery and subtype specific cancer classification. GO enrichment analysis highlighted the significant involvement of genes in synaptic signaling, ion channel regulation, and neuronal development. In the quantum phase, KEGG analysis further identified enrichment in cancer-associated pathways, including neurotrophin, MAPK, Ras, and PI3KAkt signaling, with key genes such as NGFR, NTRK2, and NTF3 suggesting a central role in neurotrophinmediated oncogenic processes. Our findings highlight the growing potential of quantum computing to advance precision oncology and next-generation biomedical analytics.
Breast cancer, the unruly development of abnormal cells in breasts, is a pressing public health issue and needs early detection for improving survival rates. Machine learning algorithms have shown promising results in breast cancer classification and detection. This study evaluates the performances of traditional and quantum machine learning techniques for data classification of breast cancer, emphasizing their effectiveness in discerning patterns using reduced set of features. An approach is proposed to reduce 30-dimensional features to 2-dimensional features using widely applied Principal Component Analysis (PCA), Incremental PCA, Truncated Singular Value Decomposition and Kernel PCA techniques. This study aims to provide an insight on the impact of reduction of features on the classification of breast cancer using classical and quantum machine learning techniques.
Introduction: In recent years, high-dimensional clinical and genomic data have gained significant importance for prognosis and personalized medicine in breast cancer. But the use of quantum machine learning (QML) on such data is limited by the availability of few qubits, the computation time of quantum simulation, and dimensionality reduction. This work systematically compares several QML architectures for breast cancer classification in the presence of realistic and simulator constraints. Methods: The experiments were performed on a dataset of METABRIC breast cancer patients (2,509 patients). After handling missing values and one-hot encoding, there were 63 features in the processed data set. The feature space was reduced by Principal Component Analysis (PCA) to 12, 4 and 2 components for the implementations of quantum computers, respectively, with 56.10 ± 0.14%, 26.78 ± 0.57% and 16.23 ± 0.33% of the variance retained. Three QML models were tested: Quantum Neural Networks (QNN), Quantum K-Nearest Neighbors (QKNN), and Quantum Support Vector Machines (QSVM), with the models being simulated. Seven classical classification models were tested: Logistic Regression, SVM with RBF kernel, K-Nearest Neighbors, Random Forest, XGBoost, LightGBM and Multilayer Perceptron, both with PCA-matched and full 63-feature representation. All primary results are reported with 5-fold cross validation. Results: Among the evaluated QML architectures, QKNN using 12 principal components achieved the strongest performance, attaining an accuracy of **75.11% ± 3.76%**, an F1-score of **0.7088 ± 0.0433**, and a ROC-AUC of **0.8148 ± 0.0394**. Even though all of the QML models performed significantly poorly in comparison to classical models trained on the entire 63-feature data set, the latter models were able to achieve about **94% accuracy** with XGBoost, Random Forest, and Logistic Regression. The comparison also showed the effect of information loss due to PCA is significant in predictive performance in both classical and quantum models. Discussion: The results show that for high dimensional breast cancer data, currently available simulator-based QML models can learn meaningful patterns with limited quantum resources, but are not as effective as powerful classical machine learning models when complete feature representations are available. The study does not report any sort of quantum advantage or clinical use, but rather a benchmark of current QML architectures that has been rigorously calculated and repeated, with a focus on the impact of dimensionality reduction, validation approaches, and simulator limitations, as well as outlining challenges that need to be overcome prior to practical implementation on real quantum hardware.