A comparative evaluation of quantum machine learning architectures for breast cancer classification using clinical and genomic data

Abstract

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.