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Journal of the American Society for Mass Spectrometry

Quantum Kernel Regression and Variational Quantum Regression for the CCS Prediction of Dissolved Organic Matter: A Comparative Benchmarking Study

Sadollah Ebrahimi, Armand Soldera, Céline Guéguen

Published Sep 10, 2026• 0 citations
Publisher

Abstract

Recent advances in quantum machine learning (QML) offer new opportunities for chemical property prediction, yet their practical performance relative to established classical models remains poorly characterized on real-world datasets. Building on our previous benchmark of classical and deep learning models for collision cross-section (CCS) predictions, we present an empirical comparison of quantum kernel regression (QKR) and a variational quantum regressor (VQR) against classical machine learning (CML) techniques, including Random Forest (RF), support vector regression (SVR), Lasso, and a Voting Regressor (VR) ensemble. Using an aquatic dissolved organic matter (DOM) dataset with five molecular descriptors and five chemical classes, we systematically investigate QKR feature map repetitions and classical readout kernels, as well as VQR circuit depths and optimizer choices, to identify performance-optimal QML configurations. Regression performance is evaluated using the mean absolute error (MAE), root mean square error (RMSE), and coefficient of determination (R2) across training-set sizes up to 600 molecules per class. Overall, RF and Lasso deliver the most robust CCS predictions, achieving R2 ≥ 0.9 for lignins, carbohydrates, lipids, and proteins. Meanwhile, the optimized QKR architecture exhibits substantial gains as data increase and achieves competitive performance on chemically homogeneous subsets such as carbohydrates and lipids. In contrast, the VQR ansatz remains consistently weaker than both QKR and the classical baselines across all classes and data sizes. The results highlight the strong influence of dataset size, feature representation, and molecular heterogeneity on QML performance while also identifying conditions under which quantum methods may become competitive in future studies.

DOI
10.1021/jasms.6c00135

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Recent advances in quantum machine learning (QML) offer new opportunities for chemical property prediction, yet their practical performance relative to established classical models remains poorly characterized on real-world datasets. Building on our previous benchmark of classical and deep learning models for collision cross-section (CCS) predictions, we present an empirical comparison of quantum kernel regression (QKR) and a variational quantum regressor (VQR) against classical machine learning (CML) techniques, including Random Forest (RF), support vector regression (SVR), Lasso, and a Voting Regressor (VR) ensemble. Using an aquatic dissolved organic matter (DOM) dataset with five molecular descriptors and five chemical classes, we systematically investigate QKR feature map repetitions and classical readout kernels, as well as VQR circuit depths and optimizer choices, to identify performance-optimal QML configurations. Regression performance is evaluated using the mean absolute error (MAE), root mean square error (RMSE), and coefficient of determination (R2) across training-set sizes up to 600 molecules per class. Overall, RF and Lasso deliver the most robust CCS predictions, achieving R2 ≥ 0.9 for lignins, carbohydrates, lipids, and proteins. Meanwhile, the optimized QKR architecture exhibits substantial gains as data increase and achieves competitive performance on chemically homogeneous subsets such as carbohydrates and lipids. In contrast, the VQR ansatz remains consistently weaker than both QKR and the classical baselines across all classes and data sizes. The results highlight the strong influence of dataset size, feature representation, and molecular heterogeneity on QML performance while also identifying conditions under which quantum methods may become competitive in future studies.
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Predicting drug-target binding affinity with limited training data remains a central challenge in computational drug discovery. We introduce a hybrid quantum-classical framework combining molecular descriptors with variational quantum circuits for interpretable binding affinity prediction. Seven physicochemical descriptors (MW, logP, TPSA, HBD/HBA, rotatable bonds, aromatic rings) were encoded into 6-qubit variational circuits using parameterized rotations and controlled-Z entanglement. Quantum kernels were extracted and used for regression on 1,200 BindingDB molecules across kinase, GPCR, and protease targets, with external validation on 300 ChEMBL compounds. Performance was compared against SVR, random forest, gradient boosting, and neural network baselines using 100-fold bootstrap validation. Variational quantum regression achieved MSE = 0.056 ± 0.009, outperforming SVR by 32% (0.082 ± 0.013), RF by 28%, and GBM by 24%. Quantum advantage was most significant in low-data regimes (n < 500), where VQR maintained R2 > 0.85 versus R2 < 0.72 for classical methods. External validation confirmed generalization (R2 = 0.83). Our Explainable Quantum Pharmacology framework revealed TPSA and logP as dominant predictive features through gradientbased sensitivity analysis, aligning with established medicinal chemistry principles. Quantum kernels provide measurable, chemically interpretable improvements for molecular property prediction in data-limited scenarios. This work demonstrates practical quantum advantage for early-stage drug discovery applications on near-term quantum hardware.
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Quantum machine learning has emerged as a promising paradigm that leverages quantum computational principles to potentially outperform classical approaches on specific learning tasks. This paper presents a comprehensive empirical investigation comparing Quantum Machine Learning (QML), specifically Quantum Support Vector Machines (QSVM) against Classical Machine Learning (CML) baselines including Logistic Regression, K Nearest Neighbors and classical SVMs. We implement quantum kernel methods using variational quantum circuits with angle embedding, IQP and ZZ feature maps on datasets exhibiting varying structural complexity. Our experiments on synthetic quantum generated datasets (Quantum Parity, Quantum Entanglement, Quantum Interference) demonstrate that QSVM achieves superior classification accuracy with improvements ranging from 2.9 % to 60 % over the best classical baselines achieving a 55.6 % overall win rate. Notably, on the Quantum Parity dataset, QSVM consistently outperformed all classical models across multiple configurations. On real-world benchmark datasets (Breast Cancer, Iris, Wine), QSVM Angle achieved 88% accuracy on Breast Cancer compared to 76% for classical SVM Linear a 15.8 % relative improvement while matching the best classical performance on Iris(100%)(100 \%)(100%)and Wine(92%)(92 \%)(92%). All experiments were conducted using quantum circuit simulation on classical hardware. These results provide empirical evidence that quantum kernel methods offer meaningful advantages over classical approaches on datasets with complex feature interactions. We discuss the theoretical foundations of these improvements including quantum feature space expressivity and kernel alignment.
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