Bridging Quantum and Classical Computing in Drug Design: Architecture Principles for Improved Molecule Generation

Abstract

Hybrid quantum-classical machine learning offers a path to leverage noisy intermediate-scale quantum (NISQ) devices for drug discovery, but optimal model architectures remain unclear. We systematically optimize the quantum-classical bridge architecture of generative adversarial networks (GANs) for molecule discovery using multi-objective Bayesian optimization. Our optimized model (BO-QGAN) significantly improves performance, achieving a 2.27-fold higher Drug Candidate Score (DCS) than prior quantum-hybrid benchmarks and 2.21-fold higher than the classical baseline, while reducing parameter count by more than 60%. Key findings favor layering multiple (3-4) shallow (4-8 qubit) quantum circuits sequentially, while classical architecture shows less sensitivity above a minimum capacity. This work provides the first empirically-grounded architectural guidelines for hybrid models, enabling more effective integration of current quantum computers into pharmaceutical research pipelines.

Published in Proceedings of the Workshop on Generative AI for Biology at the 42nd International Conference on Machine Learning 10 pages, 7 figures