Implementations of Quantum and Classical Topology-Aligned Architectures for Molecular Property Prediction

For low-data and resource-constrained regimes typical of quantum chemistry, parameter-efficient learning is a key objective. Here, we propose a topology-aligned inductive bias in which the model architecture mirrors the molecular bond graph: atoms map to a fixed register of computational units, and bonds determine which pairs interact through shared learnable parameters. This principle is instantiated in two architectures: a variational quantum circuit (Iso-QGNN), and a parameter-matched classical message-passing model (Iso-CGNN). The models are benchmarked on HOMO-LUMO and dipole moment binary classification tasks over the QM9 benchmark. With 64 trainable parameters, the implementations achieve test AUCs of approximately 0.88 (quantum) and 0.91 (classical) on the gap task, and close to 0.78 (both) on the dipole task. The models reach 90% of asymptotic performance within about 250 training molecules and gradient norms remain stable throughout training. These results indicate that the topology-aligned inductive bias is the active ingredient driving parameter efficiency at QM9 scale, with implications for matched-baseline benchmarking in quantum machine learning.

QCA-MolGAN: Quantum Circuit Associative Molecular GAN with Multi-Agent Reinforcement Learning

Navigating the vast chemical space of molecular structures to design novel drug molecules with desired target properties remains a central challenge in drug discovery. Recent advances in generative models offer promising solutions. This work presents a novel quantum circuit Born machine (QCBM)-enabled Generative Adversarial Network (GAN), called QCA-MolGAN, for generating drug-like molecules. The QCBM serves as a learnable prior distribution, which is associatively trained to define a latent space aligning with high-level features captured by the GANs discriminator. Additionally, we integrate a novel multi-agent reinforcement learning network to guide molecular generation with desired targeted properties, optimising key metrics such as quantitative estimate of drug-likeness (QED), octanol-water partition coefficient (LogP) and synthetic accessibility (SA) scores in conjunction with one another. Experimental results demonstrate that our approach enhances the property alignment of generated molecules with the multi-agent reinforcement learning agents effectively balancing chemical properties.