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arXiv · 2404.14101

Efficient molecular conformation generation with quantum-inspired algorithm

Yunting Li·Xiaopeng Cui·Zhaoping Xiong·Zuoheng Zou·Bowen Liu·Bi-Ying Wang·Runqiu Shu·Huangjun Zhu·Nan Qiao·Man-Hong Yung
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Abstract

Conformation generation, also known as molecular unfolding (MU), is a crucial step in structure-based drug design, remaining a challenging combinatorial optimization problem. Quantum annealing (QA) has shown great potential for solving certain combinatorial optimization problems over traditional classical methods such as simulated annealing (SA). However, a recent study showed that a 2000-qubit QA hardware was still unable to outperform SA for the MU problem. Here, we propose the use of quantum-inspired algorithm to solve the MU problem, in order to go beyond traditional SA. We introduce a highly-compact phase encoding method which can exponentially reduce the representation space, compared with the previous one-hot encoding method. For benchmarking, we tested this new approach on the public QM9 dataset generated by density functional theory (DFT). The root-mean-square deviation between the conformation determined by our approach and DFT is negligible (less than about 0.5 Angstrom), which underpins the validity of our approach. Furthermore, the median time-to-target metric can be reduced by a factor of five compared to SA. Additionally, we demonstrate a simulation experiment by MindQuantum using quantum approximate optimization algorithm (QAOA) to reach optimal results. These results indicate that quantum-inspired algorithms can be applied to solve practical problems even before quantum hardware become mature.

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Yunting Li, Xiaopeng Cui, Zhaoping Xiong, Zuoheng Zou, Bowen Liu, Bi-Ying Wang, Runqiu Shu, Huangjun Zhu, Nan Qiao, Man-Hong Yung. 2024-04-22. Efficient molecular conformation generation with quantum-inspired algorithm. https://arxiv.org/abs/2404.14101

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