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arXiv:1902.00462 · Science Advances

Molecular docking with Gaussian Boson Sampling

Leonardo Banchi, Mark Fingerhuth, Tomas Babej, Christopher Ing, Juan Miguel Arrazola

Published Jun 5, 2020• 169 citations
arXivHTMLPDF

Abstract

Gaussian Boson Samplers are photonic quantum devices with the potential to perform intractable tasks for classical systems. As with other near-term quantum technologies, an outstanding challenge is to identify specific problems of practical interest where these devices can prove useful. Here, we show that Gaussian Boson Samplers can be used to predict molecular docking configurations, a central problem for pharmaceutical drug design. We develop an approach where the problem is reduced to finding the maximum weighted clique in a graph, and show that Gaussian Boson Samplers can be programmed to sample large-weight cliques, i.e., stable docking configurations, with high probability, even with photon losses. We also describe how outputs from the device can be used to enhance the performance of classical algorithms. To benchmark our approach, we predict the binding mode of a ligand to the tumor necrosis factor-α converting enzyme, a target linked to immune system diseases and cancer.

DOI
10.1126/sciadv.aax1950

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Gaussian Boson Samplers are photonic quantum devices with the potential to perform intractable tasks for classical systems. As with other near-term quantum technologies, an outstanding challenge is to identify specific problems of practical interest where these devices can prove useful. Here, we show that Gaussian Boson Samplers can be used to predict molecular docking configurations, a central problem for pharmaceutical drug design. We develop an approach where the problem is reduced to finding the maximum weighted clique in a graph, and show that Gaussian Boson Samplers can be programmed to sample large-weight cliques, i.e., stable docking configurations, with high probability, even with photon losses. We also describe how outputs from the device can be used to enhance the performance of classical algorithms. To benchmark our approach, we predict the binding mode of a ligand to the tumor necrosis factor-α converting enzyme, a target linked to immune system diseases and cancer.
Gaussian boson sampling (GBS) has the potential to solve complex graph problems, such as clique finding, which is relevant to drug discovery tasks. However, realizing the full benefits of quantum enhancements requires large-scale quantum hardware with universal programmability. Here we have developed a time-bin-encoded GBS photonic quantum processor that is universal, programmable and software-scalable. Our processor features freely adjustable squeezing parameters and can implement arbitrary unitary operations with a programmable interferometer. Leveraging our processor, we successfully executed clique finding on a 32-node graph, achieving approximately twice the success probability compared to classical sampling. As proof of concept, we implemented a versatile quantum drug discovery platform using this GBS processor, enabling molecular docking and RNA-folding prediction tasks. Our work achieves GBS circuitry with its universal and programmable architecture, advancing GBS toward use in real-world applications.
Molecular docking is an important step in drug discovery, enabling the evaluation of receptor-ligand affinity while reducing experimental costs and increasing the number of possible tests. However, the high computational cost associated with molecular docking remains a limiting factor that can restrict both the experimental precision and the scale of the problems being addressed. To improve the future applicability of molecular docking, recent works have proposed the use of quantum algorithms based on Gaussian Boson Sampling quantum computers and also gate-based quantum computers. In this work, we propose the use of Quantum Circuit Evolution (QCE) for solving the molecular docking problem, a gate based and gradient-free quantum evolutionary method whose evolution is driven by the random application of unitary operations to a quantum circuit. The proposed algorithm demonstrated the ability to find the best solution to the problem in fewer steps than the methods presented in previous studies, exhibiting fast and stable convergence.
We present a quantum-inspired classical algorithm that can be used for graph-theoretical problems, such as finding the densest k subgraph and finding the maximum weight clique, which are proposed as applications of a Gaussian boson sampler. The main observation from Gaussian boson samplers is that a given graph’s adjacency matrix to be encoded in a Gaussian boson sampler is non-negative and that computing the output probability of Gaussian boson sampling restricted to a non-negative adjacency matrix is thought to be strictly easier than general cases. We first provide how to program a given graph problem into our efficient classical algorithm. We then numerically compare the performance of ideal and lossy Gaussian boson samplers, our quantum-inspired classical sampler, and the uniform sampler for finding the densest k subgraph and finding the maximum weight clique and show that the advantage from Gaussian boson samplers is not significant in general. We finally discuss the potential advantage of a Gaussian boson sampler over the proposed quantum-inspired classical sampler. Published by the American Physical Society 2024
Gaussian Boson Sampling (GBS) is capable of solving certain classes of graph problems owing to the samples produced by such a device having a connection to the hafnian matrix function. In particular, a GBS device has been shown to provide an enhancement in the search of cliques -- or complete subgraphs -- in undirected weighted graphs over classical algorithms. A graph can be mapped to a GBS experiment by configuring the squeezing parameters of the input states and programming the linear optical network. In practice, limited squeezing and photon loss degrade the performance of the GBS device for max-clique search. In comparison, coherent states -- often considered a classical resource due to their Poissonian statistics -- can be readily prepared across many modes using an attenuated laser. In this paper, we report an enhancement of the success rate of GBS in finding maximum weighted cliques by adding displacements under lossy conditions or when a limited amount of squeezing is available. Moreover, we report that this enhancement can be scaled up to large graphs with limited resource overheads.
Quantum computers, due to their superposition and entanglement properties, provide significant advantages in solving certain problems compared with classical computers. Therefore, it is crucial to identify issues that can be efficiently solved by noisy intermediate-scale quantum (NISQ) systems. Xanadu has introduced the X8 quantum chip, based on integrated photonic technology, along with important photonic platforms such as Strawberry Fields and Gaussian Boson Sampling (GBS), to solve specific computational problems. In this review article, after reviewing Boson Sampling (BS) and Gaussian Boson Sampling (GBS), we discuss the relationship between GBS and graph theory, including how graphs can be encoded in GBS. Some applications of GBS, particularly molecular docking and molecular vibrations, are also considered. The future goal of this study is to identify problems that can be represented as small graphs and solved using GBS with a limited number of optical modes.
Gaussian Boson Sampling (GBS) is a quantum computational model that leverages linear optics to solve sampling problems believed to be classically intractable. Recent experimental breakthroughs have demonstrated quantum advantage using GBS, motivating its application to real-world combinatorial optimization problems. In this work, we reformulate the graph coloring problem as an integer programming problem using the independent set formulation. This enables the use of GBS to identify cliques in the complement graph, which correspond to independent sets in the original graph. Our method is benchmarked against classical heuristics and exact algorithms on two sets of instances: Erdős-Rényi random graphs and graphs derived from a smart-charging use case. The results demonstrate that GBS can provide competitive solutions, highlighting its potential as a quantum-enhanced heuristic for graph-based optimization.