QUBO Problem Formulation of Fragment-Based Protein-Ligand Flexible Docking.

Protein-ligand docking plays a significant role in structure-based drug discovery. This methodology aims to estimate the binding mode and binding free energy between the drug-targeted protein and candidate chemical compounds, utilizing protein tertiary structure information. Reformulation of this docking as a quadratic unconstrained binary optimization (QUBO) problem to obtain solutions via quantum annealing has been attempted. However, previous studies did not consider the internal degrees of freedom of the compound that is mandatory and essential. In this study, we formulated fragment-based protein-ligand flexible docking, considering the internal degrees of freedom of the compound by focusing on fragments (rigid chemical substructures of compounds) as a QUBO problem. We introduced four factors essential for fragment-based docking in the Hamiltonian: (1) interaction energy between the target protein and each fragment, (2) clashes between fragments, (3) covalent bonds between fragments, and (4) the constraint that each fragment of the compound is selected for a single placement. We also implemented a proof-of-concept system and conducted redocking for the protein-compound complex structure of Aldose reductase (a drug target protein) using SQBM+, which is a simulated quantum annealer. The predicted binding pose reconstructed from the best solution was near-native (RMSD = 1.26 Å), which can be further improved (RMSD = 0.27 Å) using conventional energy minimization. The results indicate the validity of our QUBO problem formulation.

Optimization with photonic wave-based annealers.

Many NP-hard combinatorial optimization (CO) problems can be cast as a quadratic unconstrained binary optimization model, which maps naturally to an Ising model. The final spin configuration in the Ising model can adiabatically arrive at a solution to a Hamiltonian, given a known set of interactions between spins. We enhance two photonic Ising machines (PIMs) and compare their performance against classical (Gurobi) and quantum (D-Wave) solvers. The temporal multiplexed coherent Ising machine (TMCIM) uses the bistable response of an electro-optic modulator to mimic the spin up and down states. We compare TMCIM performance on Max-cut problems. A spatial photonic Ising machine (SPIM) convolves the wavefront of a coherent laser beam with the pixel distribution of a spatial light modulator to adiabatically achieve a minimum energy configuration, and solve a number partitioning problem (NPP). Our computational results on Max-cut indicate that classical solvers are still a better choice, while our NPP results show that SPIM is better as the problem size increases. In both cases, connectivity in Ising hardware is crucial for performance. Our results also highlight the importance of better understanding which CO problems are most likely to benefit from which type of PIM. This article is part of the theme issue 'Quantum annealing and computation: challenges and perspectives'.

Quantum Annealing in the NISQ Era: Railway Conflict Management.

We are in the noisy intermediate-scale quantum (NISQ) devices' era, in which quantum hardware has become available for application in real-world problems. However, demonstrations of the usefulness of such NISQ devices are still rare. In this work, we consider a practical railway dispatching problem: delay and conflict management on single-track railway lines. We examine the train dispatching consequences of the arrival of an already delayed train to a given network segment. This problem is computationally hard and needs to be solved almost in real time. We introduce a quadratic unconstrained binary optimization (QUBO) model of this problem, which is compatible with the emerging quantum annealing technology. The model's instances can be executed on present-day quantum annealers. As a proof-of-concept, we solve selected real-life problems from the Polish railway network using D-Wave quantum annealers. As a reference, we also provide solutions calculated with classical methods, including the conventional solution of a linear integer version of the model as well as the solution of the QUBO model using a tensor network-based algorithm. Our preliminary results illustrate the degree of difficulty of real-life railway instances for the current quantum annealing technology. Moreover, our analysis shows that the new generation of quantum annealers (the advantage system) does not perform well on those instances, either.

Dynamic Asset Allocation with Expected Shortfall via Quantum Annealing.

Recent advances in quantum hardware offer new approaches to solve various optimization problems that can be computationally expensive when classical algorithms are employed. We propose a hybrid quantum-classical algorithm to solve a dynamic asset allocation problem where a target return and a target risk metric (expected shortfall) are specified. We propose an iterative algorithm that treats the target return as a constraint in a Markowitz portfolio optimization model, and dynamically adjusts the target return to satisfy the targeted expected shortfall. The Markowitz optimization is formulated as a Quadratic Unconstrained Binary Optimization (QUBO) problem. The use of the expected shortfall risk metric enables the modeling of extreme market events. We compare the results from D-Wave's 2000Q and Advantage quantum annealers using real-world financial data. Both quantum annealers are able to generate portfolios with more than 80% of the return of the classical optimal solutions, while satisfying the expected shortfall. We observe that experiments on assets with higher correlations tend to perform better, which may help to design practical quantum applications in the near term.

Binary matrix factorization via collaborative neurodynamic optimization.

Binary matrix factorization is an important tool for dimension reduction for high-dimensional datasets with binary attributes and has been successfully applied in numerous areas. This paper presents a collaborative neurodynamic optimization approach to binary matrix factorization based on the original combinatorial optimization problem formulation and quadratic unconstrained binary optimization problem reformulations. The proposed approach employs multiple discrete Hopfield networks operating concurrently in search of local optima. In addition, a particle swarm optimization rule is used to reinitialize neuronal states iteratively to escape from local minima toward better ones. Experimental results on eight benchmark datasets are elaborated to demonstrate the superior performance of the proposed approach against six baseline algorithms in terms of factorization error. Additionally, the viability of the proposed approach is demonstrated for pattern discovery on three datasets.

Quantum computing for several AGV scheduling models.

Due to the high degree of automation, automated guided vehicles (AGVs) have been widely used in many scenarios for transportation, and traditional computing power is stretched in large-scale AGV scheduling. In recent years, quantum computing has shown incomparable performance advantages in solving specific problems, especially Combinatorial optimization problem. In this paper, quantum computing technology is introduced into the study of the AGV scheduling problem. Additionally two types of quadratic unconstrained binary optimisation (QUBO) models suitable for different scheduling objectives are constructed, and the scheduling scheme is coded into the ground state of Hamiltonian operator, and the problem is solved by using optical coherent Ising machine (CIM). The experimental results show that compared with the traditional calculation method, the optical quantum computer can save 92% computation time on average. It has great application potential.