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arXiv:2507.18003 · Applied Physics Reviews

Black-box optimization using factorization and Ising machines

Ryo Tamura, Yuya Seki, Yuki Minamoto, Koki Kitai, Yoshiki Matsuda, Shu Tanaka, Koji Tsuda

Published Apr 14, 2026• 5 citations
arXivHTMLPDF

Abstract

Black-box optimization (BBO) is used in materials design, drug discovery, and hyperparameter tuning in machine learning. The world is experiencing several of these problems. In this review, a factorization machine with quantum annealing or with quadratic-optimization annealing (FMQA) algorithm to realize fast computations of BBO using Ising machines (IMs) is discussed. The FMQA algorithm uses a factorization machine (FM) as a surrogate model for BBO. The FM model can be directly transformed into a quadratic unconstrained binary optimization model that can be solved using IMs. This makes it possible to optimize the acquisition function in BBO, which is a difficult task using conventional methods without IMs. Consequently, it has the advantage of handling large BBO problems. To be able to perform BBO with the FMQA algorithm immediately, we introduce the FMQA algorithm along with Python packages to run it. In addition, we review examples of applications of the FMQA algorithm in various fields, including physics, chemistry, materials science, and social sciences. These successful examples include binary and integer optimization problems, as well as more general optimization problems involving graphs, networks, and strings, using a binary variational autoencoder. We believe that BBO using the FMQA algorithm will become a key technology in IMs, including quantum annealers.

DOI
10.1063/5.0275450

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Black-box optimization (BBO) is used in materials design, drug discovery, and hyperparameter tuning in machine learning. The world is experiencing several of these problems. In this review, a factorization machine with quantum annealing or with quadratic-optimization annealing (FMQA) algorithm to realize fast computations of BBO using Ising machines (IMs) is discussed. The FMQA algorithm uses a factorization machine (FM) as a surrogate model for BBO. The FM model can be directly transformed into a quadratic unconstrained binary optimization model that can be solved using IMs. This makes it possible to optimize the acquisition function in BBO, which is a difficult task using conventional methods without IMs. Consequently, it has the advantage of handling large BBO problems. To be able to perform BBO with the FMQA algorithm immediately, we introduce the FMQA algorithm along with Python packages to run it. In addition, we review examples of applications of the FMQA algorithm in various fields, including physics, chemistry, materials science, and social sciences. These successful examples include binary and integer optimization problems, as well as more general optimization problems involving graphs, networks, and strings, using a binary variational autoencoder. We believe that BBO using the FMQA algorithm will become a key technology in IMs, including quantum annealers.
We introduce kernel-QA, a black-box optimization (BBO) method that constructs surrogate models analytically using low-order polynomial kernels within a quadratic unconstrained binary optimization (QUBO) framework, enabling efficient utilization of Ising machines. The method has been evaluated on artificial landscapes, ranging from uni-modal to multi-modal, with input dimensions extending to 80 for real variables and 640 for binary variables. The results demonstrate that kernel-QA is particularly effective for optimizing black-box functions characterized by local minima and high-dimensional inputs, showcasing its potential as a robust and scalable BBO approach.
In black-box combinatorial optimization, objective evaluations are often expensive, so high quality solutions must be found under a limited budget. Factorization machine with quantum annealing (FMQA) builds a quadratic surrogate model from evaluated samples and optimizes it on an Ising machine. However, FMQA requires binary decision variables, and for nonbinary structures such as integer permutations, the choice of binary encoding strongly affects search efficiency. If the encoding fails to reflect the original neighborhood structure, small Hamming moves may not correspond to meaningful modifications in the original solution space, and constrained problems can yield many infeasible candidates that waste evaluations. Recent work combines FMQA with a binary autoencoder (bAE) that learns a compact binary latent code from feasible solutions, yet the mechanism behind its performance gains is unclear. Using a small traveling salesman problem as an interpretable testbed, we show that the bAE reconstructs feasible tours accurately and, compared with manually designed encodings at similar compression, better aligns tour distances with latent Hamming distances, yields smoother neighborhoods under small bit flips, and produces fewer local optima. These geometric properties explain why bAE+FMQA improves the approximation ratio faster while maintaining feasibility throughout optimization, and they provide guidance for designing latent representations for black-box optimization.
Black-box optimization has potential in numerous applications such as hyperparameter optimization in machine learning and optimization in design of experiments. Ising machines are useful for binary optimization problems because variables can be represented by a single binary variable of Ising machines. However, conventional approaches using an Ising machine cannot handle black-box optimization problems with non-binary values. To overcome this limitation, we propose an approach for integer-variable black-box optimization problems by using Ising/annealing machines and factorization machines in cooperation with three different integer-encoding methods. The performance of our approach is numerically evaluated with different encoding methods using a simple problem of calculating the energy of the hydrogen molecule in the most stable state. The proposed approach can calculate the energy using any of the integer-encoding methods. However, one-hot encoding is useful for problems with a small size.
This paper presents an initialization method that can approximate a given approximate Ising model with a high degree of accuracy using a factorization machine (FM), a machine learning model. The construction of an Ising models using an FM is applied to black-box combinatorial optimization problems using factorization machine with quantum annealing (FMQA). It is anticipated that the optimization performance of FMQA will be enhanced through an implementation of the warm-start method. Nevertheless, the optimal initialization method for leveraging the warm-start approach in FMQA remains undetermined. Consequently, the present study compares initialization methods based on random initialization and low-rank approximation, and then identifies a suitable one for use with warm-start in FMQA through numerical experiments. Furthermore, the properties of the initialization method by the low-rank approximation for the FM are analyzed using random matrix theory, demonstrating that the approximation accuracy of the proposed method is not significantly influenced by the specific Ising model under consideration. The findings of this study will facilitate advancements of research in the field of black-box combinatorial optimization through the use of Ising machines.
A black-box optimization algorithm such as Bayesian optimization finds the extremum of an unknown function by alternating the inference of the underlying function and optimization of an acquisition function. In a high-dimensional space, such algorithms perform poorly due to the difficulty of acquisition function optimization. Herein, we apply Ising machines to overcome the difficulty in the continuous black-box optimization. As an Ising machine specializes in optimization of binary problems, a continuous vector has to be encoded to binary, and the solution by Ising machines has to be translated back. Our method has the following three parts: (1) random subspace coding based on axis-parallel hyperrectangles from continuous vector to binary vector, (2) a quadratic unconstrained binary optimization (QUBO) defined by the acquisition function based on the nonnegative-weighted linear regression model, which is solved by Ising machines, and (3) a penalization scheme to ensure that the solution can be translated back. It is shown with benchmark tests that its performance using the D-Wave Advantage quantum annealer and simulated annealing is competitive with a state-of-the-art method based on the Gaussian process in high-dimensional problems. Our method may open up the possibility of Ising machines and other QUBO solvers, including a quantum approximate optimization algorithm using gated-quantum computers, and may expand its range of application to continuous-valued problems.
Ising machines including quantum annealers have attracted attention as efficient solvers for combinatorial optimization problems (COPs). To use Ising machines, the objective function and constraints of a COP must be expressed in a QUBO (quadratic unconstrained binary optimization) form. However, their application range is practically limited since some COPs are difficult to formulate in a QUBO form, or require a large number of binary variables. Quadratic three-dimensional assignment problem (Q3AP) is a challenging problem for Ising machines to solve since the number of required binary variables rapidly increases with the problem size N. In this paper, to overcome the difficulty, we propose a method to reduce the number of necessary variables fromN3N^{3}N3to2N22N^{2}2N2by using a factorization machine with quantum annealing (FMQA) to estimate QUBO through machine learning. Experimental results with a real Ising machine demonstrate that the proposed method can obtain the best-known solution in a short time.