Physics-Inspired Optimization for Quadratic Unconstrained Problems Using a Digital Annealer

Recently, inspired by quantum annealing, many solvers specialized for unconstrained binary quadratic programming problems have been developed. For further improvement and application of these solvers, it is important to clarify the differences in their performance for various types of problems. In this study, the performance of four quadratic unconstrained binary optimization problem solvers, namely D-Wave Hybrid Solver Service (HSS), Toshiba Simulated Bifurcation Machine (SBM), Fujitsu Digital Annealer (DA), and simulated annealing on a personal computer, was benchmarked. The problems used for benchmarking were instances of real problems in MQLib, instances of the SAT-UNSAT phase transition point of random not-all-equal 3-SAT (NAE 3-SAT), and the Ising spin glass Sherrington-Kirkpatrick (SK) model. Concerning MQLib instances, the HSS performance ranked first; for NAE 3-SAT, DA performance ranked first; and regarding the SK model, SBM performance ranked first. These results may help understand the strengths and weaknesses of these solvers.

Low-density parity-check (LDPC) codes have previously been considered as combinatorial optimization problems (COPs) in respect to its decoding. However, after defining it as such, none have gone so far as to convert the LDPC code into a quadratic unconstrained binary optimization (QUBO) problem. Thus, a new method is created: one that converts the LDPC code to a QUBO problem, inputs the QUBO problem into Ising machines (computers based on the Ising model that are designed to solve the QUBO problem), obtains the QUBO solution and converts it to a LDPC solution. By utilizing an actual Ising machine, LDPC solutions with code length of 256-bits have been obtained with an accuracy of 93.9% by average annealing time 214.0ms. The benefit of this newfound methodology goes beyond its theoretical imprint of obtaining LDPC solutions more accurately. It has only been a few years since the Ising machine has been developed. Therefore, in formulating this method, one expands the currently scope of studies involving Ising machines, helping current and future researchers unlock its full range of capabilities and possibilities.

Current hardware limitations restrict the potential when solving quadratic unconstrained binary optimization (QUBO) problems via the quantum approximate optimization algorithm (QAOA) or quantum annealing (QA). Thus, we consider training neural networks in this context. We first discuss QUBO problems that originate from translated instances of the traveling salesman problem (TSP): Analyzing this representation via autoencoders shows that there is way more information included than necessary to solve the original TSP. Then we show that neural networks can be used to solve TSP instances from both QUBO input and autoencoders' hidden state representation. We finally generalize the approach and successfully train neural networks to solve arbitrary QUBO problems, sketching means to use neuromorphic hardware as a simulator or an additional co-processor for quantum computing.

We propose a new kernel that quantifies success for the task of computing a core-periphery partition for an undirected network. Finding the associated optimal partitioning may be expressed in the form of a quadratic unconstrained binary optimization (QUBO) problem, to which a state-of-the-art quantum annealer may be applied. We therefore make use of the new objective function to (a) judge the performance of a quantum annealer, and (b) compare this approach with existing heuristic core-periphery partitioning methods. The quantum annealing is performed on a commercially available D-Wave machine. The QUBO problem involves a full matrix even when the underlying network is sparse. Hence, we develop and test a sparsified version of the original QUBO which increases the available problem dimension for the quantum annealer. Results are provided on both synthetic and real data sets, and we conclude that the QUBO/quantum annealing approach offers benefits in terms of optimizing this new quantity of interest.

We consider the problem of computing a sparse binary representation of an image. To be precise, given an image and an overcomplete, non-orthonormal basis, we aim to find a sparse binary vector indicating the minimal set of basis vectors that when added together best reconstruct the given input. We formulate this problem with an L2 loss on the reconstruction error, and an L0 (or, equivalently, an L1) loss on the binary vector enforcing sparsity. This yields a so-called Quadratic Unconstrained Binary Optimization (QUBO) problem, whose solution is generally NP-hard to find. The contribution of this work is twofold. First, the method of unsupervised and unnormalized dictionary feature learning for a desired sparsity level to best match the data is presented. Second, the binary sparse coding problem is then solved on the Loihi 1 neuromorphic chip by the use of stochastic networks of neurons to traverse the non-convex energy landscape. The solutions are benchmarked against the classical heuristic simulated annealing. We demonstrate neuromorphic computing is suitable for sampling low energy solutions of binary sparse coding QUBO models, and although Loihi 1 is capable of sampling very sparse solutions of the QUBO models, there needs to be improvement in the implementation in order to be competitive with simulated annealing.

Recent hardware advances in quantum and quantum-inspired annealers promise substantial speedup for solving NP-hard combinatorial optimization problems compared to general-purpose computers. These special-purpose hardware are built for solving hard instances of Quadratic Unconstrained Binary Optimization (QUBO) problems. In terms of number of variables and precision of these hardware are usually resource-constrained and they work either in Ising space {-1,1} or in Boolean space {0,1}. Many naturally occurring problem instances are higher-order in nature. The known method to reduce the degree of a higher-order optimization problem uses Rosenberg's polynomial. The method works in Boolean space by reducing the degree of one term by introducing one extra variable. In this work, we prove that in Ising space the degree reduction of one term requires the introduction of two variables. Our proposed method of degree reduction works directly in Ising space, as opposed to converting an Ising polynomial to Boolean space and applying previously known Rosenberg's polynomial. For sparse higher-order Ising problems, this results in a more compact representation of the resultant QUBO problem, which is crucial for utilizing resource-constrained QUBO solvers.

Earthquake rupture forecasting is a critical component of seismic hazard analysis and requires identifying physically plausible rupture paths across complex fault networks. At its core, this task could be formulated as a large-scale combinatorial optimization problem, which involves selecting an optimal subset of fault segments from a set of candidates. Such problems pose significant challenges for traditional algorithms, as the number of admissible multi-fault ruptures grows combinatorially. Current operational workflows rely on locally applied plausibility filters. While computationally efficient, such greedy local heuristics risk excluding globally competitive rupture scenarios, particularly in regions with dense fault connectivity and competing rupture pathways. This work investigates whether quantum annealing hardware can serve as a sampling accelerator for exploring the ensemble of physically plausible ruptures beyond what is currently accessible to classical approaches. Designing a problem formulation that remains scientifically meaningful while respecting the constraints of current quantum hardware (size, noise, etc.) is nontrivial, and naïve encodings often collapse under these limitations. We encode rupture plausibility modeling as low energy solutions to a quadratic unconstrained binary optimization (QUBO) problem defined on a fault-network middle graph. Binary variables represent activated fault segments, while local interaction terms encode Coulomb stress transfer (as a proxy for pairwise rupture compatibility), continuity preferences, and branching behavior. Here, we adopt a classical-quantum hybrid workflow: the quantum annealer is used to sample globally competitive rupture candidates, while classical post-processing implements physical constraints to filter out non-physical ruptures. The workflow is demonstrated on a subset of the fault network used in the 2023 USGS National Seismic Hazard Model including over 200 fault segments, using both simulated thermal and quantum annealing on D-Wave hardware. Results show that our hardware-aware formulation and conditioning enable robust sampling on comparatively large fault-network instances. Views on quantum computing are polarized: some overstate its power, while others dismiss it as impractical. Our results help bridge this by establishing a concrete, testable pathway for integrating quantum annealing into rupture-modeling workflows on existing purpose-built quantum devices.—---This work is supported by the ICSC National Research Centre for High Performance Computing, Big Data and Quantum Computing (CN00000013, CUP D53C22001300005) within the European Union-NextGenerationEU program (National Recovery and Resilience Plan (PNRR) - Mission 4 Component 2 Investment 1.4.)

Quantum annealing is a model for quantum computing that is aimed at solving hard optimization problems by representing them as quadratic unconstrained binary optimization (QUBO) problems. Although many NP-hard problems can easily be formulated as binary-variable problems with a quadratic objective function, such formulations typically also include constraints, which are not allowed in a QUBO. Hence, such constraints are usually incorporated in the objective function as additive penalty terms. While there is substantial previous work on implementing linear equality constraints, the case of inequality constraints has not much been studied. In this paper, we propose a new approach for formulating and embedding inequality constraints as penalties and describe early implementation results.

One of the biggest obstacles to creating precise machine learning models is choosing representative and pertinent characteristics from big, unbalanced datasets. While too many features raise the risk of overfitting and computational expense, class imbalance frequently results in decreased accuracy and bias. The Simulated Annealing technique is used in this study to tackle a Quadratic Unconstrained Binary Optimization (QUBO) problem that is formulated as a quantum-assisted feature selection method to handle these problems. The technique seeks to reduce inter-feature redundancy and the number of selected features. There are 102,487 samples in the majority class and 11,239 in the minority class, totaling 28 characteristics in the experimental dataset. Nine ideal features were found during the feature selection method (12, 14, 15, 22, 23, 24, 25, 27, and 28). Ten-fold cross-validation was used to assess a Random Forest Classifier that was trained using an 80:20 split. With precision, recall, f1-score, and accuracy all hitting 1.00, the suggested QUBO+SMOTE method demonstrated exceptional performance. Comparatively, QUBO without SMOTE performed worse with accuracy 0.95 and minority-class f1-score of only 0.71, whereas a traditional Recursive Feature Elimination (RFE) approach obtained accuracy 0.97 with minority-class f1-score of 0.94. These findings indicate that QUBO can reduce dimensionality and address class imbalance which requires its integration with SMOTE. This study demonstrates how quantum computing can enhance the effectiveness and efficiency of machine learning, especially for large-scale imbalanced datasets

Quantum computations are very important branch of modern cryptology. According to the number of working physical qubits available in general-purpose quantum computers and in quantum annealers, there is no coincidence, that nowadays quantum annealers allow to solve larger problems. In this paper we focus on solving discrete logarithm problem (DLP) over binary fields using quantum annealing. It is worth to note, that however solving DLP over prime fields using quantum annealing has been considered before, no author, until now, has considered DLP over binary fields using quantum annealing. Therefore, in this paper, we aim to bridge this gap. We present a polynomial transformation of the discrete logarithm problem over binary fields to the Quadratic Unconstrained Binary Optimization (QUBO) problem, using approximately 3n2 logical variables for the binary field F2n. In our estimations, we assume the existence of an optimal normal base in the given fields. Such a QUBO instance can then be solved using quantum annealing.

Steric clashes pose a challenge when exploring dense protein systems using conventional explicit-chain methods. A minimal example is a single lattice protein confined on a minimal grid, with no free sites. Finding its minimum energy is a hard optimization problem, with similarities to scheduling problems. It can be recast as a quadratic unconstrained binary optimization (QUBO) problem amenable to classical and quantum approaches. We show that this problem in its QUBO form can be swiftly and consistently solved for chain length 48, using either classical simulated annealing or hybrid quantum-classical annealing on a D-Wave system. In fact, the latter computations required about 10 s. We also test linear and quadratic programming methods, which work well for a lattice gas but struggle with chain constraints. All methods are benchmarked against exact results obtained from exhaustive structure enumeration, at a high computational cost.

The hydrophobic polarity (HP) protein folding model is a simplified computation model utilized to study the folding of proteins into their three-dimensional structures. Understanding how proteins fold and misfold is fundamental to designing effective, safe drugs, allowing for targeted therapies and better patient outcomes. The amino acids of a protein can be categorized as either hydrophobic or polar, where the hydrophobic beads tend to cluster together in a properly folded protein to minimize exposure to the surrounding environment. Determining the lowest energy configurations of the HP model is a non-deterministic polynomial (NP) hard problem. One method is formulating the HP model as a quadratic unconstrained binary optimization (QUBO) problem which can be mapped to an Ising machine. In the Ising model, the lowest energy state of the system represents the correct lattice configuration of the folded protein. The Ising machine technique utilized of simulated annealing allows for future application of the work on an integrated silicon photonic chip. Alternatively, reinforcement learning designed with an energy-based reward function can optimize the HP model by adapting to the environment without the consequence of remaining in local minima like that of the Ising machine. A hybrid pipeline combining the Ising machine and reinforcement learning sequentially was designed to determine the two-dimensional lattice configurations of various protein chain lengths and sequences, combining the parallel optimization of the Ising machine on an integrated photonic platform and the adaptability of the reinforcement learning algorithm. Results found that this hybrid model improved the accuracy and ability of determining the lowest energy state in contrast to the Ising machine alone as well as improved the efficiency by reducing the number of iterations required when compared solely to reinforcement learning. Future work focuses on implementing a parallel pipeline approach as well as adapting to a three-dimensional model.

Quadratic unconstrained binary optimization (QUBO) has gained popularity over the past ten years both for the wide range of problems that can be expressed in this form and for its compatibility with many quantum computing architectures. More recently, quantum annealers have advanced to the point where the scaling of qubits makes real-world applications increasingly feasible; however, current architectures remain restricted to solving quadratic unconstrained binary optimization problems, which can represent at most two-body interactions. Here we systematically examine the shortcomings of the QUBO framework and modern quantum annealers through the lens of the high-dimensional, exponentially scaling problem of RNA structure prediction, and find results that are generalizable to QUBO formalisms writ large. We find that using the QUBO framework to predict RNA structures results in poor accuracy, which becomes worse as system size scales. We determine that the fundamental constraint of two-body interactions prevents emergent correlations in the system, which are crucial to accurate structure prediction. Furthermore, we highlight that explicit, higher-order, empirical terms that are needed to improve structure prediction are incompatible with a QUBO framework. Finally, we show that our energy landscape has many deep local minima, which lead to local minima trapping and prevent permutation invariance. The relevance of these findings to other applications of QUBO, and therefore to modern quantum annealers more broadly, are discussed, with our work providing the first explicit explanation of why these formalisms have failed and will continue to fail in high-dimensional systems with similar constraints.

In the field of microlithography, conventional computers are widely used for mask optimization. Recent progress of quantum and quantum-inspired computers has encouraged the development of quantum algorithms for numerous applications. So far, no method has been established for solving mask optimization problems with quantum computers. We introduced a simple model that describes the mask optimization problem as a quadratic unconstrained binary optimization (QUBO) problem, which is easily implemented on these computers. For simplicity, we assume there exists a target image profile on the wafer. The target can be the image of an existing mask or a virtual ideal mask which may be designed as a pixelated mask having a continuous transmission distribution. The solution is evaluated as the difference between the simulated image profile on the wafer surface and the target profile.

Resource allocation of wide-area internet networks is inherently a combinatorial optimization problem that if solved quickly, could provide near real-time adaptive control of internet-protocol traffic ensuring increased network efficacy and robustness, while minimizing energy requirements coming from power-hungry transceivers. In recent works we demonstrated how such a problem could be cast as a quadratic unconstrained binary optimization (QUBO) problem that can be embedded onto the D-Wave Advantage™ quantum annealer system, demonstrating proof of principle. Our initial studies left open the possibility for improvement of D-Wave solutions via judicious choices of system run parameters. Here we report on our investigations for optimizing these system parameters, and how we incorporate machine learning (ML) techniques to further improve on the quality of solutions. In particular, we use the Hamming distance to investigate correlations between various system-run parameters and solution vectors. We then apply a decision tree neural network (NN) to learn these correlations, with the goal of using the neural network to provide further guesses to solution vectors. We successfully implement this NN in a simple integer linear programming (ILP) example, demonstrating how the NN can fully map out the solution space that was not captured by D-Wave. We find, however, for the 3-node network problem the NN is not able to enhance the quality of space of solutions.