Quantum Annealing (QA) and QAOA are promising quantum optimisation algorithms used for finding approximate solutions to combinatorial problems on near-term NISQ systems. Many NP-hard problems can be reformulated as Quadratic Unconstrained Binary Optimisation (QUBO), which maps naturally onto quantum Hamiltonians. However, the limited qubit counts of current NISQ devices restrict practical deployment of such algorithms. In this study, we present the Hamiltonian Auto-Decomposition Optimisation Framework (HADOF), which leverages an iterative strategy to automatically divide the Quadratic Unconstrained Binary Optimisation (QUBO) Hamiltonian into sub-Hamiltonians which can be optimised separately using Hamiltonian based optimisers such as QAOA, QA or Simulated Annealing (SA) and aggregated into a global solution. We compare HADOF with Simulated Annealing (SA) and the CPLEX exact solver, showing scalability to problem sizes far exceeding available qubits while maintaining competitive accuracy and runtime. Furthermore, we realise HADOF for a toy problem on an IBM quantum computer, showing promise for practical applications of quantum optimisation.
Quantum Annealing (QA) and QAOA are promising quantum optimisation algorithms used for finding approximate solutions to combinatorial problems on near-term NISQ systems. Many NP-hard problems can be reformulated as Quadratic Unconstrained Binary Optimisation (QUBO), which maps naturally onto quantum Hamiltonians. However, the limited qubit counts of current NISQ devices restrict practical deployment of such algorithms. In this study, we present the Hamiltonian Auto-Decomposition Optimisation Framework (HADOF), which leverages an iterative strategy to automatically divide the Quadratic Unconstrained Binary Optimisation (QUBO) Hamiltonian into sub-Hamiltonians which can be optimised separately using Hamiltonian based optimisers such as QAOA, QA or Simulated Annealing (SA) and aggregated into a global solution. We compare HADOF with Simulated Annealing (SA) and the CPLEX exact solver, showing scalability to problem sizes far exceeding available qubits while maintaining competitive accuracy and runtime. Furthermore, we realise HADOF for a toy problem on an IBM quantum computer, showing promise for practical applications of quantum optimisation.
Practical applicability of quantum optimisation on near term devices is constrained by limited qubit counts and hardware noise, which restricts the scalability of quantum optimisation algorithms for combinatorial problems. The simulation of large quantum circuits is also difficult and constrained by memory requirement. The Hamiltonian Auto Decomposition Optimisation Framework (HADOF) addresses this by decomposing large QUBOs into smaller subproblems that can be solved iteratively on quantum or classical backends. This allows the scalability of quantum QUBO algorithms beyond device limits, as well as their simulation on classical devices. In this research, we extend the evaluation of HADOF by benchmarking on real IBM QPUs across sequential, single-QPU parallel, and multi-QPU parallel execution modes, advancing toward High Performance Quantum (HPQ) computing for combinatorial optimisation problems.
Experimental results on IBM quantum hardware demonstrate up to 3-4x reduction in wall clock time when utilising four QPUs compared to sequential execution baseline, while maintaining comparable solution quality. Notably, even single QPU execution benefits from parallelised job orchestration and execution, yielding up to 3x speedup. Simulated results predict over 5x speed-up in parallel execution mode. We further validate the practical applicability of the approach on real world genome assembly instances, showing that both sequential and parallel HADOF variants achieve competitive accuracy while significantly improving time to solution. These results highlight the importance of parallelism at both the algorithmic and system levels, positioning HADOF as a viable pathway toward scalable quantum optimisation.
Abstract Genome assembly is important in infectious disease surveillance, antimicrobial resistance monitoring, and cancer genomics. The task of reconstructing full genomic sequences from fragmented reads, can be framed as a large scale combinatorial optimisation problem. Recent advances in quantum computing have introduced new optimisation algorithms with potential advantages for navigating complex combinatorial search spaces. However, practical deployment is limited by noisy intermediate-scale quantum (NISQ) hardware, including restricted qubit counts, limited connectivity, and high error rates. In this research, we employ the Hamiltonian Auto Decomposition Optimisation Framework (HADOF), an algorithm agnostic framework that enables scalable quantum optimisation through federated solving across small subproblems. HADOF enabled the quantum-assisted genome assembly of a 7.1 Million base pairs Pseudomonas aeruginosa genome, to our knowledge, representing the largest genome assembly graph studied on real quantum hardware to date. The results achieved a 99.348% genome fraction and 1.0 duplication ratio, demonstrating that biologically plausible genome reconstructions can be obtained despite current hardware limitations.
Quadratic Unconstrained Binary Optimization (QUBO) provides a versatile framework for representing NP-hard combinatorial problems, yet existing solvers often face trade-offs among speed, accuracy, and scalability. In this work, we introduce a quantum-inspired solver (QIS) that unites branch-and-bound pruning, continuous gradient-descent refinement, and quantum-inspired heuristics within a fully adaptive control architecture. We benchmark QIS3 against eight state-of-the-art solvers, including genetic algorithms, coherent Ising machines, simulated bifurcation, parallel tempering, simulated annealing, our prior QIS2 version, D-Wave's simulated-annealing (Neal), and Gurobi on three canonical QUBO problem classes: Max-Cut, NAE-3SAT, and Sherrington-Kirkpatrick spin glass problems. Under a uniform runtime budget, QIS3 attains the best solution on nearly all instances, achieving optimality in 94% of max-cut instances. These results establish QIS3 as a robust, high-performance solver that bridges classical exact strategies and quantum-inspired heuristics for scalable QUBO optimization.
This paper investigates several Quadratic Unconstrained Binary optimisation (QUBO) formulations for the parallel machine scheduling problem P m | | C max with the goal of assessing their suitability for quantum annealing and related heuristic optimisation methods. Three QUBO models are constructed, ranging from formulations derived from classical integer and one-hot encodings to a more compact load-balancing based representation. Extensive computational experiments using Simulated Annealing (SA) and Quantum Annealing (QA) reveal substantial differences in scalability and solution quality among the formulations. The alternative load-balanced model consistently yields near-optimal makespans, typically within 1%–3% of the theoretical lower bound, highlighting its stability and effectiveness compared to the more penalty sensitive formulations, whose performance deteriorates for larger instances. Sensitivity analyses further reveal that the appropriate selection of penalty weights and problem-specific parameter tuning significantly influences both solution accuracy and computational effort in QUBO formulations. While current quantum hardware limitations restrict experimentation to small problem sizes, the findings illustrate how compact QUBO designs can better exploit quantum optimisation frameworks. The insights gained in this study provide practical modelling guidelines for future quantum scheduling research and lay the groundwork for extending QUBO-based approaches to more complex scheduling environments. • Three QUBO formulations are compared for identical parallel machine scheduling. • A compact load-balancing QUBO avoids auxiliary variables. • Load balancing yields makespans on average within 1–3%. • Both simulated and quantum annealing produce near-optimal schedules. • Penalty selection and encoding strongly affect scalability and solution quality.
As quantum computing advances, quantum approximate optimization algorithms (QAOA) have shown promise in addressing combinatorial optimization problems. However, the limitations of Noisy Intermediate Scale Quantum (NISQ) devices hinder the scalability of QAOA for large-scale optimization tasks. To overcome these challenges, we propose Backbone-Driven QAOA, a hybrid framework that leverages adaptive Tabu search for classical preprocessing to decompose large-scale quadratic unconstrained binary (QUBO) problems into NISQ-compatible subproblems. In our approach, adaptive Tabu search dynamically identifies and fixes backbone variables to construct reduced-dimensional subspaces that preserve the critical optimization landscape. These quantum-tractable subproblems are then solved via QAOA, with the resulting solutions iteratively refining the backbone selection in a closed-loop quantum-classical cycle. Experimental results demonstrate that our approach not only competes with, and in some cases surpasses, traditional classical algorithms but also performs comparably with recently proposed hybrid classical-quantum algorithms. Our proposed framework effectively orchestrates the allocation of quantum and classical resources, thereby enabling the solution of large-scale combinatorial optimization problems on current NISQ hardware.
Large-scale combinatorial and continuous optimisation problems remain intractable for classical algorithms as problem dimensionality scales. Quantum computing offers advantages through parallelism, amplitude amplification, and tunnelling, but practical realisation on near-term noisy intermediate-scale quantum (NISQ) devices demands careful algorithm design balancing advantage against noise resilience and circuit depth constraints. This paper presents the Quantum Optimisation Algorithm Suite (QOAS), a systematic framework across four algorithmic paradigms: Adaptive QAOA with dynamic depth scheduling; Variational Quantum Eigensolver (VQE) for QUBO problems; hybrid Quantum Annealing (QA); and Grover-enhanced Branch and Bound (GBB) for constrained integer programming. QOAS is benchmarked on five problem classes (MaxCut, TSP, Portfolio, Drug-Target, Feature Selection) across n = 12-84 qubits on IBM Quantum Eagle (127-qubit) and Falcon (27-qubit). Adaptive QAOA achieves approximation ratio 0.924 (SD = 0.018) for MaxCut at n = 48 -- outperforming standard QAOA (0.848) and Goemans-Williamson (0.878) at equivalent wall-clock time. GBB achieves 28.4x speedup over classical branch-and-bound for the n = 24 drug-target problem. QOAS provides systematic methodology for algorithm selection, circuit depth optimisation, and noise mitigation for NISQ workloads.