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arXiv:2603.13160 · Journal of Chemical Theory and Computation

Resource-efficient Quantum Algorithms for Selected Hamiltonian Subspace Diagonalization

Vincent Graves, Manqoba Q. Hlatshwayo, Theodoros Kapourniotis, Konstantinos Georgopoulos

quant-phphysics.chem-phSubmitted Mar 13, 2026• Announced Mar 16, 2026• 0 citations• Revised Jul 29, 2026 (v2)
v1 · Mar 13, 2026v2 · Jul 29, 2026
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Abstract

Quantum algorithms for selecting a subspace of Hamiltonians to diagonalize have emerged as a promising alternative to variational algorithms in the NISQ era. So far, such algorithms, which include the quantum selected configuration interaction (QSCI) and sample-based quantum diagonalization (SQD), have been formulated within second-quantization in Fock space, which leads to inefficient usage of qubit resources. We introduce the first QSCI algorithm developed in the CI-matrix (CIM) framework, which is known to have optimal qubit scaling of exactly $\lceil \log_2 (N) \rceil$ where $N$ is the size of the CIM. In addition, we introduce a novel single-bit flip error mitigation which comes at the overhead of a single qubit and we combine this with a stochastic approximate Trotterization evolution adapted from qDRIFT. Simulating benchmark N$_2$ and naphthalene molecules on quantum hardware, our results achieved similar accuracy as SQD methods but with significantly less quantum resources. However, our CIM-QSCI algorithm and SQD methods could not match the performance of classical heat-bath CI (HCI) for the same task. Hence, we introduce an augmented version of QSCI called quantum selected heat-bath CI (QSHCI). This variant replaces classical heat-bath sampling with quantum sampling from QSCI to achieve performance comparable to HCI. We note that a current drawback of our approach is the preprocessing cost of $\mathcal{O}(N^2\log N)$ for constructing the CIM and performing the Pauli decomposition. This can be further improved by considering efficient CIM access models for the stochastic Trotter evolution.

DOI
10.1021/acs.jctc.6c00521
Comments
19 pages, 5 figures

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Quantum algorithms for selecting a subspace of Hamiltonians to diagonalize have emerged as a promising alternative to variational algorithms in the NISQ era. So far, such algorithms, which include the quantum selected configuration interaction (QSCI) and sample-based quantum diagonalization (SQD), have been formulated within second-quantization in Fock space, which leads to inefficient usage of qubit resources. We introduce the first QSCI algorithm developed in the CI-matrix (CIM) framework, which is known to have optimal qubit scaling of exactly ⌈log⁡2(N)⌉\lceil \log_2 (N) \rceil⌈log2​(N)⌉ where NNN is the size of the CIM. In addition, we introduce a novel single-bit flip error mitigation which comes at the overhead of a single qubit and we combine this with a stochastic approximate Trotterization evolution adapted from qDRIFT. Simulating benchmark N2_22​ and naphthalene molecules on quantum hardware, our results achieved similar accuracy as SQD methods but with significantly less quantum resources. However, our CIM-QSCI algorithm and SQD methods could not match the performance of classical heat-bath CI (HCI) for the same task. Hence, we introduce an augmented version of QSCI called quantum selected heat-bath CI (QSHCI). This variant replaces classical heat-bath sampling with quantum sampling from QSCI to achieve performance comparable to HCI. We note that a current drawback of our approach is the preprocessing cost of O(N2log⁡N)\mathcal{O}(N^2\log N)O(N2logN) for constructing the CIM and performing the Pauli decomposition. This can be further improved by considering efficient CIM access models for the stochastic Trotter evolution.
Quantum-selected configuration interaction (QSCI) methods use a quantum computer to identify dominant electronic configurations in the molecular ground state, while a classical computer diagonalizes the Hamiltonian within the reduced subspace spanned by those configurations. Sample-based quantum diagonalization (SQD), a leading QSCI approach, uses iterative classical post-processing to correct noisy quantum measurement to ensure that the corresponding configurations remain physically sensible. In this work, we show that SQD performance can be strongly influenced by uncontrolled growth of the classical diagonalization subspace. When classical resources are not explicitly constrained, classical uniform random sampling can reproduce SQD benchmarks as noise increases the diversity of sampled configurations. We show any fair benchmarking protocol of SQD must explicitly control diagonalization size over unique samples. We then address the problem of efficiently discovering physically relevant, energy-lowering configurations by introducing a measurement protocol based on non-orthogonal configuration interaction (NOCI). By distributing measurements across orbital bases optimized with respect to the molecular Hamiltonian, we obtain improved sample efficiency relative to measurements performed solely in the Hartree--Fock basis. Importantly, these improvements persist even under fixed classical resource budgets, demonstrating that the resulting configurations are of higher quality rather than being more numerous. Under our proposed benchmarking procedure, we establish measurement-basis engineering as a promising route to improving quantum sampling methods for electronic structure.
Subspace diagonalization techniques based on quantum sampling, such as quantum selected configuration interaction (QSCI) and sample-based quantum diagonalization (SQD), have recently emerged as promising quantum-centric approaches for approximating ground-state energies of many-body systems. However, their performance is fundamentally limited by an intrinsic trade-off between sampling efficiency and the sparsity of the ground-state wavefunction, which becomes particularly severe in strongly correlated systems. Here, we introduce a filter-assisted SQD protocol that engineers wavefunction sparsity via a quantum filter, i.e., a unitary transformation of the Hamiltonian designed to concentrate the ground-state weight onto a small number of computational basis states. Using the Gini coefficient as a robust sparsity measure, we establish a quantitative relationship between wavefunction sparsity and the resource requirements of SQD, providing theoretical bounds on the required subspace dimension and sampling cost. To realize the quantum filter, we employ a tensor-network-based circuit-encoding algorithm that maps target states to quantum circuits with controllable fidelity. We benchmark our approach on the quantum Ising model with transverse and longitudinal fields using both numerical simulations and quantum hardware experiments. Our results demonstrate that, compared with standard SQD, the proposed protocol significantly enhances wavefunction sparsity, reduces ground-state energy estimation errors by orders of magnitude, and substantially lowers sampling overhead. These findings establish filter-assisted subspace diagonalization as a powerful and scalable framework for quantum many-body calculations in the strongly correlated regime.
Quantum Selected Configuration Interaction (QSCI) methods (also known as Sample-based Quantum Diagonalization, SQD) have emerged as promising near-term approaches to solving the electronic Schrödinger equation with quantum computers. In this work, we perform numerical analysis to show that QSCI methods face critical limitations that severely hinder their practical applicability in chemistry. Using the nitrogen molecule and the iron-sulfur cluster [2Fe-2S] as examples, we demonstrate that while QSCI can, in principle, yield high-quality configuration interaction (CI) expansions similar to classical SCI heuristics in some cases, the method struggles with inefficiencies in finding new determinants as sampling repeatedly selects already seen configurations. This inefficiency becomes especially pronounced when targeting high-accuracy results or sampling from an approximate ansatz. In cases where the sampling problem is not present, the resulting CI expansions are less compact than those generated from classical heuristics, rendering QSCI an overall more expensive method. Our findings suggest a significant drawback in QSCI methods when sampling from the ground-state distribution as the inescapable trade-off between finding sufficiently many determinants and generating compact, accurate CI expansions. This ultimately hinders utility in quantum chemistry applications, as QSCI falls behind more efficient classical counterparts.
Quantum Selected Configuration Interaction (QSCI) and an extended protocol known as Sample-based Quantum Diagonalization (SQD) have emerged as promising algorithms to solve the electronic Schrödinger equation with noisy quantum computers. In QSCI/SQD a quantum circuit is repeatedly prepared on the quantum device, and measured configurations form a subspace of the many-body Hilbert space in which the Hamiltonian is diagonalized classically. For the dissociation of N 2 and a model [2Fe – 2S] cluster (correlating 10 electrons in 26 orbitals and 30 electrons in 20 orbitals, respectively) we show that a nonperturbative stochastic approach, phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC), using truncated SQD trial wave functions obtained from quantum hardware can recover a substantial amount (e.g., O (100) mHa) of correlation energy. This hybrid quantum-classical combination has the potential to greatly reduce the sampling burden placed on the QSCI/SQD procedure, and is a compelling alternative to recently proposed hybrid ph-AFQMC algorithms that rely on quantum state tomography.
Sample-based Quantum Diagonalization (SQD), an extension of Quantum Selected Configuration Interaction (QSCI), has emerged as a promising hybrid quantum-classical paradigm for computing molecular ground state energies. By leveraging quantum sampling instead of variational optimization, QSCI avoids barren plateaus and enables direct reconstruction of correlated electronic wavefunctions. However, existing configuration recovery techniques primarily enforce symmetry constraints without guaranteeing optimal selection of the most physically relevant configurations, often leading to unnecessarily large subspaces and increased classical diagonalization costs. In this work, we introduce a machine-learned compact subspace generation protocol based on Restricted Boltzmann Machines (RBMs), termed QSCI-RBM, and integrate it within the Density Matrix Embedding Theory (DMET) framework. The RBM is trained on quantum-sampled configurations to learn the underlying probability distribution of dominant determinants, enabling the targeted generation of high-probability configurations. We apply this framework to the simulation of a protein-ligand complex involving the inhibitor Carmofur bound to the SARS-CoV-2 main protease (MproM^{\text{pro}}Mpro). Our results demonstrate that DMET-QSCI-RBM achieves energies within the chemical accuracy threshold by accessing only approximately 4% of the configuration subspace. In contrast, standard DMET-SQD simulations failed to reach chemical accuracy while accessing up to 20% of the subspace, even as the chemical potential itself nearly converged. These findings highlight that RBM-assisted configuration generation produces significantly more compact subspaces while preserving physical accuracy, thereby reducing classical computational overhead and enabling the scalable quantum embedding simulation of complex biological systems.
We present a quantum-classical hybrid algorithm for calculating the ground state and its energy of the quantum many-body Hamiltonian by proposing an adaptive construction of a quantum state for the quantum-selected configuration interaction (QSCI) method. QSCI allows us to select important electronic configurations in the system to perform configuration interaction (CI) calculation (subspace diagonalization of the Hamiltonian) by sampling measurement for a proper input quantum state on a quantum computer, but how we prepare a desirable input state remains a challenge. We propose an adaptive construction of the input state for QSCI in which we run QSCI repeatedly to grow the input state iteratively. We numerically illustrate that our method, dubbed ADAPT-QSCI, can yield accurate ground-state energies for small molecules, including a noisy situation for eight qubits where error rates of two-qubit gates and the measurement are both as large as 1%. ADAPT-QSCI serves as a promising method to take advantage of current noisy quantum devices and pushes forward its application to quantum chemistry.