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arXiv:2608.11569

Improved quantum sampling methods for molecular simulations

Connor van Rossum, Jeffery Cohn, Sally Shrapnel, Riddhi Gupta

quant-phphysics.chem-phphysics.comp-phSubmitted Aug 12, 2026• Announced Aug 13, 2026• 0 citations• Revised Oct 6, 2026 (v2)
v1 · Aug 12, 2026v2 · Oct 6, 2026
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Abstract

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.

Comments
19 pages, 8 figures

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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.
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.
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.
Predicting many molecular properties requires accurate ground-state energies of molecular Hamiltonians. Quantum-selected configuration interaction (QSCI) obtains such energies by measuring an input state to select important electronic configurations and classically diagonalizing the Hamiltonian in the subspace they span. ADAPT-QSCI, an adaptive extension of QSCI, improves the input state through iterative circuit growth. For single-reference molecules, the sampling distribution is dominated by the Hartree-Fock (HF) configuration, so most measurements reproduce a configuration already known. We reduce this redundancy by placing the HF configuration in the diagonalization subspace classically, before any measurement. This invalidates the operator-selection criterion of ADAPT-QSCI, and we derive a consistent replacement with energy and gradient in closed form, adding no query to the quantum device. At the per-iteration shot budgets previously used for ADAPT-QSCI, the proposed scheme reaches chemical accuracy with approximately 63%63\%63% and 43%43\%43% of the CNOT gates for H4\mathrm{H}_4H4​ and H6\mathrm{H}_6H6​, and 44%44\%44% and 40%40\%40% of the total shots. The advantage depends on the budget, however: in the infinite-shot limit the H4\mathrm{H}_4H4​ CNOT count increases to 125%125\%125% of that of ADAPT-QSCI. These results identify the per-iteration shot budget as a key design variable governing resource savings in QSCI-based algorithms.
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.
Sample-based quantum diagonalization (SQD), equivalently quantum-selected configuration interaction (QSCI), has become a centre of gravity of pre-fault-tolerant quantum chemistry: a processor samples electronic configurations and the Hamiltonian is diagonalized classically in the resulting subspace. Accuracy is governed entirely by which configurations enter it -- a machine-learning selection problem, made acute by a coupon-collector bottleneck. We review the generative and learned selectors by what each generates and the signal it exploits, and identify one gap: no reward-proportional generative-flow-network proposer has been built for tail discovery. On the field's central question -- whether the quantum sampler beats classical selected CI -- the negative verdict is not ours to claim: priority belongs to Reinholdt et al. [JCTC 21, 6811 (2025)], and polynomial-time classical estimation of the flagship circuits has reinforced it. We state that verdict at the precision a falsifiable claim requires -- it concerns reproducible, same-active-space comparisons on molecular electronic structure -- and weigh the claims outside those qualifiers. We show that alpha-string weights are not invariant under rotations inside degenerate orbital shells, so determinant counts are undefined until the orbital gauge is declared. We distil a ten-element benchmarking standard and apply it to our own deposit, which returned defects that changed numbers printed here and retracted one from v1. FCI-exact experiments confirm one prediction and refute another: the single generative advantage we find keeps no consistent sign along the dissociation coordinate at device-calibrated noise and reverses under a symmetric readout model. It does beat a noise-matched classical recovery loop on N2 by a margin five seeds cannot resolve, and loses by over a factor of two to a classical selector that needs no sampler.
We present QSCI-CMP, a quantum-classical hybrid algorithm for molecular ground-state calculations that reduces both the query count and the gate count of sample-based quantum diagonalization with amplitude amplification (SQD-AA). SQD-AA mitigates the measurement bottleneck of quantum-selected configuration interaction (QSCI) by amplifying the basis states that have not yet been measured. Its oracle, however, specifies the measured states by listing them one by one, so its gate count grows with the number of collected states. Moreover, the quantum resources are spent even on states whose importance is evident from chemical knowledge, such as low-order excitations from the Hartree-Fock reference, which could be collected classically at the outset. We therefore propose to fix such chemically trivial states in advance, include them in the diagonalization subspace from the start, and exclude them from the amplification target, using a low-cost oracle that recognizes them through the excitation level and the seniority number of each basis state. We numerically demonstrate that QSCI-CMP reduces the query count and the gate count required to reach chemical accuracy by up to approximately 68% and 72% relative to SQD-AA for 24-qubit systems. The chemically trivial subspace is freely tunable within the classical computational budget. A larger subspace shifts more work onto the classical solver and increases the reduction in quantum cost, and when it captures the ground state sufficiently well, no quantum sampling is needed at all. We also point out that a query-optimal iteration count known from the analysis of quantum search further reduces the query count of both methods by approximately 12%.