arXiv subjects

Alexey Galda

Publications and source records attributed to Alexey Galda.

At least 19 recordsLinked to original sources

arXiv2026

Pauli Correlation Encoding for mRNA Secondary Structure Prediction: Problem-Aware Decoding for Dense-Constraint QUBOs

Pauli Correlation Encoding (PCE) compresses $m$ binary variables onto $n=O(m^{1/k})$ qubits by mapping them to commuting Pauli correlators, but its continuous expectation values must be decoded into feasible binary solutions, a challenge for dense-constraint problems. We apply PCE to mRNA secondary-structure prediction, formulated as a densely constrained QUBO, and train with a QUBO-space sigmoid loss thatpreserves the QUBO penalty structure. For decoding, we introduce the Problem-Aware Guided Decoder (PAGD), which scores candidate variable commitments by combining marginal QUBO energy reduction with a trained expectation-value prior and constraint-aware feasibility pruning. On six benchmark mRNA sequences (30-60 nt, 50-240 variables, 7-14 qubits), PAGD with 100 restarts achieves 75-100 percent near-optimal recovery, defined as $P(\mathrm{gap}<1\%)$, for sequences up to 152 variables, compared with 0-30 percent for a sign-rounding plus local-search baseline. On the 240-variable instance, trained PAGD reaches 50 percent $P(\mathrm{gap}<1\%)$ at 200 restarts, outperforming untrained-circuit and random-expectation-value controls. Hardware-scale tests extend the pipeline to three 102-105 nt instances (694-745 variables, 172,000-193,000 pair constraints, 23 qubits) on IBM Heron processors. The circuits transpile SWAP-free into 480 native two-qubit gates at depth 256, and PAGD decoded gaps on QPU runs match or beat simulator means for all three instances, including exact CPLEX-optimum recovery for one sequence. These results show that PCE-trained priors can survive deployment to noisy superconducting hardware at biologically relevant scale.

quant-ph↗

arXiv2026

Molecular Excited States using Quantum Subspace Methods: Accuracy, Resource Reduction, and Error-Mitigated Hardware Implementation of q-sc-EOM

Problems in quantum chemical simulations, especially achieving accurate excited-state potential energy surfaces, are among the primary applications to achieve quantum utility. On near-term quantum hardware, variants of the variational quantum eigensolver (VQE) algorithms are the primary choice for chemistry simulation. In this study, a combination of leading ground and excited state quantum algorithms for general excited states, namely, ADAPT-VQE/LUCJ and q-sc-EOM, are utilized to calculate accurate excited state potential energy surfaces in challenging bond-breaking scenarios and compared with the classical scalable EOM-CCSD method. This work investigates avenues toward quantum utility in excited-state quantum chemistry using the q-sc-EOM approach. We assess its accuracy while mitigating major scaling bottlenecks through the Davidson algorithm and basis rotation grouping, reducing the measurement scaling from O(N$^{12}$) to O(N$^{5}$), and implementing the method on quantum hardware with various error mitigation strategies to reduce gate and measurement errors in excited states. The hardware implementation of the q-sc-EOM algorithm, augmented by mitigation of M3 readout error and symmetry projection, produces reasonably accurate excited-state energies with gate noise identified as the predominant source of error. This paves the way for accurate and scalable, generally applicable quantum excited-state methods with potential for quantum utility while identifying critical problems that require advancements.

quant-ph↗

arXiv2025

Sample-based Quantum Diagonalization Methods for Modeling the Photochemistry of Diazirine and Diazo Compounds

Diazirines and diazo compounds are widely employed as photoreactive precursors for generating carbenes, key intermediates in chemical biology and materials science. However, computationally modeling their reaction pathways remains challenging due to a need for large active spaces and the requirement to accurately capture excited-state surfaces along with transition states and conical intersections. In this work, we utilize a hybrid quantum-classical workflow for investigating carbene formation in representative diazirine-diazomethane systems. Our approach leverages Sample-based Quantum Diagonalization (SQD) and its extended variant (Ext-SQD) for ground and excited-state analysis, combined with classical tools for geometry optimization, active-space selection, and diagnostic evaluation. Quantum computations were carried out on superconducting quantum processors, and results for both aliphatic and aryl-substituted diazirine-diazomethane pairs were benchmarked against established classical methods, including DFT, CCSD, CASCI, and SCI. SQD achieves accuracy surpassing the chemical accuracy threshold for nearly all stationary points on the potential energy surface of parent diazirine relative to the CASCI(12,10) reference, and remains close to chemical accuracy for phenyl-substituted diazirine in a (30,30) active space, with an average deviation of 1.1 kcal/mol relative to the SCI benchmark. SQD closely follows CASCI and SCI trends, showing consistent agreement. The findings demonstrate the promise of quantum computing frameworks in modeling photochemical transformations of electronically complex and pharmacologically relevant molecules.

physics.chem-ph↗

arXiv2025

Co-optimization of codon usage and mRNA secondary structure using quantum computing

Co-optimizing mRNA sequences for both codon optimality and secondary structure is crucial for producing stable and efficacious mRNA therapeutics. Codon optimization, which adjusts nucleotide sequences to enhance translational efficiency, inherently influences mRNA secondary structure - a key determinant of molecular stability both in-vial and in-cell. Because both properties are governed by the same underlying sequence, optimizing one directly impacts the other. To address this interdependence, we introduce a novel variational framework that simultaneously optimizes codon usage and secondary structure. Our method employs a dual-objective function that balances the codon adaptation index (CAI) and minimum free energy (MFE), incorporating variational parameters for codon selection. Leveraging a hybrid quantum-classical computational strategy and building on prior advancements in quantum algorithms for secondary structure prediction, we effectively navigate this complex optimization space. We demonstrate the feasibility of executing this end-to-end workflow on real quantum hardware, using IBM's 127-qubit Eagle processor. We validate our approach through both simulations and quantum hardware experiments on sequences of up to 30 nucleotides. These results highlight the potential of our framework to accelerate the design of optimal mRNA constructs for therapeutic and research applications.

quant-ph↗

arXiv2025

Towards secondary structure prediction of longer mRNA sequences using a quantum-centric optimization scheme

Accurate prediction of mRNA secondary structure is critical for understanding gene expression, translation efficiency, and advancing mRNA-based therapeutics. However, the combinatorial complexity of possible foldings, especially in long sequences, poses significant computational challenges for classical algorithms. In this work, we propose a scalable, quantum-centric optimization framework that integrates quantum sampling with classical post-processing to tackle this problem. Building on a Quadratic Unconstrained Binary Optimization (QUBO) formulation of the mRNA folding task, we develop two complementary workflows: a Conditional Value at Risk (CVaR)-based variational quantum algorithm enhanced with gauge transformations and local search, and an Instantaneous Quantum Polynomial (IQP) circuit-based scheme where training is done classically and sampling is delegated to quantum hardware. We demonstrate the effectiveness of these approaches using IBM quantum processors, solving problem instances with up to 156 qubits and circuits containing up to 950 nonlocal gates, corresponding to mRNA sequences of up to 60 nucleotides. Additionally, we validate scalability of the CVaR algorithm on a tensor network simulator, reaching up to 354 qubits in noiseless settings. These results demonstrate the growing practical capabilities of hybrid quantum-classical methods for tackling large-scale biological optimization problems.

quant-ph↗

arXiv2025

Quantum machine learning framework for longitudinal biomedical studies

Longitudinal biomedical studies play a vital role in tracking disease progression, treatment response, and the emergence of resistance mechanisms, particularly in complex disorders such as cancer and neurodegenerative diseases. However, the high dimensionality of biological data, combined with the limited size of longitudinal cohorts, presents significant challenges for traditional machine learning approaches. In this work, we explore the potential of quantum machine learning (QML) for longitudinal biomarker discovery. We propose a novel modification to the instantaneous quantum polynomial time (IQP) feature map, designed to encode temporal dependencies across multiple time points in biomedical datasets. Through numerical simulations on both synthetic and real-world datasets - including studies on follicular lymphoma and Alzheimer's disease - we demonstrate that our longitudinal IQP feature map improves the ability of quantum kernels to capture intra-subject temporal patterns, offering a promising direction for QML in clinical research.

q-bio.QM↗

arXiv2024

Quantum Machine Learning in Drug Discovery: Applications in Academia and Pharmaceutical Industries

The nexus of quantum computing and machine learning - quantum machine learning - offers the potential for significant advancements in chemistry. This review specifically explores the potential of quantum neural networks on gate-based quantum computers within the context of drug discovery. We discuss the theoretical foundations of quantum machine learning, including data encoding, variational quantum circuits, and hybrid quantum-classical approaches. Applications to drug discovery are highlighted, including molecular property prediction and molecular generation. We provide a balanced perspective, emphasizing both the potential benefits and the challenges that must be addressed.

quant-ph↗

arXiv2024

mRNA secondary structure prediction using utility-scale quantum computers

Recent advancements in quantum computing have opened new avenues for tackling long-standing complex combinatorial optimization problems that are intractable for classical computers. Predicting secondary structure of mRNA is one such notoriously difficult problem that can benefit from the ever-increasing maturity of quantum computing technology. Accurate prediction of mRNA secondary structure is critical in designing RNA-based therapeutics as it dictates various steps of an mRNA life cycle, including transcription, translation, and decay. The current generation of quantum computers have reached utility-scale, allowing us to explore relatively large problem sizes. In this paper, we examine the feasibility of solving mRNA secondary structures on a quantum computer with sequence length up to 60 nucleotides representing problems in the qubit range of 10 to 80. We use Conditional Value at Risk (CVaR)-based VQE algorithm to solve the optimization problems, originating from the mRNA structure prediction problem, on the IBM Eagle and Heron quantum processors. To our encouragement, even with ``minimal'' error mitigation and fixed-depth circuits, our hardware runs yield accurate predictions of minimum free energy (MFE) structures that match the results of the classical solver CPLEX. Our results provide sufficient evidence for the viability of solving mRNA structure prediction problems on a quantum computer and motivate continued research in this direction.

quant-ph↗

arXiv2024

Demonstration of a parity-time symmetry breaking phase transition using superconducting and trapped-ion qutrits

Scalable quantum computers hold the promise to solve hard computational problems, such as prime factorization, combinatorial optimization, simulation of many-body physics, and quantum chemistry. While being key to understanding many real-world phenomena, simulation of non-conservative quantum dynamics presents a challenge for unitary quantum computation. In this work, we focus on simulating non-unitary parity-time symmetric systems, which exhibit a distinctive symmetry-breaking phase transition as well as other unique features that have no counterpart in closed systems. We show that a qutrit, a three-level quantum system, is capable of realizing this non-equilibrium phase transition. By using two physical platforms -- an array of trapped ions and a superconducting transmon -- and by controlling their three energy levels in a digital manner, we experimentally simulate the parity-time symmetry-breaking phase transition. Our results indicate the potential advantage of multi-level (qudit) processors in simulating physical effects, where additional accessible levels can play the role of a controlled environment.

quant-ph↗

arXiv2023

Quantum computing for finance

Quantum computers are expected to surpass the computational capabilities of classical computers and have a transformative impact on numerous industry sectors. We present a comprehensive summary of the state of the art of quantum computing for financial applications, with particular emphasis on stochastic modeling, optimization, and machine learning. This Review is aimed at physicists, so it outlines the classical techniques used by the financial industry and discusses the potential advantages and limitations of quantum techniques. Finally, we look at the challenges that physicists could help tackle.

quant-ph↗

arXiv2023

Similarity-Based Parameter Transferability in the Quantum Approximate Optimization Algorithm

The quantum approximate optimization algorithm (QAOA) is one of the most promising candidates for achieving quantum advantage through quantum-enhanced combinatorial optimization. A near-optimal solution to the combinatorial optimization problem is achieved by preparing a quantum state through the optimization of quantum circuit parameters. Optimal QAOA parameter concentration effects for special MaxCut problem instances have been observed, but a rigorous study of the subject is still lacking. In this work we show clustering of optimal QAOA parameters around specific values; consequently, successful transferability of parameters between different QAOA instances can be explained and predicted based on local properties of the graphs, including the type of subgraphs (lightcones) from which graphs are composed as well as the overall degree of nodes in the graph (parity). We apply this approach to several instances of random graphs with a varying number of nodes as well as parity and show that one can use optimal donor graph QAOA parameters as near-optimal parameters for larger acceptor graphs with comparable approximation ratios. This work presents a pathway to identifying classes of combinatorial optimization instances for which variational quantum algorithms such as QAOA can be substantially accelerated.

quant-ph↗

arXiv2022

Multibody molecular docking on a quantum annealer

Molecular docking, which aims to find the most stable interacting configuration of a set of molecules, is of critical importance to drug discovery. Although a considerable number of classical algorithms have been developed to carry out molecular docking, most focus on the limiting case of docking two molecules. Since the number of possible configurations of N molecules is exponential in N, those exceptions which permit docking of more than two molecules scale poorly, requiring exponential resources to find high-quality solutions. Here, we introduce a one-hot encoded quadratic unconstrained binary optimization formulation (QUBO) of the multibody molecular docking problem, which is suitable for solution by quantum annealer. Our approach involves a classical pre-computation of pairwise interactions, which scales only quadratically in the number of bodies while permitting well-vetted scoring functions like the Rosetta REF2015 energy function to be used. In a second step, we use the quantum annealer to sample low-energy docked configurations efficiently, considering all possible docked configurations simultaneously through quantum superposition. We show that we are able to minimize the time needed to find diverse low-energy docked configurations by tuning the strength of the penalty used to enforce the one-hot encoding, demonstrating a 3-4 fold improvement in solution quality and diversity over performance achieved with conventional penalty strengths. By mapping the configurational search to a form compatible with current- and future-generation quantum annealers, this work provides an alternative means of solving multibody docking problems that may prove to have performance advantages for large problems, potentially circumventing the exponential scaling of classical approaches and permitting a much more efficient solution to a problem central to drug discovery and validation pipelines.

q-bio.BM↗

arXiv2022

Towards a scalable discrete quantum generative adversarial neural network

We introduce a fully quantum generative adversarial network intended for use with binary data. The architecture incorporates several features found in other classical and quantum machine learning models, which up to this point had not been used in conjunction. In particular, we incorporate noise reuploading in the generator, auxiliary qubits in the discriminator to enhance expressivity, and a direct connection between the generator and discriminator circuits, obviating the need to access the generator's probability distribution. We show that, as separate components, the generator and discriminator perform as desired. We empirically demonstrate the expressive power of our model on both synthetic data as well as low energy states of an Ising model. Our demonstrations suggest that the model is not only capable of reproducing discrete training data, but also of potentially generalizing from it.

quant-ph↗

arXiv2022

A Survey of Quantum Computing for Finance

Quantum computers are expected to surpass the computational capabilities of classical computers during this decade and have transformative impact on numerous industry sectors, particularly finance. In fact, finance is estimated to be the first industry sector to benefit from quantum computing, not only in the medium and long terms, but even in the short term. This survey paper presents a comprehensive summary of the state of the art of quantum computing for financial applications, with particular emphasis on stochastic modeling, optimization, and machine learning, describing how these solutions, adapted to work on a quantum computer, can potentially help to solve financial problems, such as derivative pricing, risk modeling, portfolio optimization, natural language processing, and fraud detection, more efficiently and accurately. We also discuss the feasibility of these algorithms on near-term quantum computers with various hardware implementations and demonstrate how they relate to a wide range of use cases in finance. We hope this article will not only serve as a reference for academic researchers and industry practitioners but also inspire new ideas for future research.

quant-ph↗

arXiv2022

Error rate reduction of single-qubit gates via noise-aware decomposition into native gates

In the current era of Noisy Intermediate-Scale Quantum (NISQ) technology, the practical use of quantum computers remains inhibited by our inability to aptly decouple qubits from their environment to mitigate computational errors. In this work, we introduce an approach by which knowledge of a qubit's initial quantum state and the standard parameters describing its decoherence can be leveraged to mitigate the noise present during the execution of a single-qubit gate. We benchmark our protocol using cloud-based access to IBM quantum processors. On ibmq_rome, we demonstrate a reduction of the single-qubit error rate by $38\%$, from $1.6 \times 10 ^{-3}$ to $1.0 \times 10 ^{-3}$, provided the initial state of the input qubit is known. On ibmq_bogota, we prove that our protocol will never decrease gate fidelity, provided the system's $T_1$ and $T_2$ times have not drifted above $100$ times their assumed values. The protocol can be used to reduce quantum state preparation errors, as well as to improve the fidelity of quantum circuits for which some knowledge of the qubits' intermediate states can be inferred. This work presents a pathway to using information about noise levels and quantum state distributions to significantly reduce error rates associated with quantum gates via optimized decomposition into native gates.

quant-ph↗

arXiv2022

Augmenting QAOA Ansatz with Multiparameter Problem-Independent Layer

The quantum approximate optimization algorithm (QAOA) promises to solve classically intractable computational problems in the area of combinatorial optimization. A growing amount of evidence suggests that the originally proposed form of the QAOA ansatz is not optimal, however. To address this problem, we propose an alternative ansatz, which we call QAOA+, that augments the traditional $p = 1$ QAOA ansatz with an additional multiparameter problem-independent layer. The QAOA+ ansatz allows obtaining higher approximation ratios than $p = 1$ QAOA while keeping the circuit depth below that of $p = 2$ QAOA, as benchmarked on the MaxCut problem for random regular graphs. We additionally show that the proposed QAOA+ ansatz, while using a larger number of trainable classical parameters than with the standard QAOA, in most cases outperforms alternative multiangle QAOA ansätze.

quant-ph↗

arXiv2022

Tensor Network Quantum Simulator With Step-Dependent Parallelization

In this work, we present a new large-scale quantum circuit simulator. It is based on the tensor network contraction technique to represent quantum circuits. We propose a novel parallelization algorithm based on \stepslice . In this paper, we push the requirement on the size of a quantum computer that will be needed to demonstrate the advantage of quantum computation with Quantum Approximate Optimization Algorithm (QAOA). We computed 210 qubit QAOA circuits with 1,785 gates on 1,024 nodes of the the Cray XC 40 supercomputer Theta. To the best of our knowledge, this constitutes the largest QAOA quantum circuit simulations reported to this date.

quant-ph↗

arXiv2022

Characterizing Error Mitigation by Symmetry Verification in QAOA

Hardware errors are a major obstacle to demonstrating quantum advantage with the quantum approximate optimization algorithm (QAOA). Recently, symmetry verification has been proposed and empirically demonstrated to boost the quantum state fidelity, the expected solution quality, and the success probability of QAOA on a superconducting quantum processor. Symmetry verification uses parity checks that leverage the symmetries of the objective function to be optimized. We develop a theoretical framework for analyzing this approach under local noise and derive explicit formulas for fidelity improvements on problems with global $\mathbb{Z}_2$ symmetry. We numerically investigate the symmetry verification on the MaxCut problem and identify the error regimes in which this approach improves the QAOA objective. We observe that these regimes correspond to the error rates present in near-term hardware. We further demonstrate the efficacy of symmetry verification on an IonQ trapped ion quantum processor where an improvement in the QAOA objective of up to 19.2\% is observed.

quant-ph↗