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Weiwen Jiang

Publications and source records attributed to Weiwen Jiang.

At least 19 recordsLinked to original sources
arXiv2026

A Quantum Framework for Protein Binding-Site Structure Prediction on Utility-Level Quantum Processors

Accurate prediction of protein active-site structures remains a central challenge in structural biology, particularly for short and flexible peptide fragments where conventional and simulation-based methods often fail. Here, we present a quantum computing framework specifically developed for utility-level quantum processors to address this problem. Starting from an amino acid sequence, we formulate structure prediction as a ground-state energy minimization problem using the Variational Quantum Eigensolver (VQE). Amino acid connectivity is encoded on a tetrahedral lattice model, and structural constraints-including steric, geometric, and chirality terms-are mapped into a problem-specific Hamiltonian represented as sparse Pauli operators. Optimization is performed with a two-stage architecture that separates energy estimation from measurement decoding, enabling noise mitigation under realistic device conditions. We evaluate the framework on 23 randomly selected protein fragments from the PDBbind dataset and 7 fragments from therapeutically relevant proteins, and execute experiments on the IBM-Cleveland Clinic quantum processor. Predictions are benchmarked against AlphaFold 3 (AF3) and classical simulation-based approaches using identical postprocessing and docking procedures. Our method outperforms both AF3 and classical baselines in RMSD (root-mean-square deviation) and docking efficacy. These results demonstrate an end-to-end, hardware-executable pipeline for biologically relevant structure prediction on real quantum processors, highlighting its engineering feasibility and practical advantages over existing classical and deep learning approaches.

cs.ET↗
arXiv2025

Simulating Circuit Layout for Distributed Quantum Computing

The proposed framework represents the first tool to compile a quantum circuit across photonic-connected distributed quantum processors. Its design follows a divide-and-conquer paradigm for circuit partitioning, transpilation, and assembly, producing simulable and implementable circuit layouts.

quant-ph↗
arXiv2025

An End-to-End Distributed Quantum Circuit Simulator

Quantum computing has made substantial progress in recent years; however, its scalability remains constrained on a monolithic quantum processing unit (QPU). Distributed quantum computing (DQC) offers a pathway by coordinating multiple QPUs to execute large-scale circuits. Yet, DQC still faces practical barriers, as its realization depends on advances in hardware-level components such as quantum transducers and high-fidelity entanglement-distribution modules. While these technologies continue to improve, mature DQC platforms remain unavailable. In the meantime, researchers need to assess the benefits of DQC and evaluate emerging DQC designs, but the software ecosystem lacks a circuit-level simulator that models heterogeneous backends, noisy connections, and distributed execution. To fill this gap, this paper proposes SimDisQ, the first end-to-end circuit-level DQC simulator, composed of a set of novel DQC-oriented automated simulation toolkits and communication noise models that can interoperate with existing toolkits in mainstream quantum software ecosystems. Leveraging circuit-level simulation capabilities, SimDisQ enables quantitative exploration of architectural design trade-offs, communication fidelity constraints, and new circuit optimization challenges introduced by DQC, providing a foundation for future research in this promising direction. Benchmarking experiments using SimDisQ respond to a couple of open questions in the community; for example, noisy simulation of superconducting and trapped-ion qubits, with a reasonable entanglement-distribution fidelity, reveal that heterogeneous QPUs can indeed yield higher execution fidelity.

cs.ET↗
arXiv2025

A Hybrid Quantum-AI Framework for Protein Structure Prediction on NISQ Devices

Variational quantum algorithms provide a direct, physics-based approach to protein structure prediction, but their accuracy is limited by the coarse resolution of the energy landscapes generated on current noisy devices. We propose a hybrid framework that combines quantum computation with deep learning, formulating structure prediction as a problem of energy fusion. Candidate conformations are obtained through the Variational Quantum Eigensolver (VQE) executed on IBM's 127-qubit superconducting processor, which defines a global yet low-resolution quantum energy surface. To refine these basins, secondary structure probabilities and dihedral angle distributions predicted by the NSP3 neural network are incorporated as statistical potentials. These additional terms sharpen the valleys of the quantum landscape, resulting in a fused energy function that enhances effective resolution and better distinguishes native-like structures. Evaluation on 375 conformations from 75 protein fragments shows consistent improvements over AlphaFold3, ColabFold, and quantum-only predictions, achieving a mean RMSD of 4.9 Å with statistical significance (p < 0.001). The findings demonstrate that energy fusion offers a systematic method for combining data-driven models with quantum algorithms, improving the practical applicability of near-term quantum computing to molecular and structural biology.

cs.ET↗
arXiv2025

Computational Performance Bounds Prediction in Quantum Computing with Unstable Noise

Quantum computing has significantly advanced in recent years, boasting devices with hundreds of quantum bits (qubits), hinting at its potential quantum advantage over classical computing. Yet, noise in quantum devices poses significant barriers to realizing this supremacy. Understanding noise's impact is crucial for reproducibility and application reuse; moreover, the next-generation quantum-centric supercomputing essentially requires efficient and accurate noise characterization to support system management (e.g., job scheduling), where ensuring correct functional performance (i.e., fidelity) of jobs on available quantum devices can even be higher-priority than traditional objectives. However, noise fluctuates over time, even on the same quantum device, which makes predicting the computational bounds for on-the-fly noise is vital. Noisy quantum simulation can offer insights but faces efficiency and scalability issues. In this work, we propose a data-driven workflow, namely QuBound, to predict computational performance bounds. It decomposes historical performance traces to isolate noise sources and devises a novel encoder to embed circuit and noise information processed by a Long Short-Term Memory (LSTM) network. For evaluation, we compare QuBound with a state-of-the-art learning-based predictor, which only generates a single performance value instead of a bound. Experimental results show that the result of the existing approach falls outside of performance bounds, while all predictions from our QuBound with the assistance of performance decomposition better fit the bounds. Moreover, QuBound can efficiently produce practical bounds for various circuits with over 106 speedup over simulation; in addition, the range from QuBound is over 10x narrower than the state-of-the-art analytical approach.

quant-ph↗
arXiv2025

QDockBank: A Dataset for Ligand Docking on Protein Fragments Predicted on Utility-Level Quantum Computers

Protein structure prediction is a core challenge in computational biology, particularly for fragments within ligand-binding regions, where accurate modeling is still difficult. Quantum computing offers a novel first-principles modeling paradigm, but its application is currently limited by hardware constraints, high computational cost, and the lack of a standardized benchmarking dataset. In this work, we present QDockBank-the first large-scale protein fragment structure dataset generated entirely using utility-level quantum computers, specifically designed for protein-ligand docking tasks. QDockBank comprises 55 protein fragments extracted from ligand-binding pockets. The dataset was generated through tens of hours of execution on superconducting quantum processors, making it the first quantum-based protein structure dataset with a total computational cost exceeding one million USD. Experimental evaluations demonstrate that structures predicted by QDockBank outperform those predicted by AlphaFold2 and AlphaFold3 in terms of both RMSD and docking affinity scores. QDockBank serves as a new benchmark for evaluating quantum-based protein structure prediction.

cs.ET↗
arXiv2025

$\bar\partial$ Sobolev-type inequality and an improved $L^2$-estimate of $\bar\partial$ on bounded strictly pseudoconvex domains

We prove several Sobolev-type inequalities related to the $\bar\partial$-operator on bounded domains in $\mathbb{C}^n$, which can be viewed as a $\bar\partial$-version of the classical Sobolev inequality and its various generalizations, and apply them to derive a generalization of the Sobolev Inequality with Trace in $\mathbb{R}^n$. As applications to complex analysis, we get an integral form of Maximum Modulus Principle for holomorphic functions, and an improvement of Hörmander's $L^2$-estimate for $\bar\partial$ on bounded strictly pseudoconvex domains.

math.CV↗
arXiv2025

QuSplit: Achieving Both High Fidelity and Throughput via Job Splitting on Noisy Quantum Computers

With the progression into the quantum utility era, computing is shifting toward quantum-centric architectures, where multiple quantum processors collaborate with classical computing resources. Platforms such as IBM Quantum and Amazon Braket exemplify this trend, enabling access to diverse quantum backends. However, efficient resource management remains a challenge, as quantum processors are highly susceptible to noise, which significantly impacts computation fidelity. Additionally, the heterogeneous noise characteristics across different processors add further complexity to scheduling and resource allocation. Existing scheduling strategies typically focus on mapping and scheduling jobs to these heterogeneous backends, which leads to some jobs suffering extremely low fidelity. Targeting quantum optimization jobs (e.g., VQC, VQE, QAOA) - among the most promising quantum applications in the NISQ era - we hypothesize that executing the later stages of a job on a high-fidelity quantum processor can significantly improve overall fidelity. To verify this, we use VQE as a case study and develop a Genetic Algorithm-based scheduling framework that incorporates job splitting to optimize fidelity and throughput. Experimental results demonstrate that our approach consistently maintains high fidelity across all jobs while significantly enhancing system throughput. Furthermore, the proposed algorithm exhibits excellent scalability in handling an increasing number of quantum processors and larger workloads, making it a robust and practical solution for emerging quantum computing platforms. To further substantiate its effectiveness, we conduct experiments on a real quantum processor, IBM Strasbourg, which confirm that job splitting improves fidelity and reduces the number of iterations required for convergence.

quant-ph↗
arXiv2025

QuEst: Graph Transformer for Quantum Circuit Reliability Estimation

Among different quantum algorithms, PQC for QML show promises on near-term devices. To facilitate the QML and PQC research, a recent python library called TorchQuantum has been released. It can construct, simulate, and train PQC for machine learning tasks with high speed and convenient debugging supports. Besides quantum for ML, we want to raise the community's attention on the reversed direction: ML for quantum. Specifically, the TorchQuantum library also supports using data-driven ML models to solve problems in quantum system research, such as predicting the impact of quantum noise on circuit fidelity and improving the quantum circuit compilation efficiency. This paper presents a case study of the ML for quantum part. Since estimating the noise impact on circuit reliability is an essential step toward understanding and mitigating noise, we propose to leverage classical ML to predict noise impact on circuit fidelity. Inspired by the natural graph representation of quantum circuits, we propose to leverage a graph transformer model to predict the noisy circuit fidelity. We firstly collect a large dataset with a variety of quantum circuits and obtain their fidelity on noisy simulators and real machines. Then we embed each circuit into a graph with gate and noise properties as node features, and adopt a graph transformer to predict the fidelity. Evaluated on 5 thousand random and algorithm circuits, the graph transformer predictor can provide accurate fidelity estimation with RMSE error 0.04 and outperform a simple neural network-based model by 0.02 on average. It can achieve 0.99 and 0.95 R$^2$ scores for random and algorithm circuits, respectively. Compared with circuit simulators, the predictor has over 200X speedup for estimating the fidelity.

quant-ph↗
arXiv2025

Escaping Barren Plateau: Co-Exploration of Quantum Circuit Parameters and Architectures

Barren plateaus (BP), characterized by exponentially vanishing gradients that hinder the training of variational quantum circuits (VQC), present a pervasive and critical challenge in applying variational quantum algorithms to real-world applications. It is widely recognized that the BP problem becomes more pronounced with an increase in the number of parameters. This work demonstrates that the BP problem manifests at different scales depending on the specific application, highlighting the absence of a universal VQC ansatz capable of resolving the BP issue across all applications. Consequently, there is an imminent need for an automated tool to design and optimize VQC architectures tailored to specific applications. To close the gap, this paper takes Variational Quantum Eigensolvers (VQEs) as a vehicle, and we propose a novel quantum circuit parameter and architecture co-exploration framework, namely AntiBP. Experimental results demonstrate that AntiBP effectively avoids the BP issue for circuits that are not under-parameterized in noise-free environments. Furthermore, AntiBP significantly outperforms baseline VQEs in noisy environments.

quant-ph↗
arXiv2025

$L^2$-estimates on flat vector bundles and Prékopa's theorem

In this paper, we will construct Hörmander's $L^2$-estimate of the operator $d$ on a flat vector bundle over a $p$-convex Riemannian manifold and discuss some geometric applications of it. In particular, we will generalize the classical Prékopa's theorem in convex analysis.

math.DG↗
arXiv2025

DNA: Differentiable Network-Accelerator Co-Search

Powerful yet complex deep neural networks (DNNs) have fueled a booming demand for efficient DNN solutions to bring DNN-powered intelligence into numerous applications. Jointly optimizing the networks and their accelerators are promising in providing optimal performance. However, the great potential of such solutions have yet to be unleashed due to the challenge of simultaneously exploring the vast and entangled, yet different design spaces of the networks and their accelerators. To this end, we propose DNA, a Differentiable Network-Accelerator co-search framework for automatically searching for matched networks and accelerators to maximize both the task accuracy and acceleration efficiency. Specifically, DNA integrates two enablers: (1) a generic design space for DNN accelerators that is applicable to both FPGA- and ASIC-based DNN accelerators and compatible with DNN frameworks such as PyTorch to enable algorithmic exploration for more efficient DNNs and their accelerators; and (2) a joint DNN network and accelerator co-search algorithm that enables simultaneously searching for optimal DNN structures and their accelerators' micro-architectures and mapping methods to maximize both the task accuracy and acceleration efficiency. Experiments and ablation studies based on FPGA measurements and ASIC synthesis show that the matched networks and accelerators generated by DNA consistently outperform state-of-the-art (SOTA) DNNs and DNN accelerators (e.g., 3.04x better FPS with a 5.46% higher accuracy on ImageNet), while requiring notably reduced search time (up to 1234.3x) over SOTA co-exploration methods, when evaluated over ten SOTA baselines on three datasets. All codes will be released upon acceptance.

cs.LG↗
arXiv2024

All-in-One Tuning and Structural Pruning for Domain-Specific LLMs

Existing pruning techniques for large language models (LLMs) targeting domain-specific applications typically follow a two-stage process: pruning the pretrained general-purpose LLMs and then fine-tuning the pruned LLMs on specific domains. However, the pruning decisions, derived from the pretrained weights, remain unchanged during fine-tuning, even if the weights have been updated. Therefore, such a combination of the pruning decisions and the finetuned weights may be suboptimal, leading to non-negligible performance degradation. To address these limitations, we propose ATP: All-in-One Tuning and Structural Pruning, a unified one-stage structural pruning and fine-tuning approach that dynamically identifies the current optimal substructure throughout the fine-tuning phase via a trainable pruning decision generator. Moreover, given the limited available data for domain-specific applications, Low-Rank Adaptation (LoRA) becomes a common technique to fine-tune the LLMs. In ATP, we introduce LoRA-aware forward and sparsity regularization to ensure that the substructures corresponding to the learned pruning decisions can be directly removed after the ATP process. ATP outperforms the state-of-the-art two-stage pruning methods on tasks in the legal and healthcare domains. More specifically, ATP recovers up to 88% and 91% performance of the dense model when pruning 40% parameters of LLaMA2-7B and LLaMA3-8B models, respectively.

cs.CL↗
arXiv2024

A Self-guided Multimodal Approach to Enhancing Graph Representation Learning for Alzheimer's Diseases

Graph neural networks (GNNs) are powerful machine learning models designed to handle irregularly structured data. However, their generic design often proves inadequate for analyzing brain connectomes in Alzheimer's Disease (AD), highlighting the need to incorporate domain knowledge for optimal performance. Infusing AD-related knowledge into GNNs is a complicated task. Existing methods typically rely on collaboration between computer scientists and domain experts, which can be both time-intensive and resource-demanding. To address these limitations, this paper presents a novel self-guided, knowledge-infused multimodal GNN that autonomously incorporates domain knowledge into the model development process. Our approach conceptualizes domain knowledge as natural language and introduces a specialized multimodal GNN capable of leveraging this uncurated knowledge to guide the learning process of the GNN, such that it can improve the model performance and strengthen the interpretability of the predictions. To evaluate our framework, we curated a comprehensive dataset of recent peer-reviewed papers on AD and integrated it with multiple real-world AD datasets. Experimental results demonstrate the ability of our method to extract relevant domain knowledge, provide graph-based explanations for AD diagnosis, and improve the overall performance of the GNN. This approach provides a more scalable and efficient alternative to inject domain knowledge for AD compared with the manual design from the domain expert, advancing both prediction accuracy and interpretability in AD diagnosis.

cs.LG↗
arXiv2024

Efficient Circuit Wire Cutting Based on Commuting Groups

Current quantum devices face challenges when dealing with large circuits due to error rates as circuit size and the number of qubits increase. The circuit wire-cutting technique addresses this issue by breaking down a large circuit into smaller, more manageable subcircuits. However, the exponential increase in the number of subcircuits and the complexity of reconstruction as more cuts are made poses a great practical challenge. Inspired by ancilla-assisted quantum process tomography and the MUBs-based grouping technique for simultaneous measurement, we propose a new approach that can reduce subcircuit running overhead. The approach first uses ancillary qubits to transform all quantum input initializations into quantum output measurements. These output measurements are then organized into commuting groups for the purpose of simultaneous measurement, based on MUBs-based grouping. This approach significantly reduces the number of necessary subcircuits as well as the total number of shots. Lastly, we provide numerical experiments to demonstrate the complexity reduction.

quant-ph↗
arXiv2024

Unlocking Memorization in Large Language Models with Dynamic Soft Prompting

Pretrained large language models (LLMs) have revolutionized natural language processing (NLP) tasks such as summarization, question answering, and translation. However, LLMs pose significant security risks due to their tendency to memorize training data, leading to potential privacy breaches and copyright infringement. Accurate measurement of this memorization is essential to evaluate and mitigate these potential risks. However, previous attempts to characterize memorization are constrained by either using prefixes only or by prepending a constant soft prompt to the prefixes, which cannot react to changes in input. To address this challenge, we propose a novel method for estimating LLM memorization using dynamic, prefix-dependent soft prompts. Our approach involves training a transformer-based generator to produce soft prompts that adapt to changes in input, thereby enabling more accurate extraction of memorized data. Our method not only addresses the limitations of previous methods but also demonstrates superior performance in diverse experimental settings compared to state-of-the-art techniques. In particular, our method can achieve the maximum relative improvement of 112.75% and 32.26% over the vanilla baseline in terms of discoverable memorization rate for the text generation task and code generation task respectively.

cs.CL↗
arXiv2024

Dependable Classical-Quantum Computer Systems Engineering

Quantum Computing (QC) offers the potential to enhance traditional High-Performance Computing (HPC) workloads by leveraging the unique properties of quantum computers, leading to the emergence of a new paradigm: HPC-QC. While this integration presents new opportunities, it also brings novel challenges, particularly in ensuring the dependability of such hybrid systems. This paper aims to identify integration challenges, anticipate failures, and foster a diverse co-design for HPC-QC systems by bringing together QC, cloud computing, HPC, and network security. The focus of this emerging inter-disciplinary effort is to develop engineering principles that ensure the dependability of hybrid systems, aiming for a more prescriptive co-design cycle. Our framework will help to prevent design pitfalls and accelerate the maturation of the QC technology ecosystem. Key aspects include building resilient HPC-QC systems, analyzing the applicability of conventional techniques to the quantum domain, and exploring the complexity of scaling in such hybrid systems. This underscores the need for performance-reliability metrics specific to this new computational paradigm.

quant-ph↗