arXiv subjects

Yuwen Zhang

Publications and source records attributed to Yuwen Zhang.

At least 19 recordsLinked to original sources

arXiv2026

Quantum Compressed Sensing CT Reconstruction Algorithm Based on Penalized Weighted Least Squares and Guided Total Variation

Objective. Existing quadratic unconstrained binary optimization (QUBO)-based sparse-view computed tomography (CT) reconstruction neglects photon-counting statistics and anatomical heterogeneity. We address both limitations within the QUBO framework.Approach. We propose a quantum compressed-sensing CT method combining penalized weighted least squares (PWLS) and guided total variation (GTV). PWLS weights projection residuals by photon-count reliability, whereas GTV uses gradients from a prior image reconstructed by the simultaneous algebraic reconstruction technique (SART) to preserve edges and suppress noise in homogeneous regions. After binary encoding, both terms form a unified QUBO model. Experiments used four 40 times 40 CT images under a 10-view fan-beam geometry with Poisson noise. Comparisons included conventional reconstruction methods, QUBO variants, gradient descent, simulated annealing, and a D-Wave hybrid quantum-classical solver.Main results. PWLS-GTV achieved the best reconstruction quality across all cases. In the representative chest case, it reached a peak signal-to-noise ratio (PSNR) of 36.64 dB, compared with 22.48 dB for SART, the best conventional baseline. GTV consistently outperformed conventional total variation. Simulated annealing and the D-Wave hybrid solver produced similar reconstructions, whereas gradient descent was ineffective. Repeated hybrid-solver runs showed stable performance.Significance. The framework incorporates photon-statistical weighting and structure-guided regularization into QUBO-based CT reconstruction without changing its quadratic form, providing a proof of concept for quantum-assisted sparse-view CT reconstruction.

cs.CV↗

arXiv2026

Quantum CT via Dynamic Interval Encoding and Prior-Balanced QUBO Reconstruction

Quadratic unconstrained binary optimization (QUBO)-based quantum computed tomography (CT) casts reconstruction as a binary quadratic problem for quantum annealing and hybrid quantum--classical solvers. For grayscale CT, however, image encoding is constrained by the binary-variable budget: fixed global bit-plane encodings increase QUBO size and coupling complexity as gray-level precision improves, whereas low-bit encodings introduce quantization error. We propose a QUBO-based grayscale CT reconstruction framework that combines dynamic interval encoding with prior-balanced optimization. Each refinement round encodes active pixels only within local gray-level intervals around the current estimate, and a boundary-hit-guided update rule adaptively switches between search expansion and local refinement. To improve optimization stability, the method balances projection-domain data consistency and an edge-preserving quadratic prior before forming the final QUBO. Sparse-view and limited-angle fan-beam CT experiments show that the proposed method recovers structures and gray-level distributions more faithfully than the evaluated analytic, iterative, variational, and representation-based baselines. Expressivity analysis and ablation studies further indicate that the improvement mainly arises from effective gray-level representation through dynamic local encoding and more stable data-fidelity--prior coupling. Experiments on the D-Wave hybrid binary quadratic model (BQM) solver further demonstrate that the formulation is executable on a hardware-backed hybrid quantum--classical backend.

cs.CV↗

arXiv2026

Autonomous Multi-Agent AI for High-Throughput Polymer Informatics: From Property Prediction to Generative Design Across Synthetic and Bio-Polymers

We present an integrated multiagent AI ecosystem for polymer discovery that unifies high-throughput materials workflows, artificial intelligence, and computational modeling within a single Polymer Research Lifecycle (PRL) pipeline. The system orchestrates specialized agents powered by state-of-the-art large language models (DeepSeek-V2 and DeepSeek-Coder) to retrieve and reason over scientific resources, invoke external tools, execute domain-specific code, and perform metacognitive self-assessment for robust end-to-end task execution. We demonstrate three practical capabilities: a high-fidelity polymer property prediction and generative design pipeline, a fully automated multimodal workflow for biopolymer structure characterization, and a metacognitive agent framework that can monitor performance and improve execution strategies over time. On a held-out test set of 1,251 polymers, our PolyGNN agent achieves strong predictive accuracy, reaching R2 = 0.89 for glass-transition temperature (Tg ), R2 = 0.82 for tensile strength, R2 = 0.75 for elongation, and R2 = 0.91 for density. The framework also provides uncertainty estimates via multiagent consensus and scales with linear complexity to at least 10,000 polymers, enabling high-throughput screening at low computational cost. For a representative workload, the system completes inference in 16.3 s using about 2 GB of memory and 0.1 GPU hours, at an estimated cost of about $0.08. On a dedicated Tg benchmark, our approach attains R2 = 0.78, outperforming strong baselines including single-LLM prediction (R2 = 0.67), group-contribution methods (R2 = 0.71), and ChemCrow (R2 = 0.66). We further demonstrate metacognitive control in a polystyrene case study, where the system not only produces domain-level scientific outputs but continually monitors and optimizes its own behavior through tactical, strategic, and meta-strategic self-assessment.

cond-mat.soft↗

arXiv2025

Quantum Error Mitigation with Attention Graph Transformers for Burgers Equation Solvers on NISQ Hardware

We present a hybrid quantum-classical framework augmented with learned error mitigation for solving the viscous Burgers equation on noisy intermediate-scale quantum (NISQ) hardware. Using the Cole-Hopf transformation, the nonlinear Burgers equation is mapped to a diffusion equation, discretized on uniform grids, and encoded into a quantum state whose time evolution is approximated via Trotterized nearest-neighbor circuits implemented in Qiskit. Quantum simulations are executed on noisy Aer backends and IBM superconducting quantum devices and are benchmarked against high-accuracy classical solutions obtained using a Krylov-based solver applied to the corresponding discretized Hamiltonian. From measured quantum amplitudes, we reconstruct the velocity field and evaluate physical and numerical diagnostics, including the L2 error, shock location, and dissipation rate, both with and without zero-noise extrapolation (ZNE). To enable data-driven error mitigation, we construct a large parametric dataset by sweeping viscosity, time step, grid resolution, and boundary conditions, producing matched tuples of noisy, ZNE-corrected, hardware, and classical solutions together with detailed circuit metadata. Leveraging this dataset, we train an attention-based graph neural network that incorporates circuit structure, light-cone information, global circuit parameters, and noisy quantum outputs to predict error-mitigated solutions. Across a wide range of parameters, the learned model consistently reduces the discrepancy between quantum and classical solutions beyond what is achieved by ZNE alone. We discuss extensions of this approach to higher-dimensional Burgers systems and more general quantum partial differential equation solvers, highlighting learned error mitigation as a promising complement to physics-based noise reduction techniques on NISQ devices.

quant-ph↗

arXiv2025

Intervention Efficiency and Perturbation Validation Framework: Capacity-Aware and Robust Clinical Model Selection under the Rashomon Effect

In clinical machine learning, the coexistence of multiple models with comparable performance (a manifestation of the Rashomon Effect) poses fundamental challenges for trustworthy deployment and evaluation. Small, imbalanced, and noisy datasets, coupled with high-dimensional and weakly identified clinical features, amplify this multiplicity and make conventional validation schemes unreliable. As a result, selecting among equally performing models becomes uncertain, particularly when resource constraints and operational priorities are not considered by conventional metrics like F1 score. To address these issues, we propose two complementary tools for robust model assessment and selection: Intervention Efficiency (IE) and the Perturbation Validation Framework (PVF). IE is a capacity-aware metric that quantifies how efficiently a model identifies actionable true positives when only limited interventions are feasible, thereby linking predictive performance with clinical utility. PVF introduces a structured approach to assess the stability of models under data perturbations, identifying models whose performance remains most invariant across noisy or shifted validation sets. Empirical results on synthetic and real-world healthcare datasets show that using these tools facilitates the selection of models that generalize more robustly and align with capacity constraints, offering a new direction for tackling the Rashomon Effect in clinical settings.

cs.LG↗

arXiv2025

AgenticAD: A Specialized Multiagent System Framework for Holistic Alzheimer Disease Management

Alzheimer's disease (AD) presents a complex, multifaceted challenge to patients, caregivers, and the healthcare system, necessitating integrated and dynamic support solutions. While artificial intelligence (AI) offers promising avenues for intervention, current applications are often siloed, addressing singular aspects of the disease such as diagnostics or caregiver support without systemic integration. This paper proposes a novel methodological framework for a comprehensive, multi-agent system (MAS) designed for holistic Alzheimer's disease management. The objective is to detail the architecture of a collaborative ecosystem of specialized AI agents, each engineered to address a distinct challenge in the AD care continuum, from caregiver support and multimodal data analysis to automated research and clinical data interpretation. The proposed framework is composed of eight specialized, interoperable agents. These agents are categorized by function: (1) Caregiver and Patient Support, (2) Data Analysis and Research, and (3) Advanced Multimodal Workflows. The methodology details the technical architecture of each agent, leveraging a suite of advanced technologies including large language models (LLMs) such as GPT-4o and Gemini, multi-agent orchestration frameworks, Retrieval-Augmented Generation (RAG) for evidence-grounded responses, and specialized tools for web scraping, multimodal data processing, and in-memory database querying. This paper presents a detailed architectural blueprint for an integrated AI ecosystem for AD care. By moving beyond single-purpose tools to a collaborative, multi-agent paradigm, this framework establishes a foundation for developing more adaptive, personalized, and proactive solutions. This methodological approach aims to pave the way for future systems capable of synthesizing diverse data streams to improve patient outcomes and reduce caregiver burden.

cs.MA↗

arXiv2025

Causal MAS: A Survey of Large Language Model Architectures for Discovery and Effect Estimation

Large Language Models (LLMs) have demonstrated remarkable capabilities in various reasoning and generation tasks. However, their proficiency in complex causal reasoning, discovery, and estimation remains an area of active development, often hindered by issues like hallucination, reliance on spurious correlations, and difficulties in handling nuanced, domain-specific, or personalized causal relationships. Multi-agent systems, leveraging the collaborative or specialized abilities of multiple LLM-based agents, are emerging as a powerful paradigm to address these limitations. This review paper explores the burgeoning field of causal multi-agent LLMs. We examine how these systems are designed to tackle different facets of causality, including causal reasoning and counterfactual analysis, causal discovery from data, and the estimation of causal effects. We delve into the diverse architectural patterns and interaction protocols employed, from pipeline-based processing and debate frameworks to simulation environments and iterative refinement loops. Furthermore, we discuss the evaluation methodologies, benchmarks, and diverse application domains where causal multi-agent LLMs are making an impact, including scientific discovery, healthcare, fact-checking, and personalized systems. Finally, we highlight the persistent challenges, open research questions, and promising future directions in this synergistic field, aiming to provide a comprehensive overview of its current state and potential trajectory.

cs.AI↗

arXiv2025

Mic-hackathon 2024: Hackathon on Machine Learning for Electron and Scanning Probe Microscopy

Microscopy is a primary source of information on materials structure and functionality at nanometer and atomic scales. The data generated is often well-structured, enriched with metadata and sample histories, though not always consistent in detail or format. The adoption of Data Management Plans (DMPs) by major funding agencies promotes preservation and access. However, deriving insights remains difficult due to the lack of standardized code ecosystems, benchmarks, and integration strategies. As a result, data usage is inefficient and analysis time is extensive. In addition to post-acquisition analysis, new APIs from major microscope manufacturers enable real-time, ML-based analytics for automated decision-making and ML-agent-controlled microscope operation. Yet, a gap remains between the ML and microscopy communities, limiting the impact of these methods on physics, materials discovery, and optimization. Hackathons help bridge this divide by fostering collaboration between ML researchers and microscopy experts. They encourage the development of novel solutions that apply ML to microscopy, while preparing a future workforce for instrumentation, materials science, and applied ML. This hackathon produced benchmark datasets and digital twins of microscopes to support community growth and standardized workflows. All related code is available at GitHub: https://github.com/KalininGroup/Mic-hackathon-2024-codes-publication/tree/1.0.0.1

cond-mat.mtrl-sci↗

arXiv2025

Beyond Correlation: Towards Causal Large Language Model Agents in Biomedicine

Large Language Models (LLMs) show promise in biomedicine but lack true causal understanding, relying instead on correlations. This paper envisions causal LLM agents that integrate multimodal data (text, images, genomics, etc.) and perform intervention-based reasoning to infer cause-and-effect. Addressing this requires overcoming key challenges: designing safe, controllable agentic frameworks; developing rigorous benchmarks for causal evaluation; integrating heterogeneous data sources; and synergistically combining LLMs with structured knowledge (KGs) and formal causal inference tools. Such agents could unlock transformative opportunities, including accelerating drug discovery through automated hypothesis generation and simulation, enabling personalized medicine through patient-specific causal models. This research agenda aims to foster interdisciplinary efforts, bridging causal concepts and foundation models to develop reliable AI partners for biomedical progress.

cs.AI↗

arXiv2025

Multicrossmodal Automated Agent for Integrating Diverse Materials Science Data

We introduce a multicrossmodal LLM-agent framework motivated by the growing volume and diversity of materials-science data ranging from high-resolution microscopy and dynamic simulation videos to tabular experiment logs and sprawling literature archives. While recent AI efforts have accelerated individual tasks such as property prediction or image classification, they typically treat each modality in isolation, leaving rich cross-modal correlations unexplored and forcing researchers to perform laborious manual integration. Moreover, existing multimodal foundation models often require expensive retraining or fine-tuning on domain data, and current multi-agent systems in materials informatics address only narrow subtasks. To overcome these obstacles, we design a coordinated team of specialized LLM agents, each equipped with domain-adapted prompts and plugins that project their outputs into a shared embedding space. A dynamic gating mechanism then weights and merges these insights, enabling unified reasoning over heterogeneous inputs without ever modifying the underlying LLM weights. We validate our approach on challenging case studies and demonstrate substantial gains in retrieval accuracy (85%), captioning fidelity, and integrated coverage (35%) compared to single-modality and zero-shot baselines. Our work paves the way for AI digital researchers capable of bridging data silos and accelerating the materials-discovery cycle. The code is available at https://github.com/adibgpt/Multicrossmodal-Autonomous-Materials-Science-Agent.

cond-mat.mtrl-sci↗

arXiv2025

Three-dimensional neural network driving self-interference digital holography enables high-fidelity, non-scanning volumetric fluorescence microscopy

We present a deep learning driven computational approach to overcome the limitations of self-interference digital holography that imposed by inferior axial imaging performances. We demonstrate a 3D deep neural network model can simultaneously suppresses the defocus noise and improves the spatial resolution and signal-to-noise ratio of conventional numerical back-propagation-obtained holographic reconstruction. Compared with existing 2D deep neural networks used for hologram reconstruction, our 3D model exhibits superior performance in enhancing the resolutions along all the three spatial dimensions. As the result, 3D non-scanning volumetric fluorescence microscopy can be achieved, using 2D self-interference hologram as input, without any mechanical and opto-electronic scanning and complicated system calibration. Our method offers a high spatiotemporal resolution 3D imaging approach which can potentially benefit, for example, the visualization of dynamics of cellular structure and measurement of 3D behavior of high-speed flow field.

physics.optics↗

arXiv2025

CoronaryHemodynamics: An Automated Simulation Framework for Coronary Artery Hemodynamics Using OpenFOAM

CoronaryHemodynamics is a comprehensive simulation package developed on the OpenFOAM platform, designed specifically for coronary artery hemodynamics analysis. The package integrates a complete suite of tools for simulation preparation, including automatic case setup, boundary condition configuration, computational domain meshing, and a CFD solver. It fully supports MPI parallelization, leveraging the native parallel computing capabilities of OpenFOAM. The package implements Windkessel boundary conditions at the aorta outlet and all coronary vessel outlets, with outlet parameters automatically derived from physiological metrics such as heart rate, systolic blood pressure, and myocardial volume. At the aorta inlet, a parabolic flow profile is applied based on the input flow rate waveform. CoronaryHemodynamics supports both steady-state and transient solvers, enabling the simulation of various flow conditions. Flow rate and pressure data are recorded at all boundaries during the simulation, and outputs such as wall shear stress, pressure fields, and velocity fields are automatically stored for detailed post-processing and analysis. By automating critical aspects of the simulation pipeline and integrating physiological boundary conditions, CoronaryHemodynamics offers an efficient and robust framework to study coronary hemodynamics in both research and clinical applications. The package can be found at https://github.com/alundilong/CoronaryHemodynamics.

physics.flu-dyn↗

arXiv2024

Isolated zero-energy flat-bands and intrinsic magnetism in carbon monolayers

Flat-band in twisted graphene bilayer has garnered widespread attention, and whether flat-bands can be realized in carbon monolayer is an interesting topic worth exploring in condensed matter physics. In this work, we demonstrate that, based on the theory of compact localized states, a series of two-dimensional carbon allotropes with flat-bands can be achieved. Two of them named as 191-8-66-C-r567x-1 and 191-10-90-C-r567x-1 are confirmed to be dynamically stable carbon phases with isolated or weakly overlapped flat-bands at the Fermi-level. The maximum Fermi velocities of the flat-band electrons are evaluated to be 1x10^4 m/s and 0.786x10^4 m/s, both of which are lower than the Fermi velocity of the flat-band electrons in magic-angle graphene (4x10^4 m/s). Furthermore, 191-8-66-C-r567x-1 has been confirmed to be a flat-band related magnetic half-metal with a magnetic moment of 1.854 miuB per cell, while 191-10-90-C-r567x-1 is a flat-band related magnetic normal metal with a magnetic moment of 1.663 miuB per cell. These results not only show that flat-bands can be constructed in carbon monolayer, but also indicate the potential for achieving metal-free magnetic materials with light elements based on flat-band theory.

cond-mat.mes-hall↗

arXiv2024

QESM: A Leap Towards Quantum-Enhanced ML Emulation Framework for Earth and Climate Modeling

Current climate models often struggle with accuracy because they lack sufficient resolution, a limitation caused by computational constraints. This reduces the precision of weather forecasts and long-term climate predictions. To address this issue, we explored the use of quantum computing to enhance traditional machine learning (ML) models. We replaced conventional models like Convolutional Neural Networks (CNN), Multilayer Perceptrons (MLP), and Encoder-Decoder frameworks with their quantum versions: Quantum Convolutional Neural Networks (QCNN), Quantum Multilayer Perceptrons (QMLP), and Quantum Encoder-Decoders (QED). These quantum models proved to be more accurate in predicting climate-related outcomes compared to their classical counterparts. Using the ClimSim dataset, a large collection of climate data created specifically for ML-based climate prediction, we trained and tested these quantum models. Individually, the quantum models performed better, but their performance was further improved when we combined them using a meta-ensemble approach, which merged the strengths of each model to achieve the highest accuracy overall. This study demonstrates that quantum machine learning can significantly improve the resolution and accuracy of climate simulations. The results offer new possibilities for better predicting climate trends and weather events, which could have important implications for both scientific understanding and policy-making in the face of global climate challenges.

physics.ao-ph↗

arXiv2024

A Workflow for Utilizing OpenFOAM Data Structure in Physics-Informed Deep Learning Training

This study presents a novel methodology for integrating physics-informed loss functions into deep learning models using OpenFOAM's comprehensive data structures. Leveraging the robust and flexible capabilities of OpenFOAM's data structure for handling complex geometries and boundary conditions, it is demonstrated how to construct detailed loss functions that accurately embed physics constraints and potentially enhance the training and performance of neural networks in handling industrial-level complicated geometry for computational fluid dynamics (CFD) simulations. The present work primarily focuses on the 1D Burger equation to showcase the detailed procedure of constructing initial loss, boundary loss, and residual loss. While the computational geometry employed here is relatively simple, the procedure is sufficiently general to illustrate its applicability to more complex computational domains. The results show the trained operator former (OFormer) neural network can successfully predict the simulation results subject to the OpenFOAM'data structure composed loss. This framework potentially opens new avenues for using deep learning to tackle complex industrial simulation challenges, promising significant advancements in the accuracy and practicality of CFD applications.

physics.flu-dyn↗

arXiv2024

Switchable Ferroelectricity in Subnano Silicon Thin Films

Recent advancements underscore the critical need to develop ferroelectric materials compatible with silicon. We systematically explore possible ferroelectric silicon quantum films and discover a low-energy variant (hex-OR-2*2-P) with energy just 1 meV/atom above the ground state (hex-OR-2*2). Both hex-OR-2*2 and hex-OR-2*2-P are confirmed to be dynamically and mechanically stable semiconductors with indirect gaps of 1.323 eV and 1.311 eV, respectively. The ferroelectric hex-OR-2*2-P exhibits remarkable in-plane spontaneous polarization up to 120 Pc/m and is protected by a potential barrier (13.33 meV/atom) from spontaneously transitioning to hex-OR-22. To simulate the switching ferroelectricity in electric fields of the single-element silicon bilayer, we develop a method that simultaneously learns interatomic potentials and Born effective charges (BEC) in a single equivariant model with a physically informed loss. Our method demonstrates good performance on several ferroelectrics. Simulations of hex-OR-2*2-P silicon suggest a depolarization temperature of approximately 300 K and a coercive field of about 0.05 V/{\AA}. These results indicate that silicon-based ferroelectric devices are feasible, and the ground state phase of the silicon bilayer (hex-OR-2*2) is an ideal system. Our findings highlight the promise of pure silicon ferroelectric materials for future experimental synthesis and applications in memory devices, sensors, and energy converters.

cond-mat.mtrl-sci↗

arXiv2024

Blending Is All You Need: Cheaper, Better Alternative to Trillion-Parameters LLM

In conversational AI research, there's a noticeable trend towards developing models with a larger number of parameters, exemplified by models like ChatGPT. While these expansive models tend to generate increasingly better chat responses, they demand significant computational resources and memory. This study explores a pertinent question: Can a combination of smaller models collaboratively achieve comparable or enhanced performance relative to a singular large model? We introduce an approach termed "blending", a straightforward yet effective method of integrating multiple chat AIs. Our empirical evidence suggests that when specific smaller models are synergistically blended, they can potentially outperform or match the capabilities of much larger counterparts. For instance, integrating just three models of moderate size (6B/13B paramaeters) can rival or even surpass the performance metrics of a substantially larger model like ChatGPT (175B+ paramaters). This hypothesis is rigorously tested using A/B testing methodologies with a large user base on the Chai research platform over a span of thirty days. The findings underscore the potential of the "blending" strategy as a viable approach for enhancing chat AI efficacy without a corresponding surge in computational demands.

cs.CL↗

arXiv2023

Vertical Ferroelectricity in Van der Waals Materials: Models and Devices

Ferroelectricity has a wide range of applications in functional electronics and is extremely important for the development of next-generation information storage technology, but it is difficult to achieve due to its special symmetry requirements. In this letter, based on van derWaals stacking, a generic model is proposed for realizing ferroelectric devices, where a freely movable center layer is packaged in two fixed and symmetrically stacked layers. In this model, the ferroelectric phase transition can be realized between the two equivalent and eccentric ground stacking-states with opposite polarizations. By means of first-principles calculations, taking the h-BN/h-BN/h-BN and h-BN/Graphene/h-BN as feasible models, we carefully evaluate the magnitude of ferroelectricity. The corresponding polarizations are estimated as 1.83 and 1.35 pC/m, respectively, which are comparable to the sliding ferroelectricity. Such a new tri-layer model of vertical ferroelectricity can be constructed by arbitrary van derWaals semiconducting materials, and usually holds low switching barrier. Optimized material combinations with remarkable polarization are highly expectable to be discovered from the huge candidate set for future information storage.

cond-mat.mtrl-sci↗