Yangshuai Wang

Huajie Chen, Mingjie Liao, Hao Wang et al.

QM (quantum mechenics) and MM (molecular mechenics) coupling methods are widely used in simulations of crystalline defects. In this paper, we construct a residual based a posteriori error indicator for QM/MM coupling approximations. We prove the reliability of the error indicator (upper bound of the true approximation error) and develop some sampling techniques for its efficient calculation. Based on the error indicator and Dörfler marking strategy, we design an adaptive QM/MM algorithm for crystalline defects and demonstrate the efficiency with some numerical experiments.

Yifan Yu, Yangshuai Wang

The nudged elastic band (NEB) and Dimer methods are standard tools for computing minimum-energy paths and index-one saddle points in atomistic transition problems. They are increasingly driven by surrogate or learned force models, whose force errors are often anisotropic and spatially varying near transition states and defect cores, where saddle-search iterations are most sensitive. We introduce uncertainty-aware NEB and Dimer methods (UA-NEB, UA-Dimer) that use covariance as an optimizer-level reliability metric while preserving the mean-potential saddle-search equations: an oblique normal projection for NEB and covariance-weighted rotation and translation for Dimer. Both algorithms fit Robbins--Monro recursions; under a local Lyapunov stability hypothesis, verified explicitly for a canonical UA-NEB setting and stated as a hypothesis for UA-Dimer, the stochastic iterations converge almost surely within the corresponding local stability neighborhood. In the analytic benchmark, UA-NEB reduces mean barrier error by $21\%$ relative to stochastic NEB and UA-Dimer reduces the reflected-gradient residual by $22\%$; in the 127-atom tungsten-vacancy benchmark, full UA-NEB reduces mean barrier error by $56\%$ relative to stochastic NEB and by $23\%$ relative to diagonal covariance weighting. These results show that anisotropic uncertainty is most useful when embedded in the constrained geometry of the optimizer rather than collapsed into a scalar acquisition or trust criterion.

Qingyu Meng, Yangshuai Wang

Variational quantum circuits are increasingly studied as continuous-function approximators, but quantum regression remains difficult to train when global losses, finite-shot stochasticity, and circuit-depth growth combine to produce weak or ill-conditioned gradient signals. We study this trainability problem in a controlled hybrid quantum--classical regression design. The central ingredient is a capacity-controlled classical embedding that acts as a learnable geometric preconditioner: it reshapes the input distribution seen by a data-reuploading variational circuit while preserving a low-dimensional quantum bottleneck. We pair this representation design with a curriculum protocol that grows circuit depth progressively and switches from SPSA-based stochastic exploration to Adam-based analytic-gradient fine-tuning. We formalize the mechanism through a local quantum-tangent contraction statement: in the linearized quantum-parameter dynamics, the embedding changes the empirical Gram matrix that controls residual contraction and one-step loss decrease. Across finite-size statevector audits on PDE-informed regression benchmarks and small-data tabular tasks, the Hybrid QNN lowers error relative to Pure QNN baselines under matched quantum-model budgets. Strong classical references remain competitive, and in several cases are better in absolute error; the evidence therefore supports a trainability claim for the hybrid QNN design rather than a claim of classical or hardware quantum advantage.

Li Ding, Duanyu Feng, Chen Huang et al.

Protein-Text Question Answering (QA) is crucial for interpreting biological sequences through natural language. The integration of Large Language Models (LLMs) with Retrieval-Augmented Generation (RAG) that efficiently leverages biological databases and facilitates reasoning offers a potent approach for it. However, constrained by the standard RAG pipeline, these models often rely on curated, static datasets instead of expert-proven biological workflows, lacking the fine-grained information processing and struggling to generalize to novel (OOD) proteins. To bridge this gap, we propose 2D-ProteinRAG, a novel framework that empowers LLMs to operate within the gold-standard biological research workflow (BLAST). To further extract high-quality information from noisy retrieval contexts, we introduce a dual-dimensional (2D) filtering strategy following the expert analytical paradigms. Horizontal Fine-grained Attribute Alignment utilizes a lightweight, intent-aware discriminative filter to prune irrelevant metadata and align database entries with specific user queries. Vertical Homology-based Semantic Denoising resolves functional contradictions and redundancy across multiple homologs via hierarchical clustering. Extensive evaluations on both In-Distribution and diverse biological OOD benchmarks demonstrate that 2D-ProteinRAG consistently achieves state-of-the-art performance, outperforming fine-tuned baselines and other RAG methods. Our results validate the framework's robustness and scalability, providing a practical solution for interpreting protein functions in real-world scientific scenarios.

Qinyi Zhang, Duanyu Feng, Ronghui Han et al.

Simulating microstructure evolution (MicroEvo) is vital for materials design but demands high numerical accuracy, efficiency, and physical fidelity. Although recent studies on deep learning (DL) offer a promising alternative to traditional solvers, the field lacks standardized benchmarks. Existing studies are flawed due to a lack of comparing specialized MicroEvo DL models with state-of-the-art spatio-temporal architectures, an overemphasis on numerical accuracy over physical fidelity, and a failure to analyze error propagation over time. To address these gaps, we introduce MicroEvoEval, the first comprehensive benchmark for image-based microstructure evolution prediction. We evaluate 14 models, encompassing both domain-specific and general-purpose architectures, across four representative MicroEvo tasks with datasets specifically structured for both short- and long-term assessment. Our multi-faceted evaluation framework goes beyond numerical accuracy and computational cost, incorporating a curated set of structure-preserving metrics to assess physical fidelity. Our extensive evaluations yield several key insights. Notably, we find that modern architectures (e.g., VMamba), not only achieve superior long-term stability and physical fidelity but also operate with an order-of-magnitude greater computational efficiency. The results highlight the necessity of holistic evaluation and identify these modern architectures as a highly promising direction for developing efficient and reliable surrogate models in data-driven materials science.

Haoran Zhou, Zhaohui Fu, Yangshuai Wang et al.

We study a discrete-time random feature method for nonlinear, time-dependent partial differential equations. In contrast to continuous-time formulations that treat time as an additional input variable, the method advances the solution step by step, with each time level computed from previously available states. The spatial solution at each step is represented in the random feature trial space, and the time discretization is given by an implicit-explicit Runge--Kutta (IMEX-RK, 4 stages, third-order) scheme. After splitting the operator into linear and nonlinear parts, each stage admits a linear least-squares formulation, which avoids nonlinear least-squares solves. We also derive a global error estimate for the fully discrete method, separating the contributions of the stage-wise RFM approximation, perturbations in the least-squares coefficients, and the temporal discretization. Numerical experiments for the Allen--Cahn, Burgers, Korteweg--De Vries, and Cahn--Hilliard equations show relative $L^2$-errors of order $10^{-6}$ and convergence rates consistent with the third-order IMEX scheme. A comparison with an IMEX-PINN variant shows that the proposed method achieves higher accuracy at substantially lower computational cost.

Yifan Yu, Cheuk Hin Ho, Yangshuai Wang

Physics-Informed Neural Networks (PINNs) have emerged as a powerful framework for solving PDEs, yet existing uncertainty quantification (UQ) approaches for PINNs generally lack rigorous statistical guarantees. In this work, we bridge this gap by introducing a distribution-free conformal prediction (CP) framework for UQ in PINNs. This framework calibrates prediction intervals by constructing nonconformity scores on a calibration set, thereby yielding distribution-free uncertainty estimates with rigorous finite-sample coverage guarantees for PINNs. To handle spatial heteroskedasticity, we further introduce local conformal quantile estimation, enabling spatially adaptive uncertainty bands while preserving theoretical guarantee. Through systematic evaluations on typical PDEs (damped harmonic oscillator, Poisson, Allen-Cahn, and Helmholtz equations) and comprehensive testing across multiple uncertainty metrics, our results demonstrate that the proposed framework achieves reliable calibration and locally adaptive uncertainty intervals, consistently outperforming heuristic UQ approaches. By bridging PINNs with distribution-free UQ, this work introduces a general framework that not only enhances calibration and reliability, but also opens new avenues for uncertainty-aware modeling of complex PDE systems.

Yangshuai Wang, Hao Wang, Lei Zhang

Nonlinear elastic models are widely used to describe the elastic response of crystalline solids, for example, the well-known Cauchy-Born model. While the Cauchy-Born model only depends on the strain, effects of higher order strain gradients are significant and higher order continuum models are preferred, in various applications such as defect dynamics and modeling of carbon nanotubes. In this paper, we rigorously derive a higher order nonlinear elasticity model for crystals from its atomistic description in one dimension. We show that, compared to the second order accuracy of the Cauchy-Born model, the higher order continuum model in this paper is of fourth oder accuracy with respect to the interatomic spacing in the thermal dynamic limit. In addition, we discuss the key issues for the derivation of higher order continuum models in more general cases. The theoretical convergence results are demonstrated by numerical experiments.