arXiv subjects

Ziduo Yang

Publications and source records attributed to Ziduo Yang.

7 recordsLinked to original sources

arXiv2026

An Efficient High-Degree, High-Order Equivariant Graph Neural Network for Direct Crystal Structure Optimization

Crystal structure optimization is fundamental to materials modeling but remains computationally expensive when performed with density-functional theory (DFT). Machine-learning (ML) approaches offer substantial acceleration, yet existing methods face three key limitations: (i) most models operate solely on atoms and treat lattice vectors implicitly, despite their central role in structural optimization; (ii) they lack efficient mechanisms to capture high-degree angular information and higher-order geometric correlations simultaneously, which are essential for distinguishing subtle structural differences; and (iii) many pipelines are multi-stage or iterative rather than truly end-to-end, making them prone to error accumulation and limiting scalability. Here we present E$^{3}$Relax-H$^{2}$, an end-to-end high-degree, high-order equivariant graph neural network that maps an initial crystal directly to its relaxed structure. The key idea is to promote both atoms and lattice vectors to graph nodes, enabling a unified and symmetry-consistent representation of structural degrees of freedom. Building on this formulation, E$^{3}$Relax-H$^{2}$ introduces two message-passing mechanisms: (i) a high-degree, high-order message-passing module that efficiently captures high-degree angular representations and high-order many-body correlations; and (ii) a lattice-atom message-passing module that explicitly models the bidirectional coupling between lattice deformation and atomic displacement. In addition, we propose a differentiable periodicity-aware Cartesian displacement loss tailored for one-shot structure prediction under periodic boundary conditions.

cond-mat.mtrl-sci↗

arXiv2025

Equivariant Atomic and Lattice Modeling Using Geometric Deep Learning for Crystal Structure Optimization

Structure optimization, which yields the relaxed structure (minimum-energy state), is essential for reliable materials property calculations, yet traditional ab initio approaches such as density-functional theory (DFT) are computationally intensive. Machine learning (ML) has emerged to alleviate this bottleneck but suffers from two major limitations: (i) existing models operate mainly on atoms, leaving lattice vectors implicit despite their critical role in structural optimization; and (ii) they often rely on multi-stage, non-end-to-end workflows that are prone to error accumulation. Here, we present E3Relax, an end-to-end equivariant graph neural network that maps an unrelaxed crystal directly to its relaxed structure. E3Relax promotes both atoms and lattice vectors to graph nodes endowed with dual scalar-vector features, enabling unified and symmetry-preserving modeling of atomic displacements and lattice deformations. A layer-wise supervision strategy forces every network depth to make a physically meaningful refinement, mimicking the incremental convergence of DFT while preserving a fully end-to-end pipeline. We evaluate E3Relax on four benchmark datasets and demonstrate that it achieves remarkable accuracy and efficiency. Through DFT validations, we show that the structures predicted by E3Relax are energetically favorable, making them suitable as high-quality initial configurations to accelerate DFT calculations.

cond-mat.mtrl-sci↗

arXiv2025

Modeling crystal defects using defect-informed neural networks

Most AI-for-Materials research to date has focused on ideal crystals, whereas real-world materials inevitably contain defects that play a critical role in modern functional technologies. The defects break geometric symmetry and increase interaction complexity, posing particular challenges for traditional ML models. Here, we introduce Defect-Informed Equivariant Graph Neural Network (DefiNet), a model specifically designed to accurately capture defect-related interactions and geometric configurations in point-defect structures. DefiNet achieves near-DFT-level structural predictions in milliseconds using a single GPU. To validate its accuracy, we perform DFT relaxations using DefiNet-predicted structures as initial configurations and measure the residual ionic steps. For most defect structures, regardless of defect complexity or system size, only 3 ionic steps are required to reach the DFT-level ground state. Finally, comparisons with scanning transmission electron microscopy (STEM) images confirm DefiNet's scalability and extrapolation beyond point defects, positioning it as a valuable tool for defect-focused materials research.

cond-mat.mtrl-sci↗

arXiv2024

Scalable Crystal Structure Relaxation Using an Iteration-Free Deep Generative Model with Uncertainty Quantification

In computational molecular and materials science, determining equilibrium structures is the crucial first step for accurate subsequent property calculations. However, the recent discovery of millions of new crystals and complex twisted structures has challenged traditional computational methods, both ab initio and machine-learning-based, due to their computationally intensive iterative processes. To address these scalability issues, here we introduce DeepRelax, a deep generative model capable of performing geometric crystal structure relaxation rapidly and without iterations. DeepRelax learns the equilibrium structural distribution, enabling it to predict relaxed structures directly from their unrelaxed ones. The ability to perform structural relaxation at the millisecond level per structure, combined with the scalability of parallel processing, makes DeepRelax particularly useful for large-scale virtual screening. We demonstrate DeepRelax's reliability and robustness by applying it to five diverse databases, including oxides, Materials Project, two-dimensional materials, van der Waals crystals, and crystals with point defects. DeepRelax consistently shows high accuracy and efficiency, validated by density functional theory calculations. Finally, we enhance its trustworthiness by integrating uncertainty quantification. This work significantly accelerates computational workflows, offering a robust and trustworthy machine-learning method for material discovery and advancing the application of AI for science. Code for DeepRelax is available at https://github.com/Shen-Group/DeepRelax.

cond-mat.mtrl-sci↗

arXiv2023

Lightweight equivariant model for efficient machine learning interatomic potentials

In modern computational materials science, deep learning has shown the capability to predict interatomic potentials, thereby supporting and accelerating conventional simulations. However, existing models typically sacrifice either accuracy or efficiency. Moreover, lightweight models are highly demanded for offering simulating systems on a considerably larger scale at reduced computational costs. Here, we introduce a lightweight equivariant interaction graph neural network (LEIGNN) that can enable accurate and efficient interatomic potential and force predictions for molecules and crystals. Rather than relying on higher-order representations, LEIGNN employs a scalar-vector dual representation to encode equivariant features. By learning geometric symmetry information, our model remains lightweight while ensuring prediction accuracy and robustness through the equivariance. Our results show that LEIGNN consistently outperforms the prediction performance of the representative baselines and achieves significant efficiency across diverse datasets, which include catalysts, molecules, and organic isomers. Furthermore, we conduct molecular dynamics (MD) simulations using the LEIGNN force field across solid, liquid, and gas systems. It is found that LEIGNN can achieve the accuracy of \textit{ab initio} MD across all examined systems.

cs.CE↗

arXiv2023

MedAugment: Universal Automatic Data Augmentation Plug-in for Medical Image Analysis

Data augmentation (DA) has been widely leveraged in computer vision to alleviate data shortage, while its application in medical imaging faces multiple challenges. The prevalent DA approaches in medical image analysis encompass conventional DA, synthetic DA, and automatic DA. However, these approaches may result in experience-driven design and intensive computation costs. Here, we propose a suitable yet general automatic DA method for medical images termed MedAugment. We propose pixel and spatial augmentation spaces and exclude the operations that can break medical details and features. Besides, we propose a sampling strategy by sampling a limited number of operations from the two spaces. Moreover, we present a hyperparameter mapping relationship to produce a rational augmentation level and make the MedAugment fully controllable using a single hyperparameter. These configurations settle the differences between natural and medical images. Extensive experimental results on four classification and four segmentation datasets demonstrate the superiority of MedAugment. Compared with existing approaches, the proposed MedAugment prevents producing color distortions or structural alterations while involving negligible computational overhead. Our method can serve as a plugin without an extra training stage, offering significant benefits to the community and medical experts lacking a deep learning foundation. The code is available at https://github.com/NUS-Tim/MedAugment.

eess.IV↗

arXiv2022

Recent Progress in Transformer-based Medical Image Analysis

The transformer is primarily used in the field of natural language processing. Recently, it has been adopted and shows promise in the computer vision (CV) field. Medical image analysis (MIA), as a critical branch of CV, also greatly benefits from this state-of-the-art technique. In this review, we first recap the core component of the transformer, the attention mechanism, and the detailed structures of the transformer. After that, we depict the recent progress of the transformer in the field of MIA. We organize the applications in a sequence of different tasks, including classification, segmentation, captioning, registration, detection, enhancement, localization, and synthesis. The mainstream classification and segmentation tasks are further divided into eleven medical image modalities. A large number of experiments studied in this review illustrate that the transformer-based method outperforms existing methods through comparisons with multiple evaluation metrics. Finally, we discuss the open challenges and future opportunities in this field. This task-modality review with the latest contents, detailed information, and comprehensive comparison may greatly benefit the broad MIA community.

eess.IV↗