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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.

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.

Data augmentation (DA) has been widely leveraged in computer vision to alleviate the data shortage, whereas the DA in medical image analysis (MIA) faces multiple challenges. The prevalent DA approaches in MIA encompass conventional DA, synthetic DA, and automatic DA. However, utilizing these approaches poses various challenges such as experience-driven design and intensive computation cost. Here, we propose an efficient and effective automatic DA method termed MedAugment. We propose a pixel augmentation space and spatial augmentation space and exclude the operations that can break medical details and features, such as severe color distortions or structural alterations that can compromise image diagnostic value. Besides, we propose a novel 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, such as high sensitivity to certain attributes such as brightness and posterize. Extensive experimental results on four classification and four segmentation datasets demonstrate the superiority of MedAugment. Compared with existing approaches, the proposed MedAugment serves as a more suitable yet general processing pipeline for medical images without producing color distortions or structural alterations and involving negligible computational overhead. We emphasize that our method can serve as a plugin for arbitrary projects without any extra training stage, thereby holding the potential to make a valuable contribution to the medical field, particularly for medical experts without a solid foundation in deep learning. Code is available at https://github.com/NUS-Tim/MedAugment., Comment: 29 pages, 8 figures

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., Comment: Computers in Biology and Medicine Accepted