The rapid expansion of materials databases offers unprecedented opportunities for accelerating materials discovery via machine learning. However, the widespread assumption that larger datasets inherently produce better models does not hold in practice. We propose FUSION (Fusing Uncertainty with Structural Information for Optimal Neural training), an offline dataset pruning strategy that synergistically combines uncertainty quantification with crystallographic structure analysis via geometric fingerprinting, framing dataset pruning as a discrete optimization problem. Through evaluation across 3 benchmark datasets, FUSION consistently outperforms baselines, including random pruning, uncertainty sampling, weighting factor pruning, diversity sampling, and active learning. It demonstrates robust transferability across 11 diverse architectures, outperforming random pruning by 1.91–13.65% across different datasets, with an average improvement of 6.36%. Moreover, our analysis suggests that different models exhibit varying robustness characteristics when faced with pruned training data, highlighting the importance of model selection tailored to dataset composition. We identify optimal pruning points where removing just 0–8% of training data improves model performance, yielding gains up to 12.67% in specific model–dataset combinations. These results establish a new paradigm for materials informatics that prioritizes data quality over quantity, offering a pathway toward more efficient and sustainable machine learning workflows in computational materials science.

Supervised machine learning techniques are increasingly being adopted to speed up electronic structure predictions, serving as alternatives to first-principles methods like Density Functional Theory (DFT). Although current DFT datasets mainly emphasize chemical properties and atomic forces, the precise prediction of electronic charge density is essential for accurately determining a system's total energy and ground state properties. In this study, we introduce a novel electronic charge density dataset named ECD, which encompasses 140,646 stable crystal geometries with medium-precision Perdew–Burke–Ernzerhof (PBE) functional data. Within this dataset, a subset of 7,147 geometries includes high-precision electronic charge density data calculated using the Heyd–Scuseria–Ernzerhof (HSE) functional in DFT. By designing various benchmark tasks for crystalline materials and emphasizing training with large-scale PBE data while fine-tuning with a smaller subset of high-precision HSE data, we demonstrate the efficacy of current machine learning models in predicting electronic charge densities. The ECD dataset and baseline models are open-sourced to support community efforts in developing new methodologies and accelerating materials design and applications.

In addressing the challenge of Crystal Structure Prediction (CSP), symmetry-aware deep learning models, particularly diffusion models, have been extensively studied, which treat CSP as a conditional generation task. However, ensuring permutation, rotation, and periodic translation equivariance during diffusion process remains incompletely addressed. In this work, we propose EquiCSP, a novel equivariant diffusion-based generative model. We not only address the overlooked issue of lattice permutation equivariance in existing models, but also develop a unique noising algorithm that rigorously maintains periodic translation equivariance throughout both training and inference processes. Our experiments indicate that EquiCSP significantly surpasses existing models in terms of generating accurate structures and demonstrates faster convergence during the training process.

Superconductivity is a fascinating phenomenon observed in certain materials under certain conditions. However, some critical aspects of it, such as the relationship between superconductivity and materials' chemical/structural features, still need to be understood. Recent successes of data-driven approaches in material science strongly inspire researchers to study this relationship with them, but a corresponding dataset is still lacking. Hence, we present a new dataset for data-driven approaches, namely SuperCon3D, containing both 3D crystal structures and experimental superconducting transition temperature (Tc) for the first time. Based on SuperCon3D, we propose two deep learning methods for designing high Tc superconductors. The first is SODNet, a novel equivariant graph attention model for screening known structures, which differs from existing models in incorporating both ordered and disordered geometric content. The second is a diffusion generative model DiffCSP-SC for creating new structures, which enables high Tc-targeted generation. Extensive experiments demonstrate that both our proposed dataset and models are advantageous for designing new high Tc superconducting candidates.

Oriented object detectors have achieved great success in aerial detection tasks with the help of ample labeled data. Unlabeled images are easier and less expensive to obtain than labeled aerial images. Therefore, semi-supervised oriented object detection (SSOOD) is becoming a hot task, which can leverage both labeled and unlabeled data to train oriented detectors. Most SSOOD approaches focus on well-designed approaches to generate high-quality pseudo labels (PLs) or positive learning regions, which are limited to complex and variable aerial scenes. This study first analyzes key factors influencing the performance of SSOOD and proposes a global focal learning method (termed as focal teacher) without artificial priori design. It relies on global region and soft regression approaches to blur the boundaries between positive and negative samples, mainly through localization focal loss to achieve. It leverages the localization consistency between the teacher and student model to focus more on hard regions. Moreover, we organize a large remote sensing unlabeled (RSUL) dataset to exploit the performance potential of oriented detectors on mainstream aerial detection datasets (DOTA and DIOR). Adequate experiments reveal that the proposed method achieves the best performance compared with other mainstream SSOOD methods, including partly, fully, and additional data settings on DOTA and DIOR datasets. Semi-supervised mechanisms without preset learning regions can be better applied in dense and complex aerial scenes.

Crystal Structure Prediction (CSP) is crucial in various scientific disciplines. While CSP can be addressed by employing currently-prevailing generative models (**e.g.** diffusion models), this task encounters unique challenges owing to the symmetric geometry of crystal structures---the invariance of translation, rotation, and periodicity. To incorporate the above symmetries, this paper proposes DiffCSP, a novel diffusion model to learn the structure distribution from stable crystals. To be specific, DiffCSP jointly generates the lattice and atom coordinates for each crystal by employing a periodic-E(3)-equivariant denoising model, to better model the crystal geometry. Notably, different from related equivariant generative approaches, DiffCSP leverages fractional coordinates other than Cartesian coordinates to represent crystals, remarkably promoting the diffusion and the generation process of atom positions. Extensive experiments verify that our DiffCSP remarkably outperforms existing CSP methods, with a much lower computation cost in contrast to DFT-based methods. Moreover, the superiority of DiffCSP is still observed when it is extended for ab initio crystal generation.

SUMMARY: VSTH is a user-friendly web server with the complete workflow for virtual screening. By self-customized visualization software, users can interactively prepare protein files, set docking sites as well as view binding conformers in a target protein in a few clicks. We provide serval purchasable ligand libraries for selection. And, we integrate six open-source docking programs as computing engine, or as conformational sampling tools for DLIGAND2. Users can select various docking methods simultaneously and personalize computing parameters. After docking processing, user can filter docking conformations by ranked scores, or cluster-based molecular similarity to find highly populated clusters of low-energy conformations. AVAILABILITY AND IMPLEMENTATION: The VSTH web server is free and open to all users at https://matgen.nscc-gz.cn/VirtualScreening.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: The human major histocompatibility complex (MHC), also known as human leukocyte antigen (HLA), plays an important role in the adaptive immune system by presenting non-self-peptides to T cell receptors. The MHC region has been shown to be associated with a variety of diseases, including autoimmune diseases, organ transplantation and tumours. However, structural analytic tools of HLA are still sparse compared to the number of identified HLA alleles, which hinders the disclosure of its pathogenic mechanism. RESULT: To provide an integrative analysis of HLA, we first collected 1296 amino acid sequences, 256 protein data bank structures, 120 000 frequency data of HLA alleles in different populations, 73 000 publications and 39 000 disease-associated single nucleotide polymorphism sites, as well as 212 modelled HLA heterodimer structures. Then, we put forward two new strategies for building up a toolkit for transplantation and tumour immunotherapy, designing risk alignment pipeline and antigenic peptide prediction pipeline by integrating different resources and bioinformatic tools. By integrating 100 000 calculated HLA conformation difference and online tools, risk alignment pipeline provides users with the functions of structural alignment, sequence alignment, residue visualization and risk report generation of mismatched HLA molecules. For tumour antigen prediction, we first predicted 370 000 immunogenic peptides based on the affinity between peptides and MHC to generate the neoantigen catalogue for 11 common tumours. We then designed an antigenic peptide prediction pipeline to provide the functions of mutation prediction, peptide prediction, immunogenicity assessment and docking simulation. We also present a case study of hepatitis B virus mutations associated with liver cancer that demonstrates the high legitimacy of our antigenic peptide prediction process. HLA3D, including different HLA analytic tools and the prediction pipelines, is available at http://www.hla3d.cn/.

Architecture frameworks are methods used in architecture modeling. They provide a structured and systematic approach to designing systems. To date there has been little analysis on their roles in system and software engineering and if they are satisfactory. This study provides a model of understanding through analyzing the goals, inputs and outcomes of six architecture frameworks. It characterizes two classes of architecture frameworks and identifies some of their deficiencies. To overcome these deficiencies, we propose to use costs, benefits and risks for architecture analysis. We also propose a method to delineate architecture activities from detailed design activities.