Kui Xu

Fuyao Huang, Xiaozhu Yu, Kui Xu et al.

High-resolution structure determination by cryo-electron microscopy (cryo-EM) requires the accurate fitting of an atomic model into an experimental density map. Traditional refinement pipelines such as Phenix.real_space_refine and Rosetta are computationally expensive, demand extensive manual tuning, and present a significant bottleneck for researchers. We present CryoNet.Refine, an end-to-end deep learning framework that automates and accelerates molecular structure refinement. Our approach utilizes a one-step diffusion model that integrates a density-aware loss function with robust stereochemical restraints, enabling rapid optimization of a structure against experimental data. CryoNet.Refine provides a unified and versatile solution capable of refining protein complexes as well as DNA/RNA-protein complexes. In benchmarks against Phenix.real_space_refine, CryoNet.Refine consistently achieves substantial improvements in both model-map correlation and overall geometric quality metrics. By offering a scalable, automated, and powerful alternative, CryoNet.Refine aims to serve as an essential tool for next-generation cryo-EM structure refinement. Web server: https://cryonet.ai/refine; Source code: https://github.com/kuixu/cryonet.refine.

Guojie Hu, Qingqing Wu, Lipeng Zhu et al.

Through adaptive antenna repositioning, the movable antenna (MA) technology enables on-demand reconfiguration of wireless channels, thereby creating an additional spatial degree of freedom in improving communication performance. This paper investigates a multiuser uplink communication system aided by MAs, where a base station (BS) equipped with multiple MAs serves multiple single-antenna users. Specifically, given that an optimized array geometry cannot guarantee rate fairness, we focus on designing antenna trajectory at the BS to maximize the minimum achievable rate among all users over a finite time period. The resulting optimization problem is fundamentally challenging to solve due to the continuous-time nature. To address it, we first examine an ideal case with infinitely fast MA movement and demonstrate that the relaxed problem can be optimally solved via the Lagrangian dual method. The obtained trajectory solution reveals that the BS should employ a finite set of MA deployment patterns, each allocated an optimal time duration. Building on this, we then study the general case with limited MA movement speed and propose a heuristic trajectory design inspired by the optimal patterns identified in the ideal scenario. Several insights are also gained by examining the simplified special case. Finally, numerical results are provided to validate the effectiveness of the proposed designs compared to competitive benchmarks.

Weining Fu, Kai Shu, Kui Xu et al.

Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling near-atomic-level visualization of biomolecular assemblies. However, the exponential growth in cryo-EM data throughput and complexity, coupled with diverse downstream analytical tasks, necessitates unified computational frameworks that transcend current task-specific deep learning approaches with limited scalability and generalizability. We present CryoLVM, a foundation model that learns rich structural representations from experimental density maps with resolved structures by leveraging the Joint-Embedding Predictive Architecture (JEPA) integrated with SCUNet-based backbone, which can be rapidly adapted to various downstream tasks. We further introduce a novel histogram-based distribution alignment loss that accelerates convergence and enhances fine-tuning performance. We demonstrate CryoLVM's effectiveness across three critical cryo-EM tasks: density map sharpening, density map super-resolution, and missing wedge restoration. Our method consistently outperforms state-of-the-art baselines across multiple density map quality metrics, confirming its potential as a versatile model for a wide spectrum of cryo-EM applications.

Hongwei Yi, Shaoshuai Shi, Mingyu Ding et al.

3D vehicle detection based on point cloud is a challenging task in real-world applications such as autonomous driving. Despite significant progress has been made, we observe two aspects to be further improved. First, the semantic context information in LiDAR is seldom explored in previous works, which may help identify ambiguous vehicles. Second, the distribution of point cloud on vehicles varies continuously with increasing depths, which may not be well modeled by a single model. In this work, we propose a unified model SegVoxelNet to address the above two problems. A semantic context encoder is proposed to leverage the free-of-charge semantic segmentation masks in the bird's eye view. Suspicious regions could be highlighted while noisy regions are suppressed by this module. To better deal with vehicles at different depths, a novel depth-aware head is designed to explicitly model the distribution differences and each part of the depth-aware head is made to focus on its own target detection range. Extensive experiments on the KITTI dataset show that the proposed method outperforms the state-of-the-art alternatives in both accuracy and efficiency with point cloud as input only.

Kui Xu, Zhe Wang, Jiangping Shi et al.

Constructing of molecular structural models from Cryo-Electron Microscopy (Cryo-EM) density volumes is the critical last step of structure determination by Cryo-EM technologies. Methods have evolved from manual construction by structural biologists to perform 6D translation-rotation searching, which is extremely compute-intensive. In this paper, we propose a learning-based method and formulate this problem as a vision-inspired 3D detection and pose estimation task. We develop a deep learning framework for amino acid determination in a 3D Cryo-EM density volume. We also design a sequence-guided Monte Carlo Tree Search (MCTS) to thread over the candidate amino acids to form the molecular structure. This framework achieves 91% coverage on our newly proposed dataset and takes only a few minutes for a typical structure with a thousand amino acids. Our method is hundreds of times faster and several times more accurate than existing automated solutions without any human intervention.