Renmin Han

Bintao He, Yiran Cheng, Hongjia Li et al.

Understanding protein flexibility and its dynamic interactions with other molecules is essential for studying protein function. Although cryogenic electron microscopy(cryo-EM) provides an opportunity to observe macromolecular dynamics directly, computational analysis of datasets mixing continuous and discrete structural states remains a formidable challenge. Here we introduce GaussianEM, a Gaussian-based pseudo-atomic framework that simultaneously resolves compositional and conformational heterogeneity from cryo-EM images. GaussianEM employs a dual-encoder-single-decoder architecture to decompose images into learnable Gaussian components, with variability encoded through modulated parameters. This explicit parameterization yields a continuous, intuitive representation of conformational dynamics that inherently preserves local structural integrity. By modeling displacements in Gaussian space, we capture atomic-scale conformational landscapes, bridging density maps and all-atom models. In comprehensive experiments, GaussianEM successfully reconstructs complex compositional and conformational variability,and resolves previously unobserved details in public datasets. Quantitative evaluations further confirm its ability to capture broader conformational diversity without sacrificing structural fidelity.

Bintao He, Fa Zhang, Chenjie Feng et al.

Advances on cryo-electron imaging technologies have led to a rapidly increasing number of density maps. Alignment and comparison of density maps play a crucial role in interpreting structural information, such as conformational heterogeneity analysis using global alignment and atomic model assembly through local alignment. Here, we propose a fast and accurate global and local cryo-electron microscopy density map alignment method CryoAlign, which leverages local density feature descriptors to capture spatial structure similarities. CryoAlign is the first feature-based EM map alignment tool, in which the employment of feature-based architecture enables the rapid establishment of point pair correspondences and robust estimation of alignment parameters. Extensive experimental evaluations demonstrate the superiority of CryoAlign over the existing methods in both alignment accuracy and speed.

Lifa Zhu, Haining Guan, Changwei Lin et al.

In feature-learning based point cloud registration, the correct correspondence construction is vital for the subsequent transformation estimation. However, it is still a challenge to extract discriminative features from point cloud, especially when the input is partial and composed by indistinguishable surfaces (planes, smooth surfaces, etc.). As a result, the proportion of inlier correspondences that precisely match points between two unaligned point clouds is beyond satisfaction. Motivated by this, we devise several techniques to promote feature-learning based point cloud registration performance by leveraging inlier correspondences proportion: a pyramid hierarchy decoder to characterize point features in multiple scales, a consistent voting strategy to maintain consistent correspondences and a geometry guided encoding module to take geometric characteristics into consideration. Based on the above techniques, We build our Geometry-guided Consistent Network (GCNet), and challenge GCNet by indoor, outdoor and object-centric synthetic datasets. Comprehensive experiments demonstrate that GCNet outperforms the state-of-the-art methods and the techniques used in GCNet is model-agnostic, which could be easily migrated to other feature-based deep learning or traditional registration methods, and dramatically improve the performance. The code is available at https://github.com/zhulf0804/NgeNet.

Yu Li, Fan Xu, Fa Zhang et al.

Super-resolution fluorescence microscopy, with a resolution beyond the diffraction limit of light, has become an indispensable tool to directly visualize biological structures in living cells at a nanometer-scale resolution. Despite advances in high-density super-resolution fluorescent techniques, existing methods still have bottlenecks, including extremely long execution time, artificial thinning and thickening of structures, and lack of ability to capture latent structures. Here we propose a novel deep learning guided Bayesian inference approach, DLBI, for the time-series analysis of high-density fluorescent images. Our method combines the strength of deep learning and statistical inference, where deep learning captures the underlying distribution of the fluorophores that are consistent with the observed time-series fluorescent images by exploring local features and correlation along time-axis, and statistical inference further refines the ultrastructure extracted by deep learning and endues physical meaning to the final image. Comprehensive experimental results on both real and simulated datasets demonstrate that our method provides more accurate and realistic local patch and large-field reconstruction than the state-of-the-art method, the 3B analysis, while our method is more than two orders of magnitude faster. The main program is available at https://github.com/lykaust15/DLBI

Tianyang Xue, Lin Lu, Yang Liu et al.

2D irregular packing is a classic combinatorial optimization problem with various applications, such as material utilization and texture atlas generation. This NP-hard problem requires efficient algorithms to optimize space utilization. Conventional numerical methods suffer from slow convergence and high computational cost. Existing learning-based methods, such as the score-based diffusion model, also have limitations, such as no rotation support, frequent collisions, and poor adaptability to arbitrary boundaries, and slow inferring. The difficulty of learning from teacher packing is to capture the complex geometric relationships among packing examples, which include the spatial (position, orientation) relationships of objects, their geometric features, and container boundary conditions. Representing these relationships in latent space is challenging. We propose GFPack++, an attention-based gradient field learning approach that addresses this challenge. It consists of two pivotal strategies: \emph{attention-based geometry encoding} for effective feature encoding and \emph{attention-based relation encoding} for learning complex relationships. We investigate the utilization distribution between the teacher and inference data and design a weighting function to prioritize tighter teacher data during training, enhancing learning effectiveness. Our diffusion model supports continuous rotation and outperforms existing methods on various datasets. We achieve higher space utilization over several widely used baselines, one-order faster than the previous diffusion-based method, and promising generalization for arbitrary boundaries. We plan to release our source code and datasets to support further research in this direction.