GFPack++: Improving 2D Irregular Packing by Learning Gradient Field with Attention

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.

CryoAlign: feature-based method for global and local 3D alignment of EM density maps

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.

Neighborhood-aware Geometric Encoding Network for Point Cloud Registration

The distinguishing geometric features determine the success of point cloud registration. However, most point clouds are partially overlapping, corrupted by noise, and comprised of indistinguishable surfaces, which makes it a challenge to extract discriminative features. Here, we propose the Neighborhood-aware Geometric Encoding Network (NgeNet) for accurate point cloud registration. NgeNet utilizes a geometric guided encoding module to take geometric characteristics into consideration, a multi-scale architecture to focus on the semantically rich regions in different scales, and a consistent voting strategy to select features with proper neighborhood size and reject the specious features. The awareness of adaptive neighborhood points is obtained through the multi-scale architecture accompanied by voting. Specifically, the proposed techniques in NgeNet are model-agnostic, which could be easily migrated to other networks. Comprehensive experiments on indoor, outdoor and object-centric synthetic datasets demonstrate that NgeNet surpasses all of the published state-of-the-art methods. The code will be available at https://github.com/zhulf0804/NgeNet.

DLBI: Deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy

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