CryoCCD: Conditional Cycle-consistent Diffusion with Biophysical Modeling for Cryo-EM Synthesis

Cryo-electron microscopy (cryo-EM) offers near-atomic resolution imaging of macromolecules, but developing robust models for downstream analysis is hindered by the scarcity of high-quality annotated data. While synthetic data generation has emerged as a potential solution, existing methods often fail to capture both the structural diversity of biological specimens and the complex, spatially varying noise inherent in cryo-EM imaging. To overcome these limitations, we propose CryoCCD, a synthesis framework that integrates biophysical modeling with generative techniques. Specifically, CryoCCD produces multi-scale cryo-EM micrographs that reflect realistic biophysical variability through compositional heterogeneity, cellular context, and physics-informed imaging. To generate realistic noise, we employ a conditional diffusion model, enhanced by cycle consistency to preserve structural fidelity and mask-aware contrastive learning to capture spatially adaptive noise patterns. Extensive experiments show that CryoCCD generates structurally accurate micrographs and enhances performance in downstream tasks, outperforming state-of-the-art baselines in both particle picking and reconstruction.

PolyhedronNet: Representation Learning for Polyhedra with Surface-attributed Graph

Ubiquitous geometric objects can be precisely and efficiently represented as polyhedra. The transformation of a polyhedron into a vector, known as polyhedra representation learning, is crucial for manipulating these shapes with mathematical and statistical tools for tasks like classification, clustering, and generation. Recent years have witnessed significant strides in this domain, yet most efforts focus on the vertex sequence of a polyhedron, neglecting the complex surface modeling crucial in real-world polyhedral objects. This study proposes \textbf{PolyhedronNet}, a general framework tailored for learning representations of 3D polyhedral objects. We propose the concept of the surface-attributed graph to seamlessly model the vertices, edges, faces, and their geometric interrelationships within a polyhedron. To effectively learn the representation of the entire surface-attributed graph, we first propose to break it down into local rigid representations to effectively learn each local region's relative positions against the remaining regions without geometric information loss. Subsequently, we propose PolyhedronGNN to hierarchically aggregate the local rigid representation via intra-face and inter-face geometric message passing modules, to obtain a global representation that minimizes information loss while maintaining rotation and translation invariance. Our experimental evaluations on four distinct datasets, encompassing both classification and retrieval tasks, substantiate PolyhedronNet's efficacy in capturing comprehensive and informative representations of 3D polyhedral objects. Code and data are available at {https://github.com/dyu62/3D_polyhedron}.