CryoLVM: Self-supervised Learning from Cryo-EM Density Maps with Large Vision Models

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 a SCUNet-based backbone, enabling rapid adaptation to various downstream tasks. We further introduce a novel histogram-based distribution alignment loss that accelerates convergence and enhances fine-tuning performance. Through comprehensive evaluation across three critical cryo-EM tasks—density map sharpening, density map super-resolution, and missing wedge restoration—CryoLVM consistently outperforms state-of-the-art baselines across multiple density map quality metrics, confirming its potential as a versatile foundation model for a wide spectrum of cryo-EM applications.