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

arXiv: https://arxiv.org/abs/2602.02620 · HTML: https://mlsanity.com/paper/2602.02620/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 14 of its 56 references that are in the map.
- First posted on arXiv 2 Feb 2026.

## Builds on (most cited first, 14 of 14)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [A ConvNet for the 2020s](https://mlsanity.com/paper/2201.03545/) (2022)
- [Emergent Abilities of Large Language Models](https://mlsanity.com/paper/2206.07682/) (2022)
- [Self-Supervised Learning from Images with a Joint-Embedding Predictive Architecture](https://mlsanity.com/paper/2301.08243/) (2023)
- [Practical Blind Image Denoising via Swin-Conv-UNet and Data Synthesis](https://mlsanity.com/paper/2203.13278/) (2022)
- [Brain-JEPA: Brain Dynamics Foundation Model with Gradient Positioning and Spatiotemporal Masking](https://mlsanity.com/paper/2409.19407/) (2024)
- [SUNet: Swin Transformer UNet for Image Denoising](https://mlsanity.com/paper/2202.14009/) (2022)
- [A Deep Learning Method for Simultaneous Denoising and Missing Wedge Reconstruction in Cryogenic Electron Tomography](https://mlsanity.com/paper/2311.05539/) (2023)
- [A^2-Net: Molecular Structure Estimation from Cryo-EM Density Volumes](https://mlsanity.com/paper/1901.00785/) (2019)
- [CryoFM: A Flow-based Foundation Model for Cryo-EM Densities](https://mlsanity.com/paper/2410.08631/) (2024)
- [DRACO: A Denoising-Reconstruction Autoencoder for Cryo-EM](https://mlsanity.com/paper/2410.11373/) (2024)
- [CryoFastAR: Fast Cryo-EM Ab Initio Reconstruction Made Easy](https://mlsanity.com/paper/2506.05864/) (2025)

## Abstract (arXiv)

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.