# DRACO: A Denoising-Reconstruction Autoencoder for Cryo-EM

arXiv: https://arxiv.org/abs/2410.11373 · HTML: https://mlsanity.com/paper/2410.11373/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 30 of its 69 references that are in the map.
- First posted on arXiv 15 Oct 2024.

## Builds on (most cited first, 30 of 30)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Hierarchical Text-Conditional Image Generation with CLIP Latents](https://mlsanity.com/paper/2204.06125/) (2022)
- [LAION-5B: An open large-scale dataset for training next generation image-text models](https://mlsanity.com/paper/2210.08402/) (2022)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [BEiT: BERT Pre-Training of Image Transformers](https://mlsanity.com/paper/2106.08254/) (2021)
- [DUSt3R: Geometric 3D Vision Made Easy](https://mlsanity.com/paper/2312.14132/) (2023)
- [CoCa: Contrastive Captioners are Image-Text Foundation Models](https://mlsanity.com/paper/2205.01917/) (2022)
- [Revisiting Unreasonable Effectiveness of Data in Deep Learning Era](https://mlsanity.com/paper/1707.02968/) (2017)
- [iBOT: Image BERT Pre-Training with Online Tokenizer](https://mlsanity.com/paper/2111.07832/) (2021)
- [Exploring Plain Vision Transformer Backbones for Object Detection](https://mlsanity.com/paper/2203.16527/) (2022)
- [Noise2Noise: Learning Image Restoration without Clean Data](https://mlsanity.com/paper/1803.04189/) (2018)
- [Image as a Foreign Language: BEiT Pretraining for All Vision and Vision-Language Tasks](https://mlsanity.com/paper/2208.10442/) (2022)
- [Noise2Void - Learning Denoising from Single Noisy Images](https://mlsanity.com/paper/1811.10980/) (2018)
- [Scaling Language-Image Pre-training via Masking](https://mlsanity.com/paper/2212.00794/) (2022)
- [BEiT v2: Masked Image Modeling with Vector-Quantized Visual Tokenizers](https://mlsanity.com/paper/2208.06366/) (2022)
- [Towards Generalist Foundation Model for Radiology by Leveraging Web-scale 2D&3D Medical Data](https://mlsanity.com/paper/2308.02463/) (2023)
- [Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs](https://mlsanity.com/paper/1803.08207/) (2018)
- [Denoising Masked AutoEncoders Help Robust Classification](https://mlsanity.com/paper/2210.06983/) (2022)
- [DeepPicker: a Deep Learning Approach for Fully Automated Particle Picking in Cryo-EM](https://mlsanity.com/paper/1605.01838/) (2016)
- [Cryo-CARE: Content-Aware Image Restoration for Cryo-Transmission Electron Microscopy Data](https://mlsanity.com/paper/1810.05420/) (2018)
- [A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy](https://mlsanity.com/paper/1605.05543/) (2016)
- [CryoMAE: Few-Shot Cryo-EM Particle Picking with Masked Autoencoders](https://mlsanity.com/paper/2404.10178/) (2024)

## Built on by (most cited first, 4 of 4)

- [CryoFastAR: Fast Cryo-EM Ab Initio Reconstruction Made Easy](https://mlsanity.com/paper/2506.05864/) (2025)
- [Towards Foundation Models for Cryo-ET Subtomogram Analysis](https://mlsanity.com/paper/2509.24311/) (2025)
- [CryoLVM: Self-supervised Learning from Cryo-EM Density Maps with Large Vision Models](https://mlsanity.com/paper/2602.02620/) (2026)
- [Score-Based Matching with Target Guidance for Cryo-EM Denoising](https://mlsanity.com/paper/2604.17734/) (2026)

## Abstract (arXiv)

Foundation models in computer vision have demonstrated exceptional performance in zero-shot and few-shot tasks by extracting multi-purpose features from large-scale datasets through self-supervised pre-training methods. However, these models often overlook the severe corruption in cryogenic electron microscopy (cryo-EM) images by high-level noises. We introduce DRACO, a Denoising-Reconstruction Autoencoder for CryO-EM, inspired by the Noise2Noise (N2N) approach. By processing cryo-EM movies into odd and even images and treating them as independent noisy observations, we apply a denoising-reconstruction hybrid training scheme. We mask both images to create denoising and reconstruction tasks. For DRACO's pre-training, the quality of the dataset is essential, we hence build a high-quality, diverse dataset from an uncurated public database, including over 270,000 movies or micrographs. After pre-training, DRACO naturally serves as a generalizable cryo-EM image denoiser and a foundation model for various cryo-EM downstream tasks. DRACO demonstrates the best performance in denoising, micrograph curation, and particle picking tasks compared to state-of-the-art baselines.