# CryoMAE: Few-Shot Cryo-EM Particle Picking with Masked Autoencoders

arXiv: https://arxiv.org/abs/2404.10178 · HTML: https://mlsanity.com/paper/2404.10178/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 12 of its 43 references that are in the map.
- First posted on arXiv 15 Apr 2024.

## Builds on (most cited first, 12 of 12)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [You Only Look Once: Unified, Real-Time Object Detection](https://mlsanity.com/paper/1506.02640/) (2015)
- [Represent, Compare, and Learn: A Similarity-Aware Framework for Class-Agnostic Counting](https://mlsanity.com/paper/2203.08354/) (2022)
- [Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs](https://mlsanity.com/paper/1803.08207/) (2018)
- [DeepPicker: a Deep Learning Approach for Fully Automated Particle Picking in Cryo-EM](https://mlsanity.com/paper/1605.01838/) (2016)
- [A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy](https://mlsanity.com/paper/1605.05543/) (2016)

## Built on by (most cited first, 3 of 3)

- [DRACO: A Denoising-Reconstruction Autoencoder for Cryo-EM](https://mlsanity.com/paper/2410.11373/) (2024)
- [Advanced POD-Based Performance Evaluation of Classifiers Applied to Human Driver Lane Changing Prediction](https://mlsanity.com/paper/2408.15722/) (2024)
- [Reconstruction-Aware Cryo-EM Particle Picking](https://mlsanity.com/paper/2608.28838/) (2026)

## Abstract (arXiv)

Cryo-electron microscopy (cryo-EM) emerges as a pivotal technology for determining the architecture of cells, viruses, and protein assemblies at near-atomic resolution. Traditional particle picking, a key step in cryo-EM, struggles with manual effort and automated methods' sensitivity to low signal-to-noise ratio (SNR) and varied particle orientations. Furthermore, existing neural network (NN)-based approaches often require extensive labeled datasets, limiting their practicality. To overcome these obstacles, we introduce cryoMAE, a novel approach based on few-shot learning that harnesses the capabilities of Masked Autoencoders (MAE) to enable efficient selection of single particles in cryo-EM images. Contrary to conventional NN-based techniques, cryoMAE requires only a minimal set of positive particle images for training yet demonstrates high performance in particle detection. Furthermore, the implementation of a self-cross similarity loss ensures distinct features for particle and background regions, thereby enhancing the discrimination capability of cryoMAE. Experiments on large-scale cryo-EM datasets show that cryoMAE outperforms existing state-of-the-art (SOTA) methods, improving 3D reconstruction resolution by up to 22.4%.