UPicker: a semi-supervised particle picking transformer method for cryo-EM micrographs

Chi Zhang, Yiran Cheng, Kaiwen Feng, Fa Zhang, Renmin Han*, Jieqing Feng*

*此作品的通讯作者

科研成果: 期刊稿件文章同行评审

摘要

Automatic single particle picking is a critical step in the data processing pipeline of cryo-electron microscopy structure reconstruction. In recent years, several deep learning-based algorithms have been developed, demonstrating their potential to solve this challenge. However, current methods highly depend on manually labeled training data, which is labor-intensive and prone to biases especially for high-noise and low-contrast micrographs, resulting in suboptimal precision and recall. To address these problems, we propose UPicker, a semi-supervised transformer-based particle-picking method with a two-stage training process: unsupervised pretraining and supervised fine-tuning. During the unsupervised pretraining, an Adaptive Laplacian of Gaussian region proposal generator is proposed to obtain pseudo-labels from unlabeled data for initial feature learning. For the supervised fine-tuning, UPicker only needs a small amount of labeled data to achieve high accuracy in particle picking. To further enhance model performance, UPicker employs a contrastive denoising training strategy to reduce redundant detections and accelerate convergence, along with a hybrid data augmentation strategy to deal with limited labeled data. Comprehensive experiments on both simulated and experimental datasets demonstrate that UPicker outperforms state-of-the-art particle-picking methods in terms of accuracy and robustness while requiring fewer labeled data than other transformer-based models. Furthermore, ablation studies demonstrate the effectiveness and necessity of each component of UPicker. The source code and data are available at https://github.com/JachyLikeCoding/UPicker.

源语言英语
文章编号bbae636
期刊Briefings in Bioinformatics
26
1
DOI
出版状态已出版 - 1 1月 2025

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引用此

Zhang, C., Cheng, Y., Feng, K., Zhang, F., Han, R., & Feng, J. (2025). UPicker: a semi-supervised particle picking transformer method for cryo-EM micrographs. Briefings in Bioinformatics, 26(1), 文章 bbae636. https://doi.org/10.1093/bib/bbae636