Yang Yan

Yang Yan

Ph.D. candidate in AI for science, computer vision, representation learning, and structural biology.

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Machine Learning for Structure Determination in Single-Particle Cryo-Electron Microscopy: A Systematic Review

Published in IEEE Transactions on Neural Networks and Learning Systems, 2021

Systematic review of machine-learning methods for single-particle cryo-EM structure determination.

Recommended citation: Jia-Geng Wu, Yang Yan, Dong-Xu Zhang, Bo-Wen Liu, Qing-Bing Zheng, Xiao-Liang Xie, Shi-Qi Liu, Sheng-Xiang Ge, Zeng-Guang Hou, Ning-Shao Xia. (2022). "Machine Learning for Structure Determination in Single-Particle Cryo-Electron Microscopy: A Systematic Review." IEEE Transactions on Neural Networks and Learning Systems, 33(2), 452-472. DOI: 10.1109/TNNLS.2021.3131325.
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A deep learning-based computer-aided diagnosis method of X-ray images for bone age assessment

Published in Complex & Intelligent Systems, 2022

Computer-aided diagnosis method for bone-age assessment from hand-wrist X-ray images.

Recommended citation: Shaowei Li, Bowen Liu, Shulian Li, Xinyu Zhu, Yang Yan, Dongxu Zhang. (2022). "A deep learning-based computer-aided diagnosis method of X-ray images for bone age assessment." Complex & Intelligent Systems, 8(3), 1929-1939. DOI: 10.1007/s40747-021-00376-z.
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Unsupervised Cryo-EM Images Denoising and Clustering Based on Deep Convolutional Autoencoder and K-Means++

Published in IEEE Transactions on Medical Imaging, 2023

Deep autoencoder and balanced K-means++ framework for cryo-EM denoising and clustering.

Recommended citation: Dongxu Zhang, Yang Yan, Yulin Huang, Bowen Liu, Qingbing Zheng, Jun Zhang, Ningshao Xia. (2023). "Unsupervised Cryo-EM Images Denoising and Clustering Based on Deep Convolutional Autoencoder and K-Means++." IEEE Transactions on Medical Imaging, 42(5), 1509-1521. DOI: 10.1109/TMI.2022.3231626.
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An Automated TW3-RUS Bone Age Assessment Method with Ordinal Regression-Based Determination of Skeletal Maturity

Published in Journal of Digital Imaging, 2023

Automated TW3-RUS bone-age assessment using ordinal regression to determine skeletal maturity.

Recommended citation: Dongxu Zhang, Bowen Liu, Yulin Huang, Yang Yan, Shaowei Li, Jinshui He, Shuyun Zhang, Jun Zhang, Ningshao Xia. (2023). "An Automated TW3-RUS Bone Age Assessment Method with Ordinal Regression-Based Determination of Skeletal Maturity." Journal of Digital Imaging, 36(3), 1001-1015. DOI: 10.1007/s10278-023-00794-0.
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A comprehensive foundation model for cryo-EM image processing

Published in Nature Methods, 2026

Introduced Cryo-IEF as a foundation model for cryo-EM particle processing, pretrained on approximately 65 million particle images.

Recommended citation: Yang Yan, Shiqi Fan, Fajie Yuan, Huaizong Shen. (2026). "A comprehensive foundation model for cryo-EM image processing." Nature Methods, 23(1), 88-95. DOI: 10.1038/s41592-025-02916-8.
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CryoDECO: Deconstructing Extreme Compositional and Conformational Heterogeneity in Cryo-EM via Foundation Model Priors

Published in LangTaoSha Preprint Server, 2026

Foundation-prior model for heterogeneous cryo-EM reconstruction and panoramic analysis of complex structural mixtures.

Recommended citation: Yang Yan, Yanwanyu Xi, Shiqi Fan, Yifei Wang, Ziyun Tang, Fajie Yuan, Huaizong Shen. (2026). "CryoDECO: Deconstructing Extreme Compositional and Conformational Heterogeneity in Cryo-EM via Foundation Model Priors." LangTaoSha Preprint Server. DOI: 10.65215/LTSpreprints.2025.12.30.000075.
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