See google scholar for the full publication list.

Citations in latex bib format. The source code in AITom publication list.

Selected papers

  1. [ET] Zeng X, Kahng A, Xue L, Mahamid J, Chang Y, Xu M. High-throughput cryo-ET structural pattern mining by deep unsupervised clustering. Proceedings of the National Academy of Sciences. doi:10.1073/pnas.2213149120
  2. [AS,CV] Sarker N, Hakim Z, Dabouei A, Uddin M, Freyberg Z, Macwilliams A, Kangas J, Xu M. Detecting Anomalies from Liquid Transfer Videos in Automated Laboratory Setting. Frontiers in Molecular Biosciences. doi:10.3389/fmolb.2023.1147514
  3. [CV,ML,ET,EM] Uddin M, Howe G, Zeng X, Xu M. Harmony: A Generic Unsupervised Approach for Disentangling Semantic Content from Parameterized Transformations. IEEE conference on computer vision and pattern recognition (CVPR 2022). Paper
  4. [ML] Wang T, Li X, Yang P, Hu G, Zeng X, Huang S, Xu C, Xu M. Boosting Active Learning via Improving Test Performance. AAAI Conference on Artificial Intelligence. (AAAI 2022) arXiv:2112.05683
  5. [CV,ET] Zeng X, Howe G, Xu M. End-to-end robust joint unsupervised image alignment and clustering. International Conference on Computer Vision (ICCV 2021). doi:10.1109/iccv48922.2021.00383
  6. [CV,ET] Zhu X, Chen J, Zeng X, Liang J, Li C, Liu S, Behpour S, Xu M. Weakly Supervised 3D Semantic Segmentation Using Cross-Image Consensus and Inter-Voxel Affinity Relations. International Conference on Computer Vision (ICCV 2021). doi:10.1109/icv48922.2021.00283
  7. [ET] Du X, Wang H, Zhu Z, Zeng X, Chang Y, Zhang J, Xu M. Active learning to classify macromolecular structures in situ for less supervision in cryo-electron tomography. Bioinformatics. doi:10.1093/bioinformatics/btab123 arXiv:2102.12040
  8. [ET] Zeng X, Xu M. Gum-Net: Unsupervised geometric matching for fast and accurate 3D subtomogram image alignment and averaging. In Proceedings of the IEEE conference on computer vision and pattern recognition (CVPR 2020). Paper
  9. [ET] Li R, Yu L, Zhou B, Zeng X, Wang Z, Yang X, Zhang J, Gao X, Jang R, Xu M. Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms. PLOS Computational Biology. doi:10.1371/journal.pcbi.1008227
  10. [ET] Du X, Zeng X, Zhou B, Singh A, Xu M. Open-set Recognition of Unseen Macromolecules in Cellular Electron Cryo-Tomograms by Soft Large Margin Centralized Cosine Loss. British Machine Vision Conference (BMVC 2019 spotlight with acceptance rate < 5%). pdf
  11. [ET] Zhao G, Zhou B, Wang K, Jiang R, Xu M. Respond-CAM: Analyzing Deep Models for 3D Imaging Data by Visualizations. Medical Image Computing & Computer Assisted Intervention (MICCAI) 2018. arXiv:1806.00102
  12. [ET] Zhao Y, Zeng X, Guo Q, Xu M. An integration of fast alignment and maximum-likelihood methods for electron subtomogram averaging and classification. ISMB 2018. Bioinformatics. 2018 Jul 1; 34(13): i227–i236. doi:10.1093/bioinformatics/bty267. arXiv:1804.01203
  13. [ET] Zeng X, Leung M, Zeev-Ben-Mordehai T, Xu M. A convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation. Journal of Structural Biology. 2018 May;202(2):150-160. doi:10.1016/j.jsb.2017.12.015 arXiv:1706.04970 [code]
  14. [ET] Xu M, Singla J, Tocheva E, Chang Y, Stevens R, Jensen G, Alber F. De novo structural pattern mining in cellular electron cryo-tomograms. Structure. 2019 Apr 2;27(4):679-691.e14. doi:10.1016/j.str.2019.01.005. (Appeared on Structure volume cover and highlighted in Nature Methods 16, page 285 (2019), doi:10.1038/s41592-019-0382-2)
  15. [OM] Wang W, Taft D, Chen Y, Zhang J, Wallace C, Xu M, Watkins S, Xing J. Learn to segment single cells with deep distance estimator and deep cell detector. Computers in Biology and Medicine. doi:10.1016/j.compbiomed.2019.04.006
  16. [ET] Xu M, Beck M, Alber F. High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching. Journal of Structural Biology. 2012 May;178(2):152-64. Epub 2012 Mar 7.
  17. [GE] Xu M, Li W, James GM, Mehan MR, Zhou XJ. Automated multidimensional phenotype profiling using large public microarray repositories. Proc Natl Acad Sci U S A. (PNAS). 2009; 106(30), 12323 - 12328. (Highlighted in Nature Methods 6, 632; Selected and re-published in 2010 International Medical Informatics Association Yearbook of Medical Informatics)
  18. [GE] Xu M, Kao MJ, Nunez-Iglesias J, Nevins JR, West M, Zhou XJ. An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer. BMC Genomics. 2008; 9 Suppl 1:S12.


  • ET: Cryo-Electron Tomography
  • EM: Cryo-Electron Microscopy
  • AS: Automated Science
  • CV: Computer Vision
  • ML: Machine Learning
  • OM: Optical Microscopy
  • GE: Computational Genomics