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List of publications and locations of corresponding code in AITom

Particle Picking

  1. Pei L, Xu M, Frazier Z, Alber F. Simulating Cryo-Electron Tomograms of Crowded Mixtures of Macromolecular Complexes and Assessment of Particle Picking. BMC Bioinformatics. 2016; 17: 405 code (pei2016simulating)

Subtomogram Classification

  1. Xu M, Chai X, Muthakana H, Liang X, Yang G, Zeev-Ben-Mordehai T, Xing E. Deep learning based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms. ISMB 2017, Bioinformatics doi:10.1093/bioinformatics/btx230. code (xu2017deep)

  2. Liu C, Zeng X, Wang K, Guo Q, Xu M. Multi-task learning for macromolecule classification, segmentation and coarse structural recovery in cryo-tomography. 2018, arXiv preprint arXiv:1805.06332 code (liu2018multi)

  3. Lin R, Zeng X, Kitani K, Xu M. Adversarial domain adaptation for cross data source macromolecule in situ structural classification in cellular electron cryo-tomograms code (lin2019adversarial)

  4. Che C, Xian Z, Zeng X, Gao X, Xu M. Domain Randomization for Macromolecule Structure Classification and Segmentation in Electron Cyro-tomograms, 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2019: 6-11. code (che2019domain)

  5. Yu L, Li R, Zeng X, Wang H, Jin J, Yang G, Jiang R, Xu M. Few Shot Domain Adaptation Macromolecule Classification]{Few Shot Domain Adaptation for in situ Macromolecule Structural Classification in Cryo-electron Tomograms. Bioinformatics (2020). doi:10.1093/bioinformatics/btaa671. arXiv:2007.15422 code (yu2020few)

  6. 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 code (li2020few)

  7. Zhou B, Yu H, Zeng X, Yang X, Zhang J, Xu M. One-shot Learning with Attention-guided Segmentation in Cryo-Electron Tomography. Frontiers in Molecular Biosciences. doi:10.3389/fmolb.2020.613347 code (zhou2020one)

  8. Du X, Wang H, Zhu Z, Zeng X, Chang Y, Zhang J, Xing E, 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 code

  9. 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 code

  10. Zeng X, Kahng A, Xue L, Mahamid J, Chang YW, Xu M. High-throughput cryo-et structural pattern mining by deep iterative unsupervised clustering (PNAS 2023). Paper code

Subtomogram Segmentation

  1. Xu M, and Frank A. Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms. Bioinformatics 29, no. 13 (2013): i274-i282 code (xu2013automated)
  2. 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 code (zeng2018convolutional)
  3. 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. code (zhao2018respond)
  4. Yang Y, Ma Y, Zhang J, Gao X, Xu M. AttPNet: Attention-Based Deep Neural Network for 3D Point Set Analysis. Sensors, 2020, 20(19): 5455. code (yang2020attpnet)
  5. Chen F, Jiang Y, Zeng X, Zhang J, Gao X, Min X. PUB-SalNet: A Pre-Trained Unsupervised Self-Aware Backpropagation Network for Biomedical Salient Segmentation. Algorithms 13.5 (2020): 126 code (chen2020pub)

Subtomogram Alignment and Averaging

  1. Xu M, Martin B, Frank A. High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching. Journal of structural biology 178, no. 2 (2012): 152-164. code (xu2012high-throughput)
  2. 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). code (zeng2020gum)

Simulation

  1. Wu X, Zeng X, Li C, Wei H, Deng H, Zhang J, Xu M. CryoETGAN: Cryo-electron Tomography Image Synthesis Via Unpaired Image Translation. Frontiers Physiology. doi:10.3389/fphys.2022.760404 code (wu2022cryoetgan)

Tomogram Segmentation and Object Detection

  1. Zhou B, Guo Q, Zeng X, Gao X, Xu M. Feature Decomposition Based Saliency Detection in Electron Cryo-Tomograms. arXiv:1801.10562. IEEE International Conference on Bioinformatics & Biomedicine, Workshop on Machine Learning in High Resolution Microscopy (BIBM-MLHRM 2018) code (zhou2018feature)
  2. Li R, Zeng X, Siegmund S, Lin R, Zhou B, Liu C, Wang K, Jiang R, Freyberg Z, Lv H, Xu M. Automatic Localization and Identification of Mitochondria in Cellular Electron Cryo-Tomography using Faster-RCNN. BMC Bioinformatics. 201920 (Suppl 3) :132 doi:10.1186/s12859-019-2650-7. code (li2019automatic)
  3. Zhao Y, Bian H, Mu M, Uddin M, Li Z, Li X, Wang T, Xu M. Training-free CryoET Tomogram Segmentation. arxiv:2407.06833. code (zhao2024training)

Tomominer

  1. 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.code (xu2019novo)
  2. Frazier Z, Xu M, Alber F. Tomominer and tomominer cloud: A software platform for large-scale subtomogram structural analysis. Structure, Volume 25, Issue 6, p951–961.e2, 6 June 2017 code (frazier2017tomominer)

Machine Learning and Computer Vision

  1. Wang T, Li X, Yang P, Hu G, Zeng X, Huang S, Xu C, Xu M. Boosting Active Learning via Improving Test Performance. arXiv: 2112.05683. Thirty-Sixth AAAI Conference on Artificial Intelligence, AAAI 2022. code (wang2022boosting)