学术论文|杨林实验室-人工智能与生物医学影像实验室

Book Chapters

1.J. Cai, L. Lu, F. Xing, and L. Yang, "Pancreas segmentation in ct and mrivia task-specific network design and recurrent neural contextual learning", in Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics. Springer, pp. 3–21, 2019.
2.L.Lu, X.Wang,G. Carneiro,and L.Yang, "Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics", Springer, 2019.
3.X. Shi and L. Yang, "Deep hashing and its application for histopathology image analysis", in Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics. Springer, pp. 219–237, 2019.
4.Y. Xie, F. Liu, F. Xing, and L. Yang, "Deep learning for muscle pathology image analysis", in Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics. Springer, pp. 23–41, 2019.
5.Le Lu, Yefeng Zheng, Gustavo Carneiro, Lin Yang, "Deep Learning and Convolutional Neural Networks for Medical Image Computing - Precision Medicine, High Performance and Large-Scale Datasets", Advances in Computer Vision and Pattern Recognition, Springer , ISBN 978-3-319-42998-4, 2017
6.Lin Yang and David J. Foran, "Parametric and geometric deformable models: An application in biomaterials and medical imaging", Suri/Farag, eds, Vol. 2, Chapter 4, pp. 95-122, Springer, ISBN: 0-387-31204-8,2006.
7.Xiaoping Shen and Lin Yang, "Handbook of medical image analysis: segmentation and registration models", Suri/Wilson/Laxminarayan, eds, Vol. 1, Chapter 1, 47 pp., Kluwer, ISBN: 0306485508, 2005.

Peer-reviewed Journal Articles

1.Hansheng Li, Yuxin Kang, Wentao Yang, Zhuoyue Wu, Xiaoshuang Shi, Feihong Liu, Jianye Liu, Lingyu Hu, Qian Ma, Lei Cui, Jun Feng, Lin Yang, "A Robust Training Method for Pathological Cellular Detector via Spatial Loss Calibration", Frontiers in Medicine, Vol.8, 2021.
2.Boju Pan, Yuxin Kang, Yan Jin, Lin Yang, Yushuang Zheng, Lei Cui, Jian Sun, Jun Feng, Yuan Li, Lingchuan Guo and Zhiyong Liang, "Automated tumor proportion scoring for PD-L1 expression based on multistage ensemble strategy in non-small cell lung cancer", Journal of Translational Medicine, 19(1):249, 202
3.Jinzheng Cai, Adam P. Harrison, Youjing Zheng, Ke Yan, Yuankai Huo, Jing Xiao, Lin Yang, Le Lu, "Lesion-Harvester: Iteratively Mining Unlabeled Lesions and Hard-Negative Examples at Scale", IEEE Transactions on Medical Imaging, 40(1): 59-70 ,2021.
4.Xiaoshuang Shi, Fuyong Xing, Zizhao Zhang, Manish Sapkota, Zhenhua Guo, Lin Yang, "A Scalable Optimization Mechanism for Pairwise Based Discrete Hashing", IEEE Transactions on Image Processing,Vol. 30: 1130-1142, 2021.
5.Zizhao Zhang, Pingjun Chen, Xiaoshuang Shi, Lin Yang, "Text-Guided Neural Network Training for Image Recognition in Natural Scenes and Medicine", IEEE Trans Pattern Anal Mach Intell,43(5): 1733-1745 ,2021.
6.Pingjun Chen, Yun Liang, Xiaoshuang Shi, Lin Yang, Paul D. Gader, "Automatic whole slide pathology image diagnosis framework via unit stochastic selection and attention fusion", Neurocomputing,453: 312-325, 2021.
7.X Shi, H Su, F Xing, Y Liang, G Qu, L Yang, "Graph temporal ensembling based semi-supervised convolutional neural network with noisy labels for histopathology image analysis", Medical Image Analysis, 2020.
8.Lei Cui, Hansheng Li, Wenli Hui, Sitong Chen, Lin Yang, Yuxin Kang, Qirong Bo, Jun Feng, "A deep learning-based framework for lung cancer survival analysis with biomarker interpretation", BMC Bioinformatics, 2020, 21(1): 1-14.
9.Xuhong Zhang, Toby C. Cornish, Lin Yang, Tellen D. Bennett, Debashis Ghosh, Fuyong Xing, "Generative Adversarial Domain Adaptation for Nucleus Quantification in Images of Tissue Immunohistochemically Stained for Ki-67", JCO Clinical Cancer Informatics, vol. 4, pp. 666-679, 2020.
10.X. Shi, F. Xing, Z. Zhang, M. Sapkota, Z. Guo, and L. Yang, "A scalable opti- mization mechanism for pairwise based discrete hashing", IEEE Transactions on Image Processing, vol. 30, pp. 1130–1142, 2020.
11.Xiaoshuang Shi,Zhenhua Guo,Fuyong Xing,Yun Liang,Lin Yang, "Anchor-based self-ensembling for semi-supervised deep pairwise hashing", International Journal of Computer Vision, pp. 1-18, 2020.
12.P. Chen, X. Shi, Y. Liang, Y. Li, L. Yang, and P. D. Gader, "Interactive thyroid whole slide image diagnostic system using deep representation", Computer Methods and Programs in Biomedicine, vol. 195, p. 105630, 2020.
13.Y. Li, P. Chen, Z. Li, H. Su, L. Yang, and D. Zhong, "Rule-based automatic diagnosis of thyroid nodules from intraoperative frozen sections using deep learning", Artificial Intelligence in Medicine, vol. 108, p. 101918, 2020.
14.Manish Sapkota, Xiaoshuang Shi, Fuyong Xing, Lin Yang, " Deep Convolutional Hashing for Low Dimensional Binary Embedding of Histopathological Images", IEEE Journal of Biomedical and Health Informatics, vol. 23, no. 2, pp. 805-816, 2019.
15.Zizhao Zhang, Pingjun Chen, Mason McGough, Fuyong Xing, Chunbao Wang, Marilyn Bui, Yuanpu Xie, Manish Sapkota, Lei Cui, Jasreman Dhillon, Nazeel Ahmad, Farah K. Khalil, Shohreh I. Dickinson, Xiaoshuang Shi, Fujun Liu, Hai Su, Jinzheng Cai, Lin Yang, "Pathology-level interpretable whole-slide cancer diagnosis with deep learning", Accepted to Nature Machine Intelligence, Vol. 1, pp. 236-245, 2019.
16.Cui L, Feng J, Yang L, "Towards Fine Whole-Slide Skeletal Muscle Image Segmentation through Deep Hierarchically Connected Networks", Journal of Healthcare Engineering, 2019.
17.Lei Cui, Jun Feng,Zizhao Zhang, Lin Yang, "High throughput automatic muscle image segmentation using parallel framework", BMC bioinformatics, 2019, 20(1): 158.
18.Z. Zhang, P. Chen, X. Shi, and L. Yang, "Text-guided neural network training for image recognition in natural scenes and medicine", IEEE transactions on pattern analysis and machine intelligence, 2019.
19.F. Xing, T. C. Cornish, T. Bennett, D. Ghosh, and L. Yang, "Pixel-to-pixel learning with weak supervision for single-stage nucleus recognition in ki67 images", IEEE Transactions on Biomedical Engineering, vol. 66, no. 11, pp. 3088–3097, 2019.
20.J. Cai, F. Xing, A. Batra, F. Liu, G. A. Walter, K. Vandenborne, and L. Yang, "Texture analysis for muscular dystrophy classification in mri with improved class activation mapping", Pattern recognition, vol. 86, pp. 368–375, 2019.
21.J. Cai, Z. Zhang, L. Cui, Y. Zheng, and L. Yang, "Towards cross-modal organ translation and segmentation: a cycle-and shape-consistent generative adversarial network", Medical image analysis, vol. 52, pp. 174–184, 2019.
22.P. Chen and L. Yang, "tissueloc: Whole slide digital pathology image tissue local- ization", Journal of Open Source Software, vol. 4, no. 33, p. 1148, 2019.
23.X. Shi, F. Xing, Z. Guo, H. Su, F. Liu, and L. Yang, "Structured orthogonal matching pursuit for feature selection", Neurocomputing, vol. 349, pp. 164–172, 2019.
24.P. Chen, L. Gao, X. Shi, K. Allen, and L. Yang, "Fully automatic knee osteoarthritis severity grading using deep neural networks with a novel ordinal loss", Computer- ized Medical Imaging and Graphics, vol. 75, pp. 84–92, 2019.
25.F. Xing, Y. Xie, X. Shi, P. Chen, Z. Zhang, and L. Yang, "Towards pixel-to-pixel deep nucleus detection in microscopy images", BMC bioinformatics, vol. 20, no. 1, pp. 1–16, 2019.
26.Zizhao Zhang, Fuyong Xing, Xiaoshuang Shi, Lin Yang, "Revisiting Graph Construction for Fast Image Segmentation", Pattern Recognition (PR), 2018.
27.Yuanpu Xie, Fuyong Xing, Lin Yang, "Deep Voting and Structured Regression for Microscopy Image Analysis", In Deep Learning for Medical Image Analysis (pp. 155-175), 2018.
28.Xiaoshuang Shi, Manish Sapkota, Fuyong Xing, Fujun Liu, Lei Cui, Lin Yang, "Pairwise based deep ranking hashing for histopathology image classification and retri", accepted to Pattern Recognition, 2018.
29.Xiaoshuang Shi, Fuyong Xing, Jinzheng Cai, Lin Yang, "Self-learning for face clustering", accepted to Pattern Recognition, 2018.
30.Youbao Tang, Jinzheng Cai, Le Lu, Adam P. Harrison, Ke Yan, Jing Xiao, Lin Yang,Ronald M. Summers, "CT Image Enhancement Using Stacked Generative Adversarial Networks and Transfer Learning for Lesion Segmentation Improvement", MLMI, 2018: 46-54.
31.Fuyong Xing, Yuanpu Xie, Hai Su, Fujun Liu, Lin Yang, "Deep Learning in Microscopy Image Analysis: A Survey", IEEE Trans Neural Netw Learn Syst, 29(10): 4550-4568 , 2018.
32.Xiaoshuang Shi, Fuyong Xing, Kaidi Xu, Yuanpu Xie, Hai Su, Lin Yang, "Supervised graph hashing for histopathology image retri and classification", Medical Image Analysis, Vol. 22, pp. 117-128, 2017.
33.Yuanpu Xie, Fuyong Xing, Xiaoshuang Shi, Xiaofei Kong, Hai Su, Lin Yang, "Efficient and robust cell detection: A structured regression approach", Medical Image Analysis, 2017.
34.Manish Sapkota, Fujun Liu, Yuanpu Xie, Hai Su, Fuyong Xing, Lin Yang, "AIIMD: An integrated framework of automatic idiopathic inflammatory myopathy diagnosis for muscle", IEEE Journal of Biomedical and Health Informatics, 2017.
35.Zizhao Zhang, Fuyong Xing, Hai Su, Xiaoshuang Shi, Lin Yang, "Recent Advances in the Applications of Convolutional Neural Networks to Medical Image Contour Detection", CoRR abs/1708.07281 ,2017.
36.Gustavo Carneiro, Yefeng Zheng, Fuyong Xing, Lin Yang, "Review of Deep Learning Methods in Mammography, Cardiovascular, and Microscopy Image Analysis", Deep Learning and Convolutional Neural Networks for Medical Image Computing,11-32, 2017
37.Xiaoshuang Shi, Fuyong Xing, Kaidi Xu, Yuanpu Xie, Hai Su, Lin Yang, "Supervised graph hashing for histopathology image retri and classification", Medical Image Analysis, Vol. 22, pp. 117-128, 2017.
38.Zizhao Zhang, Fuyong Xing, Hai Su, Xiaoshuang Shi, Lin Yang, "Recent Advances in the Applications of Convolutional Neural Networks to Medical Image Contour Detection", CoRR abs/1708.07281 ,2017.
39.Le Lu, Yefeng Zheng, Gustavo Carneiro, Lin Yang, "Deep Learning and Convolutional Neural Networks for Medical Image Computing-Precision Medicine, High Performance and Large-Scale Datasets", Advances in Computer Vision and Pattern Recognition, Springer, ISBN 978-3-319-42998-4, 2017.
40.Hai Su, Fuyong Xing, Lin Yang, "Robust cell detection of histopathological brain tumor images using sparse reconstruction and adaptive dictionary selection", IEEE Transaction on Medical Imaging, Vol. 35, No. 6, 2016.
41.Xiaoshuang Shi, Zhenhuo Guo, Feiping Nie, Lin Yang, Jane You, and Dacheng Tao, "Two-dimensional whitening reconstruction for enhancing robustness of principle component analysis", IEEE Transaction on Pattern Analysis and Machine Intelligence, Vol. 38, No. 10, pp. 2130-2136, 2016.
42.Fuyong Xing, Lin Yang, "Robust nucleus/cell detection and segmentation for digital pathology and microscopic images: A comprehensive review", IEEE Reviews in Biomedical Engineering, No. 9, pp. 234-263, 2016.
43.Fuyong Xing, Lin Yang, "An automatic learning-based framework for robust nucleus segmentation", IEEE Transaction on Medical Imaging, Vol. 35, No. 2, pp. 550-566, 2016.
44.Tahsin Kurc, Xin Qi, Daihou Wang, Fusheng Wang, George Teodoro, Lee Cooper, Michael Nalisnik, Lin Yang, Joel Saltz, David J Foran, "Scalable Analysis of Big Pathology Image Data Cohorts using Efficient Methods and High-Performance Computing Strategies", BMC Bioinformatics, Vol. 16, No. 399, 2015.
45.Xiaofan Zhang, Fuyong Xing, Hai Su, Lin Yang,Shaoting Zhang, "High throughput histopathology image analysis via robust cell segmentation and hashing", Medical Image Analysis, Vol. 26, No. 1, pp. 306-315, 2015.
46.Christopher S. Fry, Jonah D. Lee, Jyothi Mula, Tyler J. Kirby, Janna R. Jackson, Fujun Liu, Lin Yang, Esther E. Dupont-Versteegden, John J. McCarthy, Charlotte A. Peterson, "Inducible depletion of satellite cells in adult, sedentary mice impairs muscle regenerative capacity without affecting sarcopenia", Nature Medicine, Vol. 21, pp. 76-80, 2015.
47.Fuyong Xing, Hai Su, Janna Neltner, Lin Yang, "Automatic Ki-67 Counting Using Robust Cell Detection and Online Dictionary Learning", IEEE Transaction on Biomedical Engineering (TBME), Vol. 61, No. 3, pp. 859-870, 2014.
48.Nicolas Wein, Adeline Vulin, Maria Sofia Falzarano, Christina Al-Khalili Szigyarto, Baijayanta Maiti, Andrew Findlay, Kristin H. Heller, Mathias Uhlen, Baskar Bakthavachalu, Sonia Messina, Giuseppe Vita, Chiara Passarelli, Francesca Gualandi, Steve D. Wilton, Louise Rodino-Klapec, Lin Yang, Diane M. Dunn, Daniel Schoenberg, Robert B. Weiss, Michael T. Howard, Alessandra Ferlini, Kevin M. Flanigan, "A novel DMD IRES results in a functional N-truncated dystrophin, providing a potential route to therapy for patients with 5’ mutations", Nature Medicine, Vol. 20, No. 9, pp. 992-1000, 2014.
49.Sandra Donkervoort, Ying Hu, Tanya Stojkovic, Nicol Voermans, A. Reghan Foley, Meganne E Leach, Jahannaz Dastgir, Veronique Bolduc, Thomas Cullup, Alix de Becdelievre, Lin Yang, Hai Su, Katherine Meilleur, Alice Schindler, Erik-Jan Kamsteeg, Pascale Richard, Russell Butterfield, Thomas L. Winder, Thomas Crawford, Robert B. Weiss, Francesco Muntoni, Valerie Allamand, Carsten G. Bonnemann, "Mosaicism for dominant COLVI mutations as a cause for intra-familial phenotypic variability", Human Mutation, Vol. 36, No. 1, pp. 48-56, 2014.
50.Xin Qi, Daihou Wang, Ivan Rodero, Javier Diaz-Montes, Rebekah H Gensure, Fuyong Xing, Hua Zhong, Lauri Goodell, Manish Parashar, David J Foran, Lin Yang, "Content-based histopathology image retri using CometCloud", BMC Bioinformatics, Vol. 15, pp. 287-300, 2014.
51.Hongyuan Wang, Fuyong Xing, Hai Su, Arnold Stromberg, and Lin Yang, "Novel image markers for non-small cell lung cancer classification and survival prediction", BMC Bioinformatics, Vol. 19, No. 15, pp. 310-324, 2014.
52.Michael W. Lawlor, Marissa G. Viola, Hui Meng, Rachel V. Edelstein, Fujun Liu, Ke Yang, Elizabeth J. Luna, Alexandra Lerch-Gaggl, Raymond G. Hoffmann, Christopher R. Pierson, Anna Buj-Bello, Jennifer L. Lachey, Scott Pearsall, Lin Yang, Cecilia Hillard, Alan H. Beggs, "Differential Muscle Hypertrophy Is Associated With Satellite Cell Numbers And Akt Pathway Activation Following Activin Type IIB Receptor Inhibition In Mtm1 p.R69C Mice", American Journal of Pathology, Vol. 184, No. 6, pp. 1831-1842, 2014.
53.Lin Yang, Xin Qi, Fuyong Xing, Tahsin Kurc, Joel Saltz, David J. Foran, "Parallel Content Based Sub-image Retri Using Hierarchical Searching", Bioinformatics, Vol. 30, No. 7, pp. 996-1002, 2014.
54.Fujun Liu, Christopher S. Fry, Jyothi Mula, Janna R. Jackson, Jonah D. Lee, Charlotte A. Peterson, Lin Yang, "Automated Fiber-type-specific Cross-sectional Area Assessment and Myonuclei Counting in Skeletal Muscle", Journal of Applied Physiology (JAP), Vol. 115, No. 11, pp. 1714-1724, 2013.
55.Hai Su, Fuyong Xing, Jonah Lee, Charlotte Peterson, Lin Yang, "Automatic Myonuclear Detection in Isolated Single Muscle Fiber Using Robust Ellipse Fitting and Sparse Optimization", IEEE/ACM Transaction on Computational Biology and Bioinformatics (TCBB), 14 pages, 2013
56.Fujun Liu, Abigail L. Mackey, Ratchakrit Srikuea, Karyn Esser, Lin Yang, "Automated Image Segmentation of Hemotoxylin and Eosin Stained Skeletal Muscle Cross-Sections", Journal of Microscopy, Vol. 253, No. 3, pp. 275-285, 2013
57.Joythi Mula, Jonah D. Lee, Fujun Liu, Lin Yang, Charlotte A. Peterson, "Automated Image Analysis of Skeletal Muscle Fiber Cross-sectional Area", Journal of Applied Physiology (JAP), Vol. 114, No. 1, pp. 148-155, 2013
58.Baiyang Liu, Junzhou Huang, Casimir Kulikowski, Lin Yang, "Robust Visual Tracking Using Local Sparse Appearance Model and K-selection", IEEE Transaction on Pattern Analysis and Machine Intelligence (TPAMI), Vol. 35, No. 12, pp. 2968-2981, 2013
59.Xin Qi, Fuyong Xing, David J. Foran, Lin Yang, "A Fast, Automatic Segmentation Algorithm for Locating and Delineating Touching Cell Boundaries in Imaged Histopathology ", Journal of Methods in Medical Informatics, Vol. 51, No. 3, pp. 91- 102, 2012.
60.Rebekah H. Gensure, David J. Foran, Vincent M. Lee, Vyacheslav M Gendal, Salma K Jabbour, Darren R Carpizo, John L. Nosher, and Lin Yang, "E valuation of hepatic tumor response to yttrium-90 radioembolization therapy using texture signatures generated from contrast-enhanced CT", Academic Radiology, Vol. 19, No. 10, pp. 1201-1207, 2012.
61.Xin Qi, Fuyong Xing, David J. Foran and Lin Yang, "Robust segmentation of overlapping cells in histopathology specimens using parallel seed detection and repulsive level set", IEEE Transaction on Biomedical Engineering (TBME), Vol. 59, No. 3, pp. 754-765, 2012.
62.Xin Qi, Hyunjoo Kim, Fuyong Xing, Manish Parashar, David J. Foran, Lin Yang, "The Analysis of Image Feature Robustness Using CometCloud", Vol. 3. No. 33, pp. 1-13, Journal of Pathology Informatics, 2012.
63.Fuyong Xing, Baiyang Liu, Xin Qi, David J. Foran, Lin Yang, "Digitized tissue microarray classification using sparse reconstruction", Medical Imaging: Image Processing, 83144W,2012.
64.David J. Foran , Lin Yang, Wenjin Chen, Jun Hu, Lauri A. Goodell, Michael Reiss, Fusheng Wang, Tahsin Kurc, Tony Pan, Ashish Sharma, and Joel Saltz., "Image miner: Comparative analysis of tissue microarrays using content based image retri, high performance computing, and Grid technology", Journal of American Medical Information Association (JAMIA), Vol. 18, No. 4, pp. 403-415, 2011.
65.Lin Yang, Bogdan Georgescu, Yefeng Zheng, Wang Yang, Peter Meer and Dorin Comaniciu, "Prediction based collaborative trackers (PCT): A robust and accurate approach toward 3D medical object tracking", IEEE Transaction on Medical Imaging (TMI), Vol. 30, No. 11, pp. 1921-1932, 2011.
66.David J. Foran, Wenjin Chen and Lin Yang, "Automated image interpretation computer-assisted diagnosis", Analytical Cellular Pathology, Vol. 34, No. 6, pp. 279-300, 2011.
67.Jianqin Qu, Leiguang Gong and Lin Yang, "A 3D point matching algorithm for affine registration", International Journal of Computer Assisted Radiology and Surgery, Vol. 6, No. 2, pp. 229-236, 2010.
68.Lin Yang, Oncel Tuzel, Wenjin Chen, Peter Meer, Gratian Salaru, Lauri A. Goodell and David J. Foran, "PathMiner: A web-based tool for computer assisted diagnostics in pathology", IEEE Transaction on Information Technology in Biomedicine (TITB). Vol. 13, No. 3, pp. 291-299, 2009.
69.Lin Yang, Wenjin Chen, Peter Meer, Gratian Salaru, Viktors Berstis and David J. Foran, "Virtual microscopy and grid-enabled decision support for large scale analysis of imaged pathology specimens", IEEE Transaction on Information Technology in Biomedicine (TITB), Vol. 13, No. 4, pp. 636-644, 2009.
70.Oncel Tuzel, Lin Yang, Peter Meer and David J. Foran, "Classification of hematologic malignancies using texton signatures", Pattern Analysis and Applications (PAA), Vol. 10, No. 4, pp. 277-290, 2007.
71.Lin Yang, Peter Meer and David J. Foran, "Unsupervised analysis of imaged pathology specimens based on robust estimation and color active contour models", IEEE Transaction on Information Technology in Biomedicine (TITB), Vol. 9, No. 1, pp. 475-486, 2005.

Peer-reviewed Selected Conference Publications

1.Sunyi Zheng*, Jingxiong Li*, Zhongyi Shui, Chenglu Zhu, Yunlong Zhang, Pingyi Chen, Lin Yang, "ChrSNet: Chromosome Straightening using Self-attention Guided Networks", MICCAI, 2022.
2.Yunlong Zhang*, Yuxuan Sun*, Honglin Li, Sunyi Zheng, Chenglu Zhu, Lin Yang, "Benchmarking the Robustness of Deep Neural Networks to Common Corruptions in Digital Pathology", MICCAI, 2022.
3.Zhongyi Shui*, Shichuan Zhang*, Chenglu Zhu, Bingchuan Wang, Pingyi Chen, Sunyi Zheng, Lin Yang, "End-to-End cell recognition by point annotation", MICCAI, 2022.
4.Shichuan Zhang, Chenglu Zhu, Honglin Li, Jiatong Cai, Lin Yang, "Weakly Supervised Learning for Cell Recognition in Immunohistochemical Cytoplasm Staining Images", IEEE International Symposium on Biomedical Imaging（ISBI）,2022.
5.Jiatong Cai, Chenglu Zhu, Pingyi Chen, Shichuan Zhang, Honglin Li, Lin Yang, "Category Separation for Weakly Supervised Multi-Class Cell Counting", IEEE International Symposium on Biomedical Imaging（ISBI）,2022.
6.Chenglu Zhu, Yuxuan Sun, Honglin Li, Can Cui, Shichuan Zhang, Jiatong Cai, Lin Yang, "Weakly supervised classification using multi-level instance-aware optimization on cervical cytologic image", IEEE International Symposium on Biomedical Imaging（ISBI）,2022.
7.Yuxin Kang *, Hansheng Li *, Zhuoyue Wu, Feihong Liu, Dongqing Hu, Lei Cui, Jun Feng, Lin Yang, "Boosting Boundary Representation for Gland Instance Segmentation", IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2021.
8.Zhuoyue Wu, Hansheng Li, Lei Cui, Yuxin Kang, Jianye Liu, Haider Ali, Jun Feng, Lin Yang, "Interpretable Histopathology Image Diagnosis via Whole Tissue Slide Level Supervision", Machine Learning in Medical Imaging(MLMI), 2021.
9.Jiatong Cai, Chenglu Zhu, Can Cui, Honglin Li, Tong Wu, Shichuan Zhang, Lin Yang, "Generalizing Nucleus Recognition Model in Multi-source Ki67 Immunohistochemistry Stained Images via Domain-specific Pruning", MICCAI, 2021
10.Hansheng Li, Yuxin Kang, Lingyu Hu, Qian Ma, Lei Cui, Jun Feng, Lin Yang,Wentao Yang, "Robust Pathological Detector Training Method on Sparsely Annotated Datasets via Spatial Cues", BIBM, 1396-1401,2021.
11.Yuxin Kang, Hansheng Li, Xin Han, Boju Pan, Yuan Li, Yan Jin, Qirong Bu, Lei Cui, Jun Feng, Lin Yang, "Automated Tumor Proportion Scoring for Assessment of PD-L1 Expression Based on Multi-Stage Ensemble Strategy", MICCAI, 2020.
12.Hansheng Li, Xin Han, Yuxin Kang, Xiaoshuang Shi, Mengdi Yan, Zixu Tong, Qirong Bu, Lei Cui, Jun Feng, Lin Yang, "A Novel Loss Calibration Strategy for Object Detection Networks Training on Sparsely Annotated Pathological Datasets", MICCAI, 2020.
13.P. Chen, J. Cai, and L.Yang, "Chromosome segmentation via data simulation and shape learning", in 2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC).IEEE, pp. 1637–1640, 2020.
14.X. Shi, F. Xing, Y. Xie, Z. Zhang, L. Cui, and L. Yang, "Loss-based attention for deep multiple instance learning", in Proceedings of the AAAI Conference on Artificial Intelligence, vol. 34, no. 04, pp. 5742–5749, 2020.
15.Z. Zhang, A. Romero, M. J. Muckley, P. Vincent, L. Yang, and M. Drozdzal, "Reducing uncertainty in undersampled mri reconstruction with active acquisition", in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, pp. 2049–2058, 2019.
16.M. Yan, H. Li, B. Kang, J. Feng, Y. Kang, T. Zhang, L. Yang, and L. Cui, "net: Trained on a small sample segmentation network for biomedical image anal- ysis", in 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, pp. 1402–1408, 2019.
17.H. Su, X. Shi, J. Cai, and L. Yang, "Local and global consistency regularized mean teacher for semi-supervised nuclei classification", in International Conference on Medical Image Computing and Computer-Assisted Intervention. Springer, pp. 559–567, 2019.
18. H. Li, B. Kang, Y. Kang, F. Liu, W. Hui, Q. Bo, C. Wang, L. Yang, L. Cui, and J. Feng, "Global bank: A guided pathway of encoding and decoding for pathological image analysis", in 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, pp. 415–422, 2019.
19.Zizhao Zhang, Lin Yang, Y. Zheng, "Translating and Segmenting Multimodal Medical Volumes with Cycle- and Shape-Consistency Generative Adversarial Network", International Conference on Computer Vision and Pattern Recognition (CVPR), 2018.
20.Zizhao Zhang*, Yuanpu Xie*, Lin Yang, "Photographic Text-to-Image Synthesis with a Hierarchically-nested Adversarial Network", International Conference on Computer Vision and Pattern Recognition (CVPR), 2018, Spotlight (~8%) * indicates equal contribution.
21.Lei Cui, Jun Feng, Lin Yang, "Semi-supervised Deep Linear Discriminant Analysis for Histopathology Image Classification", 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2018: 2333-2337.
22.Jinzheng Cai, Youbao Tang, Le Lu, Adam P. Harrison, Ke Yan, Jing Xiao, Lin Yang, Ronald M. Summers, "Accurate Weakly Supervised Deep Lesion Segmentation on CT Scans: Self-Paced 3D Mask Generation from RECIST", CoRR abs/18008614 ,2018.
23.Jinzheng Cai, Le Lu, Adam P. Harrison, Xiaoshuang Shi, Pingjun Chen, Lin Yang, "Iterative Attention Mining for Weakly Supervised Thoracic Disease Pattern Localization in Chest X-Rays", MICCAI,(2) 589-598,2018.
24.Jinzheng Cai, Youbao Tang, Le Lu, Adam P. Harrison, Ke Yan, Jing Xiao, Lin Yang, Ronald M. Summers, "Accurate Weakly-Supervised Deep Lesion Segmentation Using Large-Scale Clinical Annotations: Slice-Propagated 3D Mask Generation from 2D RECIST", MICCAI, (4) 396-404, 2018.
25.Xiaoshuang Shi, Fuyong Xing, Yuanpu Xie, Lin Yang, "Cell encoding for histopathology image classification", International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2017.
26.Jinzheng Cai, Le Lu, Yuanpu Xie, Fuyong Xing, Lin Yang, "Improving deep pancreas segmentation in CT and MRI image via recurrent neural contextual learning and direct loss function", International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2017
27.Xiaoshuang Shi, Fuyong Xing, Kaidi Xu, Manish Sapkota, Lin Yang, "Asymmetric discrete graph hashing", The thirty-first AAAI conference on Artificial Intelligence (AAAI), 2017.
28.Zizhao Zhang, Pingjun Chen, Manish Sapkota, Lin Yang, "TandemNet: Distilling Knowledge from Medical Images Using Diagnostic Reports as Optional Semantic References", International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2017 oral (3.6% acceptance rate)
29.Zizhao Zhang, Yuanpu, Xie, Fuyong Xing, Mason Mcgough, Lin Yang, "MDNet: A Semantically and Visually Interpretable Medical Image Diagnosis Network", IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 2017 oral (2.7% acceptance rate)
30.Xiaoshuang Shi, Fuyong Xing, Jinzheng Cai, Zizhao Zhang, Yuanpu Xie, Lin Yang, "Kernel-based supervised discrete hashing for image retri", European Conference on Computer Vision (ECCV), 2016.
31.Zizhao Zhang, Fuyong Xing, Xiaoshuang Shi, Lin Yang, "SemiContour: A semi-supervised learning approach for contour detection", IEEE International Conference on Computer Vision and Pattern Recognition (CVPR), 2016.
32.Jinzheng Cai, Le Lu, Qian Yin, Zizhao Zhang, Fuyong Xing, Lin Yang, "Pancreas Segmentation using Graph based Data Fusion with Convolutional Neural Networks", Accepted to The 19th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2016.
33.Fuyong Xing, Xiaoshuang Shi, Zizhao Zhang, Jinzheng Cai, Yuanpu Xie, Lin Yang, "Transfer Shape Priors Towards High-throughput Microscopy Image Segmentation", Accepted to The 19th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2016.
34.Yuanpu Xie, Zizhao Zhang, Manish Sapkota, Lin Yang, "Spatial Clockwork Recurrent Neural Network for Muscle Perimysium Segmentation", Accepted to The 19th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2016.
35.Menglin Jiang, Shaoting Zhang, Junzhou Huang, Lin Yang, Dimitris Metaxas, "Joint Kernel-Based Supervised Hashing for Scalable Histopathological Image Analysis", Accepted to The 18th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Munich, Germany, 8 pages, 2015.
36.Hai Su, Fuyong Xing, Xiangfei Kong, Yuanpu Xie, Shaoting Zhang, Lin Yang, "Robust Cell Detection and Segmentation in Histopathological Images using Sparse Reconstruction and Stacked Denoising Autoencoders", Accepted to The 18th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Munich, Germany, 8 pages, 2015.
37.Yuanpu Xie, Xiangfei Kong, Fuyong Xing, Fujun Liu, Hai Su, Lin Yang, "Deep Voting: A Robust Approach Towards Nucleus Localization In Microscopy Images", Accepted to The 18th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Munich, Germany, 8 pages, 2015.
38.Yuanpu Xie, Fuyong Xing, Xiangfei Kong, Hai Su, Lin Yang, "Beyond Classification: Structured Regression For Robust Cell Detection Using Convolutional Neural Network", Accepted to The 18th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Munich, Germany, 8 pages, 2015.
39.Fujun Liu, Lin Yang, "A Novel Cell Detection Method Using Deep Convolutional Neural Network and Maximum-Weight Independent Set", Accepted to The 18th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Munich, Germany, 8 pages, 2015.
40.Fujun Liu, Fuyong Xing, Zizhao Zhang, Mason Mcgough, Lin Yang, "Robust Muscle Cell Quantification Using Structured Edge Detection and Hierarchical Segmentation", Accepted to The 18th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Munich, Germany, 8 pages, 2015.
41.Fuyong Xing, Lin Yang, "Fast Cell Segmentation Using Scalable Sparse Manifold Learning and Affine Transform-approximated Active Contour", Accepted to The 18th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Munich, Germany, 8 pages, 2015.
42.Xiaofan Zhang, Hai Su, Lin Yang, Shaoting Zhang, "Scalable analysis of histopathology images via robust cellular segmentation and weighted hashing", Accepted to the 2015 International Conference on Computer Vision and Patter Recognition (CVPR), 2015.
43.Xiaofan Zhang, Hai Su, Lin Yang,Shaoting Zhang, "Weighted hashing with multiple cues for cell-level analysis of histopathology images", Accepted to the 2015 International 24th Biennial International Conference on Information Processing in Medical Imaging (IPMI), 2015.
44.Manish Sapkota, Fuyong Xing, Hai Su, Lin Yang, "Automatic muscle perimysium annotation using deep convolutional neural network", Accepted to the 2015 International Symposium on Biomedical Imaging (ISBI), 2015.
45.Fuyong Xing, Lin Yang, "Unsupervised shape prior modeling for cell segmentation in neuroendocrine tumor", Accepted to the 2015 International Symposium on Biomedical Imaging (ISBI), 2015.
46.Hai Su, Fujun Liu, Yuanpu Xie, Fuyong Xing, Sreenivasan Meyyappan, Lin Yang, "Region segmentation in histopathological breast cancer images using deep convolutional neural network", Accepted to the 2015 International Symposium on Biomedical Imaging (ISBI), 2015.
47.Xiaoshuang Shi, Zhenhua Guo, Yujiu Yang, Lin Yang, "Within-class penalty based multi-class support vector machine", ICIP ,2746-2750,2015.
48.Hai Su, Yong Shen, Fuyong Xing, Xin Qi, Kim M. Hirshfield, Lin Yang, David J. Foran, "Robust automatic breast cancer staging using a combination of functional genomics and image-omics", EMBC,7226-722,2015.
49.Xiaofan Zhang, Lin Yang, Wei Liu, Hai Su, Shaoting Zhang, "Mining histopathology images via composite hashing and online learning", Accepted to The 17th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Boston, MA, U. S. A., 2014.
50.Fujun Liu, Fuyong Xing, Hai Su, Lin Yang, "Touching adipocyte cells decomposition using combinatorial optimization", Accepted to 2014 International Symposium on Biomedical Imaging (ISBI), 2014.
51.Fujun Liu, Fuyong Xing, Lin Yang, "Robust muscle cell segmentation using region selection with dynamic programming", Accepted to 2014 International Symposium on Biomedical Imaging (ISBI), 2014.
52.Fuyong Xing, Hai Su, Lin Yang, "An Integrated Framework for Automatic Ki-67 Scoring in Pancreatic Neuroendocrine Tumor", The 16th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Nagoya, Japan, 2013.
53.Fuyong Xing, Lin Yang, "Robust Selection-based Sparse Shape Model for Lung Cancer Image Segmentation", The 16th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Nagoya, Japan, 2013.
54.Hai Su, Fuyong Xing, Jonah Lee, Charlotte Peterson, Lin Yang, "Learning based automatic detection of myonuclei in isolated single skeletal muscle fibers using multi-focus image fusion", International Symposium on Biomedical Imaging (ISBI), 2013.
55.Fuyong Xing, Lin Yang, "Robust non-small cell lung cancer classification using molecular morphological features", International Symposium on Biomedical Imaging (ISBI), 2013.
56.Baiyang Liu, Junzhou Huang, Casimir Kulikowski, Lin Yang, "Robust tracking using local sparse appearance model and K-Selection", Proc. IEEE International Conference on Computer Vision and Pattern Recognition (CVPR), Vol. 1, pp. 1-8, 2011.
57.Xin Qi, Fuyong Xing, David J. Foran, Lin Yang, "Comparative performance analysis of stained histopathology specimens using RGB and multispectral imaging", Medical Imaging: Computer-Aided Diagnosis ,79633B, 2011.
58.Baiyang Liu, Lin Yang, Junzhou Huang, P. Meer, Leiguang Gong, Casimir Kulikowski, "Robust and fast visual tracking with two stage sparse optimization", European Conference on Computer Vision (ECCV), Vol. 6314, pp. 624-637, 2010.
59.Baiyang Liu, Lin Yang, Casimir Kulikowski, Jinghao Zhou, Leiguang Gong, David J. Foran, Salma J. Jabbour and Ning J. Yue, "An adaptive tracking algorithm of lung tumors in fluoroscopy using online learned collaborative trackers", IEEE International Symposium on Biomedical Imaging (ISBI), Vol. 1, pp. 209-212, 2010.
60.David J. Foran, Lin Yang, Oncel Tuzel, Wenjin Chen, Jun Hu, Tahsin Kurc, Renato Ferreira, Joel Saltz, "A caGrid-enabled, learning based image segmentation method for histopathology specimens", Proc. IEEE International Symposium on Biomedical Imaging (ISBI), Vol. 1, pp. 1306-1309, 2009.
61.Hong Zhang, Lin Yang, David J. Foran, John Nosher, Peter Yim, "3D segmentation of the liver using free-form deformation based on boosting and deformation gradients", Proc. IEEE International Symposium on Biomedical Imaging (ISBI), Vol. 1, pp. 494-497, 2009.
62.Lin Yang, Oncel Tuzel, Peter Meer and David J. Foran, "Automatic image analysis of histopathology specimens using concave vertex graph", Proc. International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Vol. 11, pp. 833-841, 2008.
63.Lin Yang, Bogdan Georgescu, Yefeng Zheng, Peter Meer and Dorin Comaniciu, "3D Ultrasound tracking of the left ventricle using one-step forward prediction and data fusion of collaborative trackers", Proc. IEEE International Conference on Computer Vision and Pattern Recognition (CVPR), Vol. 1, pp. 1-8, 2008.
64.Lin Yang, Bogdan Georgescu, Yefeng Zheng, David J. Foran and Dorin Comaniciu, "A fast and accurate tracking algorithm of left ventricles in 3D echocardiography", Proc. International Symposium on Biomedical Imaging (ISBI), Vol. 5, pp. 221-224, 2008.
65.Lin Yang, Wenjin Chen, Peter Meer, Gratian Salaru, Michael D. Feldman and David J. Foran, "High throughput analysis of breast cancer specimens on the Grid", Proc. International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Vol. 10, pp. 617-625, 2007.
66.Lin Yang, Peter Meer and David J. Foran, "Multiple class segmentation using a unified framework over mean-shift patches", Proc. IEEE International Conference on Computer Vision and Pattern Recognition (CVPR), Vol. 1, pp. 1-8, June 2007.

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