Publications in Conferences and Workshops
- Hao Zheng, Hongming Li, Yong Fan, Coupled Reconstruction of Cortical Surfaces by Diffeomorphic Mesh Deformation, Thirty-seventh Conference on Neural Information Processing Systems, 2023
- Hongming Li and Yong Fan, Cascaded convolutional networks for unsupervised brain tissue segmentation and bias field estimation, Proc. SPIE 12655, Emerging Topics in Artificial Intelligence (ETAI) 2023, 1265506 (28 September 2023).
- B. Hou, H. Li, Z. Jiao, Z. Zhou, H. Zheng and Y. Fan, "Deep Clustering Survival Machines with Interpretable Expert Distributions," 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI), Cartagena, Colombia, 2023, pp. 1-4, doi: 10.1109/ISBI53787.2023.10230844.
- H. Zheng, H. Li and Y. Fan, "SurfNN: Joint Reconstruction of Multiple Cortical Surfaces from Magnetic Resonance Images," 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI), Cartagena, Colombia, 2023, pp. 1-4, doi: 10.1109/ISBI53787.2023.10230488.
- J. Wu and Y. Fan, "HNAS-Reg: Hierarchical Neural Architecture Search for Deformable Medical Image Registration," 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI), Cartagena, Colombia, 2023, pp. 1-4, doi: 10.1109/ISBI53787.2023.10230534.
- H. Cheng, Z. Ren, H. Ding, D. Li and Y. Fan, "Bipartite Organization of Cerebellar-Cortical Networks Identified based on Intrinsic Functional Connectivity," 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI), Cartagena, Colombia, 2023, pp. 1-4, doi: 10.1109/ISBI53787.2023.10230616.
- X. Liu, H. Li and Y. Fan, "Predicting Alzheimer’s Disease and Quantifying Asymmetric Degeneration of the Hippocampus Using Deep Learning of Magnetic Resonance Imaging Data," 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI), Cartagena, Colombia, 2023, pp. 1-4, doi: 10.1109/ISBI53787.2023.10230830.
- Chongyue Zhao, Hongming Li, Zhicheng Jiao, Tianming Du, Yong Fan: A 3D Convolutional Encapsulated Long Short-Term Memory (3DConv-LSTM) Model for Denoising fMRI Data, MICCAI 2020, In: Martel A.L. et al. (eds) Medical Image Computing and Computer Assisted Intervention – MICCAI 2020. MICCAI 2020. Lecture Notes in Computer Science, vol 12267. Springer, Cham. Oct 2020, pp 479-488
- Sarthak Pati, Ashish Singh, Saima Rathore, Aimilia Gastounioti, Mark Bergman, Phuc Ngo, Sung Min Ha, Dimitrios Bounias, James Minock, Grayson Murphy, Hongming Li, Amit Bhattarai, Adam Wolf, Patmaa Sridaran, Ratheesh Kalarot, Hamed Akbari, Aristeidis Sotiras, Siddhesh P. Thakur, Ragini Verma, Russell T. Shinohara, Paul Yushkevich, Yong Fan, Despina Kontos, Christos Davatzikos, Spyridon Bakas: The Cancer Imaging Phenomics Toolkit (CaPTk): Technical Overview. In: Crimi A., Bakas S. (eds) Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. BrainLes 2019. Lecture Notes in Computer Science, vol 11993. Springer, Cham. May 19, 2020
- Shi Yin, Qinmu Peng, Hongming Li, Zhengqiang Zhang, Xinge You, Fischer Katherine, Susan Furth, Gregory Tasian, Yong Fan: Computer-aided diagnosis of congenital abnormalities of the kidney and urinary tract in children using a multi-instance deep learning method based on ultrasound imaging data, Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI 2020), Page: 1347-1350, April 3-7, 2020, Iowa City, Iowa, USA
- Zhicheng Jiao, Hongming Li, Yong Fan: Improving diagnosis of autism spectrum disorder and disentangling its heterogeneous functional connectivity patterns using capsule networks, Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI 2020), Page:1331-1334, April 3-7, 2020, Iowa City, Iowa, USA
- Yuemeng Li, Yong Fan: DeepSEED: 3D Squeeze-and-Excitation Encoder-Decoder ConvNets for Pulmonary Nodule Detection, Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI 2020), Page:1866-1869, April 3-7, 2020, Iowa City, Iowa, USA
- Shi Yin, Qinmu Peng, Hongming Li, Zhengqiang Zhang, Xinge You, HangfanLiu, Katherine Fischer, Susan L. Furth, Gregory E. Tasian, Yong Fan: Multi-instance deep learning with graph convolutional neural networks for diagnosis of kidney diseases using ultrasound imaging. In: Greenspan H. et al. (eds) Uncertainty for Safe Utilization of Machine Learning in Medical Imaging and Clinical Image-Based Procedures. CLIP 2019, UNSURE 2019. Lecture Notes in Computer Science, vol 11840. Springer, Cham, Page: 146-154, Oct 2019 Best paper award of the 8th Clinical Image-based Procedures Workshop (CLIP)
- Hangfan Liu, Hongming Li, Yuemeng Li, Shi Yin, Pamela Boimel, James Janopaul-Naylor, Haoyu Zhong, Ying Xiao, Edgar Ben-Josef, Yong Fan: Adaptive Sparsity Regularization Based Collaborative Clustering for Cancer Prognosis. In: Shen D. et al. (eds) Medical Image Computing and Computer Assisted Intervention – MICCAI 2019. Lecture Notes in Computer Science, vol 11767. Springer, Cham, Page: 583-592, Oct 2019
- Sarthak Pati, Ashish Singh, Saima Rathore, Aimilia Gastounioti, Mark Bergman, Phuc Ngo, Sung Min Ha, Dimitrios Bounias, James Minock, Grayson Murphy, Hongming Li, Amit Bhattarai, Adam Wolf, Patmaa Sridaran, Ratheesh Kalarot, Hamed Akbari, Aristeidis Sotiras, Siddhesh P. Thakur, Ragini Verma, Russell T. Shinohara, Paul Yushkevich, Yong Fan, Despina Kontos, Christos Davatzikos, Spyridon Bakas: The Cancer Imaging Phenomics Toolkit (CaPTk): Technical Overview, Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. BrainLes 2019. Lecture Notes in Computer Science, Vol. 11993, Page: 380-394, May 19, 2020
- Hongming Li, Pamela Boimel, James Janopaul-Naylor, Haoyu Zhong, Ying Xiao, Edgar Ben-Josef, and Yong Fan: Deep convolutional neural networks for imaging data-based survival analysis of rectal cancer. Proceedings of IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) Page: 846-849, Apr 2019
- Hangfan Liu, Hongming Li, Pamela Boimel, James Janopaul-Naylor, Haoyu Zhong, Ying Xiao, Edgar Ben-Josef, and Yong Fan: Collaborative clustering of subjects and radiomic features for predicting clinical outcomes of rectal cancer patients. Proceedings of IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) Page: 1303-1306, Apr 2019
- Hongming Li, Yong Fan: Early prediction of Alzheimer's disease dementia based on baseline hippocampal MRI and 1-year follow-up cognitive measures using deep recurrent neural networks. Proceedings of IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) Page: 368-371, Apr 2019
- Shi Yin, Zhengqiang Zhang, Hongming Li, Qinmu Peng, Xinge You, Susan L. Furth, Gregory E. Tasian, Yong Fan: Fully-automatic segmentation of kidneys in clinical ultrasound images using a boundary distance regression network. Proceedings of IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) Page: 1741-1744, Apr 2019
- Hongming Li, Xiaofeng Zhu, Yong Fan: Identification of multi-scale hierarchical brain functional networks using deep matrix factorization. In: Frangi A., Schnabel J., Davatzikos C., Alberola-López C., Fichtinger G. (eds) Medical Image Computing and Computer Assisted Intervention – MICCAI 2018. MICCAI 2018. Lecture Notes in Computer Science, vol 11072. Springer, Cham, pp 223-231, Sep 2018
- Hongming Li and Yong Fan: Brain decoding from functional MRI using long short-term memory recurrent neural networks. In: Frangi A., Schnabel J., Davatzikos C., Alberola-López C., Fichtinger G. (eds) Medical Image Computing and Computer Assisted Intervention – MICCAI 2018. MICCAI 2018. Lecture Notes in Computer Science, vol 11072. Springer, Cham, pp 320-328, Sep 2018
- Hongming Li and Yong Fan: Identification of temporal transition of functional states using recurrent neural networks from functional MRI. In: Frangi A., Schnabel J., Davatzikos C., Alberola-López C., Fichtinger G. (eds) Medical Image Computing and Computer Assisted Intervention – MICCAI 2018. MICCAI 2018. Lecture Notes in Computer Science, vol 11072. Springer, Cham, pp 232-239, Sep 2018
- Hongming Li and Yong Fan: Non-rigid image registration using self-supervised fully convolutional networks without training data. Proceedings of IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018) Page: 1075-1078, Apr 2018
- Hongming Li, Theodore D. Satterthwaite, Yong Fan: Brain age prediction based on resting-state functional connectivity patterns using convolutional neural networks. Proceedings of IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018) Page: 101-104, Apr 2018
- Qiang Zhen, Greg Tasian, Yong Fan: Transfer learning for diagnosis of congenital abnormalities of the kidney and urinary tract in children based on ultrasound imaging data. Proceedings of IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018) Page: 1487-1490, Apr 2018
- Qiang Zheng and Yong Fan: Integrating semi-supervised label propagation and random forests for multi-atlas based hippocampus segmentation. Proceedings of IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018) Page: 154-157, Apr 2018
- Xuesong Yang and Yong Fan: Coupled dictionary learning for joint MR image restoration and segmentation. Proc. SPIE Medical Imaging 2018: Image Processing 10574(105742Z): 1-8, Mar 2018
- Xuesong Yang and Yong Fan: Feature extraction using convolutional neural networks for multi-atlas based image segmentation. Proc. SPIE Medical Imaging 2018: Image Processing 10574(1057439): 1-8, Mar 2018
- Xiaofeng Zhu, Hongming Li, Yong Fan: Parameter-free centralized multi-task learning for characterizing developmental sex differences in resting state functional connectivity. Proceedings of the Thirty-Second AAAI Conference on Artificial Intelligence (AAAI-18). AAAI Publications, Page: 2260-2267, Feb 2018
- Yong Fan and Christos Davatzikos: Pattern recognition of functional brain networks. Proceedings of IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP 2017) Page: 6309-6313, Mar 2017
- Hanyang Peng and Yong Fan: A General Framework for Sparsity Regularized Feature Selection via Iteratively Reweighted Least Square Minimization. Proceedings of the Thirty-First AAAI Conference on Artificial Intelligence (AAAI-17) Page: 2471-2477, Feb 2017
- Hanyang Peng and Yong Fan: Direct Sparsity Optimization Based Feature Selection for Multi-Class Classification. Proceedings of the 25th International Joint Conference on Artificial Intelligence (IJCAI-16) Page: 1918-1924, Jul 2016
- Hancan Zhu, Hewei Cheng, Xuesong Yang, and Yong Fan: Metric Learning for Label Fusion in Multi-Atlas Based Image Segmentation. Proceedings of IEEE 11th International Symposium on Biomedical Imaging (ISBI 2016) Page: 1338-1341, Apr 2016
- Hongming Li and Yong Fan: Individualized brain parcellation with integrated functional and morphological information. Proceedings of IEEE 11th International Symposium on Biomedical Imaging (ISBI 2016) Page: 992-995, Apr 2016
- Hongming Li, Theodore D. Satterthwaite, and Yong Fan: Identification of Subject-Specific Brain Functional Networks Using a Collaborative Sparse Nonnegative Matrix Decomposition Method. Proceedings of IEEE 11th International Symposium on Biomedical Imaging (ISBI 2016). IEEE, Page: 984-987, Apr 2016
- Hancan Zhu, Hewei Cheng, and Yong Fan: Random local binary pattern based label learning for multi-atlas segmentation. Proc. SPIE Medical Imaging: Image Processing 9413: 9413-46, Feb 2015
- Zhuo Sun, Yong Fan, Boudewijn P. F. Lelieveldt, and Martijn van de Giessen: Detection of Alzheimer's disease using group lasso SVM-based region selection. Proc. SPIE Medical Imaging: Computer-Aided Diagnosis 941414: 9414-39, Mar 2015
- Hewei Cheng and Yong Fan: Semi-supervised clustering for amygdala parcellation based on resting state fMRI data. Proc. SPIE Medical Imaging: Image Processing. Sebastien Ourselin; Martin A. Styner (eds.). SPIE: the international society for optics and photonics, 9034(903427): 1-8, Mar 2014
- Hewei Cheng and Yong Fan: Functional parcellation of the hippocampus by clustering resting state fMRI signals. Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI 2014) Page: 5-8, May 2014
- Hongming Li and Yong Fan: Hierarchical organization of the functional brain identified using floating aggregation of functional signals. Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI 2014). IEEE, Page: 537-540, May 2014
- Hongming Li and Yong Fan: Spatial alignment of human cortex by matching hierarchical patterns of functional connectivity. Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI 2014). IEEE, Page: 329-332, May 2014
- Hongming Li and Yong Fan: Functional brain atlas construction for brain network analysis. Proc. SPIE Medical Imaging: Image Processing. Sebastien Ourselin and David R. Haynor (eds.). SPIE: the international society for optics and photonics, 8669(86690C): 1-8, Mar 2013
- Zhenyu Tang, Di Jiang, Yong Fan: Image registration based on dynamic directed graphs with groupwise image similarity. Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI 2013). IEEE, Page: 492-495, Apr 2013
- Zhenyu Tang, Di Jiang, Hongming Li, and Yong Fan: Matching functional connectivity patterns for spatial correspondence detection in fMRI registration. In: Liao H., Linte C.A., Masamune K., Peters T.M., Zheng G. (eds) Augmented Reality Environments for Medical Imaging and Computer-Assisted Interventions. MIAR 2013, AE-CAI 2013. Lecture Notes in Computer Science, vol 8090. Springer, Berlin, Heidelberg, pp 249-257Sep 2013
- D. Jiang, Y. Du, H. Cheng, T. Jiang, and Yong Fan: fMRI alignment based on local functional connectivity patterns. Proc. SPIE Medical Imaging: Image Processing. David R. Haynor and Sébastien Ourselin (eds.). SPIE: the international society for optics and photonics, 8314(831415): 1-8, Feb 2012
- H. Cheng, Dandan Song, H. Wu, and Yong Fan: Intrinsic functional connectivity pattern based brain parcellation using normalized cut. Proc. SPIE Medical Imaging: Image Processing. David R. Haynor and Sébastien Ourselin (eds.). SPIE: the international society for optics and photonics, 8314(83144F): 1-9, Feb 2012
- Xin Zhang, Haijing Niu, Yan Song, Yong Fan: Activation detection in fNIRS by cross wavelet coherence. Proc. SPIE Medical Imaging: Biomedical Applications in Molecular, Structural, and Functional Imaging. SPIE: the international society for optics and photonics, 8317(831712): 1-7, Feb 2012
- Yongfu Hao, Jieqiong Liu, Yunyun Duan, Xinqing Zhang, Chunshui Yu, Tianzi Jiang, Yong Fan: Local Label Learning (L3) for multi-atlas based segmentation. Proc. SPIE Medical Imaging: Image Processing. David R. Haynor and Sébastien Ourselin (eds.). 8314(83142E): 1-8, Feb 2012
- Yongfu Hao, Tianzi Jiang, and Yong Fan: Shape-constrained multi-atlas based segmentation with Multi-channel Registration. Proc. SPIE Medical Imaging: Image Processing. David R. Haynor and Sébastien Ourselin (eds.). 8314(83143N): 1-8, Feb 2012
- Yuhui Du, Hongming Li, Hong Wu, and Yong Fan: Identification of subject specific and functional consistent ROIs using semi-supervised learning. Proc. SPIE Medical Imaging: Image Processing. David R. Haynor and Sébastien Ourselin (eds.). SPIE: the international society for optics and photonics, 8314(83144S): 1-7, Feb 2012
- Di Jiang, Tianzi Jiang, and Yong Fan: Groupwise fMRI registration using multi-range functional connectivity patterns. Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI 2012). IEEE, Page: 1763-1766, May 2012
- Hongming Li and Yong Fan: Label propagation with robust initialization for brain tumor segmentation. Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI 2012). IEEE, Page: 1715-1718, May 2012
- Yongfu Hao, Tianzi Jiang, and Yong Fan: Iterative multi-atlas based segmentation with multi-channel image registration and jackknife context model. Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI 2012). IEEE, Page: 900-903, May 2012
- Yong Fan: Ordinal ranking for detecting mild cognitive impairment and Alzheimer's disease based on multimodal neuroimages and CSF biomarkers. In: Liu T., Shen D., Ibanez L., Tao X. (eds) Multimodal Brain Image Analysis. MBIA 2011. Lecture Notes in Computer Science, vol 7012. Springer, Berlin, Heidelberg, pp 44-51, Sep 2011
- Yong Fan, Yong Liu, Tianzi Jiang, Zhening Liu, Yihui Hao, and Haihong Liu: Discriminant Analysis of Resting-state Functional Connectivity Patterns on the Grassmann Manifold. Proc. SPIE Medical Imaging: Image Processing. Benoit M. Dawant and David R. Haynor (eds.). SPIE: the international society for optics and photonics, 7623(76231J): 1-8, Feb 2010
- Feng Shi, Pew-Thian Yap, Yong Fan, John H. Gilmore, Weili Lin, Dinggang Shen: Neonatal brain MRI segmentation by building multi-region-multireference atlases. Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI 2010). IEEE, Page: 964-967, Apr 2010
- Yong Fan, Daniel Kaufer, Dinggang Shen: Joint estimation of multiple clinical variables of neurological diseases from imaging patterns. Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI 2010). IEEE, Page: 852-855, Apr 2010
- Hongming Li, Ming Song, Yong Fan: Segmentation of Brain Tumors in Multi-parametric MR Images via Robust Statistic Information Propagation. In: Kimmel R., Klette R., Sugimoto A. (eds) Computer Vision – ACCV 2010. ACCV 2010. Lecture Notes in Computer Science, vol 6495. Springer, Berlin, Heidelberg, pp 606-617, Nov 2010
- Feng Shi, Yong Fan, Songyuan Tang, John Gilmore, Weili Lin, and Dinggang Shen: Brain Tissue Segmentation of Neonatal MR images using a Longitudinal Subject-specific Probabilistic Atlas. Proc. SPIE Medical Imaging: Image Processing. Josien P. W. Pluim and Benoit M. Dawant (eds.). 7259(725942): 1-8, Feb 2009
- Yong Fan and Dinggang Shen: Integrated feature extraction and selection for neuroimage classification. Proc. SPIE Medical Imaging: Image Processing. Josien P. W. Pluim and Benoit M. Dawant (eds.). 7259(72591U): 1-8, Feb 2009
- Songyuan Tang, Yong Fan, Minjeong Kim, and Dinggang Shen: RABBIT: Rapid Alignment of Brains by Building Intermediate Templates. Proc. SPIE Medical Imaging: Image Processing. SPIE: the international society for optics and photonics, 7259(725909): 1-8, Mar 2009
- Feng Shi, Pew-Thian Yap, Yong Fan, Jie-Zhi Cheng, Lawrence L. Wald, Guido Gerig, Weili Lin, and Dinggang Shen: Cortical Enhanced Tissue Segmentation of Neonatal Brain MR Images Acquired by a Dedicated Phased Array Coil. Proceedings of IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops: Mathematical Methods in Biomedical Image Analysis. IEEE, Page: 39-45, Jun 2009
- Songyuan Tang, Yong Fan, Hongtu Zhu, Pew-Thian Yap, Wei Gao, Weili Lin, and Dinggang Shen: Regularization of Diffusion Tensor Field Using Coupled Robust Anisotropic Diffusion. Proceedings of IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops: Mathematical Methods in Biomedical Image Analysis. IEEE, Page: 52-57, Jun 2009
- Yong Fan, Susan M. Resnick, and Christos Davatzikos: Feature selection and classification of multi-parametric medical images using bagging and SVM. Proc. SPIE Medical Imaging: Image Processing. Joseph M. Reinhardt and Josien P. W. Pluim (eds.). SPIE: the international society for optics and photonics, 6914(69140Q): 1-10, Feb 2008
- Yong Fan, Hengyi Rao, Joan Giannetta, Hallam Hurt, Jiongjiong Wang, Christos Davatzikos, Dinggang Shen: Diagnosis of brain abnormality using both structural and functional MR images. Proceedings of Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, Page: 1044-1047, Aug 2006
- Yong Fan, Dinggang Shen, Christos Davatzikos: Detecting Cognitive States from fMRI Images by Machine Learning and Multivariate Classification. Proceedings of the Conference on Computer Vision and Pattern Recognition Workshop Page: 1-8, Jun 2006
- Yong Fan, Dinggang Shen, and Christos Davatzikos: Classification of structural images via high-dimensional image warping, robust feature extraction, and SVM. Lecture Notes in Computer Science (Medical Image Computing and Computer-Assisted Intervention-MICCAI 2005). Springer, LNCS 3749: 1-8, Oct 2005
- Dinggang Shen, Hari Sundar, Zhong Xue, Yong Fan, Harold Litt: Consistent estimation of cardiac motions by 4D image registration. Lecture Notes in Computer Science (Medical Image Computing and Computer-Assisted Intervention-MICCAI 2005) LNCS 3750: 902-910, Oct 2005
- Tianzi Jiang and Yong Fan: Parallel genetic algorithm for 3D medical image analysis. IEEE International Conference on Systems, Man and Cybernetics 6: 1-6, Oct 2002
- Yong Fan and Tianzi Jiang: Fast and robust mutual information based registration for images of the head. Proceedings of International Conference on Diagnostic Imaging and analysis Page: 162-167, Aug 2002.
- Yong Fan, Tianzi Jiang, and David J. Evans: Medical Image Registration Using Parallel Genetic Algorithms. Lecture Notes in Computer Science (Applications of Evolutionary Computing) LNCS 2279: 304-314, Apr 2002