WEIDONG (TOM) CAI  PhD

 

Associate Professor, Director of Multimedia Laboratory

Biomedical & Multimedia Info. Tech. (BMIT) Research Group

School of Computer Science

Faculty of Engineering, The University of Sydney

1 Cleveland Street, Building J12, Office 3E-344

Sydney, NSW 2006, Australia

Phone: +61 2 9351 3271

Email: tom dot cai at sydney.edu.au

Web: http://sydney.edu.au/engineering/people/tom.cai.php

 

Dr. Weidong Cai is an Associate Professor in the School of Computer Science, Director of the Multimedia Laboratory, and Associate Director of the Biomedical & Multimedia Information Technology (BMIT) Research Group at the University of Sydney. He was a Lead Investigator / Visiting Professor on medical image analysis and medical computer vision at Harvard Medical School in 2014. He received his PhD degree in Computer Science from the Basser Department of Computer Science, The University of Sydney, in 2001. His research interests include image/video processing, medical image computing, computer vision, pattern recognition, machine learning, multimedia computing, and computational neuroscience. He has published more than 300 peer-reviewed papers in leading international journals and proceedings of top international conferences. Some of his recent professional services / activities can be found here.

 

 

Selected Recent Publications

 

CONFERENCE PAPERS:

 

- Jianhui Yu, Chaoyi Zhang, Weidong Cai,
"Rethinking Rotation Invariance with Point Cloud Registration",
The 37th AAAI Conference on Artificial Intelligence (AAAI 2023), 2023. [Link] [Project] [Code]


- Dingxin Zhang, Jianhui Yu, Chaoyi Zhang, Weidong Cai,
"PaRot: Patch-Wise Rotation-Invariant Network via Feature Disentanglement and Pose Restoration",
The 37th AAAI Conference on Artificial Intelligence (AAAI 2023), 2023. [Link] [Project] [Code]


- Runkai Zhao, Heng Wang, Chaoyi Zhang, Weidong Cai,
"PointNeuron: 3D Neuron Reconstruction via Geometry and Topology Learning of Point Clouds",
IEEE/CVF Winter Conference on Applications of Computer Vision (WACV 2023), pp5787-5797, 2023. [Link] [Code]


- H. Wang, C. Zhang, J. Yu, W. Cai,
"Spatiality-guided Transformer for 3D Dense Captioning on Point Clouds",
The 31st International Joint Conference on Artificial Intelligence (IJCAI 2022), pp1393-1400, 2022. [Link] [Project] [Code]
(IJCAI Travel Grant / Award)


- S. Mao, C. Zhang, H. Wang, W. Cai,
"Towards Generalisable Audio Representations for Audio-Visual Navigation",
IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR 2022) Workshop on Embodied AI, 2022.
[Project] [Paper] [Code] [2nd@SoundSpaceChallenge - SR & dist2goal]

- Q. Yu, D. Liu, C. Zhang, X. Zhang, W. Cai,
"Unsupervised Domain Adaptive Fundus Image Segmentation with Few Labeled Source Data",
The 33rd British Machine Vision Conference (BMVC 2022), 2022. [Link] [Poster] [Video] [+Supplementary]


- C. Li, D. Liu, H. Li, Z. Zhang, G. Lu, X. Chang, W. Cai,
"Domain Adaptive Nuclei Instance Segmentation and Classification via Category-aware Feature Alignment and Pseudo-labelling",
The 25th Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2022),
Lecture Notes in Computer Science, LNCS Vol.13437, pp715-724, 2022. [Link]


- Y. Chen, F. Zhang, C. Zhang, T. Xue, L. Zekelman, J. He, Y. Song, N. Makris, Y. Rathi, A.J. Golby, W. Cai, L. O'Donnell,
"White Matter Tracts are Point Clouds: Neuropsychological Score Prediction and Critical Region Localization via Geometric Deep Learning",
The 25th Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2022),
Lecture Notes in Computer Science, LNCS Vol.13431, pp174-184, 2022. [Link]


- F. Zhang, T. Xue, W. Cai, Y. Rathi, C-F. Westin, L. O'Donnell,
"TractoFormer: A Novel Fiber-level Whole Brain Tractography Analysis Framework Using Spectral Embedding and Vision Transformers",
The 25th Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2022),
Lecture Notes in Computer Science, LNCS Vol.13431, pp196-206, 2022. [Link]


- Z. Tang, X. Wang, M. Cabezas, A. D'Souza, F. Calamante, D. Liu, M. Barnett, C. Wang, W. Cai,
"Diffusion MRI Fiber Orientation Distribution Inpainting",
The 25th Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2022)
Workshop on Computational Diffusion MRI (CDMRI), Lecture Notes in Computer Science, LNCS Vol.13722, 2022. [Link]

- T. Xue, F. Zhang, C. Zhang, Y. Chen, Y. Song, N. Makris, Y. Rathi, W. Cai, L. O'Donnell,
"SupWMA: Consistent and Efficient Tractography Parcellation of Superficial White Matter with Deep Learning",
The 19th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2022), 2022. [Link] [Project] [Code]
(IEEE ISBI Best Paper Award Finalist)


- H. Jia, C. Bai, W. Cai, H. Huang, Y. Xia,
"HNF-Netv2 for Brain Tumor Segmentation using Multi-modal MR Imaging",
Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries (BrainLes 2021),
Lecture Notes in Computer Science, LNCS Vol.12963, pp106-115, 2022. [Link]
(RSNA 2021 Brain Tumor AI Challenge Top Solution Prize)

- C. Zhang, J. Yu, Y. Song, W. Cai,
"Exploiting Edge-Oriented Reasoning for 3D Point-based Scene Graph Analysis",
The 34th IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR 2021), pp9705-9715, 2021. [Link] [Project] [Video] [Code]


- S. Gao, F. Huang, W. Cai, H. Huang
"Network Pruning via Performance Maximization",
The 34th IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR 2021), pp9270-9280, 2021. [Link]


- T. Xiang, C. Zhang, Y. Song, J. Yu, W. Cai,
"Walk in the Cloud: Learning Curves for Point Clouds Shape Analysis",
2021 IEEE/CVF International Conference on Computer Vision (ICCV 2021), pp915-924, 2021. [Link] [Project] [Code] [SOTA@ModelNet40]


- X. Wang, T. Xiang, C. Zhang, Y. Song, D. Liu, H. Huang, W. Cai,
"BiX-NAS: Searching Efficient Bi-directional Architecture for Medical Image Segmentation",
The 24th Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021),
Lecture Notes in Computer Science, LNCS Vol.12901, pp229-238, 2021. [Link] [Project] [Video] [Code]


- Z. Tang, M. Cabezas, D. Liu, M. Barnett, W. Cai, C. Wang,
"LG-Net: Lesion Gate Network for Multiple Sclerosis Lesion Inpainting",
The 24th Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021),
Lecture Notes in Computer Science, LNCS Vol.12907, pp660-669, 2021. [Link] [Code]
(MICCAI Student Travel Award)

- Y. Chen, C. Zhang, Y. Song, N. Makris, Y. Rathi, W. Cai, F. Zhang, L. O'Donnell,
"Deep Fiber Clustering: Anatomically Informed Unsupervised Deep Learning for Fast and Effective White Matter Parcellation",
The 24th Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021),
Lecture Notes in Computer Science, LNCS Vol.12907, pp497-507, 2021. [Link] [Project] [Code]
(MICCAI Student Travel Award)

- H. Wang, C. Zhang, J. Yu, Y. Song, S. Liu, W. Chrzanowski, W. Cai,
"Voxel-wise Cross-Volume Representation Learning for 3D Neuron Reconstruction",
The 24th Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021)
Workshop on Machine Learning in Medical Imaging (MLMI), Lecture Notes in Computer Science, LNCS Vol.12966, pp248-257, 2021. [Link]

- J. Yu, C. Zhang, Y. Song, W. Cai,
"ICE-GAN: Identity-aware and Capsule-Enhanced GAN with Graph based Reasoning for Micro-Expression Recognition and Synthesis",
2021 International Joint Conference on Neural Networks (IJCNN 2021), 2021. [Project] [Code]


- Y. Chen, Y. Song, C. Zhang, F. Zhang, L. O'Donnell, W. Chrzanowski, W. Cai,
"CellTrack R-CNN: A Novel End-to-End Deep Neural Network for Cell Segmentation and Tracking in Microscopy Images",
2021 IEEE 18th International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2021), pp779-782, 2021. [Link]

- H. Wang, Y. Song, C. Zhang, J. Yu, S. Liu, H. Peng, W. Cai,
"Single Neuron Segmentation using Graph-based Global Reasoning with Auxiliary Skeleton Loss from 3D Optical Microscope Images",
2021 IEEE 18th International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2021), pp934-938, 2021. [Link]

- D. Liu, D. Zhang, Y. Song, F. Zhang, L. O'Donnell, H. Huang, M. Chen, W. Cai,
"Unsupervised Instance Segmentation in Microscopy Images via Panoptic Domain Adaptation and Task Re-weighting",
The 33rd IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR 2020), pp4243-4252, 2020. [Link] [Code]


- C. Zhang, Y. Song, L. Yao, W. Cai,
"Shape-Oriented Convolution Neural Network for Point Cloud Analysis",
The 34th AAAI Conference on Artificial Intelligence (AAAI-20), pp12773-12780, 2020. [Link]
(AAAI-20 Scholarship Award)

- T. Xiang, C. Zhang, D. Liu, Y. Song, H. Huang, W. Cai,
"BiO-Net: Learning Recurrent Bi-directional Connections for Encoder-Decoder Architecture",
The 23rd Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2020),
Lecture Notes in Computer Science, LNCS Vol.12261, pp74-78, 2020. [Project] [Video] [Code]


- H. Jia, Y. Xia, W. Cai, H. Huang,
"Learning High Resolution and Efficient Non-local Features for Brain Gliomas Segmentation in MR Images",
The 23rd Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2020),
Lecture Notes in Computer Science, LNCS Vol.12264, pp480-490, 2020.

- A. Ganjdanesh, K. Ghasedi, L. Zhan, W. Cai, H. Huang,
"Predicting Potential Propensity of Adolescents to Drugs via New Semi-Supervised Deep Ordinal Regression Model",
The 23rd Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2020),
Lecture Notes in Computer Science, LNCS Vol.12261, pp635-645, 2020.

- H. Jia, W. Cai, H. Huang, Y. Xia,
"H2NF-Net for Brain Tumor Segmentation using Multimodal MR Imaging: 2nd Place Solution to BraTS Challenge 2020 Segmentation Task",
The 23rd Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2020):
Brain Tumor Segmentation (BraTS) Challenge, Lecture Notes in Computer Science, 2020.

- V. Dodballapur, R. Calisa, Y. Song, W. Cai,
"Automatic Dropout for Deep Neural Networks",
The 27th International Conference on Neural Information Processing (ICONIP 2020),
Lecture Notes in Computer Science (LNCS 12534), Theoretical Computer Science and General Issues (LNTCS 12543), pp185-196, 2020.
(Finalist for Best Paper Award)

- Z. Tang, D. Zhang, Y. Song, H. Wang, D. Liu, C. Zhang, S. Liu, H. Peng, W. Cai,
"3D Conditional Adversarial Learning for Synthesizing Microscopic Neuron Image using Skeleton-to-Neuron Translation",
The 17th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2020), pp1775-1779, 2020.

- D. Liu, D. Zhang, Y. Song, C. Zhang, F. Zhang, L. O'Donnell, W. Cai,
"Nuclei Segmentation via a Deep Panoptic Model with Semantic Feature Fusion",
The 28th International Joint Conference on Artificial Intelligence (IJCAI 2019), Main track, pp861-868, 2019. [Link] [Code]
(IJCAI Travel Grant/Award)

- Y. Wu, Y. Xia, Y. Song, D. Zhang, D. Liu, C. Zhang, W. Cai,
"Vessel-Net: Retinal Vessel Segmentation under Multi-path Supervision",
The 22nd Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2019),
Lecture Notes in Computer Science, LNCS Vol.11764, pp264-272, 2019.

- H. Jia, Y. Song, H. Huang, W. Cai, Y. Xia,
"HD-Net: Hybrid Discriminative Network for Prostate Segmentation in MR Images",
The 22nd Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2019),
Lecture Notes in Computer Science, LNCS Vol.11765, pp110-118, 2019.

- Y. Zhang, L. Zhan, W. Cai, P. Thompson, H. Heng,
"Integrating Heterogeneous Brain Networks for Predicting Brain Disease Conditions",
The 22nd Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2019),
Lecture Notes in Computer Science, LNCS Vol.11767, pp214-222, 2019.

- S.W. Chu, Y. Song, J.J. Zou, W. Cai,
"Human Pose Estimation using Deep Convolutional DenseNet Hourglass Network with Intermediate Points Voting",
IEEE International Conference on Image Processing (ICIP 2019), pp594-598, 2019.

- V. Dodballapur, Y. Song, H. Huang, M. Chen, W. Chrzanowski, W. Cai,
"Mask-Driven Mitosis Detection in Histopathology Images",
The 16th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2019), pp1855-1859, 2019.

- H. Wang, D. Zhang, Y. Song, S. Liu, D. Feng, Y. Wang, H. Peng, W. Cai,
"Segmenting Neuronal Structure in 3D Optical Microscope Images via Knowledge Distillation with Teacher-Student Network",
The 16th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2019), pp228-231, 2019.

- D. Zhang, Y. Song, D. Liu, C. Zhang, Y. Wu, H. Wang, F. Zhang, Y. Xia, L. O'Donnell, W. Cai,
"Efficient 3D Depthwise and Separable Convolutions with Dilation for Brain Tumor Segmentation",
The 32nd Australasian Joint Conference on Artificial Intelligence (AI 2019), Lecture Notes in Computer Science, Vol.11919, pp563-573, 2019.
(ACS AI Committee Travel Award)

- D. Zhang, Y. Song, D. Liu, H. Jia, S. Liu, Y. Xia, H. Huang, W. Cai,
"Panoptic Segmentation with an End-to-End Cell R-CNN for Pathology Image Analysis",
The 21st Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2018),
Lecture Notes in Computer Science, LNCS Vol.11071, pp237-244, 2018.

- Y. Wu, Y. Xia, Y. Song, Y. Zhang, W. Cai,
"Multiscale Network Followed Network Model for Retinal Vessel Segmentation",
The 21st Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2018),
Lecture Notes in Computer Science, LNCS Vol.11071, pp119-126, 2018.

- X. Wang, W. Cai, D. Shen, H. Huang,
"Temporal Correlation Structure Learning for MCI Conversion Prediction",
The 21st Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2018),
Lecture Notes in Computer Science, LNCS Vol.11072, pp446-454, 2018.

- S. Liu, D. Xu, S.K. Zhou, O. Pauly, S. Grbic, T. Mertelmeier, J. Wicklein, A. Jerebko, W. Cai, D. Cornaniciu,
"3D Anisotropic Hybrid Network: Transferring Convolutional Features from 2D Images to 3D Anisotropic Volumes",
The 21st Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2018),
Lecture Notes in Computer Science, LNCS Vol.11071, pp851-858, 2018.

- Z. Tang, C. Wang, P. Hoang, S. Liu, W. Cai, D. Soligo, R. Oliver, M. Barnett, C. Fomusek,
"Automatic Segmentation of Thigh Muscle in Longitudinal 3D T1-weighted Magnetic Resonance (MR) Images",
The 21st Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2018)
Workshop on Data-Driven Treatment Response Assessment (DATRA), LNCS Vol.11076, pp14-21, 2018.

- D. Liu, D. Zhang, Y. Song, C. Zhang, H. Huang, M. Chen, W. Cai,
"Large Kernel Refine Fusion Net for Neuron Membrane Segmentation",
IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2018)
Workshop on Computer Vision for Microscopy Image Analysis, pp2325-2333, 2018.

- C. Zhang, Y. Song, D. Zhang, S. Liu, M. Chen, W. Cai,
"Whole Slide Image Classification via Iterative Patch Labelling",
IEEE International Conference on Image Processing (ICIP 2018), pp1408-1412, 2018.

- D. Liu, D. Zhang, S. Liu, Y. Song, H. Jia, D. Feng, Y. Xia, W. Cai,
"Densely Connected Large Kernel Convolutional Network for Semantic Membrane Segmentation in Microscopy Images",
IEEE International Conference on Image Processing (ICIP 2018), pp2461-2465, 2018.
(IEEE SPS Travel Award)

- S. Liu, A. Klistorner, C. Wang, Y. Gao, B. Gilchrist, Y. Song, Y. You, J. Yao, W. Cai, M. Barnett,
"Personalized Lesion Profiling in Multiple Sclerosis",
Annual Meeting for International Society for Magnetic Resonance in Medicine (ISMRM 2018), 2018.

- Y. Song, H. Chang, Y. Gao, S. Liu, D. Zhang, J. Yao, W. Chrzanowski, W. Cai,
"Feature Learning with Component Selective Encoding for Histopathology Image Classification",
The 15th IEEE International Symposium on Biomedical Imaging (ISBI 2018), pp257-260, 2018.

- D. Zhang, Y. Song, S. Liu, D. Feng, Y. Wang, W. Cai,
"Nuclei Instance Segmentation with Dual Contour-Enhanced Adversarial Network",
The 15th IEEE International Symposium on Biomedical Imaging (ISBI 2018), pp409-412, 2018.

- X. Wang, H. Chen, W. Cai, D. Shen, H. Huang,
"Regularized Modal Regression with Applications in Cognitive Impairment Prediction",
The 31st Annual Conference on Neural Information Processing Systems (NIPS 2017), pp1447-1457, 2017.

- Y. Song, F. Zhang, Q. Li, H. Huang, L. O'Donnell, W. Cai,
"Locally-Transferred Fisher Vectors for Texture Classification",
The IEEE International Conference on Computer Vision (ICCV 2017), pp4912-4920, 2017.

- K.G. Dizaji, A. Herandi, C. Deng, W. Cai, H. Huang,
"Deep Clustering via Joint Convolutional Autoencoder Embedding and Relative Entropy Minimization",
The IEEE International Conference on Computer Vision (ICCV 2017), pp5736-5745, 2017.

- Z. Tang, D. Zhang, S. Liu, Y. Song, H. Peng, W. Cai,
"Automatic 3D Single Neuron Reconstruction with Exhaustive Tracing",
The IEEE International Conference on Computer Vision (ICCV 2017)
Workshop on Bioimage Computing, pp126-133, 2017.

- Y. Song, H. Chang, H. Huang, W. Cai,
"Supervised Intra-Embedding of Fisher Vectors for Histopathology Image Classification",
The 20th Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2017),
Lecture Notes in Computer Science, LNCS Vol.10435, pp99-106, 2017.

- Y. Xie, Y. Xia, J. Zhang, D. Feng, M. Fulham, W. Cai,
"Transferable Multi-Model Ensemble for Benign-Malignant Lung Nodule Classification on Chest CT",
The 20th Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2017),
Lecture Notes in Computer Science, LNCS Vol.10435, pp656-664, 2017.

- F. Zhang, W. Wu, L. Ning, G. McAnulty, D. Waber, B. Gagoski, K. Sarill, H. Hamoda, Y. Song, W. Cai, Y. Rathi, L. O'Donnell,
"Supra-threshold Fiber Cluster Statistics for Data-driven Whole Brain Tractography Analysis",
The 20th Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2017),
Lecture Notes in Computer Science, LNCS Vol.10433, pp556-565, 2017.

- S. Liu, D. Zhang, Y. Song, H. Peng, W. Cai,
"Triple-Crossing 2.5D Convolutional Neural Network for Detecting Neuronal Arbours in 3D Microscopic Images",
The 20th Intl. Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI 2017),
Workshop on Machine Learning in Medical Imaging, Lecture Notes in Computer Science, LNCS Vol.10541, pp185-193, 2017.

- F. Zhang, I. Norton, W. Cai, Y. Song, W. Wells, L. O'Donnell,
"Comparison between Two White Matter Segmentation Strategies: An Investigation into White Matter Segmentation Consistency",
The IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2017), pp796-799, 2017.
(NIH / NIBIB Travel Award) [Link]


- F. Zhang, P. Kahaliardabili, Y. Suter, I. Norton, R. Laura, P. Savadjiev, Y. Song, Y. Rathi, W. Cai, W. Wells, A. Golby, L. O'Donnell,
"Automated Connectivity-Based Groupwise Cortical Atlas Generation: Application to Data of Neurosurgical Patients with Brain Tumors for Cortical Parcellation Prediction",
The IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2017), pp774-777, 2017.
(NIH / NIBIB Travel Award) [Link]


- Z. Huo, S. Gao, W. Cai, H. Huang,
"Video Recovery via Learning Variation and Consistency of Images",
The 31st AAAI Conference on Artificial Intelligence (AAAI 2017), pp4082-4088, 2017. [Link]


- Z. Zhou, X. Liu, A. Ramanathan, H. Chen, Y. Li, M. Prabhat, K. Bouchard, L. Gu, L. Cheng, Z. Wan, J. Yang, N. Zhong, L. Qu, J.Z. Yang, S. Liu, W. Cai, H. Zhou, S. Zeng, C-W Wang, A. Sironi, P. Glowacki, P. Fua, M. Radojevic, D. Jin, T. Zhao, J. Zhou, Z. Zheng, P. Hong, T. Zeng, R. Li, S. Ji, H. Ikeno, Y-T Ching, T. Liu, E. Bas, B. Roysam, S. Sorensen, Al Nern, G. Tourassi, J. Wells, R. Kanzaki, K. Ito, J.S. Kim, G. Jefferis, Y. Wang, E. Rubel, P.T. Gonzalez-Bellido, R. Wong, B. Ye, H. Zeng, E. Lein, H. Cline, A-S Chiang, G.M. Rubin, S. Hill, M. Hawrylycz, A. Jones, C. Koch, E. Meijering, G.A. Ascoli, H. Peng,
"BigNeuron Algorithm - Porting and Bench-Testing for Automatic, Massive-Scale Neuron Reconstruction",
2016 Society for Neuroscience (SfN) Annual Meeting (Neuroscience 2016), 2016. [Link]


- S. Liu, Y. Song, F. Zhang, D. Feng, M. Fulham, W. Cai,
"Clique Identification and Propagation for Multimodal Brain Tumor Image Segmentation",
2016 International Conference on Brain Informatics and Health (BIH 2016), Lecture Notes in Computer Science, Vol.9919, pp285-294, 2016.
(BIH'16 Best Paper Award) [Link]


- Y. Song, Q. Li, H. Huang, D. Feng, M. Chen, W. Cai,
"Histopathology Image Categorization with Discriminative Dimension Reduction of Fisher Vectors",
The 14th European Conference on Computer Vision (ECCV 2016) Workshop on Bioimage Computing,
Lecture Notes in Computer Science, Vol.9913, pp306-317, 2016. [Link]


- H. Chen, H. Xia, W. Cai, H. Huang
"Error Analysis of Generalized Nystrom Kernel Regression",
The 30th Annual Conference on Neural Information Processing Systems (NIPS 2016) ,
Advances in Neural Information Processing Systems 29, pp2541-2549, 2016. [PDF]


- Ju Han, Yunfu Wang, Weidong Cai, Alexander Borowsky, Bahram Parvin, Hang Chang,
"Integrative Analysis of Cellular Morphometric Context Reveals Clinically Relevant Signatures in Lower Grade Glioma",
The 19th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2016),
Lecture Notes in Computer Science, Vol.9900, pp72-80, 2016. [Link]


- Yutong Xie, Jianpeng Zhang, Sidong Liu, Weidong Cai, Yong Xia,
"Lung Nodule Classification by Jointly using Visual Descriptors and Deep Features",
The 19th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2016),
Workshop on Medical Computer Vision, pp116-125, 2016. [Link]


- Donghao Zhang, Siqi Liu, Sidong Liu, Dagan Feng, Hanchuan Peng, Weidong Cai,
"Reconstruction of 3D Neuron Morphology using Rivulet Back-Tracking",
The IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2016), pp598-601, 2016. [Link]


- Yang Song, Weidong Cai, Fan Zhang, Heng Huang, Dagan Feng, Yue Wang, Mei Chen,
"Texture Analysis of Tissue Aging using Global and Cluster Constrained Local Coding",
The IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2016), pp1229-1232, 2016. [Link]


- Afaf Tareef, Yang Song, Weidong Cai, Yue Wang, Dagan Feng, Mei Chen,
"Automatic Nuclei and Cytoplasm Segmentation of Leukocytes with Color and Texture-based Image Enhancement",
The IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2016), pp935-938, 2016. [Link]


- Fan Zhang, Peter Savadjiev, Weidong Cai, Yang Song, Ragini Verma, Carl-Fredrik Westin, Lauren J O'Donnell,
"Fiber Clustering based White Matter Connectivity Analysis for Prediction of Autism Spectrum Disorder using Diffusion Tensor Imaging",
The IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2016), pp564-567, 2016.
(Finalist for Best Student Paper Award) [Link]


- Hongchang Gao, Lin Yan, Weidong Cai, Heng Huang,
"Anatomical Annotations for Drosophila Gene Expression Patterns via Multi-Dimensional Visual Descriptors Integration",
The 21st ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD 2015), pp339-348, 2015. [Link]


- Fan Zhang, Yang Song, Siqi Liu, Paul Young, Daniela Traini, Lucy Morgan, Hui-Xin Ong, Lachlan Buddle, Sidong Liu, Dagan Feng, Weidong Cai,
"Motion Representation of Ciliated Cell Images with Contour-Alignment for Automated CBF Estimation",
The 18th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2015),
Lecture Notes in Computer Science 9351, pp300-307, 2015. (MICCAI Travel Award) [Link]


- Yang Song, Weidong Cai, Fan Zhang, Heng Huang, Yun Zhou, Dagan Feng, Michael Fulham,
"Latent Discriminative Modeling for Lesion Detection in PET-CT Images",
The 18th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2015),
Workshop on Computational Methods for Molecular Imaging, pp52-62, 2015. [PDF]


- Yang Song, Weidong Cai, Qing Li, Fan Zhang, Dagan Feng, Heng Huang,
"Fusing Subcategory Probabilities for Texture Classification",
The 28th IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2015), pp4409-4417, 2015. [Link]


- Changyang Li, Yuchen Yuan, Weidong Cai, Yong Xia, Dagan Feng,
"Robust Saliency Detection via Regularized Random Walks Ranking",
The 28th IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2015), pp2710-2717, 2015. [Link]


- Sidong Liu, Weidong Cai, Siqi Liu, Sonia Pujol, Ron Kikinis, Dagan Feng,
"Subject-Centered Multi-View Feature Fusion for Neuroimaging Retrieval and Classification",
The IEEE International Conference on Image Processing (ICIP 2015), 2015. [PDF]


- Fan Zhang, Weidong Cai, Yang Song, Paul Young, Daniela Traini, Lucy Morgan, Hui-Xin Ong, Lachlan Buddle, Dagan Feng,
"Beating Cilia Identification in Fluorescence Microscope Images for Accurate CBF Measurement",
The IEEE International Conference on Image Processing (ICIP 2015), 2015. [PDF]


- Peng Li, Weidong Cai, Heng Huang,
"Weakly Supervised Natural Language Processing Framework for Abstractive Multi-Document Summarization",
The 24th ACM International Conference on Information and Knowledge Management (CIKM 2015), pp1401-1410, 2015. [Link]


- Hongchang Gao, Feiping Nie, Weidong Cai, Heng Huang,
"Robust Capped Norm Nonnegative Matrix Factorization",
The 24th ACM International Conference on Information and Knowledge Management (CIKM 2015), pp871-880, 2015. [Link]


- Siqi Liu, Sidong Liu, Fan Zhang, Weidong Cai, Sonia Pujol, Ron Kikinis, Dagan Feng, ADNI,
"Longitudinal Brain MR Retrieval with Diffeomorphic Demons Registration: What Happened to Those Patients with Similar Changes?",
The IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2015), pp588-591, 2015. [Link]


- Yang Song, Weidong Cai, Fan Zhang, Heng Huang, Yun Zhou, Dagan Feng,
"Bone Texture Characterization with Fisher Encoding of Local Descriptors",
The IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2015), pp5-8, 2015. [Link]


- Siqi Liu, Nur Hadi, Sidong Liu, Sonia Pujol, Ron Kikinis, Fan Zhang, Dagan Feng, Weidong Cai,
"Content-based Retrieval of Brain Diffusion Magnetic Resonance Image",
The 37th European Conference on Information Retrieval (ECIR 2015) Workshop on Multimodal Retrieval in the Medical Domain, 2015. [PDF]


- Fan Zhang, Yang Song, Weidong Cai, Adrien Depeursinge, Henning Muller,
"USYD/HES-SO in the VISCERAL Retrieval Benchmark",
The 37th European Conference on Information Retrieval (ECIR 2015) Workshop on Multimodal Retrieval in the Medical Domain, 2015. [PDF]


- Siqi Liu, Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis, Dagan Feng,
"Multi-Phase Feature Representation Learning for Neurodegenerative Disease Diagnosis",
First Australasian Conference on Artificial Life and Computational Intelligence (ACALCI 2015),
Lecture Notes in Artificial Intelligence 8955, pp350-359, 2015. [PDF]


- Fan Zhang, Yang Song, Weidong Cai, Alex G. Hauptmann, Sidong Liu, Siqi Liu, Dagan Feng, Mei Chen,
"Ranking-based Vocabulary Pruning in Bag-of-Features for Image Retrieval",
First Australasian Conference on Artificial Life and Computational Intelligence (ACALCI 2015),
Lecture Notes in Artificial Intelligence 8955, pp436-445, 2015. [PDF]


- Yang Song, Weidong Cai, Heng Huang, Yun Zhou, Dagan Feng, Mei Chen,
"Large Margin Aggregation of Local Estimates for Medical Image Classification",
The 17th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2014),
Lecture Notes in Computer Science 8674, pp196-203, 2014. [PDF]


- De Wang, Yang Wang, Feiping Nie, Jingwen Yan, Weidong Cai, Andrew J Saykin, Li Shen, Heng Huang,
"Human Connectome Module Pattern Detection Using A New Multi-Graph MinMax Cut Model",
The 17th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2014),
Lecture Notes in Computer Science 8675, pp313-320, 2014. [PDF]


- Weidong Cai, Sidong Liu, Yang Song, Sonia Pujol, Ron Kikinis, Dagan Feng,
"A 3D Difference-of-Gaussian-based Lesion Detector for Brain PET",
IEEE International Symposium on Biomedical Imaging (ISBI 2014), pp677-680, 2014. [Link]


- Weidong Cai, Fan Zhang, Yang Song, Sidong Liu, Lingfeng Wen, Stefan Eberl, Michael Fulham, Dagan Feng,
"Automated Feedback Extraction for Medical Imaging Retrieval",
IEEE International Symposium on Biomedical Imaging (ISBI 2014), pp907-910, 2014. [Link]


- Yang Song, Weidong Cai, Heng Huang, Yun Zhou, Yue Wang, Dagan Feng,
"Boosted Multifold Sparse Representation with Application to ILD Classification",
IEEE International Symposium on Biomedical Imaging (ISBI 2014), pp1023-1026, 2014. [Link]


- Fan Zhang, Weidong Cai, Yang Song, Paul Young, Daniela Traini, Lucy Morgan, Hui-Xin Ong, Lachlan Buddle, Dagan Feng,
"Image-based Ciliary Beating Frequency Estimation for Therapeutic Assessment on Defective Mucociliary Clearance Diseases",
IEEE International Symposium on Biomedical Imaging (ISBI 2014), pp193-196, 2014. [Link]


- Hangyu Che, Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis, Dagan Feng,
"Co-neighbor Multi-view Spectral Embedding for Medical Content-based Retrieval",
IEEE International Symposium on Biomedical Imaging (ISBI 2014), pp911-914, 2014. [Link]


- Siqi Liu, Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis, Dagan Feng,
"Early Diagnosis of Alzheimer's Disease with Deep Learning",
IEEE International Symposium on Biomedical Imaging (ISBI 2014), pp1015-1018, 2014. [Link]


- Fan Zhang, Yang Song, Weidong Cai, Yun Zhou, Michael Fulham, Stefan Eberl, Shimin Shan, Dagan Feng,
"A Ranking-based Lung Nodule Image Classification Method using Unlabeled Image Knowledge",
IEEE International Symposium on Biomedical Imaging (ISBI 2014), pp1356-1359, 2014. [Link]


- Afaf Tareef, Yang Song, Weidong Cai, Dagan Feng, Mei Chen,
"Automated Three-Stage Nucleus and Cytoplasm Segmentation of Overlapping Cells",
The 13th International Conference on Control, Automation, Robotics and Vision (ICARCV 2014), pp865-870, 2014. (Finalist for Best Paper Award) [Link]


- Sidong Liu, Siqi Liu, Sonia Pujol, Ron Kikinis, Dagan Feng, Weidong Cai,
"Propagation Graph Fusion for Multi-Modal Medical Content-based Retrieval",
The 13th International Conference on Control, Automation, Robotics and Vision (ICARCV 2014), pp849-854, 2014. [Link]


- Qing Li, Weidong Cai, Xiaogang Wang, Yun Zhou, Dagan Feng, Mei Chen,
"Medical Image Classification with Convolutional Neural Network",
The 13th International Conference on Control, Automation, Robotics and Vision (ICARCV 2014), pp844-848, 2014. [Link]


- Peng Fu, Changyang Li, Quansen Sun, Weidong Cai, Dagan Feng,
"Image Noise Level Estimation Based on A New Adaptive Superpixel Classification",
The 21st IEEE International Conference on Image Processing (ICIP 2014), pp2617-2621, 2014. [Link]


- Xiao Cai, Feiping Nie, Weidong Cai, Heng Huang,
"New Graph Structured Sparsity Model for Multi-Label Image Annotations",
The IEEE International Conference on Computer Vision (ICCV 2013), pp801-808, 2013. [Link]


- Hua Wang, Feiping Nie, Weidong Cai, Heng Huang,
"Semi-Supervised Robust Dictionary Learning via Efficient L2,0+-Norms Minimization",
The IEEE International Conference on Computer Vision (ICCV 2013), pp1145-1152, 2013. [Link]


- Xiao Cai, Feiping Nie, Weidong Cai, Heng Huang,
"Heterogeneous Image Features Integration via Multi-Modal Semi-Supervised Learning Model",
The IEEE International Conference on Computer Vision (ICCV 2013), pp1737-1744, 2013. [Link]


- Yang Song, Weidong Cai, Heng Huang, Xiaogang Wang, Stefan Eberl, Michael Fulham, Dagan Feng,
"Similarity Guided Feature Labeling for Lesion Detection",
The 16th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2013),
Lecture Notes in Computer Science 8149, pp284-291, 2013. (MICCAI Travel Award) [PDF]


- Sidong Liu, Yang Song, Weidong Cai, Sonia Pujol, Ron Kikinis, Xiaogang Wang, Dagan Feng,
"Multifold Bayesian Kernelization in Alzheimer's Diagnosis",
The 16th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2013),
Lecture Notes in Computer Science 8150, pp303-310, 2013. (MICCAI Travel Award) [PDF]


- Yang Song, Weidong Cai, Seungil Huh, Mei Chen, Takeo Kanade, Yun Zhou, Dagan Feng,
"Discriminative Data Transform for Image Feature Extraction and Classification",
The 16th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2013),
Lecture Notes in Computer Science 8150, pp452-459, 2013. (MICCAI Travel Award) [PDF]


- Heng Huang, Jingwen Yan, Feiping Nie, Jin Huang, Weidong Cai, Andrew J. Saykin, Li Shen,
"A New Sparse Simplex Model for Brain Anatomical and Genetic Network Analysis",
The 16th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2013),
Lecture Notes in Computer Science 8150, pp625-632, 2013. [PDF]


- Sidong Liu, Weidong Cai, Yang Song, Sonia Pujol, Ron Kikinis, Dagan Feng,
"A Bag of Semantic Words Model for Medical Content-based Retrieval",
The 16th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2013)
Workshop on Medical Content-Based Retrieval for Clinical Decision Support
, pp6-12, 2013. [PDF]


- Sidong Liu, Lelin Zhang, Weidong Cai, Yang Song, Zhiyong Wang, Lingfeng Wen, Dagan Feng,
"A Supervised Multiview Spectral Embedding Method for Neuroimaging Classification",
The 20th IEEE International Conference on Image Processing (ICIP 2013), pp602-605, 2013. [Link]


- Lelin Zhang, Sidong Liu, Zhiyong Wang, Weidong Cai, Yang Song, Dagan Feng,
"Graph Cuts based Relevance Feedback in Image Retrieval",
The 20th IEEE International Conference on Image Processing (ICIP 2013), pp4358-4362, 2013. [Link]


- Sidong Liu, Weidong Cai, Lingfeng Wen, Dagan Feng,
"Neuroimaging Biomarker based Prediction of Alzheimer's Disease Severity with Optimized Graph Construction",
IEEE International Symposium on Biomedical Imaging (ISBI 2013), pp1324-1327, 2013. [Link]


- Yang Song, Weidong Cai, Yun Zhou, Lingfeng Wen, Dagan Feng,
"Pathology-centric Medical Image Retrieval with Hierarchical Contextual Spatial Descriptor",
IEEE International Symposium on Biomedical Imaging (ISBI 2013), pp202-205, 2013. [Link]


- Sidong Liu, Weidong Cai, Lingfeng Wen, Dagan Feng,
"Multi-channel Brain Atrophy Pattern Analysis in Neuroimaging Retrieval",
IEEE International Symposium on Biomedical Imaging (ISBI 2013), pp206-209, 2013. [Link]


- Yang Song, Weidong Cai, Yun Zhou, Dagan Feng,
"Thoracic Abnormality Detection with Data Adaptive Structure Estimation",
The 15th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2012),
Lecture Notes in Computer Science 7510, pp74-81, 2012. [PDF]


- Yang Song, Weidong Cai, Heng Huang, Yue Wang, Dagan Feng,
"Object Localization in Medical Images based on Graphical Model with Contrast and Interest-Region Terms",
The 25th IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2012)
Workshop on Medical Computer Vision
, pp1-7, 2012. [PDF]


- Weidong Cai, Yang Song, Dagan Feng,
"Regression and Classification based Distance Metric Learning for Medical Image Retrieval",
IEEE International Symposium on Biomedical Imaging (ISBI 2012), pp1775-1778, 2012. [Link]


- Yang Song, Weidong Cai, Yue Wang, Dagan Feng,
"Location Classification of Lung Nodules with Optimized Graph Construction",
IEEE International Symposium on Biomedical Imaging (ISBI 2012), pp1439-1442, 2012. [Link]


- Yang Song, Weidong Cai, Dagan Feng,
"Global Context Inference for Adaptive Abnormality Detection in PET-CT Images",
IEEE International Symposium on Biomedical Imaging (ISBI 2012), pp482-485, 2012. [Link]


- Sidong Liu, Weidong Cai, Lingfeng Wen, Dagan Feng,
"Multiscale and Multiorientation Feature Extraction with Degenerative Patterns for 3D Neuroimaging Retrieval",
The 19th IEEE International Conference on Image Processing (ICIP 2012), pp1249-1252, 2012. [Link]


- Yang Song, Weidong Cai, Dagan Feng,
"Disease-Specific Context Modeling and Retrieval with Fast Structure Localization",
The 12th IEEE Workshop on Mathematical Methods in Biomedical Image Analysis
in conjunction with the IEEE Workshop on the Applications of Computer Vision (WACV / MMBIA 2012)
, pp89-94, 2012. [PDF]


- Yang Song, Weidong Cai, Dagan Feng,
"Hierarchical Spatial Matching for Medical Image Retrieval",
The 19th Annual ACM International Conference on Multimedia (ACM MM2011)
Workshop on Medical Multimedia Analysis and Retrieval
, pp1-6, 2011. [PDF]


- Sidong Liu, Weidong Cai, Lingfeng Wen, Dagan Feng,
"Volumetric Congruent Local Binary Patterns for 3D Neurological Image Retrieval",
The 26th International Conference on Image and Vision Computing New Zealand (IVCNZ2011), pp272-276, 2011. [PDF]


- Yang Song, Weidong Cai, Stefan Eberl, Michael Fulham, Dagan Feng,
"Region and Learning Based Retrieval for Multi-Modality medical Images",
The 8th International Conference on Biomedical Engineering (Biomed 2011), Track 723-063, 2011. [PDF]


- Sidong Liu, Weidong Cai, Lingfeng Wen, Stefan Eberl, Michael Fulham, Dagan Feng,
"Optimized Pathological and Visual Content-based Neuroimaging Retrieval",
Proceedings of SPIE Medical Imaging (SPIE-MI 2011), Track 7963-23, 2011. [PDF]


- Yang Song, Weidong Cai, Stefan Eberl, Michael Fulham, Dagan Feng,
"Thoracic Image Case Retrieval with Spatial and Contextual Information",
IEEE International symposium on Biomedical Imaging: From Nano to Macro (ISBI 2011), pp1885-1888, 2011.
[Link]


- Sidong Liu, Weidong Cai, Lingfeng Wen, Stefan Eberl, Michael Fulham, Dagan Feng,
"Localized Functional Neuroimaging Retrieval using 3D Discrete Curvelet Transform",
IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2011), pp1877-1880, 2011.
[Link]


- Yang Song, Weidong Cai, Stefan Eberl, Michael Fulham, Dagan Feng,
"Discriminative Pathological Context Detection in Thoracic Images based on Multi-level Inference",
The 14th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2011),
Lecture Notes in Computer Science 6893, pp191-198, 2011. [PDF]


 

JOURNAL PAPERS:

 

- T. Xue, F. Zhang, C. Zhang, Y. Chen, Y. Song, N. Makris, Y. Rathi, W. Cai, L. O'Donnell,
"Superficial White Matter Analysis: An Efficient Point-cloud-based Deep Learning Framework with Supervised Contrastive Learning for Consistent Tractography Parcellation across Populations and dMRI Acquisitions",
Medical Image Analysis, Vol.85, 102759, 2023. [Link] [Project]


- Linus Manubens-Gil, Zhi Zhou, Hanbo Chen, Arvind Ramanathan, Xiaoxiao Liu, Yufeng Liu, Alessandro Bria, Todd Gillette, Zongcai Ruan, Jian Yang, Miroslav Radojevic, Ting Zhao, Li Cheng, Lei Qu, Siqi Liu, Kristofer E. Bouchard, Lin Gu, Weidong Cai, Shuiwang Ji, Badrinath Roysam, Ching-Wei Wang, Hongchuan Yu, Amos Sironi, Daniel Maxim Iascone, Jie Zhou, Erhan Bas, Eduardo Conde-Sousa, Paulo Aguiar, Xiang Li, Yujie Li, Sumit Nanda, Yuan Wang, Leila Muresan, Pascal Fua, Bing Ye, Hai-yan He, Jochen F. Staiger, Manuel Peter, Daniel N. Cox, Michel Simonneau, Marcel Oberlaender, Gregory Jefferis, Kei Ito, Paloma Gonzalez-Bellido, Jinhyun Kim, Edwin Rubel, Hollis T. Cline, Hongkui Zeng, Aljoscha Nern, Ann-Shyn Chiang, Jianhua Yao, Jane Roskams, Rick Livesey, Janine Stevens, Tianming Liu, Chinh Dang, Yike Guo, Ning Zhong, Georgia Tourassi, Sean Hill, Michael Hawrylycz, Christof Koch, Erik Meijering, Giorgio A. Ascoli, Hanchuan Peng,
"BigNeuron: A resource to benchmark and predict best-performing algorithms for automated reconstruction of neuronal morphology",
Nature Methods, 2023. [Link]


- D. Liu, C. Zhang, Y. Song, H. Huang, C. Wang, M. Barnett, W. Cai,
"Decompose to Adapt: Cross-domain Object Detection via Feature Disentanglement",
IEEE Transactions on Multimedia, 2022. [Link] [Code]


- T. Xiang, C. Zhang, X. Wang, Y. Song, D. Liu, H. Huang, W. Cai,
"Towards Bi-directional Skip Connections in Encoder-Decoder Architectures and Beyond",
Medical Image Analysis, Vol.78, 102420, 2022. [Link] [Project]


- H. Jia, W. Cai, H. Huang, Y. Xia,
"Learning Multi-scale Synergic Discriminative Features for Prostate Image Segmentation",
Pattern Recognition, Vol.126, 108556, 2022. [Link]


- T. Xiang, Y. Song, C. Zhang, D. Liu, M. Chen, F. Zhang, H. Huang, L. O'Donnell, W. Cai,
"DSNet: A Dual-Stream Framework for Weakly-Supervised Gigapixel Pathology Image Analysis",
IEEE Transactions on Medical Imaging, Vol.41, No.8, pp2180-2190, 2022. [Link]


- D. Liu, D. Zhang, Y. Song, H. Huang, W. Cai,
"Panoptic Feature Fusion Net: A Novel Instance Segmentation Paradigm for Biomedical and Biological Images",
IEEE Transactions on Image Processing, Vol.30, pp2045-2059, 2021. [Link] [Code]


- D. Liu, D. Zhang, Y. Song, F. Zhang, L. O'Donnell, H. Huang, M. Chen, W. Cai,
"PDAM: A Panoptic-level Feature Alignment Framework for Unsupervised Domain Adaptive Instance Segmentation in Microscopy Images",
IEEE Transactions on Medical Imaging, Vol.40, No.1, pp154-165, 2021. [Link] [Code]


- H. Jia, Y. Xia, Y. Song, D. Zhang, H. Huang, Y. Zhang, W. Cai,
"3D APA-Net: 3D Adversarial Pyramid Anisotropic Convolutional Network for Prostate Segmentation in MR Images",
IEEE Transactions on Medical Imaging, Vol.39, No.2, pp447-457, 2020. [Link]


- Y. Shi, Z. Guo, X. Su, L. Meng, M. Zhang, J. Sun, C. Wu, M. Zheng, X. Shang, X. Zou, W. Cheng, Y. Yu, Y. Cai, C. Zhang, W. Cai, L. Da, G. He, Z. Han,
"DeepAntigen: A Novel Method for Neoantigen Prioritization via 3D Genome and Deep Sparse Learning",
Bioinformatics, Vol.36, Issue.19, pp4894-4901, 2020. [Link]


- Y. Wu, Y. Xia, Y. Song, Y. Zhang, W. Cai,
"NFN+: A Novel Network Followed Network for Retinal Vessel Segmentation", Special Issue on Advanced Deep Learning Methods for Biomedical Image Analysis,
Neural Networks, Vol.126, No.6, pp153-162, 2020. [Link]


- M. Russell, J.J. Zou, G. Fang, W. Cai,
"Feature-based Image Patch Classification for Moving Shadow Detection",
IEEE Transactions on Circuits and Systems for Video Technology, Vol.29, Issue.9, pp2652-2666, 2019. [Link]


- Y. Xie, Y. Xia, J. Zhang, Y. Song, D. Feng, M. Fulham, W. Cai,
"Knowledge-based Collaborative Deep Learning for Benign-Malignant Lung Nodule Classification on Chest CT",
IEEE Transactions on Medical Imaging, Vol.38, Issue.4, pp991-1004, 2019. [Link]


- S. Liu, D. Zhang, Y. Song, H. Peng, W. Cai,
"Automated 3D Neuron Tracing with Precise Branch Erasing and Confidence Controlled Back-Tracking",
IEEE Transactions on Medical Imaging, Vol.37, Issue.11, pp2441-2452, 2018. [Link]


- A. Tareef, Y. Song, H. Huang, D. Feng, M. Chen, Y. Wang, W. Cai,
"Multi-pass Fast Watershed for Accurate Segmentation of Overlapping Cervical Cells",
IEEE Transactions on Medical Imaging, Vol.37, Issue.9, pp2044-2059, 2018. [Link]


- F. Zhang, P. Savadjiev, W. Cai, Y. Song, Y. Rathi, B. Tunc, D. Parker, T. Kapur, R.T. Schultz, N. Makris, R. Verma, L.J. O'Donnell,
"Whole Brain White Matter Connectivity Analysis using Machine Learning: An Application to Autism",
NeuroImage, Vol.172, pp826-837, 2018. [Link]


- Y. Yuan, C. Li, J. Kim, W. Cai, D. Feng,
"Reversion Correction and Regularized Random Walk Ranking for Saliency Detection",
IEEE Transactions on Image Processing, Vol.27, Issue.3, pp1311-1322, 2018. [Link]


- F. Zhang, W. Wu, L. Ning, G. McAnulty, D. Waber, B. Gagoski, K. Sarill, H.M. Hamoda, Y. Song, W. Cai, Y. Rathi, L.J. O'Donnell,
"Suprathreshold Fiber Cluster Statistics: Leveraging White Matter Geometry to Enhance Tractography Statistical Analysis",
NeuroImage, Vol.171, pp341-354, 2018. [Link]


- Y. Yuan, Y. Shi, X. Su, X. Zou, Q. Luo, D. Feng, W. Cai, Z. Han,
"Cancer Type Prediction based on Copy Number Aberration and Chromatin 3D Structure with Convolutional Neural Networks",
BMC Genomics, Vol.19, Supp.6, pp97-104, 2018. [Link]


- D. Zhang, S. Liu, Y. Song, D. Feng, H. Peng, W. Cai,
"Automated 3D Soma Segmentation with Morphological Surface Evolution for Neuron Reconstruction",
Neuroinformatics, Springer, Vol.16, Issue.2, pp153-166, 2018. [Link]


- Y. Yuan, C. Li, J. Kim, W. Cai, D. Feng,
"Dense and Sparse Labeling with Multi-Dimensional Features for Saliency Detection",
IEEE Transactions on Circuits and Systems for Video Technology, Vol.28, Issue.5, pp1130-1143, 2018. [Link]


- Y. Song, Q. Li, H. Huang, D. Feng, M. Chen, W. Cai,
"Low Dimensional Representation of Fisher Vectors for Microscopy Image Classification",
IEEE Transactions on Medical Imaging, Vol.36, No.8, pp1636-1649, 2017. [Link]


- Y. Song, Q. Li, F. Zhang, H. Huang, D. Feng, Y. Wang, M. Chen, W. Cai,
"Dual Discriminative Local Coding for Tissue Aging Analysis",
Medical Image Analysis, Vol.38, pp65-76, 2017. [Link]


- F. Zhang, Y. Song, W. Cai, S. Liu, S.Q. Liu, S. Pujol, R. Kikinis, Y. Xia, M. Fulham, D. Feng, ADNI,
"Pairwise Latent Semantic Association for Similarity Computation in Medical Imaging",
IEEE Transactions on Biomedical Engineering, Vol.63, Issue 5, pp1058-1069, 2016. [Link]


- Y. Song, W. Cai, H. Huang, D. Feng, Y. Wang, M. Chen,
"Bioimage Classification with Subcategory Discriminant Transform of High Dimensional Visual Descriptors",
BMC Bioinformatics, 17:465, DOI 10.1186/s12859-016-1318-9, 2016. [Link] [Code]


- Siqi Liu, Donghao Zhang, Sidong Liu, Dagan Feng, Hanchuan Peng, Weidong Cai,
"Rivulet: 3D Neuron Morphology Tracing with Iterative Back-Tracking",
Neuroinformatics, Vol.14, Issue 4, pp387-401, 2016. [Link] [Toolbox/Code] [Vaa3D Plugin]


- Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis, Dagan Feng, ADNI,
"Cross-View Neuroimage Pattern Analysis in Alzheimer's Disease Staging",
Frontiers in Aging Neuroscience, 8:23, doi:10.3389/fnagi.2016.00023, 2016. [Link]


- Y. Yuan, Y. Shi, C. Li, J. Kim, W. Cai, Z. Han, D. Feng,
"DeepGene: An Advanced Cancer Type Classifier Based on Deep Learning and Somatic Point Mutations",
BMC Bioinformatics, 17(Suppl 17):476, DOI 10.1186/s12859-016-1334-9, 2016. [Link]


- Yang Song, Weidong Cai, Heng Huang, Yun Zhou, Dagan Feng, Yue Wang, Michael Fulham, Mei Chen,
"Large Margin Local Estimate with Applications to Medical Image Classification",
IEEE Transactions on Medical Imaging, Vol.34, No.6, pp1362-1377, 2015. [Link] [Code]


- Sidong Liu, Weidong Cai, Siqi Liu, Fan Zhanng, Michael Fulham, Dagan Feng, Sonia Pujol, Ron Kikinis,
"Multimodal Neuroimaging Computing: A Review of the Applications in Neuropsychiatric Disorders",
Brain Informatics
, Vol.2, No.3, Springer, 2015. (Invited paper) [Link]


- Sidong Liu, Weidong Cai, Siqi Liu, Fan Zhanng, Michael Fulham, Dagan Feng, Sonia Pujol, Ron Kikinis,
"Multimodal Neuroimaging Computing: The Workflows, Methods and Platforms",
Brain Informatics
, Vol.2, No.3, Springer, 2015. (Invited paper) [Link]


- Siqi Liu, Sidong Liu, Weidong Cai, Hangyu Che, Sonia Pujol, Ron Kikinis, Dagan Feng, Michael Fulham, ADNI,
"Multi-Modal Neuroimaging Feature Learning for Multi-Class Diagnosis of Alzheimers's Disease",
IEEE Transactions on Biomedical Engineering
, Vol.62, Issue 4, pp1132-1140, 2015. [Link]


- Yang Song, Weidong Cai, Heng Huang, Yun Zhou, Yue Wang, Dagan Feng,
"Locality-constrained Subcluster Representation Ensemble for Lung Image Classification",
Medical Image Analysis, Vol.22, Issue 1, pp102-113, 2015. [PDF]


- Yang Song, Weidong Cai, Heng Huang, Xiaogang Wang, Yun Zhou, Michael Fulham, Dagan Feng,
"Lesion Detection and Characterization with Context Driven Approximation in Thoracic FDG PET-CT Images of NSCLC Studies",
IEEE Transactions on Medical Imaging, Vol.33, No.2, pp408-421, 2014. [Link]


- Fan Zhang, Yang Song, Weidong Cai, Min-Zhao Lee, Yun Zhou, Heng Huang, Shimin Shan, Michael Fulham, Dagan Feng,
"Lung Nodule Classification with Multi-Level Patch-based Context Analysis",
IEEE Transactions on Biomedical Engineering, Vol.61, No.4, pp1155-1166, 2014. [Link]


- Yang Song, Weidong Cai, Yun Zhou, Dagan Feng,
"Feature-based Image Patch Approximation for Lung Tissue Classification",
IEEE Transactions on Medical Imaging, Vol.32, No.4, pp797-808, 2013. [Link] [Code]


- Yang Song, Weidong Cai, Heng Huang, Yue Wang, Dagan Feng, Mei Chen,
"Region-based Progressive Localization of Cell Nuclei in Microscopic Images with Data Adaptive Modeling",
BMC Bioinformatics, 14:173, pp1-16, 2013. [Link]


- Yang Song, Weidong Cai, Jinman Kim, Dagan Feng,
"A Multi-Stage Discriminative Model for Tumor and Lymph Node Detection in Thoracic Images",
IEEE Transactions on Medical Imaging, Vol.31, No.5, pp1061-1075, 2012. (The Google Publication Prize 2012) [Link]


 

BOOK CHAPTERS:

 

- H. Wang, Y. Song, Z. Tang, C. Zhang, J. Yu, D. Liu, D. Zhang, S. Liu, W. Cai,
"AI-enhanced 3D Biomedical Data Analytics for Neuronal Structure Reconstruction",
Invited book chapter, in Humanity Driven AI: Productivity, Wellbeing, Sustainability and Partnership, Edited by F. Chen and J. Zhou,
Springer, pp135-163, 2022. [Link]


- Y. Song, W. Cai,
"Visual Feature Representation in Microscopy Image Classification",
Invited book chapter, in Computer Vision for Microscopy Image Analysis, Edited by M. Chen,
Elsevier, pp73-100, 2021. [Link]


- S. Liu, D. Xu, S.K. Zhou, S. Grbic, W. Cai, D. Comaniciu,
"Anisotropic Hybrid Network for Cross-Dimension Transferable Feature Learning in 3D Medical Images",
Invited book chapter, in Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics, Edited by L. Lu, X. Wang, G. Carneiro, L. Yang,
Springer, pp199-216, 2019. [Link]


- Y. Song, W. Cai,
"Handling of Feature Space Complexity for Texture Analysis in Medical Images",
Invited book chapter, in Biomedical Texture Analysis: Fundamentals, Tools and Challenges, Edited by A. Depeursinge, O.S. Al-Kadi, J.R. Mitchell,
Elsevier: Academic Press, pp163-191, 2017. [Link]


- F. Zhang, Y. Song, W. Cai, A. Depeursinge, H. Muller,
"Text- and Content-based Medical Image Retrievals in the VISCERAL Retrieval Benchmark",
Invited book chapter, in Cloud-Based Benchmarking of Medical Image Analysis, Edited by A. Hanbury, H. Muller, G. Langs,
Springer, pp237-249, 2017. [PDF] [Link]


- Y. Song, W. Cai, S. Eberl, M. Fulham, D. Feng,
"Feature-Centric Lesion Detection and Retrieval in Thoracic Images",
Invited book chapter, in Computer Vision in Medical Imaging, Edited by C. H. Chen,
Volume 2 of Book Series in Computer Vision, pp75-94, World Scientific Publishing, 2014. [PDF] [Link]


- Y. Song, W. Cai, H. Huang, Y. Wang, D. Feng,
"Context Enhanced Graphical Model for Object Localization in Medical Images",
Invited book chapter, in Medical Computer Vision: Recognition Techniques and Applications in Medical Imaging,
Edited by B.H. Menze, G. Langs, L. Lu, A. Montillo, Z. Tu, A. Criminisi, pp194-205, Springer Berlin Heidelberg, 2013. [PDF] [Link]


 

EDITED BOOKS / PROCEEDINGS / SPECIAL ISSUES:

 

- M. Chen, W. Cai, A. Liu, D. Metaxas, T. Tasdizen, S. Zhang (Eds.),
Special Issue: Learning and understanding of biomedical big data, Machine Vision and Applications, Vol.29, Issue 8, Springer, November 2018. [Link]


- H. Muller, M. Kelm, T. Arbel, W. Cai, J. Cardoso, G. Langs, B. Menze, D. Metaxas, A. Montillo, W. Wells III, S. Zhang, A. Chung, M. Jenkinson, A. Ribbens (Eds.),
Medical Computer Vision and Bayesian and Graphical Models for Biomedical Imaging, ISBN: 978-3-319-61188-4, Springer, 2017. [Link]


- Y. Guo, H. Li, W. Cai, M. Murshed, Z. Wang, J. Gao, D. Feng,
Proceedings of 2017 International Conference on Digital Image Computing: Techniques and Applications (DICTA 2017), ISBN: 978-1-5386-2839-3, IEEE, 2017. [Link]


- Y. Zheng, S. Zhang, J. Huang, W. Cai (Eds.),
Special Issue: Advances in computering techniques for big medical image data, Neurocomputing, Vol.229, Elsevier, March 2017. [Link]


- B. Menze, G. Langs, A. Montillo, M. Kelm, H. Muller, S. Zhang, W. Cai, D. Metaxas (Eds.),
Medical Computer Vision: Algorithms for Big Data - MCV 2015, ISBN: 978-3-319-42016-5, Springer Switzerland, 2016. [Link]


- B. Menze, G. Langs, A. Montillo, M. Kelm, H. Muller, S. Zhang, W. Cai, D. Metaxas (Eds.),
Medical Computer Vision: Algorithms for Big Data, ISBN: 978-3-319-13971-5, Springer Switzerland, 2014. [Link]


 

* Full publication list: Google Scholar