1. Medical Image Computing

Recent advances in AI and machine/deep learning have witnessed great success in medical image computing. Dr. Zhang and his colleagues have designed and developed novel computing models and methods (including Machine Learning/Deep Learning and Statistical Analysis methods) to solve medical imaging tasks such as image segmentation, registration and classification, and clinical problems such as disease classification and between-population statistical analysis. 

Selected publications:

DDMReg Fan Zhang, William M Wells, and Lauren J O'Donnell.
Deep Diffusion MRI Registration (DDMReg): A Deep Learning Method for Diffusion MRI Registration.
IEEE TMI, 2022. 
Publisher's Version, Code
DDSeg Fan Zhang, Anna Breger, Kang Ik Kevin Cho, Lipeng Ning, Carl-Fredrik Westin, Lauren J O'Donnell, and Ofer Pasternak.
Deep learning based segmentation of brain tissue from diffusion MRI.
NeuroImage, 233, Pp. 117934, 2021. 
Publisher's Version, Code
DFC

Yuqian Chen, Chaoyi Zhang, Yang Song, Nikos Makris, Yogesh Rathi, Weidong Cai, Fan Zhang, and Lauren J O'Donnell.
Deep Fiber Clustering: Anatomically Informed Unsupervised Deep Learning for Fast and Effective White Matter Parcellation.
MICCAI (Student Travel Award; Early Acceptance), Pp. 497-507. 2021.
Publisher's Version

DeepWMA Fan Zhang, Suheyla Cetin Karayumak, Nico Hoffmann, Yogesh Rathi, Alexandra J Golby, and Lauren J O'Donnell.
Deep white matter analysis (DeepWMA): fast and consistent tractography segmentation.
MedIA, 65, Pp. 101761, 2020. 
Publisher's Version, Conference Version (MICCAI 2019)Code
PDAM

Dongnan Liu, Donghao Zhang, Yang Song, Fan Zhang, Lauren J O'Donnell, Heng Huang, Mei Chen, and Weidong Cai.
PDAM: A Panoptic-level Feature Alignment Framework for Unsupervised Domain Adaptive Instance Segmentation in Microscopy Images.
IEEE TMI, 40, 1, Pp. 154–165. 2020.
Publisher's VersionConference Version (CVPR 2020)Code

MK-Curve Fan Zhang, Lipeng Ning, Lauren J O'Donnell, and Ofer Pasternak.
MK–curve: Characterizing the relation between mean kurtosis and alterations in the diffusion MRI signal.
NeuroImage, 196, Pp. 68–80. 2019.
Publisher's VersionCode
AUT_SVM Fan Zhang, Peter Savadjiev, Weidong Cai, Yang Song, Yogesh Rathi, Birkan Tunç, Drew Parker, Tina Kapur, Robert T. Schultz, Nikos Makris, Ragini Verma, and Lauren J. O'Donnell.
Whole brain white matter connectivity analysis using machine learning: an application to autism.
NeuroImage, 172, Pp. 826-837, 2018. 
Publisher's VersionConference Version (ISBI 2020; Finalist for Best Student Paper Award)
STFC Fan Zhang, Weining Wu, Lipeng Ning, Gloria McAnulty, Deborahand Waber, Borjan Gagoski, Kiera Sarill, Hesham Hamoda, Yang Song, Weidong Cai, Yogesh Rathi, and Lauren J. O'Donnell.
Suprathreshold fiber cluster statistics: Leveraging white matter geometry to enhance tractography statistical analysis.
NeuroImage, 171, Pp. 341-354. 2018.
Publisher's VersionConference Version (MICCAI 2017)Code
LFV Yang Song, Fan Zhang, Qing Li, Heng Huang, Lauren J. O'Donnell, and Weidong Cai.
Locally-Transferred Fisher Vectors for Texture Classification.
ICCV, Pp. 4912-4920. 2017.
Publisher's Version
PD-LST Fan Zhang, Yang Song, Weidong Cai, Alexander G Hauptmann, Sidong Liu, Sonia Pujol, Ron Kikinis, Michael J Fulham, David Dagan Feng, and Mei Chen.
Dictionary pruning with visual word significance for medical image retrieval.
Neurocomputing, 177, Pp. 75–88. 2016. 
Publisher's Version
CCA-PairLDA Fan Zhang, Yang Song, Weidong Cai, Sidong Liu, Siqi Liu, Sonia Pujol, Ron Kikinis, Yong Xia, Michael J Fulham, and David Dagan Feng.
Pairwise latent semantic association for similarity computation in medical imaging.
IEEE TBME, 63, 5, Pp. 1058–1069. 2016. 
Publisher's Version
Clique-seg Sidong Liu, Yang Song, Fan Zhang, Dagan Feng, Michael Fulham, and Weidong Cai.
Clique Identification and Propagation for Multimodal Brain Tumor Image Segmentation.
BIH (Best Paper Award), Pp. 285–294. 2016.
Publisher's Version
CBP-Contour-Alignment.png

Fan Zhang, Yang Song, Siqi Liu, Paul Young, Daniela Traini, Lucy Morgan, Hui-Xin Ong, Lachlan Buddle, Sidong Liu, David Dagan Feng, and Weidong Cai.
Motion Representation of Ciliated Cell Images with Contour-Alignment for Automated CBF Estimation.
MICCAI (Student Travel Award), Pp. 300–307. 2015.
Publisher's Version, Suppl GIF 1, Suppl GIF 2

LungNodule.png Fan Zhang, Yang Song, Weidong Cai, Min-Zhao Lee, Yun Zhou, Heng Huang, Shimin Shan, Michael J Fulham, and Dagan D Feng.
Lung nodule classification with multilevel patch-based context analysis.
IEEE TBME (USYD-SIT Best Research Project Award based on results in the paper), 61, 4, Pp. 1155–1166. 2014.
Publisher's Version