1. Payam Ahmadvand. Machine Learning Driven Active Surfaces for 3D Segmentation of Tumour Lesions in PET Images. Master's Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, May 2017.



2. Colin J. Brown. Modelling and Prediction of Neurodevelopment in Preterm Infants using Structural Connectome Data. Doctoral Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, April 2017.



3. Mian Huang. Interactive Extraction of 3D Trees from Medical Images Supporting Gaming and Crowdsourcing. Master's Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, April 2017.

1. Alborz Amir-Khalili, Ghassan Hamarneh, and Rafeef Abugharbieh. Modelling and Extraction of Pulsatile Radial Distension and Compression Motion for Automatic Vessel Segmentation from Video. Medical Image Analysis (MedIA), 40:184-198, 2017. Keyword(s): Spatio-Temporal, Segmentation, Image-Guided Surgery.



2. Alborz Amir-Khalili, Ghassan Hamarneh, Roja Zakariaee, Ingrid Spadinger, and Rafeef Abugharbieh. Propagation of Registration Uncertainty During Multi-Fraction Cervical Cancer Brachytherapy. Physics in Medicine and Biology (PMB), 62(30):8116-81135, 2017. Keyword(s): Registration and Matching, Brachytherapy, Uncertainty.



3. Aicha BenTaieb, Hector Li-Chang, David Huntsman, and Ghassan Hamarneh. A Structured Latent Model for Ovarian Carcinoma Subtyping from Histopathology Slides. Medical Image Analysis (MedIA), 39:194-205, 2017. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Microscopy, Deep Learning, Datasets.



4. Jeremy Kawahara, Colin J. Brown, Steven Miller, Brian G. Booth, Vann Chau, Ruth Grunau, Jill Zwicker, and Ghassan Hamarneh. BrainNetCNN: Convolutional Neural Networks for Brain Networks; Towards Predicting Neurodevelopment (Brown and Kawahara: Joint first authors). NeuroImage, 146(1):1038-1049, 2017. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome, Machine Learning, Deep Learning.



5. Saeid Asgari Taghanaki, Jeremy Kawahara, Brandon Miles, and Ghassan Hamarneh. Pareto-Optimal Multi-objective Dimensionality Reduction Deep Auto-Encoder for Mammography Classification. Computer Methods and Programs in Biomedicine, 145:85-93, 2017. Keyword(s): Machine Learning, Deep Learning, Optimization.



6. Saeid Asgari Taghanaki, Yonghuai Liu, Brandon Miles, and Ghassan Hamarneh. Geometry Based Pectoral Muscle Segmentation from MLO Mammogram Views. IEEE Transactions on Biomedical Engineering (IEEE TBME), 64(1):2662-2671, 2017. Keyword(s): Segmentation.



7. Roja Zakariaee, Ghassan Hamarneh, Colin J. Brown, Marc Gaudet, Christina Aquino-Parsons, and Ingrid Spadinger. Association of Bladder Dose with Late Urinary Side Effects in Cervical Cancer High-Dose-Rate Brachytherapy. Brachytherapy, 16(6):1175-1183, 2017. Keyword(s): Registration and Matching, Brachytherapy.

1. Payam Ahmadvand, Noirin Duggan, Francois Benard, and Ghassan Hamarneh. Tumour Lesion Segmentation from 3D PET using a Machine Learning driven Active Surface. In 2nd Annual Health Technology Symposium, Vancouver, Canada, pages 1, 2017. Keyword(s): Machine Learning, Segmentation, Functional/Molecular/Dynamic Imaging.



2. Aicha BenTaieb and Ghassan Hamarneh. Artificial Pathologists: Machine Learning Models for Histopathology. In Annual SFU Health Research Day - Women's Health Research Symposium, 2017. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Microscopy, Deep Learning.



3. Aicha BenTaieb and Ghassan Hamarneh. Topology Aware Fully Convolutional Networks For Histology Gland Segmentation. In 2nd Annual Health Technology Symposium, Vancouver, Canada, pages 1, 2017. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Microscopy, Deep Learning.



4. Aicha BenTaieb and Ghassan Hamarneh. Uncertainty Driven Multi-Loss Fully Convolutional Networks for Histopathology. In Medical Image Computing and Computer-Assisted Intervention Workshop on Large-scale Annotation of Biomedical data and Expert Label Synthesis (MICCAI LABELS), volume 10552, pages 155-163, 2017. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Microscopy, Deep Learning.



5. Colin J. Brown, Kathleen Moriarty, Steven Miller, Brian G. Booth, Vann Chau, Anne Synnes, Ruth Grunau, and Ghassan Hamarneh. Prediction of Brain Network Age and Factors of Delayed Maturation in Very Preterm Infants. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 10433, pages 84-91, 2017. Keyword(s): Neurodevelopment, Machine Learning.



6. Mian Huang and Ghassan Hamarneh. SwifTree: Interactive Extraction of 3D Trees Supporting Gaming and Crowdsourcing. In Medical Image Computing and Computer-Assisted Intervention Workshop on Large-scale Annotation of Biomedical data and Expert Label Synthesis (MICCAI LABELS), volume 10552, pages 116-125, 2017. Keyword(s): Anatomical Trees and Tubular Structures, Gaming, Crowdsourcing.



7. Arafat Hussain, Alborz Amir-Khalili, Ghassan Hamarneh, and Rafeef Abugharbieh. Collage CNN for Renal Cell Carcinoma Detection from CT. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 10541, pages 229-237, 2017. Keyword(s): Machine Learning, Deep Learning, Segmentation, Localization.



8. Arafat Hussain, Alborz Amir-Khalili, Ghassan Hamarneh, and Rafeef Abugharbieh. Segmentation-Free Kidney Localization and Volume Estimation Using Aggregated Orthogonal Decision CNNs. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 10435, pages 612-620, 2017. Keyword(s): Machine Learning, Deep Learning, Segmentation, Localization.



9. Bebart Janbek, Brian G. Booth, and Ghassan Hamarneh. A Tensor Field Mumford-Shah Segmentation of Neural Pathways in DW-MRI. In Society for Industrial and Applied Mathematics (SIAM) Annual Meeting, Pittsburgh, Pennsylvania, USA, pages 1, 2017. Keyword(s): Diffusion MRI/Tensor-valued, Segmentation, Optimization.



10. Jeremy Kawahara, Colin J. Brown, Steven Miller, Brian G. Booth, Vann Chau, Ruth Grunau, Jill Zwicker, and Ghassan Hamarneh. BrainNetCNN: Artificial Convolutional Neural Networks for Connectomes. In 2nd Annual Health Technology Symposium, Vancouver, Canada, pages 1, 2017. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome, Machine Learning, Deep Learning, Classification.



11. Jeremy Kawahara, Kathleen Moriarty, and Ghassan Hamarneh. Graph Geodesics to Find Progressively Similar Skin Lesion Images. In Medical Image Computing and Computer-Assisted Intervention Workshop on Graphs in Biomedical Image Analysis (MICCAI GRAIL), pages 1-11, 2017. Keyword(s): Machine Learning, Dermatology, Color/Multichannel/Vector-valued, Deep Learning, Graph based.



12. Ismail M. Khater, Youtao Liu, Qian Liu, Fanrui Meng, Keng C. Chou, Ivan Robert Nabi, and Ghassan Hamarneh. Distinguishing Biological and Non-Biological Networks in Single Molecule Localization Super Resolution Microscopy. In American Society for Cell Biology and European Molecular Biology Organization (ASCB-EMBO), Philadelphia, USA, pages 1, 2017. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning.



13. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Filtering, Segmenting, and Quantifying Caveolin-1 Protein Clusters in 3D Super-Resolution Microscopy via Machine-Learning and Network Analysis. In SIAM-IMAGING Manitoba Workshop on Mathematical Imaging Science, Winnipeg, Canada, pages 1, 2017. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning.



14. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Filtering, Segmenting, and Quantifying Caveolin-1 Protein Clusters in 3D Super-Resolution Microscopy via Machine-Learning and Network Analysis. In Gordon Research Conference, Andover, NH, USA, pages 1, 2017. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning.



15. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Filtering, Segmenting, and Quantifying Caveolin-1 Protein Clusters in 3D Super-Resolution Microscopy via Machine-Learning and Network Analysis. In 2nd Annual Health Technology Symposium, Vancouver, Canada, pages 1, 2017. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning.



16. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Molecular Level Quantification of Cav1 Clusters in Super-Resolution Imaging Data. In Frontiers in Biophysics, Vancouver, Canada, pages 1, 2017. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning.



17. Zahra Mirikharaji, Mengliu Zhao, and Ghassan Hamarneh. Globally-Optimal Anatomical Tree Extraction from 3D Medical Images using Pictorial Structures and Minimal Paths. In 2nd Annual Health Technology Symposium, Vancouver, Canada, pages 1, 2017. Keyword(s): Anatomical Trees and Tubular Structures, Optimization, Bifurcation/Junction.



18. Zahra Mirikharaji, Mengliu Zhao, and Ghassan Hamarneh. Globally-Optimal Anatomical Tree Extraction from 3D Medical Images using Pictorial Structures and Minimal Paths (Mirikharaji and Zhao: Joint first authors). In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 10434, pages 242-250, 2017. Keyword(s): Anatomical Trees and Tubular Structures, Optimization, Bifurcation/Junction.



19. Saeid Asgari Taghanaki, Noirin Duggan, Hillgan Ma, Anna Celler, Francois Benard, and Ghassan Hamarneh. Lesion volume Estimation from PET without Requiring Segmentation. In Quantitative Imaging Network (QIN) Annual Meeting, 2017. Keyword(s): Machine Learning, Segmentation, Functional/Molecular/Dynamic Imaging.



20. Mengliu Zhao and Ghassan Hamarneh. Bifurcation Localization in 3D Images via Evolutionary Geometric Deformable Templates. In Canadian Conference on Computer and Robot Vision (CRV), pages 124-130, 2017. Keyword(s): Anatomical Trees and Tubular Structures, Deformable Models, Shape Modelling and Analysis, Bifurcation/Junction.



21. Mengliu Zhao, Brandon Miles, and Ghassan Hamarneh. Leveraging Tree Statistics for Extracting Anatomical Trees from 3D Medical Images. In Canadian Conference on Computer and Robot Vision (CRV), pages 131-138, 2017. Keyword(s): Anatomical Trees and Tubular Structures, Shape Modelling and Analysis, Bifurcation/Junction.



22. Mengliu Zhao, Brandon Miles, and Ghassan Hamarneh. Tree Structure Analysis in 3D Medical Images. In 2nd Annual Health Technology Symposium, Vancouver, Canada, pages 1, 2017. Keyword(s): Anatomical Trees and Tubular Structures, Shape Modelling and Analysis, Bifurcation/Junction.

1. Jeremy Kawahara and Ghassan Hamarneh. Fully Convolutional Networks to Detect Clinical Dermoscopic Features. Technical report arxiv:1703.04559, 3 2017. Keyword(s): Machine Learning, Deep Learning, Dermatology, Challenge.

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