1. Aicha BenTaieb. Analyzing Cancers in Digitized Histopathology Images. Doctoral Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, September 2018.

1. Saeedeh Afshari, Aicha BenTaieb, and Ghassan Hamarneh. Automatic Localization of Normal Active Organs in 3D PET Scans. Computerized Medical Imaging and Graphics (CMIG), 70:111-118, 2018. Keyword(s): Deep Learning, Machine Learning, Functional/Molecular/Dynamic Imaging, Localization.



2. Aicha BenTaieb and Ghassan Hamarneh. Adversarial Stain Transfer for Histopathology Image Analysis. IEEE Transactions on Medical Imaging (IEEE TMI), 37(3):792-802, 2018. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Microscopy, Deep Learning, Generative Adversarial Network.



3. Colin J. Brown, Steven Miller, Brian G. Booth, Jill Zwicker, Ruth Grunau, Anne Synnes, Vann Chau, and Ghassan Hamarneh. Predictive connectome subnetwork extraction with anatomical and connectivity priors. Computerized Medical Imaging and Graphics (CMIG), 71(January):67-78, 2018. Keyword(s): Diffusion MRI/Tensor-valued, Autism, Neurodevelopment, Connectome, Machine Learning.



4. Saurabh Garg, Lisa Y. W. Tang, Ghassan Hamarneh, Allard Jongman, Joan Sereno, and Yue Wang. Computer-vision analysis shows different facial movements for the production of different Mandarin tones. The Journal of the Acoustical Society of America (JASA). Also appears in ASA Meeting, 144(3):1720-1720, 2018. Keyword(s): Tracking, Machine Learning, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal.



5. Peyman Gholami, Mohammad Ali Ahmadi-pajouh, Nabiollah Abolftahi, Ghassan Hamarneh, and Mohammad Kayvanrad. Segmentation and Measurement of Chronic Wounds for Bioprinting. IEEE Journal of Biomedical and Health Informatics (IEEE JBHI), 22(4):1269-1277, 2018. Keyword(s): Segmentation, Dermatology.



6. Ismail M. Khater, Fanrui Meng, Timothy H. Wong, Ivan Robert Nabi, and Ghassan Hamarneh. Super Resolution Network Analysis Defines the Molecular Architecture of Caveolae and Caveolin-1 Scaffolds. Nature - Scientific reports, 8(9009):1-15, 2018. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning.



7. Joan Sereno, Allard Jongman, Yue Wang, Ghassan Hamarneh, Lisa Y. W. Tang, Saurabh Garg, Paul Tupper, Bob McMurray, Charles Redmon, Yuyu Zeng, Beverly Hannah, Keith Leung, and Sylvia Cho. Linking production and perception of clear speech. The Journal of the Acoustical Society of America (JASA). Also appears in ASA Meeting, 144(3):1725-1725, 2018. Keyword(s): Tracking, Machine Learning, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal.



8. Saeid Asgari Taghanaki, Noirin Duggan, Hillgan Ma, Xinchi Hou, Anna Celler, Francois Benard, and Ghassan Hamarneh. Segmentation-Free Direct Tumor Volume and Metabolic Activity Estimation from PET Scans. Computerized Medical Imaging and Graphics (CMIG), 63(January):52-66, 2018. Keyword(s): Machine Learning, Segmentation, Functional/Molecular/Dynamic Imaging.

1. Aicha BenTaieb and Ghassan Hamarneh. Predicting Cancer with a Recurrent Visual Attention Model for Histopathology Images. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11071, pages 129-137, 2018. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Microscopy, Deep Learning.



2. Saurabh Garg, Ghassan Hamarneh, Allard Jongman, Joan Sereno, and Yue Wang. Joint Gender-, Tone-, Vowel- Classification via Novel Hierarchical Classification for Annotation of Monosyllabic Mandarin Word Tokens. In IEEE International Conference on Acoustics, Speech, and Signal Processing (IEEE ICASSP), pages 5744-5748, 2018. Keyword(s): Tracking, Segmentation, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal.



3. Saurabh Garg, Lisa Y. W. Tang, Ghassan Hamarneh, Allard Jongman, Joan Sereno, and Yue Wang. Computer-vision analysis shows different facial movements for the production of different Mandarin tones. In Acoustical Society of America Meeting (ASA), pages 1, 2018. Keyword(s): Tracking, Machine Learning, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal.



4. Arafat Hussain, Ghassan Hamarneh, and Rafeef Abugharbieh. Noninvasive Determination of Gene Mutations in Clear Cell Renal Cell Carcinoma using Multiple Instance Decisions Aggregated CNN. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11071, pages 657-665, 2018. Keyword(s): Super Resolution, Machine Learning, Deep Learning.



5. Saeed Izadi, Zahra Mirikharaji, Jeremy Kawahara, and Ghassan Hamarneh. Generative Adversarial Networks to Segment Skin Lesions. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 881-884, 2018. Keyword(s): Machine Learning, Dermatology, Color/Multichannel/Vector-valued, Deep Learning, Generative Adversarial Network, Segmentation.



6. Saeed Izadi, Kathleen Moriarty, and Ghassan Hamarneh. Can Deep Learning Relax Endomicroscopy Hardware Miniaturization Requirements?. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11070, pages 57-64, 2018. Keyword(s): Microscopy, Super Resolution, Enhancement/Restoration/Denoising, Machine Learning, Deep Learning.



7. Jeremy Kawahara, Colin J. Brown, and Ghassan Hamarneh. Connectome Priors in Deep Neural Networks to Predict Autism (Kawahara and Brown: Joint first authors). In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 110-113, 2018. Keyword(s): Diffusion MRI/Tensor-valued, Autism, Connectome, Machine Learning, Deep Learning, Classification.



8. Ismail M. Khater, Qian Liu, Keng C. Chou, Ghassan Hamarneh, and Ivan Robert Nabi. Modular Structure of Caveolin-1 Scaffolds and Caveolae Identified by Single Molecule Localization Microscopy. In American Society for Cell Biology and European Molecular Biology Organization (ASCB-EMBO), San Diego, USA, pages 1343 (Abstract P2707), 2018. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning, Graph based.



9. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Caveolin-1 Domain Characterization Using Machine Learning and Graphlet Analysis of Single Molecule Super Resolution Microscopy. In American Society for Cell Biology and European Molecular Biology Organization (ASCB-EMBO), San Diego, USA, pages 1342 (Abstract P2706), 2018. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning, Graphlets, Graph based, Biomarkers/Biosignatures.



10. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Characterization of caveolin-1 domains via graphlet decomposition of SMLM super resolution data. In Genesis BME day, Vancouver, Canada, pages 1, 2018. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning, Graphlets, Graph based, Biomarkers/Biosignatures.



11. Zahra Mirikharaji and Ghassan Hamarneh. Star Shape Prior in Fully Convolutional Networks for Skin Lesion Segmentation. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11073, pages 737-745, 2018. Keyword(s): Machine Learning, Deep Learning, Segmentation, Dermatology, Color/Multichannel/Vector-valued, Shape Modelling and Analysis.



12. Zahra Mirikharaji, Saeed Izadi, Jeremy Kawahara, and Ghassan Hamarneh. Deep Auto-context Fully Convolutional Neural Network for Skin Lesion Segmentation. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 877-880, 2018. Keyword(s): Machine Learning, Dermatology, Color/Multichannel/Vector-valued, Deep Learning, Segmentation.



13. Adria Romero-Lopez, Tory Jarmain, Latif Abid, Jevin Maltais, Albert Jimenez, Jeremy Kawahara, Ghassan Hamarneh, Shuang Ao, Mohamed Akrout, Anirudh Challa, Michael Aristocrat, Katrina Cirone, Stephen Solis, and Andrew McCann. Q&A-informed image-based deep learning for skin disease recognition in the real world. In Self-Organizing Conference on Machine Learning (SOCML), pages 1, 2018. Keyword(s): Machine Learning, Dermatology, Color/Multichannel/Vector-valued, Deep Learning, Reinforcement Learning, Classification.



14. Saeid Asgari Taghanaki, Arkadeep Das, and Ghassan Hamarneh. Vulnerability Analysis of Chest X-Ray Image Classification Against Adversarial Attacks. In Medical Image Computing and Computer-Assisted Intervention Workshop on Deep Learning Fails (MICCAI DLF), volume 11038, pages 87-94, 2018. Keyword(s): Machine Learning, Deep Learning, Adversarial Attacks.



15. Yue Wang, Beverly Hannah, Keith Leung, Sylvia Cho, Joan Sereno, Allard Jongman, Charles Redmon, Yuyu Zeng, Ghassan Hamarneh, Lisa Y. W. Tang, Saurabh Garg, Paul Tupper, and Bob McMurray. Linking production and perception of clear speech. In Acoustical Society of America Meeting (ASA), pages 1, 2018. Keyword(s): Tracking, Machine Learning, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal.



16. Hanene Ben Yedder, Aicha BenTaieb, Majid Shokoufi, Amir Zahiremami, Farid Golnaraghi, and Ghassan Hamarneh. Deep Learning based Image Reconstruction for Diffuse Optical Tomography. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning for Medical Image Reconstruction (MICCAI MLMIR), volume 11074, pages 112-119, 2018. Keyword(s): Image Reconstruction, Diffuse Optical Tomography, Machine Learning, Deep Learning.



17. Mengliu Zhao and Ghassan Hamarneh. TreeNet: Multi-Loss Deep Learning Network to Predict Branch Direction for Extracting 3D Anatomical Trees. In Medical Image Computing and Computer-Assisted Intervention Workshop on Deep Learning in Medical Image Analysis (MICCAI DLMIA), volume 11045, pages 47-55, 2018. Keyword(s): Anatomical Trees and Tubular Structures, Shape Modelling and Analysis, Machine Learning, Deep Learning, Bifurcation/Junction.

1. Ismail M. Khater, Qian Liu, Keng C. Chou, Ghassan Hamarneh, and Ivan Robert Nabi. Super-resolution modularity analysis shows that polyhedral caveolin-1 oligomers combine to form scaffolds and caveolae. Technical report biorxiv:495382, 12 2018. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning.



2. Saeid Asgari Taghanaki, Aicha BenTaieb, Anmol Sharma, S. Kevin Zhou, Yefeng Zheng, Bogdan Georgescu, Puneet Sharma, Sasa Grbic, Zhoubing Xu, Dorin Comaniciu, and Ghassan Hamarneh. Select, Attend, and Transfer: Light, Learnable Skip Connections. Technical report arxiv:1703.04559, 4 2018. Keyword(s): Machine Learning, Deep Learning, Segmentation.



3. Saeid Asgari Taghanaki, Yefeng Zheng, S. Kevin Zhou, Bogdan Georgescu, Puneet Sharma, Daguang Xu, Dorin Comaniciu, and Ghassan Hamarneh. Combo Loss: Handling Input and Output Imbalance in Multi-Organ Segmentation. Technical report arxiv:1703.04559, 5 2018. Keyword(s): Machine Learning, Deep Learning, Segmentation.

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