1. Li Wang, Yinghuan Shi, Heung-Il Suk, Alison Noble, and Ghassan Hamarneh, editors. Special Issue on Machine Learning in Medical Imaging (MLMI), volume 74. 2019. [bibtex-key = cmig2019mlmi]

1. Ismail Khater. Machine Learning and Network Analysis for Macromolecular Structure Determination from Super-resolution Microscopy. Doctoral Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, September 2019. [bibtex-key = phd2019khater]



2. 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. [bibtex-key = msc2017ahmadvand]

1. Kumar Abhishek, Colin J. Brown, and Ghassan Hamarneh. Multi-Sample $\zeta$-mixup: Richer, More Realistic Synthetic Samples from a $p$-Series Interpolant. Journal of Big Data, 11(43):1-41, 3 2024. Keyword(s): Machine Learning, Deep Learning, Synthesis/Simulation/Augmentation, Classification, Dermatology. [bibtex-key = jbd2024]



2. Nourhan Bayasi, Ghassan Hamarneh, and Rafeef Garbi. GC2: Generalizable Continual Classification of Medical Images. IEEE Transactions on Medical Imaging (IEEE TMI), 000(000):000-000, 2024. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Continual Learning, Domain Generalization. [bibtex-key = tmi2024]



3. Ivan Robert Nabi, Ben Cardoen, Khater, Guang Gao, Timothy H. Wong, and Ghassan Hamarneh. AI-based analysis of super-resolution microscopy: Biological discovery in the absence of ground truth. The Journal Of Cell Biology (JCB), 000(jcb.000):000-000, 000 2024. Keyword(s): Super Resolution Microscopy, Deep Learning, Machine Learning, Weak Supervision, Survey/Review. [bibtex-key = jcb2024]



4. Ashish Sinha, Jeremy Kawahara, Arezou Pakzad, Kumar Abhishek, Matthieu Ruthven, Enjie Ghorbel, Anis Kacem, Djamila Aouada, and Ghassan Hamarneh. DermSynth3D: Synthesis of in-the-wild Annotated Dermatology Images (Sinha, Kawahara, Pakzad: Joint first authors). Medical Image Analysis (MedIA), 000(103145):000, 2024. Keyword(s): Dermatology, Machine Learning, Deep Learning, Segmentation, Synthesis/Simulation/Augmentation, Datasets. [bibtex-key = media2024]



5. Hanene Ben Yedder, Ben Cardoen, Majid Shokoufi, Farid Golnaraghi, and Ghassan Hamarneh. Deep Orthogonal Multi-Wavelength Fusion for Tomogram-Free Diagnosis in Diffuse Optical Imaging. Computers in Biology and Medicine (CIBM), 000:000, 2024. Keyword(s): Image Reconstruction, Machine Learning, Deep Learning. [bibtex-key = cibm2024]



6. Saurabh Garg, Haoyao Ruan, Ghassan Hamarneh, Dawn M. Behne, Allard Jongman, Joan Sereno, and Yue Wang. Mouth2Audio: Intelligible Audio Synthesis From Videos With Distinctive Vowel Articulation. International Journal of Speech Technology, 000(000):000-000, 2023. Keyword(s): Synthesis/Simulation/Augmentation, Tracking, Machine Learning, Deep Learning, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal. [bibtex-key = ijst2023b]



7. Saurabh Garg, Lisa Y. W. Tang, Ghassan Hamarneh, Allard Jongman, Joan Sereno, and Yue Wang. Different facial cues for different speech styles in Mandarin tone articulation. Frontiers in Communication - Language Sciences, 8(1148240):1-19, 2023. Keyword(s): Tracking, Machine Learning, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal. [bibtex-key = frontcomm2023]



8. Zahra Mirikharaji, Kumar Abhishek, Alceu Bissoto, Catarina Barata, Sandra Avila, Eduardo Valle, M. Emre Celebi, and Ghassan Hamarneh. A Survey on Deep Learning for Skin Lesion Segmentation (Mirikharaji and Abhishek: Joint first authors; Celebi and Hamarneh: Joint senior authors). Medical Image Analysis (MedIA), pp 1-55, 2023. Keyword(s): Machine Learning, Deep Learning, Segmentation, Survey/Review, Dermatology. [bibtex-key = media2023]



9. Ben Cardoen, Timothy H. Wong, Parsa Alan, Sieun Lee, Joanne Aiko Matsubara, Ivan Robert Nabi, and Ghassan Hamarneh. SPECHT: Self-tuning Plausibility Based Object Detection Enables Quantification of Conflict in Heterogeneous Multi-scale Microscopy (Nabi and Hamarneh: Joint senior authors). PLOS ONE, 17(12):e0276726, 2022. Keyword(s): Super Resolution Microscopy, Machine Learning, Classification, Belief Theory, Biomarkers/Biosignatures, Generalizability. [bibtex-key = plosone2022]



10. Arafat Hussain, Zahra Mirikharaji, Mohammad Momeny, Mahmoud Marhamati, Ali Asghar Neshat, Rafeef Garbi, and Ghassan Hamarneh. Active Deep Learning from a Noisy Teacher for Semi-supervised 3D Image Segmentation: Application to COVID-19 Pneumonia Infection in CT. Computerized Medical Imaging and Graphics (CMIG), 102(102127):1-11, 2022. Keyword(s): Segmentation, Machine Learning, Deep Learning, COVID19, SARS-CoV-2. [bibtex-key = cmig2022]



11. Saeed Izadi, Darren Sutton, and Ghassan Hamarneh. Image Denoising in the Deep Learning Era. Artificial Intelligence Review, 000(000):1-46, 2022. Keyword(s): Enhancement/Restoration/Denoising, Machine Learning, Deep Learning, Survey/Review. [bibtex-key = aire2022]



12. M.Sadegh Saberian, Kathleen Moriarty, Andrea Olmstead, Christian Hallgrimson, François Jean, Ivan Robert Nabi, Maxwell Libbrecht, and Ghassan Hamarneh. DEEMD: Drug Efficacy Estimation against SARS-CoV-2 based on Cell Morphology with Deep Multiple Instance Learning. IEEE Transactions on Medical Imaging (IEEE TMI), 41(11):3128-3145, 2022. Keyword(s): Deep Learning, Machine Learning, COVID19, SARS-CoV-2. [bibtex-key = tmi2022]



13. Mengliu Zhao, Jeremy Kawahara, Kumar Abhishek, Sajjad Shamanian, and Ghassan Hamarneh. Skin3D: Detection and Longitudinal Tracking of Pigmented Skin Lesions in 3D Total-Body Textured Meshes (Zhao and Kawahara: Joint first authors). Medical Image Analysis (MedIA), 77(102329):1-10, 2022. Keyword(s): Dermatology, Machine Learning, Deep Learning, Optimization, Registration and Matching, Graph based, Tracking, Datasets. [bibtex-key = media2022]



14. Kumar Abhishek, Jeremy Kawahara, and Ghassan Hamarneh. Predicting the Clinical Management of Skin Lesions using Deep Learning. Nature - Scientific Reports, 11(7769):1-14, 2021. Keyword(s): Dermatology, Machine Learning, Deep Learning, Clinical Management. [bibtex-key = nature_sr2021b]



15. Arafat Hussain, Ghassan Hamarneh, and Rafeef Garbi. Cascaded Localization Regression Neural Nets for Kidney Localization and Segmentation-free Volume Estimation. IEEE Transactions on Medical Imaging (IEEE TMI), 40(6):1555-1567, 2021. Keyword(s): Machine Learning, Deep Learning, Segmentation, Localization. [bibtex-key = tmi2021]



16. Arafat Hussain, Ghassan Hamarneh, and Rafeef Garbi. Learnable Image Histograms-based Deep Radiomics for Renal Cell Carcinoma Grading and Staging. Computerized Medical Imaging and Graphics (CMIG), 90(101924):1-10, 2021. Keyword(s): Classification, Machine Learning, Deep Learning. [bibtex-key = cmig2021]



17. Saeid Asgari Taghanaki, Kumar Abhishek, Joseph Paul Cohen, Julien Cohen-Adad, and Ghassan Hamarneh. Deep Semantic Segmentation of Natural and Medical Images: A Review (Taghanaki and Abhishek: Joint first authors). Artificial Intelligence Review, 54(1):137-178, 2021. Keyword(s): Segmentation, Survey/Review, Machine Learning, Deep Learning. [bibtex-key = aire2020a]



18. Timothy H. Wong, Ismail M. Khater, Bharat Joshi, Mona Shahsavari, Ghassan Hamarneh, and Ivan Robert Nabi. Single molecule network analysis identifies structural changes to caveolae and scaffolds due to mutation of the caveolin-1 scaffolding domain (Wong and Khater: Joint first authors; Hamarneh and Nabi: Joint senior authors). Nature - Scientific Reports, 11(7810):1-14, 2021. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning. [bibtex-key = nature_sr2021]



19. Hanene Ben Yedder, Ben Cardoen, and Ghassan Hamarneh. Deep Learning for Biomedical Image Reconstruction: A Survey. Artificial Intelligence Review, 54(1):215-251, 2021. Keyword(s): Image Reconstruction, Machine Learning, Deep Learning. [bibtex-key = aire2020b]



20. Hanene Ben Yedder, Ben Cardoen, Majid Shokoufi, Farid Golnaraghi, and Ghassan Hamarneh. Multitask Deep Learning Reconstruction and Localization of Lesions in Limited Angle Diffuse Optical Tomography. IEEE Transactions on Medical Imaging (IEEE TMI), 41(3):515-530, 2021. Keyword(s): Image Reconstruction, Machine Learning, Deep Learning, Synthesis/Simulation/Augmentation,. [bibtex-key = tmi2021b]



21. Ben Cardoen, Hanene Ben Yedder, Anmol Sharma, Keng C. Chou, Ivan Robert Nabi, and Ghassan Hamarneh. ERGO: Efficient Recurrent Graph Optimized Emitter Density Estimation in Single Molecule Localization Microscopy. IEEE Transactions on Medical Imaging (IEEE TMI), 39(6):1942-1956, 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning. [bibtex-key = tmi2020]



22. Saurabh Garg, Lisa Y. W. Tang, Ghassan Hamarneh, Allard Jongman, Joan Sereno, and Yue Wang. Different facial cues for different speech styles in Mandarin tone articulation. The Journal of the Acoustical Society of America (JASA). Also appears in ASA Meeting, 148(4):2764-2764, 2020. Keyword(s): Tracking, Machine Learning, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal. [bibtex-key = jasa2020]



23. Weina Jin, Mostafa Fatehi, Kumar Abhishek, Mayur Mallya, Brian Toyota, and Ghassan Hamarneh. Artificial Intelligence in Glioma Imaging: Challenges and Advances. Journal of Neural Engineering, 17(2):021002, 2020. Keyword(s): Glioma Imaging, Machine Learning, Deep Learning, Survey/Review. [bibtex-key = jne2020]



24. Ismail M. Khater, Ivan Robert Nabi, and Ghassan Hamarneh. A Review of Super-resolution Single Molecule Localization Microscopy Cluster Analysis and Quantification Methods. Cell Patterns, 1(3):2666-3899, 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Deep Learning, Machine Learning, Classification, Graph based, Biomarkers/Biosignatures, Survey/Review. [bibtex-key = cellpatterns2020]



25. Rory Long, Kathleen Moriarty, Ben Cardoen, Guang Gao, A. Wayne Vogl, François Jean, Ghassan Hamarneh, and Ivan Robert Nabi. Super Resolution Microscopy and Deep Learning Identify Zika Virus Reorganization of the Endoplasmic Reticulum (Long and Moriarty: Joint first authors; Hamarneh and Nabi: Joint senior authors). Nature - Scientific reports, 10(20937):1-18, 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Deep Learning. [bibtex-key = nature_sr2020a]



26. Brian Smith, John Buatti, Christian Bauer, Ethan Ulrich, Payam Ahmadvand, Mikalai Budzevich, Robert Gillies, Dmitry Goldgof, Milan Grkovski, Ghassan Hamarneh, Paul Kinahan, John Muzi, Mark Muzi, Charles Laymon, James Mountz, Sadek Nehmeh, Matthew Oborski, Binsheng Zhao, John Sunderland, and Reinhard Beichel. Multi-Site Technical and Clinical Performance Evaluation of Quantitative Imaging Biomarkers from 3D FDG PET Segmentations of Head and Neck Cancer Images. Tomography, 6(2):65-76, 2020. Keyword(s): Machine Learning, Segmentation, Functional/Molecular/Dynamic Imaging. [bibtex-key = tomography2020]



27. Ismail M. Khater, Stephane Aroca-Ouellette, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Caveolae and scaffold detection from single molecule localization microscopy data using deep learning. PLOS ONE, 14(8):1-17, 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Deep Learning, Machine Learning, Classification, Graph based, Biomarkers/Biosignatures. [bibtex-key = plosone2019]



28. Ismail M. Khater, Qian Liu, Keng C. Chou, Ghassan Hamarneh, and Ivan Robert Nabi. Super-resolution modularity analysis shows polyhedral caveolin-1 oligomers combine to form scaffolds and caveolae. Nature - Scientific reports, 9(9888):1-10, 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = nature_sr2019]



29. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Identification of Caveolin-1 Domain Signatures via Graphlet Analysis of Single Molecule Super-Resolution Data. Bioinformatics, 35(18):3468-3475, 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning, Graphlets, Graph based, Biomarkers/Biosignatures. [bibtex-key = bioinformatics2019]



30. Anmol Sharma and Ghassan Hamarneh. Missing MRI Pulse Sequence Synthesis using Multi-Modal Generative Adversarial Network. IEEE Transactions on Medical Imaging (IEEE TMI), 39(4):1170-1183, 2019. Keyword(s): Machine Learning, Deep Learning, Generative Adversarial Network, Synthesis/Simulation/Augmentation, Multimodal. [bibtex-key = tmi2019]



31. 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. Computerized Medical Imaging and Graphics (CMIG), 75:24-33, 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation. [bibtex-key = cmig2019]



32. 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. [bibtex-key = cmig2018c]



33. 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. [bibtex-key = tmi2018]



34. 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. [bibtex-key = cmig2018b]



35. 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. [bibtex-key = jasa2018b]



36. 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. [bibtex-key = nature_sr2018]



37. 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. [bibtex-key = jasa2018a]



38. 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. [bibtex-key = cmig2018a]



39. 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. [bibtex-key = media2017]



40. 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. [bibtex-key = neuroimage2017]



41. 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. [bibtex-key = cmpb2017]



42. Reinhard Beichel, Brian Smith, Christian Bauer, Ethan Ulrich, Payam Ahmadvand, Mikalai Budzevich, Robert Gillies, Dmitry Goldgof, Milan Grkovski, Ghassan Hamarneh, Qiao Huang, Paul Kinahan, Charles Laymon, James Mountz, John Muzi, Mark Muzi, Sadek Nehmeh, Matthew Oborski, Yongqiang Tan, Binsheng Zhao, John Sunderland, and John Buatti. Multi-site Quality and Variability Analysis of 3D FDG PET Segmentations based on Phantom and Clinical Image Data. Medical Physics, 44(2):479-496, 2016. Keyword(s): Segmentation, Machine Learning, Functional/Molecular/Dynamic Imaging. [bibtex-key = mp2017]



43. Aicha BenTaieb, Masoud Nosrati, Hector Li-Chang, David Huntsman, and Ghassan Hamarneh. Clinically-Inspired Automatic Classification of Ovarian Carcinoma Subtypes. Journal of Pathology Informatics, 7(1):1-28, 2016. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Microscopy. [bibtex-key = jpi2016]



44. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. Skin Lesion Tracking System using Structured Graphical Models. Medical Image Analysis (MedIA) (Special Issue on Discrete Graphical Models in Biomedical Image Analysis), 27:84-92, 2015. Keyword(s): Registration and Matching, Tracking, Graph based, Dermatology, Machine Learning. [bibtex-key = media2015]



45. Ching-Wei Wang, Cheng-Ta Huang, Meng-Che Hsieh, Chung-Hsing Li, Sheng-Wei Chang, Wei-Cheng Li, Remy Vandaele, Raphael Maree, Sebastien Jodogne, Pierre Geurts, Cheng Chen, Guoyan Zheng, Chengwen Chu, Hengameh Mirzaalian, Ghassan Hamarneh, Tomaz Vrtovec, and Bulat Ibragimov. Evaluation and Comparison of Anatomical Landmark Detection Methods for Cephalometric X-Ray Images: A Grand Challenge. IEEE Transactions on Medical Imaging (IEEE TMI), 34(9):1890-900, 2015. Keyword(s): Challenge, Graph based, Optimization, Machine Learning, Registration and Matching. [bibtex-key = tmi2015b]



46. Bahareh HajGhanbari, Ghassan Hamarneh, Neda Changizi, Aaron Ward, and W. Darlene Reid. MRI-based 3D shape analysis of thigh muscles: Patients with chronic obstructive pulmonary disease versus healthy adults. Academic Radiology, 18(2):155-166, 2011. Keyword(s): Shape Modelling and Analysis, Machine Learning. [bibtex-key = ar2011]



47. Oliver van Kaick, Ghassan Hamarneh, Aaron Ward, Mark Schweitzer, and Hao (Richard) Zhang. Learning Fourier Descriptors for Computer-Aided Diagnosis of the Supraspinatus. Academic Radiology, 17(8):1040-1049, 2010. Keyword(s): Shape Modelling and Analysis, Machine Learning. [bibtex-key = ar2010a]



48. Aaron Ward, Ghassan Hamarneh, and Mark Schweitzer. 3D Bicipital Groove Shape Analysis and Relationship to Tendopathy. Journal of Digital Imaging, 21(2):219-234, 2008. Keyword(s): Shape Modelling and Analysis, Machine Learning. [bibtex-key = jdi2008a]



49. Aaron Ward, Ghassan Hamarneh, Reem Ashry, and Mark Schweitzer. 3D Shape Analysis of the Supraspinatus Muscle: A Clinical Study of the Relationship between Shape and Pathology. Academic Radiology, 14(10):1229-1241, 2007. Keyword(s): Shape Modelling and Analysis, Machine Learning. [bibtex-key = ar2007]

1. Kumar Abhishek and Ghassan Hamarneh. Lesion Elevation Prediction from Skin Images Improves Diagnosis. In Medical Image Computing and Computer-Assisted Intervention (MICCAI) ISIC Skin Image Analysis Workshop (MICCAI ISIC), pages 000–000, 2024. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning. [bibtex-key = miccai_isic2024b]



2. Kumar Abhishek, Jeremy Kawahara, and Ghassan Hamarneh. Segmentation Style Discovery: Application to Skin Lesion Images. In Medical Image Computing and Computer-Assisted Intervention (MICCAI) ISIC Skin Image Analysis Workshop (MICCAI ISIC), pages 000–000, 2024. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Segmentation. [bibtex-key = miccai_isic2024a]



3. Nourhan Bayasi, Ghassan Hamarneh, and Rafeef Garbi. Continual-Zoo: Leveraging Zoo Models for Continual Classification of Medical Images. In IEEE Computer Vision and Pattern Recognition (IEEE CVPR) Workshop on Continual Learning (CLVision), pages 000-000, 2024. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Continual Learning, Domain Generalization. [bibtex-key = cvpr_clvision2024]



4. Nourhan Bayasi, Fayyad Jamil, Alceu Bissoto, Ghassan Hamarneh, and Rafeef Garbi. BiasPruner: Debiased Continual Learning for Medical Image Classification. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 000, pages 000-000, 2024. Keyword(s): Classification, Dermatology, Machine Learning, Deep Learning, Continual Learning, AI Bias and Fairness. [bibtex-key = miccai2024a]



5. Aliasghar Khani, Saeid Asgari Taghanaki, Aditya Sanghi, Ali Mahdavi-Amiri, and Ghassan Hamarneh. SLiMe: Segment Like Me. In International Conference on Learning Representations (ICLR), 2024. Keyword(s): Deep Learning, Machine Learning, One-/Few-Shot Learning, Segmentation, Diffusion Models, Foundational Models. [bibtex-key = iclr2024]



6. Kumar Abhishek, Colin J. Brown, and Ghassan Hamarneh. $\zeta$-mixup: Richer, More Realistic Mixing of Multiple Images. In Medical Imaging with Deep Learning (MIDL), pages 1-5, 2023. Keyword(s): Machine Learning, Deep Learning, Synthesis/Simulation/Augmentation. [bibtex-key = midl2023]



7. Nourhan Bayasi, Siyi Du, Ghassan Hamarneh, and Rafeef Garbi. Continual-GEN: Continual Group Ensembling for Domain-agnostic Skin Lesion Classification. In Medical Image Computing and Computer-Assisted Intervention (MICCAI) ISIC Skin Image Analysis Workshop (MICCAI ISIC), pages 000–000, 2023. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Classification, Continual Learning. [bibtex-key = miccai_isic2023a]



8. Siyi Du, Nourhan Bayasi, Ghassan Hamarneh, and Rafeef Garbi. AViT: Adapting Vision Transformers for Small Skin Lesion Segmentation Datasets. In Medical Image Computing and Computer-Assisted Intervention (MICCAI) ISIC Skin Image Analysis Workshop (MICCAI ISIC), pages 000–000, 2023. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Segmentation, Transformers. [bibtex-key = miccai_isic2023b]



9. Siyi Du, Nourhan Bayasi, Ghassan Hamarneh, and Rafeef Garbi. MDViT: Multi-domain Vision Transformer for Small Medical Image Segmentation Datasets Segmentation. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), pages 000-000, 2023. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Transformers, Classification. [bibtex-key = miccai2023]



10. Nourhan Bayasi, Ghassan Hamarneh, and Rafeef Garbi. BoosterNet: Improving Domain Generalization of Deep Neural Nets using Culpability-Ranked Features. In IEEE Computer Vision and Pattern Recognition (IEEE CVPR), pages 528-538, 2022. Keyword(s): Machine Learning, Deep Learning, Classification, Continual Learning, Domain Generalization, Dermatology. [bibtex-key = cvpr2022]



11. Siyi Du, Ben Her, Nourhan Bayasi, Ghassan Hamarneh, and Rafeef Garbi. FairDisCo: Fairer AI in Dermatology via Disentanglement Contrastive Learning. In European Conference on Computer Vision (ECCV) ISIC Skin Image Analysis Workshop (ECCV ISIC), pages 185-202, 2022. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, AI Bias and Fairness, Classification. [bibtex-key = eccv_isic2022b]



12. Weina Jin, Xiaoxiao Li, and Ghassan Hamarneh. Evaluating Explainable AI on Multi-Modal Medical Imaging Task: Can Existing Algorithms Fulfill Clinical Requirements?. In Association for the Advancement of Artificial Intelligence Conference (AAAI), volume 36, pages 11945-11953, 2022. Keyword(s): Deep Learning, Explainable AI (XAI), Glioma Imaging, Machine Learning, MRI, Multimodal. [bibtex-key = aaai2022]



13. Ismail M. Khater, Timothy H. Wong, Christian Hallgrimson, Satish Moparthi, Stéphane Vassilopoulos, Ghassan Hamarneh, and Ivan Robert Nabi. Molecular architecture of clathrin plaques and pits defined by super-resolution network analysis (SuperResNET) (Khater and Wong: Joint first authors; Hamarneh and Nabi: Joint senior authors). In American Society of Cell Biology (ASCB) - Cell Bio, 2022. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Software and Tools, Network Modelling and Analysis, Machine Learning. [bibtex-key = ascb2022b]



14. Arezou Pakzad, Kumar Abhishek, and Ghassan Hamarneh. CIRCLe: Color Invariant Representation Learning for Unbiased Classification of Skin Lesions. In European Conference on Computer Vision (ECCV) ISIC Skin Image Analysis Workshop (ECCV ISIC), pages 203–219, 2022. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, AI Bias and Fairness, Classification. [bibtex-key = eccv_isic2022a]



15. Kumar Abhishek and Ghassan Hamarneh. Matthews Correlation Coefficient Loss for Deep Convolutional Networks: Application to Skin Lesion Segmentation. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 225-229, 2021. Keyword(s): Segmentation, Machine Learning, Deep Learning, Dermatology, Optimization. [bibtex-key = isbi2021]



16. Nourhan Bayasi, Ghassan Hamarneh, and Rafeef Garbi. Culprit-Prune-Net: Efficient Continual Sequential Multi-Domain Learning with Application to Skin Lesion Classification. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 12907, pages 165-175, 2021. Keyword(s): Classification, Dermatology, Machine Learning, Deep Learning, Continual Learning, Domain Generalization. [bibtex-key = miccai2021]



17. Ben Cardoen and Ghassan Hamarneh. Learning to look beyond what we can see: Leveraging statistical learning to improve scientific discovery from fluorescence microscopy. In Biomedical Imaging and Artificial Intelligence (BMIAI) cluster Fall Research Showcase, Vancouver, Canada, pages 1, 2021. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Deep Learning, Processing, Belief Theory. [bibtex-key = bmiai2021a]



18. Ismail M. Khater, Timothy H. Wong, Stéphane Vassilopoulos, Ivan Robert Nabi, and Ghassan Hamarneh. SuperResNET: a GUI software package for single molecule localization microscopy cluster analysis (Nabi and Hamarneh: Joint senior authors). In Single Molecule Localization Microscopy Symposium - Current Trends, pages 1, 2021. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Software and Tools, Network Modelling and Analysis, Machine Learning. [bibtex-key = smlms2021]



19. Mia McLean, Lynne Williams, Colin J. Brown, Ghassan Hamarneh, Cecil Chau, Joanne Weinberg, Anne Synnes, Steven Miller, and Ruth Grunau. Neonatal Pain-related Stress, Neonatal Structural Brain Subnetworks, Cortisol and Behavior at 4 years in Children Born Very Preterm. In 54th Annual Meeting of the International Society for Developmental Psychobiology, Chicago, USA, pages 1, 2021. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome, Machine Learning. [bibtex-key = isdp2021]



20. Mia McLean, Lynne Williams, Jeremy Kawahara, Colin J. Brown, Ghassan Hamarneh, Joanne Weinberg, Anne Synnes, Steven Miller, and Ruth Grunau. Associations Between Neonatal Pain-Related Stress, Neonatal Brain Structural Connectome, and Behavior at School Age in Children Born Very Preterm. In 6th Annual Research Day Brain, Behaviour and Development (BB&D), Vancouver, Canada, pages 1, 2021. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome, Machine Learning. [bibtex-key = bcbbd2021]



21. Zahra Mirikharaji, Kumar Abhishek, Saeed Izadi, and Ghassan Hamarneh. D-LEMA: Deep Learning Ensembles from Multiple Annotations. In Biomedical Imaging and Artificial Intelligence (BMIAI) cluster Fall Research Showcase, Vancouver, Canada, pages 1, 2021. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Segmentation. [bibtex-key = bmiai2021b]



22. Zahra Mirikharaji, Kumar Abhishek, Saeed Izadi, and Ghassan Hamarneh. D-LEMA: Deep Learning Ensembles from Multiple Annotations - Application to Skin Lesion Segmentation. In IEEE Computer Vision and Pattern Recognition (IEEE CVPR) ISIC Skin Image Analysis Workshop (CVPR ISIC), pages 1837-1846, 2021. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Segmentation. [bibtex-key = cvpr_isic2021]



23. Kumar Abhishek, Ghassan Hamarneh, and Mark S. Drew. Illumination-based Transformations Improve Skin Lesion Segmentation in Dermoscopic Images. In IEEE Computer Vision and Pattern Recognition (IEEE CVPR) ISIC Skin Image Analysis Workshop (CVPR ISIC), pages 728-729, 2020. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Segmentation. [bibtex-key = cvpr_isic2020]



24. Ali Arab, Betty Chinda, William Siu, George Medvedev, Tao Gu, Hui Guo, Sylvain Moreno, Ghassan Hamarneh, Martin Ester, and Xiaowei Song. A fully-automated convolutional neural network with deep supervision approach for haemorrhage segmentation and volume quantification in CT scans. In American Society of Neuroradiology (ASNR), pages 1, 2020. Keyword(s): Deep Learning, Machine Learning, Segmentation. [bibtex-key = asnr2020]



25. Shahab Aslani, Vittorio Murino, Michael Dayan, Roger Tam, Diego Sona, and Ghassan Hamarneh. Scanner Invariant Multiple Sclerosis Lesion Segmentation from MRI. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 781-785, 2020. Keyword(s): Segmentation, Machine Learning, Deep Learning, Multiple Sclerosis, MRI. [bibtex-key = isbi2020]



26. Ben Cardoen, Timothy H. Wong, Parsa Alan, Sieun Lee, Joanne Aiko Matsubara, Ivan Robert Nabi, and Ghassan Hamarneh. Automatic identification of protein complexes in multi-scale microscopy with applications tometastasis and Alzheimer disease. In The 2nd Annual Tri-Cluster Research Day, Canada, pages 1, 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Processing, Belief Theory. [bibtex-key = tricluster2020b]



27. Ben Cardoen, Timothy H. Wong, Parsa Alan, Sieun Lee, Joanne Aiko Matsubara, Ivan Robert Nabi, and Ghassan Hamarneh. Belief theory enables identification of protein complexes in multi-scale microscopy with applications to metastasis and Alzheimer disease. In Centre for Artificial Intelligence Decision-making and Action (CAIDA), BC's AI Showcase, Canada, pages 1, 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Processing, Belief Theory. [bibtex-key = caida2020b]



28. Saurabh Garg, Lisa Y. W. Tang, Ghassan Hamarneh, Allard Jongman, Joan Sereno, and Yue Wang. Different facial cues for different speech styles in Mandarin tone articulation. In Acoustical Society of America Meeting (ASA), pages 1, 2020. Keyword(s): Tracking, Machine Learning, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal. [bibtex-key = asa2020]



29. Saeed Izadi and Ghassan Hamarneh. Patch-based Non-Local Bayesian Networks for Blind Confocal Microscopy Denoising. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 12265, pages 46–55, 2020. Keyword(s): Microscopy, Enhancement/Restoration/Denoising, Machine Learning, Deep Learning. [bibtex-key = miccai2020]



30. Ismail M. Khater, Ivan Robert Nabi, and Ghassan Hamarneh. SuperNet: Super-resolution Network Analysis and Quantification of Single Molecule Clusters. In Single Molecule Localization Microscopy Symposium - Showtime, pages 1, 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Software and Tools, Network Modelling and Analysis, Machine Learning. [bibtex-key = smlms2020]



31. M.Sadegh Saberian, Kathleen Moriarty, Andrea Olmstead, François Jean, Ivan Robert Nabi, Maxwell Libbrecht, and Ghassan Hamarneh. Drug Repurposing Efficacy Estimation based on Morphological Analysis of SARS-CoV-2 Infected Cells within a Multiple Instance Learning Framework. In Machine learning for computational biology conference (MLCB), pages 1-13, 2020. Keyword(s): Deep Learning, Machine Learning, COVID19, SARS-CoV-2. [bibtex-key = mlcb2020]



32. Kumar Abhishek and Ghassan Hamarneh. Mask2Lesion: Mask-Constrained Adversarial Skin Lesion Image Synthesis. In Medical Image Computing and Computer-Assisted Intervention Workshop on Simulation and Synthesis in Medical Imaging (MICCAI SASHIMI), volume 11827, pages 71-80, 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation, Generative Adversarial Network, Dermatology, Synthesis/Simulation/Augmentation. [bibtex-key = miccai_sashimi2019]



33. Saeedeh Afshari, Aicha BenTaieb, Zahra Mirikharaji, and Ghassan Hamarneh. Weakly Supervised Fully Convolutional Network for PET Lesion Segmentation. In SPIE Medical Imaging, volume 10949, pages 1-7, 2019. Keyword(s): Deep Learning, Machine Learning, Functional/Molecular/Dynamic Imaging, Localization. [bibtex-key = spiemi2019]



34. Ben Cardoen, Fiona Dickson, Ismail M. Khater, Ivan Robert Nabi, and Ghassan Hamarneh. Interaction zone analysis of CAV1 - CAVIN1 in breast cancer cells. In European Molecular Biology Organization EMBO Workshop Caveolae and nanodomains: Translating structural principles and dynamics into function, Le Pouliguen, France, pages 1, 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning. [bibtex-key = embo2019a]



35. Arafat Hussain, Ghassan Hamarneh, and Rafeef Abugharbieh. ImHistNet: Learnable Image Histogram Based DNN with Application to Noninvasive Determination of Carcinoma Grades in CT Scans. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11769, pages 130-138, 2019. Keyword(s): Classification, Machine Learning, Deep Learning. [bibtex-key = miccai2019e]



36. Arafat Hussain, Ghassan Hamarneh, and Rafeef Abugharbieh. Renal Cell Carcinoma Staging with Learnable Image Histogram-based Deep Neural Network. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 11861, pages 533-540, 2019. Keyword(s): Machine Learning, Deep Learning, Classification. [bibtex-key = miccai_mlmi2019c]



37. Saeed Izadi, Zahra Mirikharaji, Mengliu Zhao, and Ghassan Hamarneh. WhiteNNer - Blind Image Denoising via Noise Whiteness Priors. In International Conference on Computer Vision workshop on Visual Recognition for Medical Images (ICCV VRMI), pages 476-484, 2019. Keyword(s): Microscopy, Enhancement/Restoration/Denoising, Machine Learning, Deep Learning. [bibtex-key = iccv_vrmi2019b]



38. Saeed Izadi, Darren Sutton, and Ghassan Hamarneh. Image Super Resolution via Bilinear Pooling: Application to Confocal Endomicroscopy. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning for Medical Image Reconstruction (MICCAI MLMIR), volume 11905, pages 236-244, 2019. Keyword(s): Microscopy, Super Resolution, Enhancement/Restoration/Denoising, Machine Learning, Deep Learning. [bibtex-key = miccai_mlmir2019]



39. Ismail M. Khater, Ivan Robert Nabi, and Ghassan Hamarneh. Identification of Cav1 Domains Using Super Resolution Microscopy and Machine Learning. In European Molecular Biology Organization EMBO Workshop Caveolae and nanodomains: Translating structural principles and dynamics into function, Le Pouliguen, France, pages 1, 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = embo2019b]



40. Zahra Mirikharaji, Yiqi Yan, and Ghassan Hamarneh. Learning to Segment Skin Lesions from Noisy Annotations. In Medical Image Computing and Computer-Assisted Intervention Workshop on Medical Image Learning with Less Labels and Imperfect Data (MICCAI MIL3ID), volume 11795, pages 207-215, 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation, Dermatology. [bibtex-key = miccai_mil3id2019]



41. Saeid Asgari Taghanaki, Kumar Abhishek, Shekoofeh Azizi, and Ghassan Hamarneh. A Kernelized Manifold Mapping to Diminish the Effect of Adversarial Perturbations. In IEEE Computer Vision and Pattern Recognition (IEEE CVPR), pages 11332-11341, 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation, Classification. [bibtex-key = cvpr2019]



42. Saeid Asgari Taghanaki, Kumar Abhishek, and Ghassan Hamarneh. Improved Inference via Deep Input Transfer. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11769, pages 819-827, 2019. Keyword(s): Segmentation, Machine Learning, Deep Learning. [bibtex-key = miccai2019b]



43. Saeid Asgari Taghanaki, Aicha BenTaieb, Anmol Sharma, S. Kevin Zhou, Yefeng Zheng, Bogdan Georgescu, Puneet Sharma, Daguang Xu, Dorin Comaniciu, and Ghassan Hamarneh. SAT: Select, Attend, and Transfer: Light, Learnable Skip Connections. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 11861, pages 417-425, 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation. [bibtex-key = miccai_mlmi2019b]



44. Saeid Asgari Taghanaki, Mohammad Havaei, Tess Berthier, Francis Dutil, Lisa Di Jorio, Ghassan Hamarneh, and Yoshua Bengio. InfoMask: Masked Variational Latent Representation to Localize Chest Disease. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11769, pages 739-747, 2019. Keyword(s): Classification, Machine Learning, Deep Learning. [bibtex-key = miccai2019a]



45. Yiqi Yan, Jeremy Kawahara, and Ghassan Hamarneh. Melanoma Recognition via Visual Attention. In Information Processing in Medical Imaging (IPMI), volume 11492, pages 793–804, 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation, Dermatology. [bibtex-key = ipmi2019]



46. Hanene Ben Yedder, Ben Cardoen, Majid Shokoufi, Farid Golnaraghi, and Ghassan Hamarneh. Limited-Angle Diffuse Optical Tomography Image Reconstruction using Deep Learning. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11764, pages 66-74, 2019. Keyword(s): Image Reconstruction, Machine Learning, Deep Learning, Diffuse Optical Tomography. [bibtex-key = miccai2019c]



47. Chris Yoon, Ghassan Hamarneh, and Rafeef Abugharbieh. Generalizable Feature Learning in the Presence of Data Bias and Domain Class Imbalance with Application to Skin Lesion Classification. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 11767, pages 365-373, 2019. Keyword(s): Classification, Dermatology, Machine Learning, Deep Learning. [bibtex-key = miccai2019d]



48. Mengliu Zhao and Ghassan Hamarneh. Retinal Image Classification via Vasculature-guided Sequential Attention. In International Conference on Computer Vision workshop on Visual Recognition for Medical Images (ICCV VRMI), pages 381-387, 2019. Keyword(s): Anatomical Trees and Tubular Structures, Classification, Shape Modelling and Analysis, Machine Learning, Deep Learning. [bibtex-key = iccv_vrmi2019a]



49. Mengliu Zhao and Ghassan Hamarneh. Tree-LSTM: Using LSTM to Encode Memory in Anatomical Tree Prediction from 3D Images. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 11861, pages 637-645, 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation, Anatomical Trees and Tubular Structures, Shape Modelling and Analysis, Bifurcation/Junction. [bibtex-key = miccai_mlmi2019a]



50. 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. [bibtex-key = miccai2018b]



51. 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. [bibtex-key = asa2018b]



52. 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. [bibtex-key = miccai2018d]



53. 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. [bibtex-key = isbi2018b]



54. 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. [bibtex-key = miccai2018c]



55. 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. [bibtex-key = isbi2018c]



56. 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. [bibtex-key = ascb2018b]



57. 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. [bibtex-key = ascb2018a]



58. 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. [bibtex-key = bme2018]



59. 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. [bibtex-key = miccai2018a]



60. 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. [bibtex-key = isbi2018a]



61. 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. [bibtex-key = socml2018]



62. 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. [bibtex-key = miccai_dlf2018]



63. 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. [bibtex-key = asa2018a]



64. 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. [bibtex-key = miccai_mlmir2018]



65. 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. [bibtex-key = miccai_dlmia2018]



66. 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. [bibtex-key = healthtech2017b]



67. 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. [bibtex-key = sfu_health2017]



68. 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. [bibtex-key = healthtech2017a]



69. 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. [bibtex-key = miccai_labels2017a]



70. 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. [bibtex-key = miccai2017b]



71. 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. [bibtex-key = miccai_mlmi2017]



72. 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. [bibtex-key = miccai2017c]



73. 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. [bibtex-key = healthtech2017c]



74. 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. [bibtex-key = miccai_grail2017]



75. 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. [bibtex-key = ascb2017]



76. 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. [bibtex-key = siam2017a]



77. 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. [bibtex-key = healthtech2017d]



78. 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. [bibtex-key = gordon2017a]



79. 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. [bibtex-key = frontiers_biophysics2017]



80. 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. [bibtex-key = qin2017]



81. Payam Ahmadvand, Noirin Duggan, Francois Benard, and Ghassan Hamarneh. Tumour Lesion Segmentation from 3D PET using a Machine Learning driven Active Surface. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 10019, pages 271-278, 2016. Keyword(s): Machine Learning, Segmentation, Functional/Molecular/Dynamic Imaging. [bibtex-key = miccai_mlmi2016b]



82. Payam Ahmadvand, Hillgan Ma, Jesse Tanguay, Anna Celler, Francois Benard, and Ghassan Hamarneh. A Level-Set based Segmentation of tumour lesions in PET images. In Quantitative Imaging Network (QIN) Annual Meeting, 2016. Keyword(s): Machine Learning, Segmentation, Functional/Molecular/Dynamic Imaging. [bibtex-key = qin2016]



83. Aicha BenTaieb and Ghassan Hamarneh. Topology Aware Fully Convolutional Networks For Histology Gland Segmentation. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 9900, pages 460-468, 2016. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Microscopy, Deep Learning. [bibtex-key = miccai2016a]



84. Aicha BenTaieb, Jeremy Kawahara, and Ghassan Hamarneh. Multi-Loss Convolutional Networks for Gland Analysis in Microscopy. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 642-645, 2016. Keyword(s): Machine Learning, Microscopy, Deep Learning. [bibtex-key = isbi2016a]



85. Colin J. Brown, Steven Miller, Brian G. Booth, Jill Zwicker, Ruth Grunau, Anne Synnes, Vann Chau, and Ghassan Hamarneh. Predictive Subnetwork Extraction with Structural Priors for Infant Connectomes. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 9900, pages 175-183, 2016. Keyword(s): Neurodevelopment, Machine Learning. [bibtex-key = miccai2016b]



86. Colin J. Brown, Steven Miller, Brian G. Booth, Jill Zwicker, Ruth Grunau, Anne Synnes, Vann Chau, and Ghassan Hamarneh. Predictive Subnetwork Extraction with Structural Priors for Infant Connectomes. In Annual Neuroscience Extravaganza, Centre for Brain Health, BC, Canada, 2016. Keyword(s): Neurodevelopment, Machine Learning. [bibtex-key = neuroscix2016b]



87. Arafat Hussain, Ghassan Hamarneh, Tim O'Connell, Mohammed Mohammed, and Rafeef Abugharbieh. Segmentation-Free Estimation of Kidney Volumes in CT with Dual Regression Forests. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 10019, pages 156-163, 2016. Keyword(s): Machine Learning, Segmentation. [bibtex-key = miccai_mlmi2016c]



88. Jeremy Kawahara, Aicha BenTaieb, and Ghassan Hamarneh. Deep Features to Classify Skin Lesions. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 1397-1400, 2016. Keyword(s): Machine Learning, Dermatology, Deep Learning. [bibtex-key = isbi2016b]



89. 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 Annual Neuroscience Extravaganza, Centre for Brain Health, BC, Canada, 2016. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome, Machine Learning, Deep Learning. [bibtex-key = neuroscix2016a]



90. Jeremy Kawahara and Ghassan Hamarneh. Multi-Resolution-Tract CNN with Hybrid Pretrained and Skin-Lesion Trained Layers. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 10019, pages 164-171, 2016. Keyword(s): Machine Learning, Dermatology, Color/Multichannel/Vector-valued, Deep Learning. [bibtex-key = miccai_mlmi2016a]



91. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Defining caveolae and scaffolds by computational network analysis of particle localization super-resolution microscopy. In American Society for Cell Biology (ASCB), San Francisco, California, pages 1, 2016. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = ascb2016]



92. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Discovering Biosignatures of Cav1 Domains: Computational Methods for Super-resolution Microscopy. In LSI Imaging Super-resolution Mini-symposium, Vancouver, Canada, pages 1, 2016. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = superres2016]



93. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Quantifying Caveolin-1 Molecular Domains via Machine Learning and Computational Network Analysis of Super-resolution Microscopy Data. In Bringing the ASCB to the LSI Imaging Mini-symposium, Vancouver, Canada, pages 1, 2016. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = ascblsi2016]



94. Aicha BenTaieb, Hector Li-Chang, David Huntsman, and Ghassan Hamarneh. Automatic Diagnosis of Ovarian Carcinomas via Sparse Multiresolution Tissue Representation. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 9349, pages 629-636, 2015. Keyword(s): Machine Learning, Microscopy, Deep Learning. [bibtex-key = miccai2015b]



95. Colin J. Brown, Steven Miller, Brian G. Booth, Ken Poskitt, Vann Chau, Anne Synnes, Jill Zwicker, Ruth Grunau, and Ghassan Hamarneh. Prediction of Motor Function in Very Preterm Infants using Connectome Features and Local Synthetic Instances. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 9349, pages 69-76, 2015. Keyword(s): Neurodevelopment, Machine Learning, Synthesis/Simulation/Augmentation. [bibtex-key = miccai2015a]



96. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Identifying Sub-Cellular Domains in PC3 cells by Analysing Caveolin-1 Proteins from Nanoscopy Super-Resolution Data. In NanoLytica, Burnaby, Canada, pages 1, 2015. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = nanolytica2015]



97. Ismail M. Khater, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Super-resolution analysis of Caveolae and Cav1 scaffolds in Prostate Cancer Cells. In Advanced Structural and Chemical Imaging (ASCI) Symposium, Pullman, Washington, pages 1, 2015. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = asci2015]



98. Fanrui Meng, Ismail M. Khater, Ghassan Hamarneh, and Ivan Robert Nabi. Super-resolution analysis of Caveolae and Cav1 scaffolds in Prostate Cancer Cells. In Canadian Cytometry and Microscopy Association (CCMA), Toronto, Canada, pages 1, 2015. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Machine Learning. [bibtex-key = ccma2015]



99. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. A computer vision tracking system for pigmented skin lesions. In World Congress of Dermatology (WCD), 2015. Keyword(s): Processing, Color/Multichannel/Vector-valued, Machine Learning, Optimization, Registration and Matching, Tracking, Graph based, Dermatology. [bibtex-key = wcd2015b]



100. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. Detecting Streaks from Dermoscopic Images of Pigmented Skin Lesions. In The International Society for Biophysics and Imaging of the Skin (ISBS), 2015. Keyword(s): Processing, Color/Multichannel/Vector-valued, Machine Learning, Dermatology. [bibtex-key = isbs2015]



101. Jeremy Kawahara, Jean-Marc Peyrat, Julien Abi-Nahed, Osama Al-Alao, Abdulla Al-Ansari, Rafeef Abugharbieh, and Ghassan Hamarneh. Automatic Labelling of Tumourous vs Tumour-Free Frames in Free-Hand Laparoscopic Ultrasound Video. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 8674, pages 677-684, 2014. Keyword(s): Spatio-Temporal, Machine Learning, Segmentation, Image-Guided Surgery. [bibtex-key = miccai2014c]



102. Hengameh Mirzaalian and Ghassan Hamarneh. Automatic Globally-Optimal Pictorial Structures with Random Decision Forest Based Likelihoods For Cephalometric X-Ray Landmark Detection. In Automatic Cephalometric X-Ray Landmark Detection Challenge 2014, in conjunction with IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 1-12, 2014. Keyword(s): Challenge, Machine Learning, Optimization. [bibtex-key = isbi2014_chlg_ceph]



103. Mengliu Zhao and Ghassan Hamarneh. Bifurcation Detection in 3D Vascular Images Using Novel Features and Random Forest. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 421-424, 2014. Keyword(s): Anatomical Trees and Tubular Structures, Machine Learning, Bifurcation/Junction. [bibtex-key = isbi2014a]



104. Jeremy Kawahara, Chris McIntosh, Roger Tam, and Ghassan Hamarneh. Augmenting Auto-context with Global Geometric Features for Spinal Cord Segmentation. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 8184, pages 212-219, 2013. Keyword(s): Segmentation, Machine Learning, Shape Modelling and Analysis, Multiple Sclerosis, MRI. [bibtex-key = miccai_mlmi2013a]



105. Jeremy Kawahara, Chris McIntosh, Roger Tam, and Ghassan Hamarneh. Novel Morphological and Appearance Features for Predicting Physical Disability from MR Images in Multiple Sclerosis Patients. In Medical Image Computing and Computer-Assisted Intervention Workshop on Computational Methods and Clinical Applications for Spine Imaging (MICCAI CSI), pages 1-13, 2013. Keyword(s): Machine Learning, Shape Modelling and Analysis, Multiple Sclerosis, MRI. [bibtex-key = miccai_csi2013]



106. Tayebeh Lotfi, Lisa Y. W. Tang, Shawn Andrews, and Ghassan Hamarneh. Improving probabilistic image registration via reinforcement learning and uncertainty evaluation. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 8184, pages 188-195, 2013. Keyword(s): Uncertainty, Registration and Matching, Machine Learning. [bibtex-key = miccai_mlmi2013b]



107. Hamidreza Mirzaei, Lisa Y. W. Tang, Rene Werner, and Ghassan Hamarneh. Decision Forests with Spatio-temporal Features for Graph-based Tumour Segmentation in 4D Lung CT. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 8184, pages 179-186, 2013. Keyword(s): Segmentation, Machine Learning, Functional/Molecular/Dynamic Imaging. [bibtex-key = miccai_mlmi2013c]



108. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. Learning Features for Streak Detection in Dermoscopic Color Images using Localized Radial Flux of Principal Intensity Curvature. In IEEE workshop on Mathematical Methods for Biomedical Image Analysis (IEEE MMBIA), pages 97-101, 2012. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Anatomical Trees and Tubular Structures, Dermatology. [bibtex-key = mmbia2012d]



109. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. Uncertainty-based Feature Learning for Skin Lesion Matching using a High Order MRF Optimization Framework. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 7511, pages 98-105, 2012. Keyword(s): Machine Learning, Uncertainty, Optimization, Dermatology. [bibtex-key = miccai2012]



110. Lisa Y. W. Tang, Alfred O Hero, and Ghassan Hamarneh. Locally-Adaptive Similarity Metric for Deformable Medical Image Registration. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 728-731, 2012. Keyword(s): Machine Learning, Registration and Matching. [bibtex-key = isbi2012a]



111. Bahareh HajGhanbari, Ghassan Hamarneh, Neda Changizi, Aaron Ward, and W. Darlene Reid. 3D shape analysis of thigh muscles: people with Chronic Obstructive Pulmonary Disease versus healthy older adults. In Canadian Physiotherapy Association Congress, pages 1, 2011. Keyword(s): Shape Modelling and Analysis, Machine Learning. [bibtex-key = cpa2011]



112. Bahareh HajGhanbari, Ghassan Hamarneh, Neda Changizi, Aaron Ward, and W. Darlene Reid. MRI-based Three dimensional shape analysis of thigh muscles: people with Chronic Obstructive Pulmonary Disease versus healthy older adults. In Heart+Lung Health Fest, pages 1, 2011. Keyword(s): Shape Modelling and Analysis, Machine Learning. [bibtex-key = hlf2011]



113. Lisa Y. W. Tang, Ghassan Hamarneh, and Tim Bressmann. A Machine Learning Approach to Tongue Motion Analysis in 2D Ultrasound Image Sequences. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 7009, pages 151-158, 2011. Keyword(s): Tracking, Machine Learning. [bibtex-key = miccai_mlmi2011]



114. Chris McIntosh and Ghassan Hamarneh. Optimal Weights for Convex Functionals in Medical Image Segmentation. In International Symposium on Visual Computing: Special Track on Optimization for Vision, Graphics and Medical Imaging: Theory and Applications (ISVC OVGMI), volume 5875-I, pages 1079-1088, 2009. Keyword(s): Optimization, Segmentation, Machine Learning. [bibtex-key = isvc2009b]



115. Chris McIntosh and Ghassan Hamarneh. Is a Single Energy Functional Sufficient? Adaptive Energy Functionals and Automatic Initialization. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 4792, pages 503-510, 2007. Keyword(s): Deformable Models, Segmentation, Optimization, Machine Learning. [bibtex-key = miccai2007c]



116. Aaron Ward, Ghassan Hamarneh, and Mark Schweitzer. Anatomical Shape Analysis: Exploring the Relationship between Shape and Pathology. In CIHR National Research Poster Competition, Canadian Student Health Research Forum (CSHRF), Winnipeg, June 6-7, 2007. Keyword(s): Shape Modelling and Analysis, Machine Learning. [bibtex-key = cshrf2007]



117. Aaron Ward, Ghassan Hamarneh, Reem Ashry, and Mark Schweitzer. 3D Shape Analysis of the Supraspinatus Muscle. In Medical Image Computing and Computer-Assisted Intervention Joint Diseases Workshop (MICCAI JD), pages 96-103, 2006. Keyword(s): Shape Modelling and Analysis, Machine Learning. [bibtex-key = miccai_jd2006b]



118. Aaron Ward, Ghassan Hamarneh, and Mark Schweitzer. 3D Shape Description of the Bicipital Groove: Correlation to Pathology. In Medical Image Computing and Computer-Assisted Intervention Joint Diseases Workshop (MICCAI JD), pages 80-87, 2006. Keyword(s): Shape Modelling and Analysis, Machine Learning. [bibtex-key = miccai_jd2006a]

1. Kumar Abhishek, Aditi Jain, and Ghassan Hamarneh. Investigating the Quality of DermaMNIST and Fitzpatrick17k Dermatological Image Datasets. Technical report arXiv:2401.14497, 1 2024. Keyword(s): Dermatology, Machine Learning, Deep Learning, Software and Tools, Datasets. [bibtex-key = arxiv:2401.14497]



2. Ashwin Samudre, Guang Gao, Ben Cardoen, Ivan Robert Nabi, and Ghassan Hamarneh. nERdy: network analysis of endoplasmic reticulum (Nabi and Hamarneh: Joint senior authors). Technical report biorxiv:2024.02.20.581259, 2 2024. Keyword(s): Super Resolution Microscopy, Software and Tools, Network Modelling and Analysis, Machine Learning, Deep Learning, Anatomical Trees and Tubular Structures, Synthesis/Simulation/Augmentation. [bibtex-key = biorxiv_2024_02_20_581259]



3. Siyi Du, Nourhan Bayasi, Ghassan Hamarneh, and Rafeef Garbi. MDViT: Multi-domain Vision Transformer for Small Medical Image Segmentation Datasets Segmentation. Technical report arxiv.2307.02100, 7 2023. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Transformers, Classification. [bibtex-key = arxiv:2307.02100]



4. Ivan Robert Nabi, Ben Cardoen, Ismail M. Khater, Guang Gao, Timothy H. Wong, and Ghassan Hamarneh. AI-based analysis of super-resolution microscopy: Biological discovery in the absence of ground truth. Technical report arxiv.2305.17193, 5 2023. Keyword(s): Machine Learning, Deep Learning, Weak Supervision, Super Resolution Microscopy, Validation. [bibtex-key = arxiv:2305.17193]



5. Ashish Sinha, Jeremy Kawahara, Arezou Pakzad, Kumar Abhishek, Matthieu Ruthven, Enjie Ghorbel, Anis Kacem, Djamila Aouada, and Ghassan Hamarneh. DermSynth3D: Synthesis of in-the-wild Annotated Dermatology Images (Sinha, Kawahara, Pakzad: Joint first authors). Technical report arxiv.2305.12621, 5 2023. Keyword(s): Dermatology, Machine Learning, Deep Learning, Segmentation, Synthesis/Simulation/Augmentation, Datasets. [bibtex-key = arxiv:2305.12621]



6. Kumar Abhishek, Colin J. Brown, and Ghassan Hamarneh. Multi-Sample $\zeta$-mixup: Richer, More Realistic Synthetic Samples from a $p$-Series Interpolant. Technical report arXiv:2204.03323, 4 2022. Keyword(s): Machine Learning, Deep Learning, Synthesis/Simulation/Augmentation. [bibtex-key = arxiv:2204.03323]



7. Parsa Alan, Kurt Vandevoorde, Bharat Joshi, Ben Cardoen, Guang Gao, Yahya Mohammadzadeh, Ghassan Hamarneh, and Ivan Robert Nabi. Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS (Alan, Vandevoorde, Joshi, and Cardoen: Joint first authors; Hamarneh and Nabi: Joint senior authors). Technical report Research Square (Preprint) 1559637, 4 2022. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Deep Learning, Image Processing, Belief Theory. [bibtex-key = research_square2022_1559637]



8. Siyi Du, Ben Her, Nourhan Bayasi, Ghassan Hamarneh, and Rafeef Garbi. FairDisCo: Fairer AI in Dermatology via Disentanglement Contrastive Learning. Technical report arXiv:2208.10013, 8 2022. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, AI Bias and Fairness, Classification. [bibtex-key = arxiv:2208.10013]



9. Zahra Mirikharaji, Kumar Abhishek, Alceu Bissoto, Catarina Barata, Sandra Avila, Eduardo Valle, M. Emre Celebi, and Ghassan Hamarneh. A Survey on Deep Learning for Skin Lesion Segmentation (Mirikharaji and Abhishek: Joint first authors; Celebi and Hamarneh: Joint senior authors). Technical report arXiv:2206.00356, 6 2022. Keyword(s): Machine Learning, Deep Learning, Segmentation, Survey/Review, Dermatology. [bibtex-key = arxiv:2206.00356]



10. Arezou Pakzad, Kumar Abhishek, and Ghassan Hamarneh. CIRCLe: Color Invariant Representation Learning for Unbiased Classification of Skin Lesions. Technical report arXiv:2208.13528, 8 2022. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, AI Bias and Fairness, Classification. [bibtex-key = arxiv:2208.13528]



11. Hanene Ben Yedder, Ben Cardoen, Majid Shokoufi, Farid Golnaraghi, and Ghassan Hamarneh. Orthogonal Multi-frequency Fusion Based Image Reconstruction and Diagnosis in Diffuse Optical Tomography. Technical report techrxiv:21574533, 11 2022. Keyword(s): Image Reconstruction, Machine Learning, Deep Learning, Diffuse Optical Tomography. [bibtex-key = techrxiv_21574533]



12. Mengliu Zhao, Jeremy Kawahara, Sajjad Shamanian, Kumar Abhishek, Priyanka Chandrashekar, and Ghassan Hamarneh. Detection and Longitudinal Tracking of Pigmented Skin Lesions in 3D Total-Body Skin Textured Meshes (Zhao and Kawahara: Joint first authors). Technical report arXiv:2105.00374, 5 2021. Keyword(s): Dermatology, Machine Learning, Deep Learning, Optimization, Registration and Matching, Graph based, Tracking. [bibtex-key = arxiv:2105.00374]



13. Kumar Abhishek and Ghassan Hamarneh. Matthews Correlation Coefficient Loss for Deep Convolutional Networks: Application to Skin Lesion Segmentation. Technical report arXiv:2010.13454, 10 2020. Keyword(s): Dermatology, Machine Learning, Deep Learning, Segmentation. [bibtex-key = arxiv:2010.13454]



14. Kumar Abhishek, Ghassan Hamarneh, and Mark S. Drew. Illumination-based Transformations Improve Skin Lesion Segmentation in Dermoscopic Images. Technical report arxiv:2003.10111, 3 2020. Keyword(s): Dermatology, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Segmentation. [bibtex-key = arxiv:2003.10111]



15. Kumar Abhishek, Jeremy Kawahara, and Ghassan Hamarneh. Predicting the Clinical Management of Skin Lesions Using Deep Learning. Technical report medRxiv 2020.11.02.20223941, November 2020. Keyword(s): Dermatology, Machine Learning, Deep Learning, Clinical Management. [bibtex-key = medrxiv2020_20223941]



16. Ben Cardoen and Ghassan Hamarneh. Introduction to Causality. Technical report SFU-Summit-20939, 12 2020. Keyword(s): Machine Learning, Deep Learning, Causality. [bibtex-key = sfu_summit_cardoen_2021a]



17. Ben Cardoen, Timothy H. Wong, Parsa Alan, Sieun Lee, Joanne Aiko Matsubara, Ivan Robert Nabi, and Ghassan Hamarneh. SPECHT: Self-tuning Plausibility Based Object Detection Enables Quantification of Conflict in Heterogeneous Multi-scale Microscopy (Nabi and Hamarneh: Joint senior authors). Technical report techrxiv:12971051, 9 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Processing, Belief Theory, Object Detection, Datasets. [bibtex-key = techrxiv_12971051]



18. Saeed Izadi and Ghassan Hamarneh. Patch-based Non-Local Bayesian Networks for Blind Confocal Microscopy Denoising. Technical report arxiv:2003.11177, 3 2020. Keyword(s): Microscopy, Enhancement/Restoration/Denoising, Machine Learning, Deep Learning. [bibtex-key = arxiv:2003.11177]



19. Ivan Klyuzhin, Yixi Xu, Anthony Ortiz, Juan Lavista Ferres, Ghassan Hamarneh, and Arman Rahmim. Testing the Ability of Convolutional Neural Networks to Learn Radiomic Features. Technical report medrxiv:20198077, September 2020. Keyword(s): Deep Learning, Machine Learning, Radiomics, Functional/Molecular/Dynamic Imaging. [bibtex-key = medrxiv2020_20198077]



20. Rory Long, Kathleen Moriarty, Ben Cardoen, Guang Gao, A. Wayne Vogl, François Jean, Ghassan Hamarneh, and Ivan Robert Nabi. Super Resolution Microscopy and Deep Learning Identify Zika Virus Reorganization of the Endoplasmic Reticulum (Long and Moriarty: Joint first authors; Hamarneh and Nabi: Joint senior authors. Technical report biorxiv:091611, 5 2020. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Deep Learning. [bibtex-key = biorxiv_2020_091611]



21. Zahra Mirikharaji, Kumar Abhishek, Saeed Izadi, and Ghassan Hamarneh. D-LEMA: Deep Learning Ensembles from Multiple Annotations - Application to Skin Lesion Segmentation. Technical report arXiv:2012.07206, 12 2020. Keyword(s): Dermatology, Machine Learning, Deep Learning, Segmentation. [bibtex-key = arxiv:2012.07206]



22. Hanene Ben Yedder, Ben Cardoen, and Ghassan Hamarneh. Deep Learning for Biomedical Image Reconstruction: A Survey. Technical report arxiv:2002.12351, 2 2020. Keyword(s): Image Reconstruction, Machine Learning, Deep Learning, Survey/Review. [bibtex-key = arxiv:2002.12351]



23. Hanene Ben Yedder, Ben Cardoen, Majid Shokoufi, Farid Golnaraghi, and Ghassan Hamarneh. Multitask Deep Learning Reconstruction and Localization of Lesions in Limited Angle Diffuse Optical Tomography. Technical report techrxiv:13150805, 10 2020. Keyword(s): Image Reconstruction, Machine Learning, Deep Learning, Synthesis/Simulation/Augmentation, Diffuse Optical Tomography. [bibtex-key = techrxiv_13150805]



24. Kumar Abhishek and Ghassan Hamarneh. Mask2Lesion: Mask-Constrained Adversarial Skin Lesion Image Synthesis. Technical report arxiv:1906.05845, 6 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation. [bibtex-key = arxiv:1906.05845]



25. Shahab Aslani, Vittorio Murino, Michael Dayan, Roger Tam, Diego Sona, and Ghassan Hamarneh. Scanner Invariant Multiple Sclerosis Lesion Segmentation from MRI. Technical report arxiv:1910.10035, 10 2019. Keyword(s): Segmentation, Machine Learning, Deep Learning, Multiple Sclerosis, MRI. [bibtex-key = arxiv:1910.10035]



26. Aicha BenTaieb and Ghassan Hamarneh. Deep Learning Models for Digital Pathology. Technical report arxiv:1910.12329, 10 2019. Keyword(s): Color/Multichannel/Vector-valued, Machine Learning, Microscopy, Deep Learning, Generative Adversarial Network, Survey/Review. [bibtex-key = arxiv:1910.12329]



27. Saeed Izadi, Darren Sutton, and Ghassan Hamarneh. Image Super Resolution via Bilinear Pooling: Application to Confocal Endomicroscopy. Technical report arxiv:1906.07802, 6 2019. Keyword(s): Microscopy, Super Resolution, Enhancement/Restoration/Denoising, Machine Learning, Deep Learning. [bibtex-key = arxiv:1906.07802]



28. Weina Jin, Mostafa Fatehi, Kumar Abhishek, Mayur Mallya, Brian Toyota, and Ghassan Hamarneh. Artificial Intelligence in Glioma Imaging: Challenges and Advances. Technical report arxiv:1911.12886, 11 2019. Keyword(s): Glioma Imaging, Machine Learning, Deep Learning. [bibtex-key = arxiv:1911.12886]



29. Jeremy Kawahara and Ghassan Hamarneh. Visual Diagnosis of Dermatological Disorders: Human and Machine Performance. Technical report arxiv:1906.01256, 6 2019. Keyword(s): Survey/Review, Color/Multichannel/Vector-valued, Machine Learning, Deep Learning, Dermatology, Classification. [bibtex-key = arxiv:1906.01256]



30. Ismail M. Khater, Stephane Aroca-Ouellette, Fanrui Meng, Ivan Robert Nabi, and Ghassan Hamarneh. Caveolae and scaffold detection from single molecule localization microscopy data using deep learning. Technical report biorxiv:495382, 1 2019. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Machine Learning, Deep Learning, Network Modelling and Analysis, Machine Learning. [bibtex-key = biorxiv_2019_526327]



31. Zahra Mirikharaji, Yiqi Yan, and Ghassan Hamarneh. Learning to Segment Skin Lesions from Noisy Annotations. Technical report arxiv:1906.03815, 6 2019. Keyword(s): Machine Learning, Deep Learning, Segmentation. [bibtex-key = arxiv:1906.03815]



32. Anmol Sharma and Ghassan Hamarneh. Missing MRI Pulse Sequence Synthesis using Multi-Modal Generative Adversarial Network. Technical report arxiv:1904.12200, 4 2019. Keyword(s): Glioma Imaging, Machine Learning, Deep Learning, Generative Adversarial Network, Multimodal. [bibtex-key = arxiv:1904.12200]



33. Saeid Asgari Taghanaki, Kumar Abhishek, Joseph Paul Cohen, Julien Cohen-Adad, and Ghassan Hamarneh. Deep Semantic Segmentation of Natural and Medical Images: A Review. Technical report arxiv:1910.07655, 10 2019. Keyword(s): Survey/Review, Segmentation, Machine Learning, Deep Learning. [bibtex-key = arxiv:1910.07655]



34. Saeid Asgari Taghanaki, Kumar Abhishek, and Ghassan Hamarneh. Improved Inference via Deep Input Transfer. Technical report arxiv:1904.02307, 4 2019. Keyword(s): Machine Learning, Deep Learning. [bibtex-key = arxiv:1904.02307]



35. Saeid Asgari Taghanaki, Kumar Abhishek, and Ghassan Hamarneh. Signed Input Regularization. Technical report arxiv:1911.07086, 12 2019. Keyword(s): Machine Learning, Deep Learning. [bibtex-key = arxiv:1911.07086]



36. Saeid Asgari Taghanaki, Mohammad Havaei, Tess Berthier, Francis Dutil, Lisa Di Jorio, Ghassan Hamarneh, and Yoshua Bengio. InfoMask: Masked Variational Latent Representation to Localize Chest Disease. Technical report arxiv:1903.11741, 3 2019. Keyword(s): Machine Learning, Deep Learning. [bibtex-key = arxiv:1903.11741]



37. 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. [bibtex-key = biorxiv_2018_495382]



38. 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. [bibtex-key = arxiv:1804.05181]



39. 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. [bibtex-key = arxiv:1805.02798]



40. 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. [bibtex-key = arxiv:1703.04559]



41. Colin J. Brown and Ghassan Hamarneh. Machine Learning on Human Connectome Data from MRI. Technical report arxiv:1611.08699, 11 2016. Keyword(s): Survey/Review, Machine Learning, Connectome, Diffusion MRI/Tensor-valued. [bibtex-key = arxiv:1611.08699]

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