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Publications about 'Graph based'
Articles in journal, book chapters
  1. 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]


  2. 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]


  3. 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]


  4. 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]


  5. 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]


  6. 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]


  7. Hengameh Mirzaalian, Tim K. Lee, and Ghassan Hamarneh. Spatial Normalization of Human Back Images for Dermatological Studies. IEEE Journal of Biomedical and Health Informatics (IEEE JBHI), 18(4):1494-1501, 2013. Keyword(s): Registration and Matching, Tracking, Graph based, Dermatology. [bibtex-key = jbhi2013]


  8. Bernard Ng, Ghassan Hamarneh, and Rafeef Abugharbieh. Modeling Brain Activation in fMRI Using Group MRF. IEEE Transactions on Medical Imaging (IEEE TMI), 31(5):1113-1123, 2012. Keyword(s): Functional/Molecular/Dynamic Imaging, Segmentation, Graph based. [bibtex-key = tmi2012b]


  9. Lisa Y. W. Tang, Tim Bressmann, and Ghassan Hamarneh. Tongue contour tracking in dynamic ultrasound via higher-order MRFs and efficient fusion moves. Medical Image Analysis (MedIA), 16(8):1503-1520, 2012. Keyword(s): Tracking, Registration and Matching, Graph based. [bibtex-key = mia2012b]


  10. Miranda Poon, Ghassan Hamarneh, and Rafeef Abugharbieh. Efficient Interactive 3D Livewire Segmentation of Objects with Arbitrary Topologies. Computerized Medical Imaging and Graphics (CMIG), 32(8):639-650, 2008. Keyword(s): Segmentation, Software and Tools, User Interaction, Graph based. [bibtex-key = cmig2008]


Conference articles
  1. 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]


  2. 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]


  3. 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]


  4. 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]


  5. 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]


  6. Jeremy Kawahara, Chris McIntosh, Roger Tam, and Ghassan Hamarneh. Globally Optimal Spinal Cord Segmentation using A Minimal Path in High Dimensions. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 836-839, 2013. Keyword(s): Segmentation, Optimization, Anatomical Trees and Tubular Structures, Graph based, Multiple Sclerosis, MRI. [bibtex-key = isbi2013b]


  7. Brian G. Booth and Ghassan Hamarneh. Competitive Tractography for Extracting Brain Connectivity from Diffusion MRI. In The 6th Annual Canadian Neuroscience Meeting (CAN-ACN), 2012. Keyword(s): Diffusion MRI/Tensor-valued, Graph based. [bibtex-key = can-acn2012]


  8. Brian G. Booth and Ghassan Hamarneh. Exact Integration of Diffusion Orientation Distribution Functions for Graph-Based Diffusion MRI Analysis. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 935-938, 2011. Keyword(s): Diffusion MRI/Tensor-valued, Graph based. [bibtex-key = isbi2011]


  9. Shawn Andrews, Ghassan Hamarneh, and Ahmed Saad. Fast Random Walker with Priors using Precomputation for Interactive Medical Image Segmentation. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 6363, pages 9-16, 2010. Keyword(s): Segmentation, Graph based. [bibtex-key = miccai2010b]


  10. Hengameh Mirzaalian and Ghassan Hamarneh. Vessel Scale Selection using MRF Optimization. In IEEE Computer Vision and Pattern Recognition (IEEE CVPR), pages 3273-3278, 2010. Keyword(s): Anatomical Trees and Tubular Structures, Optimization, Graph based. [bibtex-key = cvpr2010a]


  11. Bernard Ng, Rafeef Abugharbieh, and Ghassan Hamarneh. Group MRF for fMRI Activation Detection. In IEEE Computer Vision and Pattern Recognition (IEEE CVPR), pages 2887-2894, 2010. Keyword(s): Functional/Molecular/Dynamic Imaging, Segmentation, Graph based. [bibtex-key = cvpr2010b]


  12. Bernard Ng, Ghassan Hamarneh, and Rafeef Abugharbieh. Detecting Brain Activation in fMRI Using Group Random Walker. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 6362, pages 331-338, 2010. Keyword(s): Functional/Molecular/Dynamic Imaging, Segmentation, Graph based. [bibtex-key = miccai2010d]


  13. Josna Rao, Rafeef Abugharbieh, and Ghassan Hamarneh. Adaptive Regularization for Image Segmentation Using Local Image Curvature Cues. In European Conference on Computer Vision (ECCV), pages 651-665, 2010. Keyword(s): Segmentation, Optimization, Graph based. [bibtex-key = eccv2010]


  14. Lisa Y. W. Tang and Ghassan Hamarneh. Graph-based tracking of the tongue contour in ultrasound sequences with adaptive temporal regularization. In IEEE workshop on Mathematical Methods for Biomedical Image Analysis (IEEE MMBIA) in conjunction with the IEEE Conference on Computer Vision and Pattern Recognition (IEEE CVPR), pages 154-161, 2010. Keyword(s): Tracking, Registration and Matching, Graph based. [bibtex-key = mmbia2010]


  15. Ghassan Hamarneh. Multi-Label MRF Optimization via a Least Squares s-t Cut. 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 1055-1066, 2009. Keyword(s): Optimization, Segmentation, Graph based. [bibtex-key = isvc2009a]


  16. Hengameh Mirzaalian, Ghassan Hamarneh, and Tim K. Lee. Graph-based Approach to Skin Mole Matching Incorporating Template-Normalized Coordinates. In IEEE Computer Vision and Pattern Recognition (IEEE CVPR), pages 2152-2159, 2009. Keyword(s): Registration and Matching, Tracking, Graph based, Dermatology. [bibtex-key = cvpr2009]


  17. Hengameh Mirzaalian, Ghassan Hamarneh, and Tim K. Lee. Skin Mole Matching Incorporating Template-Normalized Coordinates. In Annual UBC and CIHR Skin Research Day, 2009. Keyword(s): Registration and Matching, Tracking, Graph based, Dermatology. [bibtex-key = skin2009]


  18. Bernard Ng, Rafeef Abugharbieh, Ghassan Hamarneh, and Martin McKeown. Random Walker Based Estimation and Spatial Analysis of Probabilistic fMRI Activation Maps. In Medical Image Computing and Computer-Assisted Intervention Workshop on Statistical modeling and detection issues in intra- and inter-subject functional MRI data analysis (MICCAI fMRI), pages 37-44, 2009. Keyword(s): Functional/Molecular/Dynamic Imaging, Segmentation, Graph based. [bibtex-key = miccai_fmri2009]


  19. Maryam Sadeghi, Geoff Tien, Ghassan Hamarneh, and Stella Atkins. Hands-free Interactive Image Segmentation Using Eyegaze. In SPIE Medical Imaging, volume 72601H, pages 1-10, 2009. Keyword(s): Segmentation, User Interaction, Graph based. [bibtex-key = spiemi2009]


  20. Ahmed Saad, Ghassan Hamarneh, Torsten Moeller, and Ben Smith. Kinetic Modeling based Probabilistic Segmentation for Molecular Images. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 5241, pages 244-252, 2008. Keyword(s): Functional/Molecular/Dynamic Imaging, Segmentation, Uncertainty, Graph based. [bibtex-key = miccai2008a]


  21. Miranda Poon, Ghassan Hamarneh, and Rafeef Abugharbieh. Live-Vessel: Extending Livewire for Simultaneous Extraction of Optimal Medial and Boundary Paths in Vascular Images. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 4792, pages 444-451, 2007. Keyword(s): Deformable Models, Segmentation, Anatomical Trees and Tubular Structures, Graph based. [bibtex-key = miccai2007a]


  22. Miranda Poon, Ghassan Hamarneh, and Rafeef Abugharbieh. Segmentation of Complex Objects with Non-Spherical Topologies from Volumetric Medical Images using 3D Livewire. In SPIE Medical Imaging, volume 6512-31, pages 1-10, 2007. Keyword(s): Segmentation, User Interaction, Graph based. [bibtex-key = spiemi2007a]


  23. Ahmed Saad, Ben Smith, Ghassan Hamarneh, and Torsten Moeller. Simultaneous Segmentation, Kinetic Parameter Estimation, and Uncertainty Visualization of Dynamic PET Images. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 4792, pages 726-733, 2007. Keyword(s): Segmentation, Functional/Molecular/Dynamic Imaging, Uncertainty, Graph based. [bibtex-key = miccai2007b]


  24. Yonas Weldeselassie and Ghassan Hamarneh. DT-MRI Segmentation Using Graph Cuts. In SPIE Medical Imaging, volume 6512-1K, pages 1-9, 2007. Keyword(s): Segmentation, Diffusion MRI/Tensor-valued, Graph based. [bibtex-key = spiemi2007b]


  25. Ghassan Hamarneh and Judith Hradsky. DTMRI Segmentation using DT-Snakes and DT-Livewire. In IEEE International Symposium on Signal Processing and Information Technology (IEEE ISSPIT), pages 513-518, 2006. Keyword(s): Segmentation, Deformable Models, Diffusion MRI/Tensor-valued, Graph based. [bibtex-key = isspit2006b]


  26. Artur Chodorowski, Ulf Mattsson, Morgan Langille, and Ghassan Hamarneh. Color lesion boundary detection using live wire. In SPIE Medical Imaging, volume 5747, pages 1589-1596, 2005. Keyword(s): Segmentation, Deformable Models, Color/Multichannel/Vector-valued, Graph based. [bibtex-key = spiemi2005d]


Internal reports
  1. 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]


  2. Shawn Andrews and Ghassan Hamarneh. Multi-Region Probabilistic Dice Similarity Coefficient using the Aitchison Distance and Bipartite Graph Matching. Technical report arxiv:1509.07244, 9 2015. Keyword(s): Segmentation, Validation, Graph based, Registration and Matching. [bibtex-key = arxiv:1509.07244]


  3. Shawn Andrews, Ghassan Hamarneh, and Ahmed Saad. Fast Random Walker with Priors using Precomputation for Interactive Medical Image Segmentation. Technical report TR 2010-07, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 6 2010. Keyword(s): Segmentation, Graph based, Fast MIA. [bibtex-key = sfu_cs2010_07]


  4. Josna Rao, Rafeef Abugharbieh, and Ghassan Hamarneh. Adaptive Regularization for Image Segmentation Using Local Image Curvature Cues. Technical report TR 2010-08, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 6 2010. Keyword(s): Segmentation, Graph based. [bibtex-key = sfu_cs2010_08]


  5. Ryan Dickie, Ghassan Hamarneh, and Rafeef Abugharbieh. Live-vessel: Interactive vascular image segmentation with simultaneous extraction of optimal medial and boundary paths. Technical report TR 2009-23, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 11 2009. Keyword(s): Segmentation, Anatomical Trees and Tubular Structures, Color/Multichannel/Vector-valued, Optimization, Software and Tools, User Interaction, Medial-based Shape Representation, Graph based, Bifurcation/Junction. [bibtex-key = sfu_cs2009_23]


  6. Ghassan Hamarneh. Multi-Label MRF Optimization via Least Squares s-t Cuts. Technical report arxiv:0907.0204, 7 2009. Keyword(s): Optimization, Segmentation, Graph based. [bibtex-key = arxiv:0907.0204]


  7. Ghassan Hamarneh. Multi-Label MRF Optimization via Least Squares s-t Cuts. Technical report TR 2009-08, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 4 2009. Keyword(s): Optimization, Segmentation, Graph based. [bibtex-key = sfu_cs2009_08]


  8. Josna Rao, Ghassan Hamarneh, and Rafeef Abugharbieh. Automatic Spatially-Adaptive Balancing of Energy Terms for Image Segmentation. Technical report arxiv:0906.4131, 6 2009. Keyword(s): Segmentation, Graph based. [bibtex-key = arxiv:0906.4131]



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Last modified: Thu Aug 1 12:06:05 2024
Author: hamarneh.

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