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Publications of year 2022
Thesis
  1. Saeed Izadi. Deep Learning for Medical Image Restoration. Doctoral Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, June 2022.


  2. Mayur Mallya. Multimodal Guidance for Medical Image Classification. Master's Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, August 2022.


  3. Zahra Mirikharaji. Deep Learning for Skin Lesion Segmentation. Doctoral Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, April 2022.


Articles in journal, book chapters
  1. Parsa Alan, Bharat Joshi, Ben Cardoen, Kurt Vandevoorde, Guang Gao, Peter Overby, James D. Johnson, Ghassan Hamarneh, and Ivan Robert Nabi. Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS (Alan, Joshi, Cardoen, and Vandevoorde: Joint first authors; Hamarneh and Nabi: Joint senior authors). Cellular and Molecular Life Sciences (CMLS), 79(565):1-20, 2022. Keyword(s): Super Resolution Microscopy, Image Processing, Belief Theory.


  2. 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.


  3. 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.


  4. 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.


  5. Weina Jin, Xiaoxiao Li, Mostafa Fatehi, and Ghassan Hamarneh. Guidelines and evaluation for clinical explainable AI in medical image analysis. Medical Image Analysis (MedIA), 102684:1-30, 2022. Keyword(s): Deep Learning, Explainable AI (XAI), Multimodal.


  6. 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. Computer Methods and Programs in Biomedicine, 2019(106750):1-10, 2022. Keyword(s): Deep Learning, Functional/Molecular/Dynamic Imaging, Radiomics.


  7. 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.


  8. Darren Sutton, Zamir K. Punja, and Ghassan Hamarneh. Characterization of Trichome Phenotypes to Assess Maturation and Flower Development in Cannabis sativa L. (Cannabis) by Automatic Trichome Gland Analysis. Smart Agricultural Technology (SAT), 3(100111):1-15, 2022. Keyword(s): Agritech, Precision Agriculture, Plant Phenotyping, Trichomes, Medicinal Cannabis.


  9. 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.


Conference articles
  1. Parsa Alan, Bharat Joshi, Ben Cardoen, Kurt Vandevoorde, Guang Gao, Peter Overby, James D. Johnson, Ghassan Hamarneh, and Ivan Robert Nabi. Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS (Alan, Joshi, Cardoen, and Vandevoorde: Joint first authors; Hamarneh and Nabi: Joint senior authors). In American Society of Cell Biology (ASCB) - Cell Bio, 2022. Keyword(s): Super Resolution Microscopy, Image Processing, Belief Theory.


  2. Parsa Alan, Kurt Vandevoorde, Bharat Joshi, Ben Cardoen, Guang Goa, Ghassan Hamarneh, and Ivan Robert Nabi. Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS. In UBC SBME 2022, 2022. Keyword(s): Super Resolution Microscopy, Image Processing, Belief Theory.


  3. 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.


  4. Kayleigh Campbell, Colin J. Brown, Ghassan Hamarneh, Steven Miller, and Tim Oberlander. Disrupted structural network topology of the neonatal brain following prenatal SSRI antidepressant exposure, and its relationship with later infant neurodevelopment and behaviour at 2-years of age. In International Society for Developmental Psychobiology (ISDP), 2022. Keyword(s): Neurodevelopment, Diffusion MRI/Tensor-valued.


  5. Ben Cardoen, Kurt Vandevoorde, Guang Gao, Parsa Alan, Ellie Tiliakou, William Liu, A. Wayne Vogl, Ghassan Hamarneh, and Ivan Robert Nabi. A novel sub-precision detection method (MCS-DETECT) identifies shape complexity of mitochondria-ER contacts (MERCs) in 3D STED super-resolution microscopy (Cardoen, Vandervoorde, and Gao: Joint first authors; Hamarneh and Nabi: Joint senior authors). In American Society of Cell Biology (ASCB) - Cell Bio, 2022. Keyword(s): Object Detection, Super Resolution Microscopy.


  6. 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.


  7. Saeed Izadi, Isaac Shiri, Carlos Uribe, Parham Geramifar, Habib Zaidi, Arman Rahmim, and Ghassan Hamarneh. Context-Aware Filtering for Direct Joint Attenuation and Scatter Correction of Whole-Body PET Images. In The Society of Nuclear Medicine and Molecular Imaging (SNMMI) Annual Meeting, pages 1, 2022. Keyword(s): Enhancement/Restoration/Denoising, Deep Learning, Functional/Molecular/Dynamic Imaging.


  8. 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.


  9. Ismail M. Khater, Ivan Robert Nabi, and Ghassan Hamarneh. HDCluster: High-Degree Graph-Based Clustering Algorithm and its Application to Single Molecule Localization Microscopy. In Single Molecule Localization Microscopy Symposium, pages 1, 2022. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Network Modelling and Analysis, Clustering.


  10. 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.


  11. Mayur Mallya and Ghassan Hamarneh. Deep Multimodal Guidance for Medical Image Classification. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 13437, pages 298–308, 2022. Keyword(s): Dermatology, Deep Learning, MRI, Microscopy, Multimodal.


  12. 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.


  13. Saeid Asgari Taghanaki, Aliasghar Khani, Fereshte Khani, Ali Gholami, Linh Tran, Ali Mahdavi-Amiri, and Ghassan Hamarneh. MaskTune: Mitigating Shortcut Learning by Tuning to Explore (Asgari, Khani, Khani, Gholami: Equal contribution). In Neural Information Processing Systems (NeurIPS), pages 1-13, 2022. Keyword(s): Classification, Deep Learning.


Internal reports
  1. 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.


  2. 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.


  3. Ben Cardoen, Guang Gao, Kurt Vandevoorde, Parsa Alan, William Liu, Ghassan Hamarneh, and Ivan Robert Nabi. Automatic sub-precision membrane contact site detection identifies convoluted tubular riboMERCs (Cardoen, Gao, Vandevoorde: Joint first authors; Hamarneh and Nabi: Joint senior authors). Technical report biorxiv:2022.06.23.497346, 6 2022. Keyword(s): Super Resolution Microscopy, Single Molecule Localization Microscopy, Color/Multichannel/Vector-valued, Image Reconstruction.


  4. 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.


  5. 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. Technical report SSRN Electronic Journal 4146179, 6 2022. Keyword(s): Segmentation, Tracking, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal, Deep Learning.


  6. Saeed Izadi, Isaac Shiri, Carlos Uribe, Parham Geramifar, Habib Zaidi, Arman Rahmim, and Ghassan Hamarneh. Enhanced Direct Joint Attenuation and Scatter Correction of Whole-Body PET Images via Context-Aware Deep Networks. Technical report medRxiv 2022.05.26.22275662, May 2022. Keyword(s): Enhancement/Restoration/Denoising, Deep Learning, Functional/Molecular/Dynamic Imaging.


  7. Saeed Izadi, Darren Sutton, and Ghassan Hamarneh. Image Denoising in the Deep Learning Era. Technical report Research Square (Preprint) 1806416, 6 2022. Keyword(s): Deep Learning, Enhancement/Restoration/Denoising, Survey/Review.


  8. Weina Jin, Jianyu Fan, Diane Gromala, Philippe Pasquier, and Ghassan Hamarneh. EUCA: the End-User-Centered Explainable AI Framework. Technical report arXiv:2102.02437, 2 2022. Keyword(s): Explainable AI (XAI).


  9. Weina Jin, Jianyu Fan, Diane Gromala, Philippe Pasquier, Xiaoxiao Li, and Ghassan Hamarneh. Transcending XAI Algorithm Boundaries through End-User-Inspired Design. Technical report arXiv:2208.08739, 8 2022. Keyword(s): Deep Learning, Explainable AI (XAI), Multimodal.


  10. Weina Jin, Mostafa Fatehi, Ru Guo, and Ghassan Hamarneh. Evaluating the Clinical Utility of Artificial Intelligence Assistance and its Explanation on Glioma Grading Task. Technical report medRxiv 2022.12.07.22282726, December 2022. Keyword(s): Deep Learning, Explainable AI (XAI), Multimodal.


  11. Weina Jin, Xiaoxiao Li, Mostafa Fatehi, and Ghassan Hamarneh. Guidelines and evaluation for clinical explainable AI on medical image analysis. Technical report arXiv:2202.10553, 2 2022. Keyword(s): Deep Learning, Explainable AI (XAI).


  12. Weina Jin, Xiaoxiao Li, and Ghassan Hamarneh. Evaluating Explainable AI on a Multi-Modal Medical Imaging Task: Can Existing Algorithms Fulfill Clinical Requirements?. Technical report arXiv:2203.06487, 3 2022. Keyword(s): Deep Learning, Explainable AI (XAI), Multimodal.


  13. Mayur Mallya and Ghassan Hamarneh. Deep Multimodal Guidance for Medical Image Classification. Technical report arXiv:2203.05683, 3 2022. Keyword(s): Dermatology, Deep Learning, MRI, Microscopy, Multimodal.


  14. 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.


  15. 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.


  16. Darren Sutton, Zamir K. Punja, and Ghassan Hamarneh. Characterization of Trichome Phenotypes to Assess Maturation and Flower Development in Cannabis sativa L. (Cannabis) by Automatic Trichome Gland Analysis. Technical report SSRN Electronic Journal 4141209, 6 2022. Keyword(s): Agritech, Precision Agriculture, Plant Phenotyping, Trichomes, Medicinal Cannabis.


  17. 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.



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

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