1. Hanene Ben Yedder. Deep Learning Methods for Reconstruction and Analysis of Diffuse Optical Tomography Images of Breast Cancer Lesions. Doctoral Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, September 2023.

1. Ben Cardoen, Kurt Vandevoorde, Guang Gao, Milene Ortiz-Silva, Parsa Alan, Ellie Tiliakou, William Liu, A. Wayne Vogl, Ghassan Hamarneh, and Ivan Robert Nabi. Membrane contact site detection (MCS-DETECT) reveals dual control of rough mitochondria-ER contacts (Cardoen, Vandevoorde, Gao, and Ortiz: Joint first authors; Hamarneh and Nabi: Joint senior authors). The Journal Of Cell Biology (JCB), 1(jcb.202206109):000-000, 11 2023. Keyword(s): Super Resolution Microscopy, Object Detection, Restoration, Reconstruction, Interaction.



2. Ben Cardoen, Hanene Ben Yedder, Sieun Lee, Ivan Robert Nabi, and Ghassan Hamarneh. DataCurator.jl: Efficient, portable, and reproducible validation, curation, and transformation of large heterogeneous datasets using human-readable recipes compiled into machine verifiable templates. BioInformatics Advances, 3(1-5):000-000, 2023. Keyword(s): Microscopy, Processing, Single Molecule Localization, Super Resolution Microscopy, Software and Tools, Reproducibility.



3. 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.



4. 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.



5. Weina Jin, Mostafa Fatehi, Ru Guo, and Ghassan Hamarneh. Evaluating the Clinical Utility of Artificial Intelligence Assistance and its Explanation on the Glioma Grading Task (Jin and Fatehi: Joint first authors). Artificial Intelligence In Medicine, 000(000):000-000, 2023. Keyword(s): Deep Learning, Explainable AI (XAI).



6. Weina Jin, Xiaoxiao Li, Mostafa Fatehi, and Ghassan Hamarneh. Generating Post-Hoc Explanation from Deep Neural Networks for Multi-Modal Medical Image Analysis Tasks. MethodX, 10(102009):1-7, 2023. Keyword(s): Deep Learning, Explainable AI (XAI), Multimodal, Software and Tools.



7. 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.



8. Shubam Sachdeva, Haoyao Ruan, Ghassan Hamarneh, Dawn Behne, Allard Jongman, Joan Sereno, and Yue Wang. Plain-to-clear speech video conversion for enhanced intelligibility. International Journal of Speech Technology (IJST), pp 1-22, 2023. Keyword(s): Segmentation, Tracking, Color/Multichannel/Vector-valued, Speech and Language, Facial Analysis, Spatio-Temporal.

1. 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.



2. 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.



3. Adriano D'Alessandro, Ali Mahdavi-Amiri, and Ghassan Hamarneh. Learning-to-Count by Learning-to-Rank. In Canadian Conference on Computer and Robot Vision (CRV), pages 1-8, 2023. Keyword(s): Deep Learning, Counting, Ranking.



4. 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.



5. 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.

1. Ben Cardoen, Hanene Ben Yedder, Sieun Lee, Ivan Robert Nabi, and Ghassan Hamarneh. DataCurator.jl: Efficient, portable, and reproducible validation, curation, and transformation of large heterogeneous datasets using human-readable recipes compiled into machine verifiable templates. Technical report techrxiv:22060118, 2 2023. Keyword(s): Microscopy, Processing, Single Molecule Localization, Super Resolution Microscopy, Software and Tools, Reproducibility.



2. Ben Cardoen, Hanene Ben Yedder, Sieun Lee, Ivan Robert Nabi, and Ghassan Hamarneh. Log-Paradox: Necessary and sufficient conditions for confounding statistically significant pattern reversal under the log-transform. Technical report arxiv.2302.04780, 000 2023. Keyword(s): Microscopy, Processing, Single Molecule Localization, Super Resolution Microscopy, Software and Tools, Statistics, Geometric mean, Log-transform.



3. Adriano D'Alessandro, Ali Mahdavi-Amiri, and Ghassan Hamarneh. Counting Objects in Images using Deep Learning: Methods and Current Challenges. Technical report Research Square (Preprint) 2986682, 6 2023. Keyword(s): Deep Learning, Counting, Survey/Review, Dermatology.



4. Adriano D'Alessandro, Ali Mahdavi-Amiri, and Ghassan Hamarneh. SYRAC: Synthesize, Rank, and Count. Technical report arxiv.2310.01662, 10 2023. Keyword(s): Deep Learning, Counting, Ranking.



5. 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.



6. Weina Jin, Jianyu Fan, Diane Gromala, Philippe Pasquier, and Ghassan Hamarneh. Invisible Users: Uncovering End-Users' Requirements for Explainable AI via Explanation Forms and Goals. Technical report arxiv.2302.06609, 2 2023. Keyword(s): Deep Learning, Explainable AI (XAI), Multimodal, Software and Tools.



7. Weina Jin, Xiaoxiao Li, and Ghassan Hamarneh. The XAI Alignment Problem: Rethinking How Should We Evaluate Human-Centered AI Explainability Techniques. Technical report arxiv.2303.17707, 4 2023. Keyword(s): Explainable AI (XAI).



8. Aliasghar Khani, Saeid Asgari Taghanaki, Aditya Sanghi, Ali Mahdavi-Amiri, and Ghassan Hamarneh. SLiMe: Segment Like Me. Technical report arxiv.2309.03179, 9 2023. Keyword(s): Deep Learning, Segmentation.



9. 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.



10. 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.

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