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publications.yml
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281 lines (262 loc) · 12 KB
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#==============================================================================
# Publications (_data/publications.yml)
#
# Purpose:
# Stores all lab publications displayed on /publications page.
# Supports articles, conference papers, preprints, and technical reports.
#
# Usage:
# Add new publications at the TOP of the list (newest first).
# Displayed by: _includes/publication-item.html
#
# Required Fields:
# - id: Unique identifier (Format: "FirstAuthor_Venue_Year")
# - title: Full publication title
# - authors: Complete author list (use "others" for et al.)
# - year: Publication year (YYYY)
#
# Optional Fields:
# - status: "published" | "accepted" | "preprint" | "under_review"
# - type: "article" | "inproceedings" | "preprint" | "techreport"
# - journal/booktitle: Venue name
# - volume/pages: Citation details
# - doi: Digital Object Identifier
# - url: Publication webpage
# - github: GitHub repository URL
# - arxiv: arXiv ID (e.g., "2401.12345")
# - list_image: Thumbnail (path relative to root, e.g., "images/pubpic/fig.png")
# - highlight: 1 (featured) | 0 (regular)
#
# Example Entry:
# - id: "Hosseini_JPI2024"
# title: "Computational Pathology: A Survey Review"
# authors: "Mahdi S. Hosseini, others"
# year: 2024
# type: "article"
# journal: "Journal of Pathology Informatics"
# doi: "10.1016/j.jpi.2023.100357"
# list_image: "images/pubpic/survey.jpg"
#==============================================================================
- id: "Ali_arXiv2026_MonoLoss"
title: "MonoLoss: A Training Objective for Interpretable Monosemantic Representations"
authors: "Ali Nasiri-Sarvi, Anh Tien Nguyen, Hassan Rivaz, Dimitris Samaras, Mahdi S. Hosseini"
year: 2026
status: "under_review"
type: "article"
journal: "arXiv:2602.12403"
url: "https://atlasanalyticslab.github.io/MonoLoss/"
arxiv: "2602.12403"
github: "https://github.com/AtlasAnalyticsLab/MonoLoss"
list_image: "images/pubpic/monoloss.png"
highlight: 0
- id: "Alagha_arXiv2025_AtlasPatch"
title: "AtlasPatch: An Efficient and Scalable Tool for Whole Slide Image Preprocessing in Computational Pathology"
authors: "Ahmed Alagha, Christopher Leclerc, Yousef Kotp, Omar Abdelwahed, Calvin Moras, Peter Rentopoulos, Rose Rostami, Bich Ngoc Nguyen, Jumanah Baig, Abdelhakim Khellaf, Vincent Quoc-Huy Trinh, Rabeb Mizouni, Hadi Otrok, Jamal Bentahar, Mahdi S. Hosseini"
year: 2026
status: "under_review"
type: "article"
journal: "arxiv:2602.03998"
url: "https://atlasanalyticslab.github.io/AtlasPatch/"
arxiv: "2602.03998"
github: "https://github.com/AtlasAnalyticsLab/AtlasPatch"
list_image: "images/pubpic/atlaspatch.png"
highlight: 0
- id: "Yang_arXiv2025_ADPv2"
title: "ADPv2: A Hierarchical Histological Tissue Type-Annotated Dataset for Potential Biomarker Discovery of Colorectal Disease"
authors: "Zhiyuan Yang, Kai Li, Sophia Ghamoshi Ramandi, Patricia Brassard, Hakim Khellaf, Vincent Quoc-Huy Trinh, Jennifer Zhang, Lina Chen, Corwyn Rowsell, Sonal Varma, Konstantinos N. Plataniotis, Mahdi S. Hosseini"
year: 2025
status: "published"
type: "article"
journal: "Journal of Pathology Informatics"
pages: "100537"
url: "https://zenodo.org/records/15307021"
doi: "10.1016/j.jpi.2025.100537"
arxiv: "2507.05656"
list_image: "images/pubpic/adpv2d.png"
highlight: 0
- id: "Sharma_arXiv2025_EfficientPromptsVLMs"
title: "Investigating Zero-Shot Diagnostic Pathology in Vision-Language Models with Efficient Prompt Design"
authors: "Vineet Sharma, Ahmed Alagha, Hamza Khellaf, Vincent Quoc-Huy Trinh, Mahdi S. Hosseini"
year: 2025
status: "published"
type: "inproceedings"
booktitle: "6th International Conference on Deep Learning Theory and Applications (DeLTA 2025)"
url: "https://link.springer.com/chapter/10.1007/978-3-032-04339-9_17"
arxiv: "2505.00134"
doi: "10.1007/978-3-032-04339-9_17"
list_image: "images/pubpic/efficient_prompts.png"
highlight: 0
- id: "He_IPMI2025_PathTTT"
title: "PathTTT: Test-Time Training with Meta-auxiliary Learning for Pathology Image Classification"
authors: "Haoyu He, Mahdi S. Hosseini, Yang Wang"
year: 2025
status: "published"
type: "inproceedings"
booktitle: "Information Processing in Medical Imaging (IPMI 2025) – LNCS 15829"
url: "https://link.springer.com/chapter/10.1007/978-3-031-96628-6_3"
doi: "10.1007/978-3-031-96628-6_3"
list_image: "images/pubpic/pathttt.png"
highlight: 0
- id: "Nasiri_arXiv2025_SPARC"
title: "SPARC: Concept-Aligned Sparse Autoencoders for Cross-Model, Cross-Modal Interpretability"
authors: "Ali Nasiri-Sarvi, Hassan Rivaz, Mahdi S. Hosseini"
year: 2025
status: "under_review"
type: "article"
journal: "arXiv:2507.06265"
arxiv: "2507.06265"
github: "https://github.com/AtlasAnalyticsLab/SPARC"
list_image: "images/pubpic/SPARC.png"
highlight: 0
- id: "Zhang_arXiv2025_LBMamba"
title: "LBMamba: Locally Bi-directional Mamba"
authors: "Jingwei Zhang, Xi Han, Hong Qin, Mahdi S. Hosseini, Dimitris Samaras"
year: 2025
status: "published"
type: "article"
journal: "Transactions on Machine Learning Research (TMLR 2025)"
issn: "2835-8856"
url: "https://openreview.net/pdf?id=e1aXaIXblQ"
arxiv: "2506.15976"
github: "https://github.com/cvlab-stonybrook/LBMamba"
list_image: "images/pubpic/lbmamba.png"
highlight: 0
- id: "Rostami_arXiv2025_SegmentAnyCrack"
title: "Segment Any Crack: Deep Semantic Segmentation Adaptation for Crack Detection"
authors: "Ghordsiyeh Rostami, Po-Han Chen, Mahdi S. Hosseini"
year: 2026
status: "published"
type: "article"
journal: "Journal of Computing in Civil Engineering"
volume: "40"
issue: "3"
pages: "04026020"
url: "https://ascelibrary.org/doi/pdf/10.1061/JCCEE5.CPENG-7090"
arxiv: "2504.14138"
github:
doi: "10.1061/JCCEE5.CPENG-7090"
list_image: "images/pubpic/sac.png"
highlight: 0
# - id: "Li_LabInvest2025_IPMN_1606"
# title: "1606 Cell-Centered Deep-Learning Feature Extraction Reveals Specific Stromal Features During Intraductal Papillary Mucinous Neoplasm Progression"
# authors: "Jiaqi Li, Philippe Brassard, Zhun Yang, Youssef Kotp, Alex,re Montpetit, Bich Nguyen, Guillaume Soucy, Mahdi S. Hosseini"
# year: 2025
# status: "published"
# type: "article"
# journal: "Laboratory Investigation"
# url: "https://www.laboratoryinvestigation.org/article/S0023-6837(24)03527-X/fulltext"
# list_image: "images/pubpic/ipmn_1606.jpg"
# highlight: 0
# - id: "Brassard_LabInvest2025_UNI_567"
# title: "567 Cell-Centered UNI Feature Extraction Accurately Classifies Colon Polyps, Highlights Microenvironmental Remodeling"
# authors: "Philippe Brassard, Hamza Khellaf, Jiaqi Li, Maxime Batardière, Youssef Kotp, Zhun Yang, Alex,re Montpetit, Mahdi S. Hosseini"
# year: 2025
# status: "published"
# type: "article"
# journal: "Laboratory Investigation"
# url: "https://www.laboratoryinvestigation.org/article/S0023-6837(24)02476-0/fulltext"
# list_image: "images/pubpic/uni_567.jpg"
# highlight: 0
- id: "Freiche_SPIE2025_US_LatentDiffusion"
title: "Ultrasound Image Generation using Latent Diffusion Models"
authors: "Baptiste Freiche, Asma El-Khoury, Ali Nasiri-Sarvi, Mahdi S. Hosseini, Daniel Garcia, Adrian Basarab"
year: 2025
status: "published"
type: "inproceedings"
booktitle: "Medical Imaging 2025: Ultrasonic Imaging, Tomography (SPIE Vol. 13412)"
url: "https://www.spiedigitallibrary.org/conference-proceedings-of-spie/13412/134121F/Ultrasound-image-generation-using-latent-diffusion-models/10.1117/12.3047788.full"
arxiv: "2502.08580"
github: "https://github.com/Toterino/US-image-generation"
doi: "10.1117/12.3047788"
list_image: "images/pubpic/ultrasound.png"
highlight: 0
- id: "Zhang_CVPR2025_2DMamba"
title: "2DMamba: Efficient State Space Model for Image Representation with Applications on Giga-Pixel Whole Slide Image Classification"
authors: "Jingwei Zhang, Anh Tien Nguyen, Xi Han, Vincent Quoc-Huy Trinh, Hong Qin, Dimitris Samaras, Mahdi S. Hosseini"
year: 2025
status: "published"
type: "inproceedings"
booktitle: "Proceedings of the IEEE/CVF Conference on Computer Vision, Pattern Recognition (CVPR 2025)"
url: "https://openaccess.thecvf.com/content/CVPR2025/html/Zhang_2DMamba_Efficient_State_Space_Model_for_Image_Representation_with_Applications_CVPR_2025_paper.html"
arxiv: "2412.00678"
github: "https://github.com/AtlasAnalyticsLab/2DMamba"
doi: "10.1109/cvpr52734.2025.00339"
list_image: "images/pubpic/2dmamba.png"
highlight: 0
- id: "Thakkar_arXiv2024_DiffusionCompPath"
title: "Comparative Analysis of Diffusion Generative Models in Computational Pathology"
authors: "Denisha Thakkar, Vincent Quoc-Huy Trinh, Sonal Varma, Samira Ebrahimi Kahou, Hassan Rivaz, Mahdi S. Hosseini"
year: 2024
status: "under_review"
type: "article"
journal: "arXiv:2411.15719"
arxiv: "2411.15719"
github: "https://github.com/AtlasAnalyticsLab/Diffusion4Path"
list_image: "images/pubpic/diffusion_comp.png"
highlight: 0
- id: "Hosseini_JPI2024_Survey"
title: "Computational Pathology: A Survey Review, the Way Forward"
authors: "Mahdi S. Hosseini, Babak Ehteshami Bejnordi, Vincent Quoc-Huy Trinh, Lyndon Chan, Danial Hasan, Xiang Li, Shuo Yang, others"
year: 2024
status: "published"
type: "article"
journal: "Journal of Pathology Informatics"
volume: "15"
pages: "100357"
url: "https://pmc.ncbi.nlm.nih.gov/articles/PMC10900832/"
arxiv: "2304.05482"
doi: "10.1016/j.jpi.2023.100357"
github: "https://github.com/AtlasAnalyticsLab/CPath_Survey"
list_image: "images/pubpic/cpath_survey.jpg"
highlight: 0
- id: "Notton_arXiv2024_BarlowTwins_Colon"
title: "Efficient Self-Supervised Barlow Twins from Limited Tissue Slide Cohorts for Colonic Pathology Diagnostics"
authors: "Charles Notton, Varun Sharma, Vincent Quoc-Huy Trinh, Liang Chen, Ming Xu, Sonal Varma, Mahdi S. Hosseini"
year: 2025
status: "published"
type: "article"
journal: "Medical Image Analysis"
url: "https://www.semanticscholar.org/paper/Efficient-Self-Supervised-Barlow-Twins-from-Limited-Notton-Sharma/a3e6ce451690f49e78819afa87e6fde6a55b44a0"
arxiv: "2411.05959"
github: "https://github.com/AtlasAnalyticsLab/PathBT"
list_image: "images/pubpic/barlow_colon.png"
highlight: 0
- id: "Nasiri_LNCS2025_BreastUS_VMamba"
title: "Vision Mamba for Classification of Breast Ultrasound Images"
authors: "Ali Nasiri-Sarvi, Mahdi S. Hosseini, Hassan Rivaz"
year: 2025
status: "published"
type: "inproceedings"
booktitle: "Deep Breast Workshop on AI, Imaging for Diagnostic, Treatment Challenges in Breast Care (LNCS 15451)"
url: "https://link.springer.com/chapter/10.1007/978-3-031-77789-9_15"
github: "https://github.com/IMPACT-L/BU-Mamba"
arxiv: "2407.03552"
doi: "10.1007/978-3-031-77789-9_15"
list_image: "images/pubpic/breast-mamba.png"
highlight: 0
- id: "Gomes_ICLR2025_AdaFisher"
title: "AdaFisher: Adaptive Second Order Optimization via Fisher Information"
authors: "Daniel Martins Gomes, Yiming Zhang, Evgenii Beliakov, Guillaume Wolf, Mahdi S. Hosseini"
year: 2025
status: "published"
type: "inproceedings"
booktitle: "International Conference on Learning Representations (ICLR 2025)"
url: "https://openreview.net/pdf?id=puTxuiK2qO"
arxiv: "2405.16397"
github: "https://github.com/AtlasAnalyticsLab/AdaFisher"
poster: "https://iclr.cc/media/iclr-2025/Slides/28275_Uy3dOo0.pdf"
list_image: "images/pubpic/adafisher.png"
highlight: 0
- id: "Nasiri_CVPRW2024_Vim4Path"
title: "Vim4Path: Self-Supervised Vision Mamba for Histopathology Images"
authors: "Ali Nasiri-Sarvi, Vincent Quoc-Huy Trinh, Hassan Rivaz, Mahdi S. Hosseini"
year: 2024
status: "published"
type: "inproceedings"
booktitle: "Proceedings of the IEEE/CVF Conference on Computer Vision, Pattern Recognition (CVPR 2024)"
url: "https://openaccess.thecvf.com/content/CVPR2024W/CVMI/html/Nasiri-Sarvi_Vim4Path_Self-Supervised_Vision_Mamba_for_Histopathology_Images_CVPRW_2024_paper.html"
arxiv: "2404.13222"
github: "https://github.com/AtlasAnalyticsLab/Vim4Path"
doi: "10.1109/cvprw63382.2024.00683"
list_image: "images/pubpic/vim4path.png"
highlight: 0