diff --git a/Gemfile b/Gemfile index 5e62951..0e50aad 100644 --- a/Gemfile +++ b/Gemfile @@ -5,7 +5,7 @@ # Specifies Ruby gem dependencies for Jekyll site build. # # Ruby Version: -# 3.4.7+ (latest stable as of October 18, 2025) +# 3.4.7+; tested with Ruby 4.0.5 # # Key Dependencies: # - jekyll 4.4.1+: Static site generator @@ -24,7 +24,7 @@ source 'https://rubygems.org' -ruby "3.4.7" +ruby ">= 3.4.7", "< 5.0" gem "jekyll", "4.4.1" # gem "github-pages", "~> 232", group: :jekyll_plugins diff --git a/README.md b/README.md index a26f704..cef1feb 100644 --- a/README.md +++ b/README.md @@ -214,6 +214,7 @@ This setting affects the entire site including header, footer, and content areas ## Project Sites - **AtlasPatch:** https://atlasanalyticslab.github.io/AtlasPatch/ (linked from the header -> Projects dropdown) +- **MOOZY:** https://atlasanalyticslab.github.io/MOOZY/ (linked from the header -> Projects dropdown) --- diff --git a/_data/news.yml b/_data/news.yml index dcdc24b..932452c 100644 --- a/_data/news.yml +++ b/_data/news.yml @@ -115,6 +115,18 @@ # headline: '🎂 Happy Birthday to Omar Abdelwahed!' #============================================================================== +- date: June 17, 2026 + headline: "**MOOZY** accepted in [European Conference on Computer Vision (ECCV 2026)](https://eccv.ecva.net/Conferences/2026)! [Project page](https://atlasanalyticslab.github.io/MOOZY/)." + +- date: April 30, 2026 + headline: "**Simple Token-Efficient VLM** paper accepted in [International Conference on Deep Learning Theory and Applications (DeLTA 2026)](https://www.insticc.org/node/technicalprogram/DeLTA/2026)!" + +- date: March 20, 2026 + headline: "**SPARC** accepted in [Transactions on Machine Learning Research (TMLR)](https://openreview.net/forum?id=IJfvoc2GbZ)!" + +- date: February 6, 2026 + headline: "**Segment Any Crack** paper published in [Journal of Computing in Civil Engineering](https://ascelibrary.org/doi/10.1061/JCCEE5.CPENG-7090)!" + - date: February 5, 2026 headline: "We've released **AtlasPatch**! Visit the project page [here](https://atlasanalyticslab.github.io/AtlasPatch/)." diff --git a/_data/publications.yml b/_data/publications.yml index d2b41bd..cd61fc3 100644 --- a/_data/publications.yml +++ b/_data/publications.yml @@ -23,6 +23,8 @@ # - doi: Digital Object Identifier # - url: Publication webpage # - github: GitHub repository URL +# - huggingface: Hugging Face model/dataset/space URL +# - pypi: Python package 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) @@ -38,6 +40,61 @@ # list_image: "images/pubpic/survey.jpg" #============================================================================== +- id: "Rostami_arXiv2026_FisherAdapTune" + title: "Fisher-Guided Progressive Parameter Selection for Adaptive Fine-Tuning" + authors: "Ghodsiyeh Rostami, Po-Han Chen, Mahdi S. Hosseini" + year: 2026 + status: "under_review" + type: "article" + journal: "arXiv:2606.10196" + arxiv: "2606.10196" + github: "https://github.com/AtlasAnalyticsLab/FisherAdapTune" + list_image: "images/pubpic/FisherAdapTune.png" + highlight: 0 + +- id: "Yang_arXiv2026_TokenEfficientVLM" + title: "Simple Token-Efficient Vision-Language Model for Case-level Pathology Synoptic Report Generation" + authors: "Zhiyuan Yang, Jiahao Cheng, Vincent Quoc-Huy Trinh, Mahdi S. Hosseini" + year: 2026 + status: "published" + type: "inproceedings" + booktitle: "International Conference on Deep Learning Theory and Applications (DeLTA 2026)" + arxiv: "2605.30716" + doi: "10.48550/arXiv.2605.30716" + list_image: "images/pubpic/PathoVLM.png" + highlight: 0 + +- id: "Kotp_arXiv2026_MOOZY" + title: "MOOZY: A Patient-First Foundation Model for Computational Pathology" + authors: "Yousef Kotp, Vincent Quoc-Huy Trinh, Christopher Pal, Mahdi S. Hosseini" + year: 2026 + status: "published" + type: "inproceedings" + booktitle: "European Conference on Computer Vision (ECCV 2026)" + url: "https://atlasanalyticslab.github.io/MOOZY/" + arxiv: "2603.27048" + github: "https://github.com/AtlasAnalyticsLab/MOOZY" + huggingface: "https://huggingface.co/AtlasAnalyticsLab/MOOZY" + pypi: "https://pypi.org/project/moozy/" + doi: "10.48550/arXiv.2603.27048" + list_image: "images/pubpic/MOOZY.png" + highlight: 0 + +- id: "Notton_MedIA2026_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: 2026 + status: "published" + type: "article" + journal: "Medical Image Analysis" + volume: "111" + pages: "104004" + arxiv: "2411.05959" + github: "https://github.com/AtlasAnalyticsLab/PathBT" + doi: "10.1016/j.media.2026.104004" + list_image: "images/pubpic/barlow_colon.png" + highlight: 0 + - 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" @@ -45,15 +102,14 @@ 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" + title: "AtlasPatch: Efficient Tissue Detection and High-throughput Patch Extraction for Computational Pathology at Scale" + authors: "Ahmed Alagha, Christopher Leclerc, Yousef Kotp, Omar Metwally, Calvin Moras, Peter Rentopoulos, Ghodsiyeh 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" @@ -61,20 +117,24 @@ url: "https://atlasanalyticslab.github.io/AtlasPatch/" arxiv: "2602.03998" github: "https://github.com/AtlasAnalyticsLab/AtlasPatch" + huggingface: "https://huggingface.co/AtlasAnalyticsLab/AtlasPatch" + pypi: "https://pypi.org/project/atlas-patch/" 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 + year: 2026 status: "published" type: "article" journal: "Journal of Pathology Informatics" + volume: "20" pages: "100537" url: "https://zenodo.org/records/15307021" doi: "10.1016/j.jpi.2025.100537" arxiv: "2507.05656" + github: "https://github.com/AtlasAnalyticsLab/ADPv2" list_image: "images/pubpic/adpv2d.png" highlight: 0 @@ -103,15 +163,17 @@ list_image: "images/pubpic/pathttt.png" highlight: 0 -- id: "Nasiri_arXiv2025_SPARC" - title: "SPARC: Concept-Aligned Sparse Autoencoders for Cross-Model, Cross-Modal Interpretability" +- id: "Nasiri_TMLR2026_SPARC" + title: "SPARC: Concept-Aligned Sparse Autoencoders for Cross-Model and Cross-Modal Interpretability" authors: "Ali Nasiri-Sarvi, Hassan Rivaz, Mahdi S. Hosseini" - year: 2025 - status: "under_review" + year: 2026 + status: "published" type: "article" - journal: "arXiv:2507.06265" + journal: "Transactions on Machine Learning Research (TMLR 2026)" + url: "https://openreview.net/forum?id=IJfvoc2GbZ" arxiv: "2507.06265" github: "https://github.com/AtlasAnalyticsLab/SPARC" + doi: "10.48550/arXiv.2507.06265" list_image: "images/pubpic/SPARC.png" highlight: 0 @@ -123,9 +185,10 @@ type: "article" journal: "Transactions on Machine Learning Research (TMLR 2025)" issn: "2835-8856" - url: "https://openreview.net/pdf?id=e1aXaIXblQ" + url: "https://openreview.net/forum?id=e1aXaIXblQ" arxiv: "2506.15976" github: "https://github.com/cvlab-stonybrook/LBMamba" + doi: "10.48550/arXiv.2506.15976" list_image: "images/pubpic/lbmamba.png" highlight: 0 @@ -146,26 +209,32 @@ 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" +# - id: "Brassard_LabInvest2025_UNI_567" +# title: "567 Cell-Centered UNI Feature Extraction Accurately Classifies Colon Polyps and Highlights Microenvironmental Remodeling" +# authors: "Patricia Brassard, Abdelhakim Khellaf, Jia Lin Li, Maelle Batardiere, Yousef Kotp, Zhiyuan Yang, Alexandra Montpetit, Genevieve Soucy, Bich Nguyen, Mahdi S. Hosseini, Vincent Quoc-Huy Trinh" # 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" +# volume: "105" +# issue: "3" +# pages: "102798" +# url: "https://www.laboratoryinvestigation.org/article/S0023-6837(24)02476-0/fulltext" +# doi: "10.1016/j.labinv.2024.102798" # 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" +# - id: "Li_LabInvest2025_IPMN_1606" +# title: "1606 Cell-Centered Deep-Learning Feature Extraction Reveals Specific Stromal Features During Intraductal Papillary Mucinous Neoplasm Progression" +# authors: "Jia Lin Li, Patricia Brassard, Zhiyuan Yang, Yousef Kotp, Alexandra Montpetit, Bich Nguyen, Genevieve Soucy, Mahdi S. Hosseini, Vincent Quoc-Huy Trinh, Abdelhakim Khellaf" # 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" +# volume: "105" +# issue: "3" +# pages: "103849" +# url: "https://www.laboratoryinvestigation.org/article/S0023-6837(24)03527-X/fulltext" +# doi: "10.1016/j.labinv.2024.103849" # highlight: 0 - id: "Freiche_SPIE2025_US_LatentDiffusion" @@ -182,6 +251,19 @@ list_image: "images/pubpic/ultrasound.png" highlight: 0 +- id: "Rostami_ISARC2025_CrackRecognition" + title: "Deep Learning for Automated Crack Recognition: Insights, Challenges, and Future Directions" + authors: "Ghodsiyeh Rostami, Po-Han Chen, Mahdi S. Hosseini" + year: 2025 + status: "published" + type: "inproceedings" + booktitle: "Proceedings of the International Symposium on Automation and Robotics in Construction (ISARC 2025)" + url: "https://www.iaarc.org/publications/2025_proceedings_of_the_42nd_isarc_montreal_canada/deep_learning_for_automated_crack_recognition_insights_challenges_and_future_directions.html" + doi: "10.22260/ISARC2025/0160" + video: "https://www.youtube.com/watch?v=QzHvcjeCmUA" + list_image: "images/pubpic/CrackRecognition2025.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" @@ -224,20 +306,6 @@ 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" @@ -259,9 +327,10 @@ status: "published" type: "inproceedings" booktitle: "International Conference on Learning Representations (ICLR 2025)" - url: "https://openreview.net/pdf?id=puTxuiK2qO" + url: "https://openreview.net/forum?id=puTxuiK2qO" arxiv: "2405.16397" github: "https://github.com/AtlasAnalyticsLab/AdaFisher" + doi: "10.48550/arXiv.2405.16397" poster: "https://iclr.cc/media/iclr-2025/Slides/28275_Uy3dOo0.pdf" list_image: "images/pubpic/adafisher.png" highlight: 0 diff --git a/_includes/header.html b/_includes/header.html index ce85150..ef43323 100644 --- a/_includes/header.html +++ b/_includes/header.html @@ -50,6 +50,12 @@ AtlasPatch +
  • + + MOOZY + +
  • Funding
    • diff --git a/_includes/publication-item.html b/_includes/publication-item.html index ab281c5..a4a2cf7 100644 --- a/_includes/publication-item.html +++ b/_includes/publication-item.html @@ -21,6 +21,8 @@ {% if entry.url %}{% assign link_count = link_count | plus: 1 %}{% endif %} {% if entry.arxiv %}{% assign link_count = link_count | plus: 1 %}{% endif %} {% if entry.github %}{% assign link_count = link_count | plus: 1 %}{% endif %} +{% if entry.huggingface %}{% assign link_count = link_count | plus: 1 %}{% endif %} +{% if entry.pypi %}{% assign link_count = link_count | plus: 1 %}{% endif %} {% if entry.doi %}{% assign link_count = link_count | plus: 1 %}{% endif %} {% if entry.video %}{% assign link_count = link_count | plus: 1 %}{% endif %} {% if entry.poster %}{% assign link_count = link_count | plus: 1 %}{% endif %} @@ -52,6 +54,12 @@ {% if entry.github %} [CODE] {% endif %} + {% if entry.huggingface %} + [HUGGINGFACE] + {% endif %} + {% if entry.pypi %} + [PYPI] + {% endif %} {% if entry.doi %} [DOI] {% endif %} diff --git a/css/main.scss b/css/main.scss index d3e9ae6..1378537 100644 --- a/css/main.scss +++ b/css/main.scss @@ -142,9 +142,13 @@ p.byline { z-index: 2000; } -.navbar .dropdown-item.project-link-atlaspatch { +.navbar .dropdown-item.project-link-atlaspatch, +.navbar .dropdown-item.project-link-moozy { font-family: system-ui, -apple-system, BlinkMacSystemFont, sans-serif; font-weight: 700; +} + +.navbar .dropdown-item.project-link-atlaspatch { color: #5b5bff; } @@ -153,6 +157,15 @@ p.byline { color: #5b5bff; } +.navbar .dropdown-item.project-link-moozy { + color: #000000; +} + +.navbar .dropdown-item.project-link-moozy:hover, +.navbar .dropdown-item.project-link-moozy:focus { + color: #000000; +} + .navbar .navbar-toggler { border-color: var(--atlas-border-color); color: var(--atlas-body-text); diff --git a/images/pubpic/CrackRecognition2025.png b/images/pubpic/CrackRecognition2025.png new file mode 100644 index 0000000..4c1d2fe Binary files /dev/null and b/images/pubpic/CrackRecognition2025.png differ diff --git a/images/pubpic/FisherAdapTune.png b/images/pubpic/FisherAdapTune.png new file mode 100644 index 0000000..7da0725 Binary files /dev/null and b/images/pubpic/FisherAdapTune.png differ diff --git a/images/pubpic/MOOZY.png b/images/pubpic/MOOZY.png new file mode 100644 index 0000000..22de596 Binary files /dev/null and b/images/pubpic/MOOZY.png differ diff --git a/images/pubpic/PathoVLM.png b/images/pubpic/PathoVLM.png new file mode 100644 index 0000000..9704298 Binary files /dev/null and b/images/pubpic/PathoVLM.png differ