Feature/update publications 2026 06 29

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

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)
 
 ---
 

_data/news.yml

@@ -115,6 +115,18 @@
 #     headline: '🎂 <strong>Happy Birthday</strong> 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/)."
 

_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)
@@ -38,43 +40,101 @@
 #     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"
   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"
+  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"
   journal: "arxiv:2602.03998"
   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

_includes/header.html

@@ -50,6 +50,12 @@
                 AtlasPatch
               </a>
             </li>
+            <li>
+              <a class="dropdown-item project-link-moozy" href="https://atlasanalyticslab.github.io/MOOZY/" target="_blank"
+                 rel="noopener noreferrer">
+                MOOZY
+              </a>
+            </li>
           </ul>
         </li>
         <li class="nav-item"><a class="nav-link" href="{{ site.url }}{{ site.baseurl }}/funding/">Funding</a></li>

_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 %}
             <a href="{{ entry.github }}">[CODE]</a>
           {% endif %}
+          {% if entry.huggingface %}
+            <a href="{{ entry.huggingface }}">[HUGGINGFACE]</a>
+          {% endif %}
+          {% if entry.pypi %}
+            <a href="{{ entry.pypi }}">[PYPI]</a>
+          {% endif %}
           {% if entry.doi %}
             <a href="https://doi.org/{{ entry.doi }}">[DOI]</a>
           {% endif %}

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);