add pubs, defense

Author: davevanveen

_bibliography/papers.bib

@@ -16,18 +16,10 @@ @article{vanveen2024clinical
   poster={poster_clin_summ.pdf},
 }
 
-@article{aali2024benchmark,
-    title={A Benchmark of Domain-Adapted Large Language Models for Generating Brief Hospital Course Summaries},
-    author={A. Aali and D. {Van Veen} and Y.I. Arefeen and J. Hom and C. Bluethgen and E.P. Reis and S. Gatidis and N. Clifford and J. Daws and A.S. Tehrani and J. Kim and A.S. Chaudhari},
-    journal={arXiv preprint arXiv:2403.05720},
-    year={2024},
-    pdf={https://arxiv.org/abs/2403.05720.pdf},
-}
-
 @article{stanford-aimi-chexagent-2024,
     title={CheXagent: Towards a Foundation Model for Chest X-Ray Interpretation},
     author={Z. Chen and M. Varma and J.B. Delbrouck and M. Paschali and L. Blankemeier and D. {Van Veen} and J.M.J. Valanarasu and A. Youssef and J.P. Cohen and E.P. Reis and E.B. Tsai and A. Johnston and C. Olsen and T.M. Abraham and S. Gatidis and A.S. Chaudhari and C.P. Langlotz},
-    journal={arXiv preprint arXiv:2401.12208},
+    journal={arXiv},
     year={2024},
     pdf={https://arxiv.org/abs/2401.12208.pdf},
     code={https://github.com/Stanford-AIMI/CheXagent},
@@ -36,6 +28,27 @@ @article{stanford-aimi-chexagent-2024
     demo={http://34.31.232.110:8888/},
 }
 
+@article {Gatti2024.05.06.24306965,
+        author = {A. Gatti and L. Blankemeier and D. {Van Veen} and B. Hargreaves and S.L. Delp and G.E. Gold and F. Kogan and A.S. Chaudhari},
+        title = {ShapeMed-Knee: A Dataset and Neural Shape Model Benchmark for Modeling 3D Femurs},
+        year = {2024},
+        doi = {10.1101/2024.05.06.24306965},
+        url={https://www.medrxiv.org/content/early/2024/05/07/2024.05.06.24306965},
+        journal = {medRxiv},
+	pdf={https://www.medrxiv.org/content/10.1101/2024.05.06.24306965v1.full.pdf},
+	code={https://github.com/gattia/ShapeMedKnee},
+	model={https://huggingface.co/aagatti/ShapeMedKnee},
+	data={https://huggingface.co/datasets/aagatti/ShapeMedKnee},
+}
+
+@article{aali2024benchmark,
+    title={A Benchmark of Domain-Adapted Large Language Models for Generating Brief Hospital Course Summaries},
+    author={A. Aali and D. {Van Veen} and Y.I. Arefeen and J. Hom and C. Bluethgen and E.P. Reis and S. Gatidis and N. Clifford and J. Daws and A.S. Tehrani and J. Kim and A.S. Chaudhari},
+    journal={arXiv},
+    year={2024},
+    pdf={https://arxiv.org/abs/2403.05720.pdf},
+}
+
 @inproceedings{gatti2024neural,
   title={Neural Shape Models Meaningfully Localize Features Relevant to Osteoarthritis Disease: Data from the Osteoarthritis Initiative},
   author={A. Gatti and L. Blankemeier and D. {Van Veen} and B. Hargreaves and S. Delp and F. Kogan and G. Gold and A.S. Chaudhari},
@@ -104,7 +117,7 @@ @inproceedings{vanusing
 @article{vanveen2020compressed,
       title={Compressed Sensing with Deep Image Prior and Learned Regularization}, 
       author={D. {Van Veen} and A. Jalal and M. Soltanolkotabi and E. Price and S. Vishwanath and A.G. Dimakis},
-      journal={arXiv preprint arXiv:1806.06438},
+      journal={arXiv},
       year={2020},
       pdf={https://arxiv.org/pdf/1806.06438.pdf},
       code={https://github.com/davevanveen/compsensing_dip},

_layouts/bib.liquid

@@ -164,9 +164,6 @@
       {% if entry.bibtex_show %}
         <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a>
       {% endif %}
-      {% if entry.html %}
-        <a href="{{ entry.html }}" class="btn btn-sm z-depth-0" role="button">HTML</a>
-      {% endif %}
       {% if entry.pdf %}
         {% if entry.pdf contains '://' %}
           <a href="{{ entry.pdf }}" class="btn btn-sm z-depth-0" role="button">PDF</a>
@@ -184,6 +181,15 @@
       {% if entry.video %}
         <a class="abstract btn btn-sm z-depth-0" role="button">Video</a>
       {% endif %}
+      {% if entry.model %}
+        <a class="abstract btn btn-sm z-depth-0" role="button">Model</a>
+      {% endif %}
+      {% if entry.dataset %}
+        <a class="abstract btn btn-sm z-depth-0" role="button">Dataset</a>
+      {% endif %}
+      {% if entry.demo %}
+        <a class="abstract btn btn-sm z-depth-0" role="button">Demo</a>
+      {% endif %}
       {% if entry.blog %}
         <a href="{{ entry.blog }}" class="btn btn-sm z-depth-0" role="button">Blog</a>
       {% endif %}
@@ -204,6 +210,9 @@
           <a href="{{ entry.slides | prepend: '/assets/pdf/' | relative_url }}" class="btn btn-sm z-depth-0" role="button">Slides</a>
         {% endif %}
       {% endif %}
+      {% if entry.html %}
+        <a href="{{ entry.html }}" class="btn btn-sm z-depth-0" role="button">Project page</a>
+      {% endif %}
       {% if entry.website %}
         <a href="{{ entry.website }}" class="btn btn-sm z-depth-0" role="button">Website</a>
       {% endif %}

_news/240524_defense.md

@@ -0,0 +1,7 @@
+---
+layout: post
+date: 2024-05-24 15:59:00-0400
+inline: true
+---
+
+Successfully defended my PhD thesis entitled [Data-Efficient Machine Learning for Image Reconstruction and Text Summarization in Biomedicine](https://docs.google.com/presentation/d/1YyZCnVaYZyuvUKWBewwCtS_-rVLPQ1pgT6l-lQgxmyE/edit?usp=sharing).