carousel

Author: celrm

_bibliography/references.bib

@@ -20,7 +20,18 @@ @inproceedings{
 year={2024},
 url={https://openreview.net/forum?id=IfZwSRpqHl},
 pdf={https://openreview.net/pdf?id=IfZwSRpqHl},
-abstract={Graph neural networks exhibiting a rescale invariance, like GATs, obey a conservation law of its parameters, which has been exploited to derive a balanced state that induces good initial trainability. Yet, finite learning rates as used in practice topple the network out of balance during training. This effect is even more pronounced with larger learning rates that tend to induce improved generalization but make the training dynamics less robust. To support even larger learning rates, we propose to dynamically balance the network according to a different criterion, based on relative gradients, that promotes faster and better. In combination with large learning rates and gradient clipping, dynamic rebalancing significantly improves generalization on real-world data. We observe that rescaling provides us with the flexibility to control the order in which network layers are trained. This leads to novel insights into similar phenomena as grokking, which can further boost generalization performance.},
+abstract={Graph neural networks exhibiting a rescale invariance, like GATs, obey a conservation law of its parameters, which has been exploited to derive a balanced state that induces good initial trainability. Yet, finite learning rates as used in practice topple the network out of balance during training. This effect is even more pronounced with larger learning rates that tend to induce improved generalization but make the training dynamics less robust. To support even larger learning rates, we propose to dynamically balance the network according to a different criterion, based on relative gradients, that promotes faster and better. In combination with large learning rates and gradient clipping, dynamic rebalancing significantly improves generalization on real-world data. We observe that rescaling provides us with the flexibility to control the order in which network layers are trained. This leads to novel insights into similar phenomena as grokking, which can further boost generalization performance.}
+}
+
+@article{Hossain2024,
+author = {Hossain,  Intekhab and Fanfani,  Viola and Fischer,  Jonas and Quackenbush,  John and Burkholz,  Rebekka},
+title={Biologically informed NeuralODEs for genome-wide regulatory dynamics},
+journal={Genome Biology},
+year={2024},
+month={May},
+volume={25},
+url={https://doi.org/10.1186/s13059-024-03264-0},
+abstract={Gene regulatory network (GRN) models that are formulated as ordinary differential equations (ODEs) can accurately explain temporal gene expression patterns and promise to yield new insights into important cellular processes, disease progression, and intervention design. Learning such gene regulatory ODEs is challenging, since we want to predict the evolution of gene expression in a way that accurately encodes the underlying GRN governing the dynamics and the nonlinear functional relationships between genes. Most widely used ODE estimation methods either impose too many parametric restrictions or are not guided by meaningful biological insights, both of which impede either scalability, explainability, or both.}
 }
 
 @inproceedings{

_data/news.yml

@@ -1,5 +1,5 @@
 - date: 25. September 2024
-  headline: "Our two papers were accepted at NeurIPS 2024 (see [publications](/publications))!"
+  headline: "Our three papers were accepted at NeurIPS 2024 (see [publications](/publications))!"
 
 - date: 1. June 2024
   headline: "Welcome to Chao, Rahul, and Dong!"

_data/team_members.yml

@@ -16,6 +16,13 @@
       email: [email protected]
       url: https://chaoedisonzhouucl.github.io/
 
+    - name: Dr. Gowtham Abbavaram
+      last_name: Abbavaram
+      photo: 
+      start_date: Oct 2024
+      email: [email protected]
+      url: https://gautam0707.github.io/
+
 - role: PhD students
   members:
     - name: Advait Gadhikar

_layouts/homelay.html

@@ -5,18 +5,18 @@
 <div id="homeid" class="col-sm-8">
 
   <!-- carousel -->
-  <!-- <div id="carousel" class="carousel slide" data-ride="carousel" style="margin: auto; width: 100%;">
+  <div id="carousel" class="carousel slide" data-interval="false" data-ride="carousel" style="margin: auto; width: 100%;">
     <ol class="carousel-indicators">
         <li data-target="#carousel" data-slide-to="0" class="active"></li>
         <li data-target="#carousel" data-slide-to="1"></li>
     </ol>
     <div class="carousel-inner">
         <div class="item active">
-          <img src="{{ site.url }}{{ site.baseurl }}/images/group-cropped.jpg"  alt="Slide 1" 
+          <img src="{{ site.url }}{{ site.baseurl }}/images/group/1.jpg"  alt="Slide 1" 
           style="width: 100%; border-radius: 40px; margin-left: auto;">
         </div>
         <div class="item">
-          <img src="{{ site.url }}{{ site.baseurl }}/images/group-cropped.jpg" alt="Slide 2" 
+          <img src="{{ site.url }}{{ site.baseurl }}/images/group/2.jpg" alt="Slide 2" 
           style="width: 100%; border-radius: 40px; margin-left: auto;">
         </div>
     </div>
@@ -28,10 +28,10 @@
     <span class="glyphicon glyphicon-chevron-right" aria-hidden="true"></span>
     <span class="sr-only">Next</span>
   </a>
-</div> -->
+</div>
 
-<img src="{{ site.url }}{{ site.baseurl }}/images/group-cropped.jpg" alt="Slide 2" 
-style="width: 100%; border-radius: 40px; margin-left: auto;">
+<!-- <img src="{{ site.url }}{{ site.baseurl }}/images/group-cropped.jpg" alt="Slide 2" 
+style="width: 100%; border-radius: 40px; margin-left: auto;"> -->
 
 {{ content }}
 

_pages/team.md

@@ -8,50 +8,41 @@ permalink: /team/
 
 # Team Members
 
-{% assign first = 0 %}
 {% for group in site.data.team_members %}
 {% assign number_printed = 0 %}
 {% for member in group.members %}
 
 {% assign even_odd = number_printed | modulo: 2 %}
-{% if even_odd == 0 and first != 1 %}
+{% if even_odd == 0 %}
 <div class="row">
 {% endif %}
 
-{% if forloop.first and first > 1 %}
+{% if forloop.first %}
 <h3 style="margin-left:16px;" >{{group.role}}</h3>
 {% endif %}
 
 <div class="col-sm-6 clearfix">
 
-{% if first < 2 %}
-<h3>{{group.role}}</h3>
-{% endif %}
 
 {% if member.photo %}
-  <img src="{{ site.url }}{{ site.baseurl }}/images/team/{{ member.photo }}" 
+  <img src="{{ site.url }}{{ site.baseurl }}/images/team members/{{ member.photo }}" 
   class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" />
 {% else %}
-  <img src="{{ site.url }}{{ site.baseurl }}/images/team/blank.jpg"
+  <img src="{{ site.url }}{{ site.baseurl }}/images/team members/blank.jpg"
   class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" />
 {% endif %}
-{% if first > 1 %}
-  <h4 style="margin-top:-11px;">{{ member.name }}</h4>
-{% else %}
   <h4>{{ member.name }}</h4>
-{% endif %}
   [Homepage]({{ member.url }})
   | [Email](mailto:{{ member.email }})
   <br>
   <i>since {{ member.start_date }}</i>
 </div>
 
-{% if even_odd == 1 or forloop.last and first != 0 %}
+{% if even_odd == 1 or forloop.last %}
 </div>
 {% endif %}
 
 {% assign number_printed = number_printed | plus: 1 %}
-{% assign first = first | plus: 1 %}
 
 {% endfor %}
 {% endfor %}

_site/images/group/1.jpg

@@ -69,18 +69,18 @@
         <div id="homeid" class="col-sm-8">
 
   <!-- carousel -->
-  <!-- <div id="carousel" class="carousel slide" data-ride="carousel" style="margin: auto; width: 100%;">
+  <div id="carousel" class="carousel slide" data-interval="false" data-ride="carousel" style="margin: auto; width: 100%;">
     <ol class="carousel-indicators">
         <li data-target="#carousel" data-slide-to="0" class="active"></li>
         <li data-target="#carousel" data-slide-to="1"></li>
     </ol>
     <div class="carousel-inner">
         <div class="item active">
-          <img src="/images/group-cropped.jpg"  alt="Slide 1" 
+          <img src="/images/group/1.jpg"  alt="Slide 1" 
           style="width: 100%; border-radius: 40px; margin-left: auto;">
         </div>
         <div class="item">
-          <img src="/images/group-cropped.jpg" alt="Slide 2" 
+          <img src="/images/group/2.jpg" alt="Slide 2" 
           style="width: 100%; border-radius: 40px; margin-left: auto;">
         </div>
     </div>
@@ -92,10 +92,10 @@
     <span class="glyphicon glyphicon-chevron-right" aria-hidden="true"></span>
     <span class="sr-only">Next</span>
   </a>
-</div> -->
+</div>
 
-<img src="/images/group-cropped.jpg" alt="Slide 2" 
-style="width: 100%; border-radius: 40px; margin-left: auto;">
+<!-- <img src="/images/group-cropped.jpg" alt="Slide 2" 
+style="width: 100%; border-radius: 40px; margin-left: auto;"> -->
 
 <h1 id="relational-ml-lab">Relational ML Lab</h1>
 
@@ -121,7 +121,7 @@ <h3>News</h3>
 <div class="well">
 
 <b>25 Sep 2024</b>
-<p>Our two papers were accepted at NeurIPS 2024 (see <a href="/publications">publications</a>)!</p>
+<p>Our three papers were accepted at NeurIPS 2024 (see <a href="/publications">publications</a>)!</p>
 
 <hr/>
 

_site/images/group-cropped.jpg renamed to _site/images/group/2.jpg

@@ -72,7 +72,7 @@ <h1 id="news">News</h1>
 <hr />
 
 <h4>25 September 2024</h4>
-<p>Our two papers were accepted at NeurIPS 2024 (see <a href="/publications">publications</a>)!</p>
+<p>Our three papers were accepted at NeurIPS 2024 (see <a href="/publications">publications</a>)!</p>
 
 <hr />
 

_site/images/team/2023-10-21.jpg renamed to _site/images/group/all/2023-10-21.jpg

@@ -73,6 +73,7 @@ <h1 id="publications">Publications</h1>
     <option value="">All members</option>
     <option value="Burkholz">Dr. Rebekka Burkholz</option>
     <option value="Zhou">Dr. Chao Zhou</option>
+    <option value="Abbavaram">Dr. Gowtham Abbavaram</option>
     <option value="Gadhikar">Advait Gadhikar</option>
     <option value="Mustafa">Nimrah Mustafa</option>
     <option value="Rubio-Madrigal">Celia Rubio-Madrigal</option>
@@ -183,6 +184,56 @@ <h1 id="publications">Publications</h1>
 <li><!-- _layouts/bib.html -->
 
 
+  <div class="row" style="margin-top: 30px;" id="bib-Hossain2024" authors="HossainFanfaniFischerQuackenbushBurkholz">
+        <div class="preview"><img class="preview z-depth-1 rounded" src="/images/publications/default.png" /></div>
+        <!-- Entry bib key -->
+        <div id="Hossain2024" class="col-sm-10">
+        <!-- Title -->
+        
+          <div class="title"><a href="https://doi.org/10.1186/s13059-024-03264-0"><b>Biologically informed NeuralODEs for genome-wide regulatory dynamics</b></a></div>
+        
+        <!-- Author -->
+        <div class="author">
+        
+
+        Intekhab Hossain,&nbsp;Viola Fanfani,&nbsp;Jonas Fischer,&nbsp;John Quackenbush,&nbsp;and&nbsp;Rebekka Burkholz</div>
+
+        <!-- Journal/Book title and date -->
+        
+        
+        <div class="periodical">
+          <em>Genome Biology</em>, May 2024
+        </div>
+        <div class="periodical">
+          
+        </div>
+
+          <!-- Links/Buttons -->
+        <div class="links"><a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a>
+            <a class="abstract btn btn-sm z-depth-0" role="button">Abs</a>
+          </div>
+          
+
+          <!-- Hidden abstract block -->
+          <div class="abstract hidden">
+            <p>Gene regulatory network (GRN) models that are formulated as ordinary differential equations (ODEs) can accurately explain temporal gene expression patterns and promise to yield new insights into important cellular processes, disease progression, and intervention design. Learning such gene regulatory ODEs is challenging, since we want to predict the evolution of gene expression in a way that accurately encodes the underlying GRN governing the dynamics and the nonlinear functional relationships between genes. Most widely used ODE estimation methods either impose too many parametric restrictions or are not guided by meaningful biological insights, both of which impede either scalability, explainability, or both.</p>
+          </div><!-- Hidden bibtex block -->
+          <div class="bibtex hidden">
+            <figure class="highlight"><pre><code class="language-bibtex" data-lang="bibtex"><span class="nc">@article</span><span class="p">{</span><span class="nl">Hossain2024</span><span class="p">,</span>
+  <span class="na">author</span> <span class="p">=</span> <span class="s">{Hossain, Intekhab and Fanfani, Viola and Fischer, Jonas and Quackenbush, John and Burkholz, Rebekka}</span><span class="p">,</span>
+  <span class="na">title</span> <span class="p">=</span> <span class="s">{Biologically informed NeuralODEs for genome-wide regulatory dynamics}</span><span class="p">,</span>
+  <span class="na">journal</span> <span class="p">=</span> <span class="s">{Genome Biology}</span><span class="p">,</span>
+  <span class="na">year</span> <span class="p">=</span> <span class="s">{2024}</span><span class="p">,</span>
+  <span class="na">month</span> <span class="p">=</span> <span class="nv">may</span><span class="p">,</span>
+  <span class="na">volume</span> <span class="p">=</span> <span class="s">{25}</span><span class="p">,</span>
+  <span class="na">url</span> <span class="p">=</span> <span class="s">{https://doi.org/10.1186/s13059-024-03264-0}</span>
+<span class="p">}</span></code></pre></figure>
+          </div>
+        </div>
+      </div></li>
+<li><!-- _layouts/bib.html -->
+
+
   <div class="row" style="margin-top: 30px;" id="bib-mustafa2024gate" authors="MustafaBurkholz">
         <div class="preview"><img class="preview z-depth-1 rounded" src="/images/publications/default.png" /></div>
         <!-- Entry bib key -->

_site/images/group/all/2024-10-03.jpg

@@ -71,34 +71,47 @@ <h1 id="team-members">Team Members</h1>
 
 <div class="row">
 
-  <div class="col-sm-6 clearfix">
+  <h3 style="margin-left:16px;">Faculty</h3>
 
-    <h3>Faculty</h3>
+  <div class="col-sm-6 clearfix">
 
-    <p><img src="/images/team/rebekka.burkholz.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
+    <p><img src="/images/team members/rebekka.burkholz.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
 
     <h4>Dr. Rebekka Burkholz</h4>
-
     <p><a href="https://sites.google.com/view/rebekkaburkholz/">Homepage</a>
   | <a href="mailto:[email protected]">Email</a>
   <br />
   <i>since 2021</i></p>
   </div>
 
-  <div class="col-sm-6 clearfix">
+</div>
+
+<div class="row">
 
-    <h3>PostDocs</h3>
+  <h3 style="margin-left:16px;">PostDocs</h3>
 
-    <p><img src="/images/team/chao.zhou.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
+  <div class="col-sm-6 clearfix">
 
-    <h4>Dr. Chao Zhou</h4>
+    <p><img src="/images/team members/chao.zhou.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
 
+    <h4>Dr. Chao Zhou</h4>
     <p><a href="https://chaoedisonzhouucl.github.io/">Homepage</a>
   | <a href="mailto:[email protected]">Email</a>
   <br />
   <i>since May 2024</i></p>
   </div>
 
+  <div class="col-sm-6 clearfix">
+
+    <p><img src="/images/team members/blank.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
+
+    <h4>Dr. Gowtham Abbavaram</h4>
+    <p><a href="https://gautam0707.github.io/">Homepage</a>
+  | <a href="mailto:[email protected]">Email</a>
+  <br />
+  <i>since Oct 2024</i></p>
+  </div>
+
 </div>
 
 <div class="row">
@@ -107,10 +120,9 @@ <h3 style="margin-left:16px;">PhD students</h3>
 
   <div class="col-sm-6 clearfix">
 
-    <p><img src="/images/team/advait.gadhikar.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
-
-    <h4 style="margin-top:-11px;">Advait Gadhikar</h4>
+    <p><img src="/images/team members/advait.gadhikar.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
 
+    <h4>Advait Gadhikar</h4>
     <p><a href="https://advaitgadhikar.github.io/">Homepage</a>
   | <a href="mailto:[email protected]">Email</a>
   <br />
@@ -119,10 +131,9 @@ <h4 style="margin-top:-11px;">Advait Gadhikar</h4>
 
   <div class="col-sm-6 clearfix">
 
-    <p><img src="/images/team/nimrah.mustafa.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
-
-    <h4 style="margin-top:-11px;">Nimrah Mustafa</h4>
+    <p><img src="/images/team members/nimrah.mustafa.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
 
+    <h4>Nimrah Mustafa</h4>
     <p><a href="https://cispa.de/en/people/c01nimu">Homepage</a>
   | <a href="mailto:[email protected]">Email</a>
   <br />
@@ -135,10 +146,9 @@ <h4 style="margin-top:-11px;">Nimrah Mustafa</h4>
 
   <div class="col-sm-6 clearfix">
 
-    <p><img src="/images/team/celia.rubio-madrigal.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
-
-    <h4 style="margin-top:-11px;">Celia Rubio-Madrigal</h4>
+    <p><img src="/images/team members/celia.rubio-madrigal.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
 
+    <h4>Celia Rubio-Madrigal</h4>
     <p><a href="https://celrm.github.io/">Homepage</a>
   | <a href="mailto:[email protected]">Email</a>
   <br />
@@ -147,10 +157,9 @@ <h4 style="margin-top:-11px;">Celia Rubio-Madrigal</h4>
 
   <div class="col-sm-6 clearfix">
 
-    <p><img src="/images/team/tom.jacobs.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
-
-    <h4 style="margin-top:-11px;">Tom Jacobs</h4>
+    <p><img src="/images/team members/tom.jacobs.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
 
+    <h4>Tom Jacobs</h4>
     <p><a href="https://cispa.de/en/people/c01toja">Homepage</a>
   | <a href="mailto:[email protected]">Email</a>
   <br />
@@ -163,10 +172,9 @@ <h4 style="margin-top:-11px;">Tom Jacobs</h4>
 
   <div class="col-sm-6 clearfix">
 
-    <p><img src="/images/team/blank.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
-
-    <h4 style="margin-top:-11px;">Rahul Nittala</h4>
+    <p><img src="/images/team members/blank.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
 
+    <h4>Rahul Nittala</h4>
     <p><a href="https://cispa.de/en/people/c01rani">Homepage</a>
   | <a href="mailto:[email protected]">Email</a>
   <br />
@@ -175,10 +183,9 @@ <h4 style="margin-top:-11px;">Rahul Nittala</h4>
 
   <div class="col-sm-6 clearfix">
 
-    <p><img src="/images/team/dong.sun.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
-
-    <h4 style="margin-top:-11px;">Dong Sun</h4>
+    <p><img src="/images/team members/dong.sun.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
 
+    <h4>Dong Sun</h4>
     <p><a href="https://cispa.de/en/people/c01dosu">Homepage</a>
   | <a href="mailto:[email protected]">Email</a>
   <br />
@@ -193,10 +200,9 @@ <h3 style="margin-left:16px;">Research assistants (HiWis)</h3>
 
   <div class="col-sm-6 clearfix">
 
-    <p><img src="/images/team/adarsh.jamadandi.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
-
-    <h4 style="margin-top:-11px;">Adarsh Jamadandi</h4>
+    <p><img src="/images/team members/adarsh.jamadandi.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
 
+    <h4>Adarsh Jamadandi</h4>
     <p><a href="https://adarshmj.github.io">Homepage</a>
   | <a href="mailto:[email protected]">Email</a>
   <br />