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‎_bibliography/references.bib

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author = {Hossain, Intekhab and Fischer, Jonas and Burkholz, Rebekka and Quackenbush, John},
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booktitle={Thirty-eighth Conference on Neural Information Processing Systems},
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year={2024},
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url={https://openreview.net/forum?id=FNtsZLwkGr},
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pdf={https://openreview.net/pdf?id=FNtsZLwkGr},
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abstract={The practical utility of machine learning models in the sciences often hinges on their interpretability. It is common to assess a model's merit for scientific discovery, and thus novel insights, by how well it aligns with already available domain knowledge - a dimension that is currently largely disregarded in the comparison of neural network models. While pruning can simplify deep neural network architectures and excels in identifying sparse models, as we show in the context of gene regulatory network inference, state-of-the-art techniques struggle with biologically meaningful structure learning. To address this issue, we propose DASH, a generalizable framework that guides network pruning by using domain-specific structural information in model fitting and leads to sparser, better interpretable models that are more robust to noise. Using both synthetic data with ground truth information, as well as real-world gene expression data, we show that DASH, using knowledge about gene interaction partners within the putative regulatory network, outperforms general pruning methods by a large margin and yields deeper insights into the biological systems being studied.}
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}
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‎_data/alumni_members.yml

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- role: Research assistants (HiWis)
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members:
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- name: Adarsh Jamadandi
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last_name: Jamadandi
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photo: adarsh.jamadandi.jpg
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start_date: Nov 2022
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end_date: Oct 2024
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email: [email protected]
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url: https://adarshmj.github.io
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- name: Harsha Nelaturu
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last_name: Nelaturu
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photo: harsha.nelaturu.jpg

‎_data/team_members.yml

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- name: Dr. Gowtham Abbavaram
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last_name: Abbavaram
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photo:
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photo: gowtham.abbavaram.jpg
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start_date: Oct 2024
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email: [email protected]
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url: https://gautam0707.github.io/
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photo: dong.sun.jpg
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start_date: Jul 2024
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email: [email protected]
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url: https://cispa.de/en/people/c01dosu
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- role: Research assistants (HiWis)
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members:
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- name: Adarsh Jamadandi
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last_name: Jamadandi
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photo: adarsh.jamadandi.jpg
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start_date: Nov 2022
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email: [email protected]
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url: https://adarshmj.github.io
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url: https://cispa.de/en/people/c01dosu

‎_site/images/team members/gowtham.abbavaram.jpg

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‎_site/publications/index.html

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<option value="Jacobs">Tom Jacobs</option>
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<option value="Nittala">Rahul Nittala</option>
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<option value="Sun">Dong Sun</option>
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<option value="Jamadandi">Adarsh Jamadandi</option>
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</select></p>
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<ol class="bibliography"><li><!-- _layouts/bib.html -->
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<div id="hossain2024pruning" class="col-sm-10">
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<!-- Title -->
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<div class="title"><b>Pruning neural network models for gene regulatory dynamics using data and domain knowledge</b></div>
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<div class="title"><a href="https://openreview.net/forum?id=FNtsZLwkGr"><b>Pruning neural network models for gene regulatory dynamics using data and domain knowledge</b></a></div>
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<!-- Author -->
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<div class="author">
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<!-- Links/Buttons -->
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<div class="links"><a class="conf btn btn-sm z-depth-0">NeurIPS</a><a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a>
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<a class="abstract btn btn-sm z-depth-0" role="button">Abs</a>
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<a href="https://openreview.net/pdf?id=FNtsZLwkGr" class="btn btn-sm z-depth-0" role="button">PDF</a>
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</div>
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<span class="na">title</span> <span class="p">=</span> <span class="s">{Pruning neural network models for gene regulatory dynamics using data and domain knowledge}</span><span class="p">,</span>
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<span class="na">author</span> <span class="p">=</span> <span class="s">{Hossain, Intekhab and Fischer, Jonas and Burkholz, Rebekka and Quackenbush, John}</span><span class="p">,</span>
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<span class="na">booktitle</span> <span class="p">=</span> <span class="s">{Thirty-eighth Conference on Neural Information Processing Systems}</span><span class="p">,</span>
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<span class="na">year</span> <span class="p">=</span> <span class="s">{2024}</span>
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<span class="na">year</span> <span class="p">=</span> <span class="s">{2024}</span><span class="p">,</span>
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<span class="na">url</span> <span class="p">=</span> <span class="s">{https://openreview.net/forum?id=FNtsZLwkGr}</span><span class="p">,</span>
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<span class="p">}</span></code></pre></figure>
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</div>
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‎_site/team/index.html

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<div class="col-sm-6 clearfix">
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<p><img src="/images/team members/blank.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
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<p><img src="/images/team members/gowtham.abbavaram.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
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<h4>Dr. Gowtham Abbavaram</h4>
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<p><a href="https://gautam0707.github.io/">Homepage</a>
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</div>
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<div class="row">
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<h3 style="margin-left:16px;">Research assistants (HiWis)</h3>
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<div class="col-sm-6 clearfix">
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<p><img src="/images/team members/adarsh.jamadandi.jpg" class="img-responsive" width="20%" style="float: left; margin: 0px 22px 24px 0;" /></p>
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<h4>Adarsh Jamadandi</h4>
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<p><a href="https://adarshmj.github.io">Homepage</a>
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| <a href="mailto:[email protected]">Email</a>
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<br />
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<i>since Nov 2022</i></p>
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</div>
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</div>
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<h2 id="alumni">Alumni</h2>
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<h3>Research assistants (HiWis)</h3>
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<ul>
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<li style="margin-left:-16px;"><a href="https://adarshmj.github.io">Adarsh Jamadandi</a>:
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<i>Nov 2022 - Oct 2024</i>.</li>
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<li style="margin-left:-16px;"><a href="https://nelaturuharsha.github.io/">Harsha Nelaturu</a>:
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<i>Aug 2023 - Jul 2024</i>.</li>
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‎images/team members/gowtham.abbavaram.jpg

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