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‎_bibliography/papers.bib‎

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code={https://github.com/amirgroup-codes/cryoSENSE},
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website={https://cryosense.github.io},
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html={https://arxiv.org/abs/2511.12931},
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preview={ddpm.gif}
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preview={ddpm.gif},
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selected={true}
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}
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@article{10.1093/pnasnexus/pgaf334,
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html = {https://doi.org/10.1093/pnasnexus/pgaf334},
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website={https://life-tracer.github.io/},
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media={https://www.eurekalert.org/news-releases/1105981},
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preview={pnasnexus.png}
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preview={pnasnexus.png},
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selected={true}
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}
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‎_site/assets/jupyter/blog.ipynb.html‎

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<html lang="en">
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<head><meta charset="utf-8"/>
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<meta content="width=device-width, initial-scale=1.0" name="viewport"/>
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<title>jekyll-jupyter-notebook20251118-21031-1k4wua</title><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js"></script>
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<title>jekyll-jupyter-notebook20251118-31161-luib50</title><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js"></script>
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<style type="text/css">
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pre { line-height: 125%; }
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td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }

‎_site/blog/2024/tabs/index.html‎

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<p>With this you can generate visualizations like:</p>
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<ul id="log" class="tab" data-tab="b70bca1e-f814-4e81-a9be-bae11fe973b9" data-name="log">
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<ul id="log" class="tab" data-tab="a2621a9e-a679-4538-9b0b-ce4427cabd93" data-name="log">
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<li class="active" id="log-php">
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<a href="#">php </a>
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</li>
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</ul>
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<ul class="tab-content" id="b70bca1e-f814-4e81-a9be-bae11fe973b9" data-name="log">
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<ul class="tab-content" id="a2621a9e-a679-4538-9b0b-ce4427cabd93" data-name="log">
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<div class="language-php highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="nb">var_dump</span><span class="p">(</span><span class="s1">'hello'</span><span class="p">);</span>
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<h2 id="another-example">Another example</h2>
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<ul id="data-struct" class="tab" data-tab="7a69929c-0f36-4c83-8f19-7b357f4ac0ca" data-name="data-struct">
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<ul id="data-struct" class="tab" data-tab="b96e09c7-8023-486f-a8dd-e58ad3a5b26e" data-name="data-struct">
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<li class="active" id="data-struct-yaml">
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<a href="#">yaml </a>
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</ul>
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<ul class="tab-content" id="7a69929c-0f36-4c83-8f19-7b357f4ac0ca" data-name="data-struct">
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<ul class="tab-content" id="b96e09c7-8023-486f-a8dd-e58ad3a5b26e" data-name="data-struct">
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<div class="language-yaml highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="na">hello</span><span class="pi">:</span>
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<h2 id="tabs-for-something-else">Tabs for something else</h2>
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<ul id="something-else" class="tab" data-tab="c4bc4bb4-5636-485c-8fdb-48e04e62e111" data-name="something-else">
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<ul id="something-else" class="tab" data-tab="a3cb5924-163d-4df5-b981-0cc0db118aa7" data-name="something-else">
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<li class="active" id="something-else-text">
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<a href="#">text </a>
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</ul>
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<ul class="tab-content" id="c4bc4bb4-5636-485c-8fdb-48e04e62e111" data-name="something-else">
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<ul class="tab-content" id="a3cb5924-163d-4df5-b981-0cc0db118aa7" data-name="something-else">
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<p>Regular text</p>

‎_site/feed.xml‎

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<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" xml:lang="en"><generator uri="https://jekyllrb.com/" version="4.3.3">Jekyll</generator><link href="http://localhost:4000/feed.xml" rel="self" type="application/atom+xml" /><link href="http://localhost:4000/" rel="alternate" type="text/html" hreflang="en" /><updated>2025-11-18T10:14:34-05:00</updated><id>http://localhost:4000/feed.xml</id><title type="html">blank</title><subtitle>My personal website.
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<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" xml:lang="en"><generator uri="https://jekyllrb.com/" version="4.3.3">Jekyll</generator><link href="http://localhost:4000/feed.xml" rel="self" type="application/atom+xml" /><link href="http://localhost:4000/" rel="alternate" type="text/html" hreflang="en" /><updated>2025-11-18T10:46:28-05:00</updated><id>http://localhost:4000/feed.xml</id><title type="html">blank</title><subtitle>My personal website.
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</subtitle><entry><title type="html">Google Gemini updates: Flash 1.5, Gemma 2 and Project Astra</title><link href="http://localhost:4000/blog/2024/google-gemini-updates-flash-15-gemma-2-and-project-astra/" rel="alternate" type="text/html" title="Google Gemini updates: Flash 1.5, Gemma 2 and Project Astra" /><published>2024-05-14T00:00:00-04:00</published><updated>2024-05-14T00:00:00-04:00</updated><id>http://localhost:4000/blog/2024/google-gemini-updates-flash-15-gemma-2-and-project-astra</id><content type="html" xml:base="http://localhost:4000/blog/2024/google-gemini-updates-flash-15-gemma-2-and-project-astra/"><![CDATA[]]></content><author><name></name></author><summary type="html"><![CDATA[We’re sharing updates across our Gemini family of models and a glimpse of Project Astra, our vision for the future of AI assistants.]]></summary></entry><entry><title type="html">a post with tabs</title><link href="http://localhost:4000/blog/2024/tabs/" rel="alternate" type="text/html" title="a post with tabs" /><published>2024-04-30T20:32:13-04:00</published><updated>2024-04-30T20:32:13-04:00</updated><id>http://localhost:4000/blog/2024/tabs</id><content type="html" xml:base="http://localhost:4000/blog/2024/tabs/"><![CDATA[<p>This is how a post with <a href="https://github.com/Ovski4/jekyll-tabs">tabs</a> looks like. Note that the tabs could be used for different purposes, not only for code.</p>
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<p>With this you can generate visualizations like:</p>
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<ul id="log" class="tab" data-tab="b70bca1e-f814-4e81-a9be-bae11fe973b9" data-name="log">
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<ul id="log" class="tab" data-tab="a2621a9e-a679-4538-9b0b-ce4427cabd93" data-name="log">
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<a href="#">php </a>
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</ul>
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<ul class="tab-content" id="b70bca1e-f814-4e81-a9be-bae11fe973b9" data-name="log">
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<ul class="tab-content" id="a2621a9e-a679-4538-9b0b-ce4427cabd93" data-name="log">
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<div class="language-php highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="nb">var_dump</span><span class="p">(</span><span class="s1">'hello'</span><span class="p">);</span>
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<h2 id="another-example">Another example</h2>
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<ul id="data-struct" class="tab" data-tab="7a69929c-0f36-4c83-8f19-7b357f4ac0ca" data-name="data-struct">
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<ul id="data-struct" class="tab" data-tab="b96e09c7-8023-486f-a8dd-e58ad3a5b26e" data-name="data-struct">
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</ul>
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<ul class="tab-content" id="7a69929c-0f36-4c83-8f19-7b357f4ac0ca" data-name="data-struct">
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<ul class="tab-content" id="b96e09c7-8023-486f-a8dd-e58ad3a5b26e" data-name="data-struct">
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<div class="language-yaml highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="na">hello</span><span class="pi">:</span>
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<h2 id="tabs-for-something-else">Tabs for something else</h2>
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<ul id="something-else" class="tab" data-tab="c4bc4bb4-5636-485c-8fdb-48e04e62e111" data-name="something-else">
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<ul id="something-else" class="tab" data-tab="a3cb5924-163d-4df5-b981-0cc0db118aa7" data-name="something-else">
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<p>Regular text</p>

‎_site/index.html‎

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<figure>
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https://developer.mozilla.org/en-US/docs/Learn/HTML/Multimedia_and_embedding/Responsive_images for info on defining 'sizes' for responsive images
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-->
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<source class="responsive-img-srcset" srcset="/assets/img/publication_preview/ddpm-480.webp 480w,/assets/img/publication_preview/ddpm-800.webp 800w,/assets/img/publication_preview/ddpm-1400.webp 1400w," sizes="200px" type="image/webp">
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<img src="/assets/img/publication_preview/ddpm.gif" class="preview z-depth-1 rounded" width="100%" height="auto" alt="ddpm.gif" data-zoomable loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();">
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</source></picture>
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</figure>
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</div>
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<!-- Entry bib key -->
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<div id="saeedi2025cryosense" class="col-sm-8">
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<!-- Title -->
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<div class="title">cryoSENSE: Compressive Sensing Enables High-throughput Microscopy with Sparse and Generative Priors on the Protein Cryo-EM Image Manifold</div>
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<!-- Author -->
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<div class="author">
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Zain
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Shabeeb, Daniel
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Saeedi, Darin
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Tsui, and
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var element = $(this);
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var more_authors_text = element.text() == '2 more authors' ? 'Vida Jamali, Amirali Aghazadeh' : '2 more authors';
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">2 more authors</span>
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<em>arXiv:2511.12931</em>, 2025
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<a href="https://github.com/amirgroup-codes/cryoSENSE" class="btn btn-sm z-depth-0" role="button" rel="external nofollow noopener" target="_blank">Code</a>
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<a href="https://cryosense.github.io" class="btn btn-sm z-depth-0" role="button" rel="external nofollow noopener" target="_blank">Website</a>
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https://developer.mozilla.org/en-US/docs/Learn/HTML/Multimedia_and_embedding/Responsive_images for info on defining 'sizes' for responsive images
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-->
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<source class="responsive-img-srcset" srcset="/assets/img/publication_preview/pnasnexus-480.webp 480w,/assets/img/publication_preview/pnasnexus-800.webp 800w,/assets/img/publication_preview/pnasnexus-1400.webp 1400w," sizes="200px" type="image/webp">
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<img src="/assets/img/publication_preview/pnasnexus.png" class="preview z-depth-1 rounded" width="100%" height="auto" alt="pnasnexus.png" data-zoomable loading="eager" onerror="this.onerror=null; $('.responsive-img-srcset').remove();">
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<div id="10.1093/pnasnexus/pgaf334" class="col-sm-8">
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<!-- Title -->
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<div class="title">Discriminating abiotic and biotic organics in meteorite and terrestrial samples using machine learning on mass spectrometry data</div>
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Daniel
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Saeedi, Denise
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Buckner, Thomas A
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