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1<!DOCTYPE html> <html lang="en"> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <title>Yuqi Cheng</title> <meta name="author" content="Yuqi Cheng"> <meta name="description" content=""> <link href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha256-DF7Zhf293AJxJNTmh5zhoYYIMs2oXitRfBjY+9L//AY=" crossorigin="anonymous"> <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/css/mdb.min.css" integrity="sha256-jpjYvU3G3N6nrrBwXJoVEYI/0zw8htfFnhT9ljN3JJw=" crossorigin="anonymous"> <link defer rel="stylesheet" href="https://unpkg.com/[email protected]/dist/bootstrap-table.min.css"> <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/@fortawesome/[email protected]/css/all.min.css" integrity="sha256-mUZM63G8m73Mcidfrv5E+Y61y7a12O5mW4ezU3bxqW4=" crossorigin="anonymous"> <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/css/academicons.min.css" integrity="sha256-i1+4qU2G2860dGGIOJscdC30s9beBXjFfzjWLjBRsBg=" crossorigin="anonymous"> <link rel="stylesheet" type="text/css" href="https://fonts.googleapis.com/css?family=Roboto:300,400,500,700|Roboto+Slab:100,300,400,500,700|Material+Icons"> <link rel="stylesheet" href="https://cdn.jsdelivr.net/gh/jwarby/jekyll-pygments-themes@master/github.css" media="" id="highlight_theme_light"> <link rel="shortcut icon" href="/assets/img/DNA.png"> <link rel="stylesheet" href="/assets/css/main.css"> <link rel="canonical" href="https://yuqcheng.github.io/"> <link rel="stylesheet" href="https://cdn.jsdelivr.net/gh/jwarby/jekyll-pygments-themes@master/native.css" media="none" id="highlight_theme_dark"> 

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1 </head> <body class="fixed-top-nav "> <header> <nav id="navbar" class="navbar navbar-light navbar-expand-sm fixed-top"> <div class="container"> <button class="navbar-toggler collapsed ml-auto" type="button" data-toggle="collapse" data-target="#navbarNav" aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation"> <span class="sr-only">Toggle navigation</span> <span class="icon-bar top-bar"></span> <span class="icon-bar middle-bar"></span> <span class="icon-bar bottom-bar"></span> </button> <div class="collapse navbar-collapse text-right" id="navbarNav"> <ul class="navbar-nav ml-auto flex-nowrap"> <li class="nav-item active"> <a class="nav-link" href="/">About<span class="sr-only">(current)</span></a> </li> <li class="nav-item "> <a class="nav-link" href="/publications/">Publications</a> </li> <li class="nav-item "> <a class="nav-link" href="/experience/">Experience</a> </li> <li class="toggle-container"> <button id="light-toggle" title="Change theme"> <i class="fas fa-moon"></i> <i class="fas fa-sun"></i> </button> </li> </ul> </div> </div> </nav> <progress id="progress" value="0"> <div class="progress-container"> <span class="progress-bar"></span> </div> </progress> </header> <div class="container mt-5"> <div class="post"> <header class="post-header"> <h1 class="post-title"> <span class="font-weight-bold">Yuqi</span> Cheng </h1> <p class="desc"><a href="https://cse.gatech.edu/" rel="external nofollow noopener" target="_blank">School of Computational Science and Engineering</a>. Georgia Institute of Technology</p> </header> <article> <div class="profile float-right"> <figure> <picture> <source class="responsive-img-srcset" media="(max-width: 480px)" srcset="/assets/img/prof_pic-480.webp"></source> <source class="responsive-img-srcset" media="(max-width: 800px)" srcset="/assets/img/prof_pic-800.webp"></source> <source class="responsive-img-srcset" media="(max-width: 1400px)" srcset="/assets/img/prof_pic-1400.webp"></source> <img src="/assets/img/prof_pic.jpg" class="img-fluid z-depth-1 rounded-circle" width="auto" height="auto" alt="prof_pic.jpg" onerror="this.onerror=null; $('.responsive-img-srcset').remove();"> </picture> </figure> </div> <div class="clearfix"> <p>Hi! I’m a PhD student in the <a href="https://www.cc.gatech.edu/degree-programs/phd-computational-science-and-engineering" rel="external nofollow noopener" target="_blank">Computational Science and Engineering program</a> at Georgia Tech College of Computing, advised by <a href="https://xiuweizhang.wordpress.com/" rel="external nofollow noopener" target="_blank">Dr. Xiuwei Zhang</a>. Before starting my PhD, I did my Master’s degree in computational biology at <a href="https://gradschool.weill.cornell.edu/" rel="external nofollow noopener" target="_blank">Weill Cornell Medicine</a> (’22) and my bachelor’s double majored in biology and data science at China Agricultural University (’20).</p> <p>My research interests broadly center on the application of AI models to single-cell and spatial omics. Specifically, my current work includes (1) cell label transfer and perturbed cell detection in single-cell data and (2) predicting transcriptomic signals from histology images.</p> </div> <h2><a href="/publications/" style="color: inherit;">Selected Publications</a></h2> <div class="publications"> <ol class="bibliography"> <li> <div class="row"> <div class="col-sm-2 abbr"><abbr class="badge">scBalance</abbr></div> <div id="cheng2023scalable" class="col-sm-8"> <div class="title">A scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data</div> <div class="author"> <em>Yuqi Cheng</em>, Xingyu Fan, Jianing Zhang, and Yu Li</div> <div class="periodical"> <em>Communications Biology</em>, 2023 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> <a href="https://www.nature.com/articles/s42003-023-04928-6" class="btn btn-sm z-depth-0" role="button" rel="external nofollow noopener" target="_blank">HTML</a> </div> <div class="badges"> <span class="altmetric-embed" data-hide-no-mentions="true" data-hide-less-than="15" data-badge-type="2" data-badge-popover="right"></span> <span class="__dimensions_badge_embed__" data-pmid="" data-hide-zero-citations="true" data-style="small_rectangle" data-legend="hover-right" style="margin-bottom: 3px;"></span> </div> <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">cheng2023scalable</span><span class="p">,</span>
2  <span class="na">title</span> <span class="p">=</span> <span class="s">{A scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data}</span><span class="p">,</span>
3  <span class="na">author</span> <span class="p">=</span> <span class="s">{Cheng, Yuqi and Fan, Xingyu and Zhang, Jianing and Li, Yu}</span><span class="p">,</span>
4  <span class="na">

4journal</span> <span class="p">=</span> <span class="s">{Communications Biology}</span><span class="p">,</span>
5  <span class="na">volume</span> <span class="p">=</span> <span class="s">{6}</span><span class="p">,</span>
6  <span class="na">number</span> <span class="p">=</span> <span class="s">{1}</span><span class="p">,</span>
7  <span class="na">pages</span> <span class="p">=</span> <span class="s">{545}</span><span class="p">,</span>
8  <span class="na">year</span> <span class="p">=</span> <span class="s">{2023}</span><span class="p">,</span>
9  <span class="na">publisher</span> <span class="p">=</span> <span class="s">{Nature Publishing Group UK London}</span><span class="p">,</span>
10<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div class="col-sm-2 abbr"><abbr class="badge">CLEAR</abbr></div> <div id="han2022self" class="col-sm-8"> <div class="title">Self-supervised contrastive learning for integrative single cell RNA-seq data analysis</div> <div class="author"> Wenkai Han*, <em>Yuqi Cheng*</em>, Jiayang Chen*, Huawen Zhong, and <span class="more-authors" title="click to view 6 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '6 more authors' ? 'Zhihang Hu, Siyuan Chen, Licheng Zong, Irwin King, Xin Gao, Yu Li' : '6 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.text(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">6 more authors</span> </div> <div class="periodical"> <em>Briefings in Bioinformatics</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> <a href="https://academic.oup.com/bib/article/23/5/bbac377/6695268" class="btn btn-sm z-depth-0" role="button" rel="external nofollow noopener" target="_blank">HTML</a> </div> <div class="badges"> <span class="altmetric-embed" data-hide-no-mentions="true" data-hide-less-than="15" data-badge-type="2" data-badge-popover="right"></span> <span class="__dimensions_badge_embed__" data-pmid="" data-hide-zero-citations="true" data-style="small_rectangle" data-legend="hover-right" style="margin-bottom: 3px;"></span> </div> <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">han2022self</span><span class="p">,</span>
11  <span class="na">title</span> <span class="p">=</span> <span class="s">{Self-supervised contrastive learning for integrative single cell RNA-seq data analysis}</span><span class="p">,</span>
12  <span class="na">author</span> <span class="p">=</span> <span class="s">{Han*, Wenkai and Cheng*, Yuqi and Chen*, Jiayang and Zhong, Huawen and Hu, Zhihang and Chen, Siyuan and Zong, Licheng and King, Irwin and Gao, Xin and Li, Yu}</span><span class="p">,</span>
13  <span class="na">journal</span> <span class="p">=</span> <span class="s">{Briefings in Bioinformatics}</span><span class="p">,</span>
14  <span class="na">volume</span> <span class="p">=</span> <span class="s">{23}</span><span class="p">,</span>
15  <span class="na">number</span> <span class="p">=</span> <span class="s">{5}</span><span class="p">,</span>
16  <span class="na">year</span> <span class="p">=</span> <span class="s">{2022}</span><span class="p">,</span>
17<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div class="col-sm-2 abbr"><abbr class="badge">EpiPack</abbr></div> <div id="Cheng2025epipack" class="col-sm-8"> <div class="title">Discovering cell types and states from reference atlases with heterogeneous single-cell ATAC-seq features</div> <div class="author"> <em>Yuqi Cheng</em>, and Xiuwei Zhang</div> <div class="periodical"> <em>bioRxiv</em>, 2025 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> <a href="https://www.biorxiv.org/content/10.1101/2025.09.19.677191v1" class="btn btn-sm z-depth-0" role="button" rel="external nofollow noopener" target="_blank">HTML</a> </div> <div class="badges"> <span class="altmetric-embed" data-hide-no-mentions="true" data-hide-less-than="15" data-badge-type="2" data-badge-popover="right" data-doi="10.1101/2025.09.19.677191"></span> <span class="__dimensions_badge_embed__" data-doi="10.1101/2025.09.19.677191" data-hide-zero-citations="true" data-style="small_rectangle" data-legend="hover-right" style="margin-bottom: 3px;"></span> </div> <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">Cheng2025epipack</span><span class="p">,</span>
18  <span class="na">author</span> <span class="p">=</span> <span class="s">{Cheng, Yuqi and Zhang, Xiuwei}</span><span class="p">,</span>
19  <span class="na">title</span> <span class="p">=</span> <span class="s">{Discovering cell types and states from reference atlases with heterogeneous single-cell ATAC-seq features}</span><span class="p">,</span>
20  <span class="na">year</span> <span class="p">=</span> <span class="s">{2025}</span><span class="p">,</span>
21  <span class="na">doi</span> <span class="p">=</span> <span class="s">{10.1101/2025.09.19.677191}</span><span class="p">,</span>
22  <span class="na">publisher</span> <span class="p">=</span> <span class="s">{Cold Spring Harbor Laboratory}</span><span class="p">,</span>
23  <span class="na">

23journal</span> <span class="p">=</span> <span class="s">{bioRxiv}</span><span class="p">,</span>
24<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> </ol> </div> <div class="social"> <div class="contact-icons"> <a href="mailto:%79%63%68%65%6E%67%34%33%30@%67%61%74%65%63%68.%65%64%75" title="email"><i class="fas fa-envelope"></i></a> <a href="https://scholar.google.com/citations?user=JPFlY-UAAAAJ" title="Google Scholar" rel="external nofollow noopener" target="_blank"><i class="ai ai-google-scholar"></i></a> <a href="https://github.com/yuqcheng" title="GitHub" rel="external nofollow noopener" target="_blank"><i class="fab fa-github"></i></a> <a href="https://www.linkedin.com/in/yuqicheng" title="LinkedIn" rel="external nofollow noopener" target="_blank"><i class="fab fa-linkedin"></i></a> <a href="https://twitter.com/Yq_Cheng" title="Twitter" rel="external nofollow noopener" target="_blank"><i class="fab fa-twitter"></i></a> </div> <div class="contact-note"> </div> </div> </article> </div> </div> <footer class="fixed-bottom"> <div class="container mt-0"> © Copyright 2025 Yuqi Cheng. </div> </footer> 

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