<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" xml:lang="en"><generator uri="https://jekyllrb.com/" version="3.10.0">Jekyll</generator><link href="http://sceris.life/feed.xml" rel="self" type="application/atom+xml" /><link href="http://sceris.life/" rel="alternate" type="text/html" hreflang="en" /><updated>2026-11-03T12:25:44+00:00</updated><id>http://sceris.life/feed.xml</id><title type="html">Paper Notes</title><subtitle>Short paper reviews</subtitle><author><name>Vladimir Opaits</name><email>663vova@gmail.com</email></author><entry><title type="html">Example review: how a post is structured</title><link href="http://sceris.life/reviews/2026/11/03/example-review/" rel="alternate" type="text/html" title="Example review: how a post is structured" /><published>2026-11-03T00:00:00+00:00</published><updated>2026-11-03T00:00:00+00:00</updated><id>http://sceris.life/reviews/2026/11/03/example-review</id><content type="html" xml:base="http://sceris.life/reviews/2026/11/03/example-review/"><![CDATA[<h2 id="context">Context</h2>

<p>Plain text is written in Markdown. <strong>Bold</strong>, <em>italic</em>, <code class="language-plaintext highlighter-rouge">inline code</code>,
<a href="https://example.com">links</a>.</p>

<blockquote>
  <p>Quotes from the paper look like this.</p>
</blockquote>

<h2 id="formulas">Formulas</h2>

<p>These work when front matter has <code class="language-plaintext highlighter-rouge">math: true</code>. Inline: $z_n \sim \mathcal{N}(0, I)$,
display:</p>

\[x_{ng} \mid z_n, \ell_n \sim \mathrm{ZINB}\big(\ell_n \, \rho_g(z_n), \theta_g, \pi_g(z_n)\big)\]

<h2 id="code">Code</h2>

<div class="language-python highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="kn">import</span> <span class="nn">scanpy</span> <span class="k">as</span> <span class="n">sc</span>
<span class="kn">import</span> <span class="nn">scvi</span>

<span class="n">adata</span> <span class="o">=</span> <span class="n">sc</span><span class="p">.</span><span class="n">read_h5ad</span><span class="p">(</span><span class="s">"pbmc.h5ad"</span><span class="p">)</span>
<span class="n">scvi</span><span class="p">.</span><span class="n">model</span><span class="p">.</span><span class="n">SCVI</span><span class="p">.</span><span class="n">setup_anndata</span><span class="p">(</span><span class="n">adata</span><span class="p">,</span> <span class="n">layer</span><span class="o">=</span><span class="s">"counts"</span><span class="p">,</span> <span class="n">batch_key</span><span class="o">=</span><span class="s">"batch"</span><span class="p">)</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">scvi</span><span class="p">.</span><span class="n">model</span><span class="p">.</span><span class="n">SCVI</span><span class="p">(</span><span class="n">adata</span><span class="p">,</span> <span class="n">n_latent</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span>
<span class="n">model</span><span class="p">.</span><span class="n">train</span><span class="p">()</span>
</code></pre></div></div>

<h2 id="table">Table</h2>

<table>
  <thead>
    <tr>
      <th>Method</th>
      <th>ARI</th>
      <th>NMI</th>
    </tr>
  </thead>
  <tbody>
    <tr>
      <td>PCA</td>
      <td>0.61</td>
      <td>0.70</td>
    </tr>
    <tr>
      <td>scVI</td>
      <td>0.74</td>
      <td>0.79</td>
    </tr>
  </tbody>
</table>

<h2 id="images">Images</h2>

<p>Put files in <code class="language-plaintext highlighter-rouge">assets/img/reviews/&lt;post-name&gt;/</code> and embed them with a caption
(click opens full size):</p>

<figure class="figure">
  <a href="/assets/img/reviews/example-review/placeholder.svg" target="_blank" rel="noopener">
    <img src="/assets/img/reviews/example-review/placeholder.svg" alt="Figure 1 from the paper, with Markdown in the caption" loading="lazy" />
  </a>
  <figcaption>Figure 1 from the paper, <em>with Markdown</em> in the caption</figcaption>
</figure>

<div class="language-liquid highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="p">{%</span><span class="w"> </span><span class="nt">include</span><span class="w"> </span>figure.html<span class="w"> </span><span class="na">src</span><span class="o">=</span><span class="s2">"/assets/img/reviews/example-review/fig1.png"</span><span class="w"> </span><span class="na">caption</span><span class="o">=</span><span class="s2">"Figure 1"</span><span class="w"> </span><span class="p">%}</span>
</code></pre></div></div>

<p>Plain Markdown also works: <code class="language-plaintext highlighter-rouge">![alt text](/assets/img/reviews/example-review/fig1.png)</code>.</p>

<h2 id="my-take">My take</h2>

<p>Personal assessment of the paper goes here.</p>]]></content><author><name>Vladimir Opaits</name><email>663vova@gmail.com</email></author><category term="scrnaseq" /><category term="ml" /><summary type="html"><![CDATA[Context]]></summary></entry></feed>