index.xml

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  <channel>
    <title>Alireza Karbalayghareh</title>
    <link>https://karbalayghareh.github.io/</link>
      <atom:link href="https://karbalayghareh.github.io/index.xml" rel="self" type="application/rss+xml" />
    <description>Alireza Karbalayghareh</description>
    <generator>Wowchemy (https://wowchemy.com)</generator><language>en-us</language><lastBuildDate>Sat, 01 Jun 2030 13:00:00 +0000</lastBuildDate>
    <image>
      <url>https://karbalayghareh.github.io/media/icon_hua2ec155b4296a9c9791d015323e16eb5_11927_512x512_fill_lanczos_center_2.png</url>
      <title>Alireza Karbalayghareh</title>
      <link>https://karbalayghareh.github.io/</link>
    </image>
    
    <item>
      <title>Example Talk</title>
      <link>https://karbalayghareh.github.io/talk/example-talk/</link>
      <pubDate>Sat, 01 Jun 2030 13:00:00 +0000</pubDate>
      <guid>https://karbalayghareh.github.io/talk/example-talk/</guid>
      <description>&lt;div class=&#34;alert alert-note&#34;&gt;
  &lt;div&gt;
    Click on the &lt;strong&gt;Slides&lt;/strong&gt; button above to view the built-in slides feature.
  &lt;/div&gt;
&lt;/div&gt;
&lt;p&gt;Slides can be added in a few ways:&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;&lt;strong&gt;Create&lt;/strong&gt; slides using Wowchemy&amp;rsquo;s &lt;a href=&#34;https://wowchemy.com/docs/managing-content/#create-slides&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;&lt;em&gt;Slides&lt;/em&gt;&lt;/a&gt; feature and link using &lt;code&gt;slides&lt;/code&gt; parameter in the front matter of the talk file&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;Upload&lt;/strong&gt; an existing slide deck to &lt;code&gt;static/&lt;/code&gt; and link using &lt;code&gt;url_slides&lt;/code&gt; parameter in the front matter of the talk file&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;Embed&lt;/strong&gt; your slides (e.g. Google Slides) or presentation video on this page using &lt;a href=&#34;https://wowchemy.com/docs/writing-markdown-latex/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;shortcodes&lt;/a&gt;.&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;Further event details, including &lt;a href=&#34;https://wowchemy.com/docs/writing-markdown-latex/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;page elements&lt;/a&gt; such as image galleries, can be added to the body of this page.&lt;/p&gt;
</description>
    </item>
    
    <item>
      <title>Chromatin interaction aware gene regulatory modeling with graph attention networks</title>
      <link>https://karbalayghareh.github.io/publication/preprint/</link>
      <pubDate>Fri, 02 Apr 2021 00:00:00 +0000</pubDate>
      <guid>https://karbalayghareh.github.io/publication/preprint/</guid>
      <description></description>
    </item>
    
    <item>
      <title>GraphReg</title>
      <link>https://karbalayghareh.github.io/project/internal-project-1/</link>
      <pubDate>Fri, 02 Apr 2021 00:00:00 +0000</pubDate>
      <guid>https://karbalayghareh.github.io/project/internal-project-1/</guid>
      <description>&lt;p&gt;Linking distal enhancers to genes and modeling their impact on target gene expression are longstanding unresolved problems in regulatory genomics and critical for interpreting non-coding genetic variation. Here we present a new deep learning approach called GraphReg that exploits 3D interactions from chromosome conformation capture assays in order to predict gene expression from 1D epigenomic data or genomic DNA sequence. By using graph attention networks to exploit the connectivity of distal elements and promoters, GraphReg more faithfully models gene regulation and more accurately predicts gene expression levels than dilated convolutional neural networks (CNNs), the current state-of-the-art deep learning approach for this task. Feature attribution used with GraphReg accurately identifies functional enhancers of genes, as validated by CRISPRi-FlowFISH and TAP-seq assays, outperforming both CNNs and the recently proposed Activity-by-Contact model. GraphReg therefore represents an important advance in modeling the regulatory impact of epigenomic and sequence elements.&lt;/p&gt;
</description>
    </item>
    
    <item>
      <title>Welcome to Wowchemy, the website builder for Hugo</title>
      <link>https://karbalayghareh.github.io/post/getting-started/</link>
      <pubDate>Sun, 13 Dec 2020 00:00:00 +0000</pubDate>
      <guid>https://karbalayghareh.github.io/post/getting-started/</guid>
      <description>&lt;h2 id=&#34;overview&#34;&gt;Overview&lt;/h2&gt;
&lt;ol&gt;
&lt;li&gt;The Wowchemy website builder for Hugo, along with its starter templates, is designed for professional creators, educators, and teams/organizations - although it can be used to create any kind of site&lt;/li&gt;
&lt;li&gt;The template can be modified and customised to suit your needs. It&amp;rsquo;s a good platform for anyone looking to take control of their data and online identity whilst having the convenience to start off with a &lt;strong&gt;no-code solution (write in Markdown and customize with YAML parameters)&lt;/strong&gt; and having &lt;strong&gt;flexibility to later add even deeper personalization with HTML and CSS&lt;/strong&gt;&lt;/li&gt;
&lt;li&gt;You can work with all your favourite tools and apps with hundreds of plugins and integrations to speed up your workflows, interact with your readers, and much more&lt;/li&gt;
&lt;/ol&gt;














&lt;figure  id=&#34;figure-the-template-is-mobile-first-with-a-responsive-design-to-ensure-that-your-site-looks-stunning-on-every-device&#34;&gt;
  &lt;div class=&#34;d-flex justify-content-center&#34;&gt;
    &lt;div class=&#34;w-100&#34; &gt;&lt;img src=&#34;https://raw.githubusercontent.com/wowchemy/wowchemy-hugo-modules/master/academic.png&#34; alt=&#34;The template is mobile first with a responsive design to ensure that your site looks stunning on every device.&#34; loading=&#34;lazy&#34; data-zoomable /&gt;&lt;/div&gt;
  &lt;/div&gt;&lt;figcaption&gt;
      The template is mobile first with a responsive design to ensure that your site looks stunning on every device.
    &lt;/figcaption&gt;&lt;/figure&gt;
&lt;h2 id=&#34;get-started&#34;&gt;Get Started&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;👉 &lt;a href=&#34;https://wowchemy.com/templates/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;&lt;strong&gt;Create a new site&lt;/strong&gt;&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;📚 &lt;a href=&#34;https://wowchemy.com/docs/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;&lt;strong&gt;Personalize your site&lt;/strong&gt;&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;💬 &lt;a href=&#34;https://discord.gg/z8wNYzb&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;Chat with the &lt;strong&gt;Wowchemy community&lt;/strong&gt;&lt;/a&gt; or &lt;a href=&#34;https://discourse.gohugo.io&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;&lt;strong&gt;Hugo community&lt;/strong&gt;&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;🐦 Twitter: &lt;a href=&#34;https://twitter.com/wowchemy&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;@wowchemy&lt;/a&gt; &lt;a href=&#34;https://twitter.com/GeorgeCushen&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;@GeorgeCushen&lt;/a&gt; &lt;a href=&#34;https://twitter.com/search?q=%28%23MadeWithWowchemy%20OR%20%23MadeWithAcademic%29&amp;amp;src=typed_query&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;#MadeWithWowchemy&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;💡 &lt;a href=&#34;https://github.com/wowchemy/wowchemy-hugo-modules/issues&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;Request a &lt;strong&gt;feature&lt;/strong&gt; or report a &lt;strong&gt;bug&lt;/strong&gt; for &lt;em&gt;Wowchemy&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;⬆️ &lt;strong&gt;Updating Wowchemy?&lt;/strong&gt; View the &lt;a href=&#34;https://wowchemy.com/docs/guide/update/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;Update Guide&lt;/a&gt; and &lt;a href=&#34;https://wowchemy.com/updates/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;Release Notes&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;
&lt;h2 id=&#34;crowd-funded-open-source-software&#34;&gt;Crowd-funded open-source software&lt;/h2&gt;
&lt;p&gt;To help us develop this template and software sustainably under the MIT license, we ask all individuals and businesses that use it to help support its ongoing maintenance and development via sponsorship.&lt;/p&gt;
&lt;h3 id=&#34;-click-here-to-become-a-sponsor-and-help-support-wowchemys-future-httpswowchemycomplans&#34;&gt;&lt;a href=&#34;https://wowchemy.com/plans/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;❤️ Click here to become a sponsor and help support Wowchemy&amp;rsquo;s future ❤️&lt;/a&gt;&lt;/h3&gt;
&lt;p&gt;As a token of appreciation for sponsoring, you can &lt;strong&gt;unlock &lt;a href=&#34;https://wowchemy.com/plans/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;these&lt;/a&gt; awesome rewards and extra features 🦄✨&lt;/strong&gt;&lt;/p&gt;
&lt;h2 id=&#34;ecosystem&#34;&gt;Ecosystem&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;&lt;strong&gt;&lt;a href=&#34;https://github.com/wowchemy/hugo-academic-cli&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;Hugo Academic CLI&lt;/a&gt;:&lt;/strong&gt; Automatically import publications from BibTeX&lt;/li&gt;
&lt;/ul&gt;
&lt;h2 id=&#34;inspiration&#34;&gt;Inspiration&lt;/h2&gt;
&lt;p&gt;&lt;a href=&#34;https://academic-demo.netlify.com/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;Check out the latest &lt;strong&gt;demo&lt;/strong&gt;&lt;/a&gt; of what you&amp;rsquo;ll get in less than 10 minutes, or &lt;a href=&#34;https://wowchemy.com/user-stories/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;view the &lt;strong&gt;showcase&lt;/strong&gt;&lt;/a&gt; of personal, project, and business sites.&lt;/p&gt;
&lt;h2 id=&#34;features&#34;&gt;Features&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;&lt;strong&gt;Page builder&lt;/strong&gt; - Create &lt;em&gt;anything&lt;/em&gt; with &lt;a href=&#34;https://wowchemy.com/docs/page-builder/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;&lt;strong&gt;widgets&lt;/strong&gt;&lt;/a&gt; and &lt;a href=&#34;https://wowchemy.com/docs/writing-markdown-latex/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;&lt;strong&gt;elements&lt;/strong&gt;&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;Edit any type of content&lt;/strong&gt; - Blog posts, publications, talks, slides, projects, and more!&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;Create content&lt;/strong&gt; in &lt;a href=&#34;https://wowchemy.com/docs/writing-markdown-latex/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;&lt;strong&gt;Markdown&lt;/strong&gt;&lt;/a&gt;, &lt;a href=&#34;https://wowchemy.com/docs/import/jupyter/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;&lt;strong&gt;Jupyter&lt;/strong&gt;&lt;/a&gt;, or &lt;a href=&#34;https://wowchemy.com/docs/install-locally/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;&lt;strong&gt;RStudio&lt;/strong&gt;&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;Plugin System&lt;/strong&gt; - Fully customizable &lt;a href=&#34;https://wowchemy.com/docs/customization/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;&lt;strong&gt;color&lt;/strong&gt; and &lt;strong&gt;font themes&lt;/strong&gt;&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;Display Code and Math&lt;/strong&gt; - Code highlighting and &lt;a href=&#34;https://en.wikibooks.org/wiki/LaTeX/Mathematics&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;LaTeX math&lt;/a&gt; supported&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;Integrations&lt;/strong&gt; - &lt;a href=&#34;https://analytics.google.com&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;Google Analytics&lt;/a&gt;, &lt;a href=&#34;https://disqus.com&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;Disqus commenting&lt;/a&gt;, Maps, Contact Forms, and more!&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;Beautiful Site&lt;/strong&gt; - Simple and refreshing one page design&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;Industry-Leading SEO&lt;/strong&gt; - Help get your website found on search engines and social media&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;Media Galleries&lt;/strong&gt; - Display your images and videos with captions in a customizable gallery&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;Mobile Friendly&lt;/strong&gt; - Look amazing on every screen with a mobile friendly version of your site&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;Multi-language&lt;/strong&gt; - 34+ language packs including English, 中文, and Português&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;Multi-user&lt;/strong&gt; - Each author gets their own profile page&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;Privacy Pack&lt;/strong&gt; - Assists with GDPR&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;Stand Out&lt;/strong&gt; - Bring your site to life with animation, parallax backgrounds, and scroll effects&lt;/li&gt;
&lt;li&gt;&lt;strong&gt;One-Click Deployment&lt;/strong&gt; - No servers. No databases. Only files.&lt;/li&gt;
&lt;/ul&gt;
&lt;h2 id=&#34;themes&#34;&gt;Themes&lt;/h2&gt;
&lt;p&gt;Wowchemy and its templates come with &lt;strong&gt;automatic day (light) and night (dark) mode&lt;/strong&gt; built-in. Alternatively, visitors can choose their preferred mode - click the moon icon in the top right of the &lt;a href=&#34;https://academic-demo.netlify.com/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;Demo&lt;/a&gt; to see it in action! Day/night mode can also be disabled by the site admin in &lt;code&gt;params.toml&lt;/code&gt;.&lt;/p&gt;
&lt;p&gt;&lt;a href=&#34;https://wowchemy.com/docs/customization&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;Choose a stunning &lt;strong&gt;theme&lt;/strong&gt; and &lt;strong&gt;font&lt;/strong&gt;&lt;/a&gt; for your site. Themes are fully customizable.&lt;/p&gt;
&lt;h2 id=&#34;license&#34;&gt;License&lt;/h2&gt;
&lt;p&gt;Copyright 2016-present &lt;a href=&#34;https://georgecushen.com&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;George Cushen&lt;/a&gt;.&lt;/p&gt;
&lt;p&gt;Released under the &lt;a href=&#34;https://github.com/wowchemy/wowchemy-hugo-modules/blob/master/LICENSE.md&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;MIT&lt;/a&gt; license.&lt;/p&gt;
</description>
    </item>
    
    <item>
      <title>Hello R Markdown</title>
      <link>https://karbalayghareh.github.io/post/2020-12-01-r-rmarkdown/</link>
      <pubDate>Tue, 01 Dec 2020 21:13:14 -0500</pubDate>
      <guid>https://karbalayghareh.github.io/post/2020-12-01-r-rmarkdown/</guid>
      <description>
&lt;script src=&#34;https://karbalayghareh.github.io/post/2020-12-01-r-rmarkdown/index.en_files/header-attrs/header-attrs.js&#34;&gt;&lt;/script&gt;


&lt;div id=&#34;r-markdown&#34; class=&#34;section level1&#34;&gt;
&lt;h1&gt;R Markdown&lt;/h1&gt;
&lt;p&gt;This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see &lt;a href=&#34;http://rmarkdown.rstudio.com&#34; class=&#34;uri&#34;&gt;http://rmarkdown.rstudio.com&lt;/a&gt;.&lt;/p&gt;
&lt;p&gt;You can embed an R code chunk like this:&lt;/p&gt;
&lt;pre class=&#34;r&#34;&gt;&lt;code&gt;summary(cars)
##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00
fit &amp;lt;- lm(dist ~ speed, data = cars)
fit
## 
## Call:
## lm(formula = dist ~ speed, data = cars)
## 
## Coefficients:
## (Intercept)        speed  
##     -17.579        3.932&lt;/code&gt;&lt;/pre&gt;
&lt;/div&gt;
&lt;div id=&#34;including-plots&#34; class=&#34;section level1&#34;&gt;
&lt;h1&gt;Including Plots&lt;/h1&gt;
&lt;p&gt;You can also embed plots. See Figure &lt;a href=&#34;#fig:pie&#34;&gt;1&lt;/a&gt; for example:&lt;/p&gt;
&lt;pre class=&#34;r&#34;&gt;&lt;code&gt;par(mar = c(0, 1, 0, 1))
pie(
  c(280, 60, 20),
  c(&amp;#39;Sky&amp;#39;, &amp;#39;Sunny side of pyramid&amp;#39;, &amp;#39;Shady side of pyramid&amp;#39;),
  col = c(&amp;#39;#0292D8&amp;#39;, &amp;#39;#F7EA39&amp;#39;, &amp;#39;#C4B632&amp;#39;),
  init.angle = -50, border = NA
)&lt;/code&gt;&lt;/pre&gt;
&lt;div class=&#34;figure&#34;&gt;&lt;span id=&#34;fig:pie&#34;&gt;&lt;/span&gt;
&lt;img src=&#34;https://karbalayghareh.github.io/post/2020-12-01-r-rmarkdown/index.en_files/figure-html/pie-1.png&#34; alt=&#34;A fancy pie chart.&#34; width=&#34;672&#34; /&gt;
&lt;p class=&#34;caption&#34;&gt;
Figure 1: A fancy pie chart.
&lt;/p&gt;
&lt;/div&gt;
&lt;/div&gt;
</description>
    </item>
    
    <item>
      <title>Writing technical content in Academic</title>
      <link>https://karbalayghareh.github.io/post/writing-technical-content/</link>
      <pubDate>Fri, 12 Jul 2019 00:00:00 +0000</pubDate>
      <guid>https://karbalayghareh.github.io/post/writing-technical-content/</guid>
      <description>&lt;p&gt;Academic is designed to give technical content creators a seamless experience. You can focus on the content and Academic handles the rest.&lt;/p&gt;
&lt;p&gt;&lt;strong&gt;Highlight your code snippets, take notes on math classes, and draw diagrams from textual representation.&lt;/strong&gt;&lt;/p&gt;
&lt;p&gt;On this page, you&amp;rsquo;ll find some examples of the types of technical content that can be rendered with Academic.&lt;/p&gt;
&lt;h2 id=&#34;examples&#34;&gt;Examples&lt;/h2&gt;
&lt;h3 id=&#34;code&#34;&gt;Code&lt;/h3&gt;
&lt;p&gt;Academic supports a Markdown extension for highlighting code syntax. You can enable this feature by toggling the &lt;code&gt;highlight&lt;/code&gt; option in your &lt;code&gt;config/_default/params.toml&lt;/code&gt; file.&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;```python
import pandas as pd
data = pd.read_csv(&amp;quot;data.csv&amp;quot;)
data.head()
```
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;renders as&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-python&#34;&gt;import pandas as pd
data = pd.read_csv(&amp;quot;data.csv&amp;quot;)
data.head()
&lt;/code&gt;&lt;/pre&gt;
&lt;h3 id=&#34;charts&#34;&gt;Charts&lt;/h3&gt;
&lt;p&gt;Academic supports the popular &lt;a href=&#34;https://plot.ly/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;Plotly&lt;/a&gt; chart format.&lt;/p&gt;
&lt;p&gt;Save your Plotly JSON in your page folder, for example &lt;code&gt;chart.json&lt;/code&gt;, and then add the &lt;code&gt;{{&amp;lt; chart data=&amp;quot;chart&amp;quot; &amp;gt;}}&lt;/code&gt; shortcode where you would like the chart to appear.&lt;/p&gt;
&lt;p&gt;Demo:&lt;/p&gt;


&lt;div id=&#34;chart-835261974&#34; class=&#34;chart&#34;&gt;&lt;/div&gt;
&lt;script&gt;
  (function() {
    let a = setInterval( function() {
      if ( typeof window.Plotly === &#39;undefined&#39; ) {
        return;
      }
      clearInterval( a );

      Plotly.d3.json(&#34;./line-chart.json&#34;, function(chart) {
        Plotly.plot(&#39;chart-835261974&#39;, chart.data, chart.layout, {responsive: true});
      });
    }, 500 );
  })();
&lt;/script&gt;
&lt;p&gt;You might also find the &lt;a href=&#34;http://plotly-json-editor.getforge.io/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;Plotly JSON Editor&lt;/a&gt; useful.&lt;/p&gt;
&lt;h3 id=&#34;math&#34;&gt;Math&lt;/h3&gt;
&lt;p&gt;Academic supports a Markdown extension for $\LaTeX$ math. You can enable this feature by toggling the &lt;code&gt;math&lt;/code&gt; option in your &lt;code&gt;config/_default/params.toml&lt;/code&gt; file.&lt;/p&gt;
&lt;p&gt;To render &lt;em&gt;inline&lt;/em&gt; or &lt;em&gt;block&lt;/em&gt; math, wrap your LaTeX math with &lt;code&gt;$...$&lt;/code&gt; or &lt;code&gt;$$...$$&lt;/code&gt;, respectively.&lt;/p&gt;
&lt;p&gt;Example &lt;strong&gt;math block&lt;/strong&gt;:&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-latex&#34;&gt;$$\gamma_{n} = \frac{ 
\left | \left (\mathbf x_{n} - \mathbf x_{n-1} \right )^T 
\left [\nabla F (\mathbf x_{n}) - \nabla F (\mathbf x_{n-1}) \right ] \right |}
{\left \|\nabla F(\mathbf{x}_{n}) - \nabla F(\mathbf{x}_{n-1}) \right \|^2}$$
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;renders as&lt;/p&gt;
&lt;p&gt;$$\gamma_{n} = \frac{ \left | \left (\mathbf x_{n} - \mathbf x_{n-1} \right )^T \left [\nabla F (\mathbf x_{n}) - \nabla F (\mathbf x_{n-1}) \right ] \right |}{\left |\nabla F(\mathbf{x}_{n}) - \nabla F(\mathbf{x}_{n-1}) \right |^2}$$&lt;/p&gt;
&lt;p&gt;Example &lt;strong&gt;inline math&lt;/strong&gt; &lt;code&gt;$\nabla F(\mathbf{x}_{n})$&lt;/code&gt; renders as $\nabla F(\mathbf{x}_{n})$.&lt;/p&gt;
&lt;p&gt;Example &lt;strong&gt;multi-line math&lt;/strong&gt; using the &lt;code&gt;\\\\&lt;/code&gt; math linebreak:&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-latex&#34;&gt;$$f(k;p_{0}^{*}) = \begin{cases}p_{0}^{*} &amp;amp; \text{if }k=1, \\\\
1-p_{0}^{*} &amp;amp; \text{if }k=0.\end{cases}$$
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;renders as&lt;/p&gt;
&lt;p&gt;$$f(k;p_{0}^{*}) = \begin{cases}p_{0}^{*} &amp;amp; \text{if }k=1, \\&lt;br&gt;
1-p_{0}^{*} &amp;amp; \text{if }k=0.\end{cases}$$&lt;/p&gt;
&lt;h3 id=&#34;diagrams&#34;&gt;Diagrams&lt;/h3&gt;
&lt;p&gt;Academic supports a Markdown extension for diagrams. You can enable this feature by toggling the &lt;code&gt;diagram&lt;/code&gt; option in your &lt;code&gt;config/_default/params.toml&lt;/code&gt; file or by adding &lt;code&gt;diagram: true&lt;/code&gt; to your page front matter.&lt;/p&gt;
&lt;p&gt;An example &lt;strong&gt;flowchart&lt;/strong&gt;:&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;```mermaid
graph TD
A[Hard] --&amp;gt;|Text| B(Round)
B --&amp;gt; C{Decision}
C --&amp;gt;|One| D[Result 1]
C --&amp;gt;|Two| E[Result 2]
```
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;renders as&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-mermaid&#34;&gt;graph TD
A[Hard] --&amp;gt;|Text| B(Round)
B --&amp;gt; C{Decision}
C --&amp;gt;|One| D[Result 1]
C --&amp;gt;|Two| E[Result 2]
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;An example &lt;strong&gt;sequence diagram&lt;/strong&gt;:&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;```mermaid
sequenceDiagram
Alice-&amp;gt;&amp;gt;John: Hello John, how are you?
loop Healthcheck
    John-&amp;gt;&amp;gt;John: Fight against hypochondria
end
Note right of John: Rational thoughts!
John--&amp;gt;&amp;gt;Alice: Great!
John-&amp;gt;&amp;gt;Bob: How about you?
Bob--&amp;gt;&amp;gt;John: Jolly good!
```
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;renders as&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-mermaid&#34;&gt;sequenceDiagram
Alice-&amp;gt;&amp;gt;John: Hello John, how are you?
loop Healthcheck
    John-&amp;gt;&amp;gt;John: Fight against hypochondria
end
Note right of John: Rational thoughts!
John--&amp;gt;&amp;gt;Alice: Great!
John-&amp;gt;&amp;gt;Bob: How about you?
Bob--&amp;gt;&amp;gt;John: Jolly good!
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;An example &lt;strong&gt;Gantt diagram&lt;/strong&gt;:&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;```mermaid
gantt
section Section
Completed :done,    des1, 2014-01-06,2014-01-08
Active        :active,  des2, 2014-01-07, 3d
Parallel 1   :         des3, after des1, 1d
Parallel 2   :         des4, after des1, 1d
Parallel 3   :         des5, after des3, 1d
Parallel 4   :         des6, after des4, 1d
```
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;renders as&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-mermaid&#34;&gt;gantt
section Section
Completed :done,    des1, 2014-01-06,2014-01-08
Active        :active,  des2, 2014-01-07, 3d
Parallel 1   :         des3, after des1, 1d
Parallel 2   :         des4, after des1, 1d
Parallel 3   :         des5, after des3, 1d
Parallel 4   :         des6, after des4, 1d
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;An example &lt;strong&gt;class diagram&lt;/strong&gt;:&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;```mermaid
classDiagram
Class01 &amp;lt;|-- AveryLongClass : Cool
&amp;lt;&amp;lt;interface&amp;gt;&amp;gt; Class01
Class09 --&amp;gt; C2 : Where am i?
Class09 --* C3
Class09 --|&amp;gt; Class07
Class07 : equals()
Class07 : Object[] elementData
Class01 : size()
Class01 : int chimp
Class01 : int gorilla
class Class10 {
  &amp;lt;&amp;lt;service&amp;gt;&amp;gt;
  int id
  size()
}
```
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;renders as&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-mermaid&#34;&gt;classDiagram
Class01 &amp;lt;|-- AveryLongClass : Cool
&amp;lt;&amp;lt;interface&amp;gt;&amp;gt; Class01
Class09 --&amp;gt; C2 : Where am i?
Class09 --* C3
Class09 --|&amp;gt; Class07
Class07 : equals()
Class07 : Object[] elementData
Class01 : size()
Class01 : int chimp
Class01 : int gorilla
class Class10 {
  &amp;lt;&amp;lt;service&amp;gt;&amp;gt;
  int id
  size()
}
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;An example &lt;strong&gt;state diagram&lt;/strong&gt;:&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;```mermaid
stateDiagram
[*] --&amp;gt; Still
Still --&amp;gt; [*]
Still --&amp;gt; Moving
Moving --&amp;gt; Still
Moving --&amp;gt; Crash
Crash --&amp;gt; [*]
```
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;renders as&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-mermaid&#34;&gt;stateDiagram
[*] --&amp;gt; Still
Still --&amp;gt; [*]
Still --&amp;gt; Moving
Moving --&amp;gt; Still
Moving --&amp;gt; Crash
Crash --&amp;gt; [*]
&lt;/code&gt;&lt;/pre&gt;
&lt;h3 id=&#34;todo-lists&#34;&gt;Todo lists&lt;/h3&gt;
&lt;p&gt;You can even write your todo lists in Academic too:&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-markdown&#34;&gt;- [x] Write math example
- [x] Write diagram example
- [ ] Do something else
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;renders as&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;&lt;input checked=&#34;&#34; disabled=&#34;&#34; type=&#34;checkbox&#34;&gt; Write math example&lt;/li&gt;
&lt;li&gt;&lt;input checked=&#34;&#34; disabled=&#34;&#34; type=&#34;checkbox&#34;&gt; Write diagram example&lt;/li&gt;
&lt;li&gt;&lt;input disabled=&#34;&#34; type=&#34;checkbox&#34;&gt; Do something else&lt;/li&gt;
&lt;/ul&gt;
&lt;h3 id=&#34;tables&#34;&gt;Tables&lt;/h3&gt;
&lt;p&gt;Represent your data in tables:&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-markdown&#34;&gt;| First Header  | Second Header |
| ------------- | ------------- |
| Content Cell  | Content Cell  |
| Content Cell  | Content Cell  |
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;renders as&lt;/p&gt;
&lt;table&gt;
&lt;thead&gt;
&lt;tr&gt;
&lt;th&gt;First Header&lt;/th&gt;
&lt;th&gt;Second Header&lt;/th&gt;
&lt;/tr&gt;
&lt;/thead&gt;
&lt;tbody&gt;
&lt;tr&gt;
&lt;td&gt;Content Cell&lt;/td&gt;
&lt;td&gt;Content Cell&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;Content Cell&lt;/td&gt;
&lt;td&gt;Content Cell&lt;/td&gt;
&lt;/tr&gt;
&lt;/tbody&gt;
&lt;/table&gt;
&lt;h3 id=&#34;callouts&#34;&gt;Callouts&lt;/h3&gt;
&lt;p&gt;Academic supports a &lt;a href=&#34;https://wowchemy.com/docs/content/writing-markdown-latex/#callouts&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;shortcode for callouts&lt;/a&gt;, also referred to as &lt;em&gt;asides&lt;/em&gt;, &lt;em&gt;hints&lt;/em&gt;, or &lt;em&gt;alerts&lt;/em&gt;. By wrapping a paragraph in &lt;code&gt;{{% callout note %}} ... {{% /callout %}}&lt;/code&gt;, it will render as an aside.&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-markdown&#34;&gt;{{% callout note %}}
A Markdown aside is useful for displaying notices, hints, or definitions to your readers.
{{% /callout %}}
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;renders as&lt;/p&gt;
&lt;div class=&#34;alert alert-note&#34;&gt;
  &lt;div&gt;
    A Markdown aside is useful for displaying notices, hints, or definitions to your readers.
  &lt;/div&gt;
&lt;/div&gt;
&lt;h3 id=&#34;spoilers&#34;&gt;Spoilers&lt;/h3&gt;
&lt;p&gt;Add a spoiler to a page to reveal text, such as an answer to a question, after a button is clicked.&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-markdown&#34;&gt;{{&amp;lt; spoiler text=&amp;quot;Click to view the spoiler&amp;quot; &amp;gt;}}
You found me!
{{&amp;lt; /spoiler &amp;gt;}}
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;renders as&lt;/p&gt;
&lt;details class=&#34;spoiler &#34;  id=&#34;spoiler-2&#34;&gt;
  &lt;summary&gt;Click to view the spoiler&lt;/summary&gt;
  &lt;p&gt;You found me!&lt;/p&gt;
&lt;/details&gt;
&lt;h3 id=&#34;icons&#34;&gt;Icons&lt;/h3&gt;
&lt;p&gt;Academic enables you to use a wide range of &lt;a href=&#34;https://sourcethemes.com/academic/docs/page-builder/#icons&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;icons from &lt;em&gt;Font Awesome&lt;/em&gt; and &lt;em&gt;Academicons&lt;/em&gt;&lt;/a&gt; in addition to &lt;a href=&#34;https://sourcethemes.com/academic/docs/writing-markdown-latex/#emojis&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;emojis&lt;/a&gt;.&lt;/p&gt;
&lt;p&gt;Here are some examples using the &lt;code&gt;icon&lt;/code&gt; shortcode to render icons:&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-markdown&#34;&gt;{{&amp;lt; icon name=&amp;quot;terminal&amp;quot; pack=&amp;quot;fas&amp;quot; &amp;gt;}} Terminal  
{{&amp;lt; icon name=&amp;quot;python&amp;quot; pack=&amp;quot;fab&amp;quot; &amp;gt;}} Python  
{{&amp;lt; icon name=&amp;quot;r-project&amp;quot; pack=&amp;quot;fab&amp;quot; &amp;gt;}} R
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;renders as&lt;/p&gt;
&lt;p&gt;
  &lt;i class=&#34;fas fa-terminal  pr-1 fa-fw&#34;&gt;&lt;/i&gt; Terminal&lt;br&gt;

  &lt;i class=&#34;fab fa-python  pr-1 fa-fw&#34;&gt;&lt;/i&gt; Python&lt;br&gt;

  &lt;i class=&#34;fab fa-r-project  pr-1 fa-fw&#34;&gt;&lt;/i&gt; R&lt;/p&gt;
&lt;h3 id=&#34;did-you-find-this-page-helpful-consider-sharing-it-&#34;&gt;Did you find this page helpful? Consider sharing it 🙌&lt;/h3&gt;
</description>
    </item>
    
    <item>
      <title>Display Jupyter Notebooks with Academic</title>
      <link>https://karbalayghareh.github.io/post/jupyter/</link>
      <pubDate>Tue, 05 Feb 2019 00:00:00 +0000</pubDate>
      <guid>https://karbalayghareh.github.io/post/jupyter/</guid>
      <description>&lt;pre&gt;&lt;code class=&#34;language-python&#34;&gt;from IPython.core.display import Image
Image(&#39;https://www.python.org/static/community_logos/python-logo-master-v3-TM-flattened.png&#39;)
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;















&lt;figure  &gt;
  &lt;div class=&#34;d-flex justify-content-center&#34;&gt;
    &lt;div class=&#34;w-100&#34; &gt;&lt;img src=&#34;./index_1_0.png&#34; alt=&#34;png&#34; loading=&#34;lazy&#34; data-zoomable /&gt;&lt;/div&gt;
  &lt;/div&gt;&lt;/figure&gt;
&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-python&#34;&gt;print(&amp;quot;Welcome to Academic!&amp;quot;)
&lt;/code&gt;&lt;/pre&gt;
&lt;pre&gt;&lt;code&gt;Welcome to Academic!
&lt;/code&gt;&lt;/pre&gt;
&lt;h2 id=&#34;install-python-and-jupyterlab&#34;&gt;Install Python and JupyterLab&lt;/h2&gt;
&lt;p&gt;&lt;a href=&#34;https://www.anaconda.com/distribution/#download-section&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;Install Anaconda&lt;/a&gt; which includes Python 3 and JupyterLab.&lt;/p&gt;
&lt;p&gt;Alternatively, install JupyterLab with &lt;code&gt;pip3 install jupyterlab&lt;/code&gt;.&lt;/p&gt;
&lt;h2 id=&#34;create-or-upload-a-jupyter-notebook&#34;&gt;Create or upload a Jupyter notebook&lt;/h2&gt;
&lt;p&gt;Run the following commands in your Terminal, substituting &lt;code&gt;&amp;lt;MY-WEBSITE-FOLDER&amp;gt;&lt;/code&gt; and &lt;code&gt;&amp;lt;SHORT-POST-TITLE&amp;gt;&lt;/code&gt; with the file path to your Academic website folder and a short title for your blog post (use hyphens instead of spaces), respectively:&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-bash&#34;&gt;mkdir -p &amp;lt;MY-WEBSITE-FOLDER&amp;gt;/content/post/&amp;lt;SHORT-POST-TITLE&amp;gt;/
cd &amp;lt;MY-WEBSITE-FOLDER&amp;gt;/content/post/&amp;lt;SHORT-POST-TITLE&amp;gt;/
jupyter lab index.ipynb
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;The &lt;code&gt;jupyter&lt;/code&gt; command above will launch the JupyterLab editor, allowing us to add Academic metadata and write the content.&lt;/p&gt;
&lt;h2 id=&#34;edit-your-post-metadata&#34;&gt;Edit your post metadata&lt;/h2&gt;
&lt;p&gt;The first cell of your Jupter notebook will contain your post metadata (&lt;a href=&#34;https://sourcethemes.com/academic/docs/front-matter/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;front matter&lt;/a&gt;).&lt;/p&gt;
&lt;p&gt;In Jupter, choose &lt;em&gt;Markdown&lt;/em&gt; as the type of the first cell and wrap your Academic metadata in three dashes, indicating that it is YAML front matter:&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;---
title: My post&#39;s title
date: 2019-09-01

# Put any other Academic metadata here...
---
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;Edit the metadata of your post, using the &lt;a href=&#34;https://sourcethemes.com/academic/docs/managing-content&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;documentation&lt;/a&gt; as a guide to the available options.&lt;/p&gt;
&lt;p&gt;To set a &lt;a href=&#34;https://sourcethemes.com/academic/docs/managing-content/#featured-image&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;featured image&lt;/a&gt;, place an image named &lt;code&gt;featured&lt;/code&gt; into your post&amp;rsquo;s folder.&lt;/p&gt;
&lt;p&gt;For other tips, such as using math, see the guide on &lt;a href=&#34;https://sourcethemes.com/academic/docs/writing-markdown-latex/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;writing content with Academic&lt;/a&gt;.&lt;/p&gt;
&lt;h2 id=&#34;convert-notebook-to-markdown&#34;&gt;Convert notebook to Markdown&lt;/h2&gt;
&lt;pre&gt;&lt;code class=&#34;language-bash&#34;&gt;jupyter nbconvert index.ipynb --to markdown --NbConvertApp.output_files_dir=.
&lt;/code&gt;&lt;/pre&gt;
&lt;h2 id=&#34;example&#34;&gt;Example&lt;/h2&gt;
&lt;p&gt;This post was created with Jupyter. The orginal files can be found at &lt;a href=&#34;https://github.com/gcushen/hugo-academic/tree/master/exampleSite/content/post/jupyter&#34;&gt;https://github.com/gcushen/hugo-academic/tree/master/exampleSite/content/post/jupyter&lt;/a&gt;&lt;/p&gt;
</description>
    </item>
    
    <item>
      <title>Slides</title>
      <link>https://karbalayghareh.github.io/slides/example/</link>
      <pubDate>Tue, 05 Feb 2019 00:00:00 +0000</pubDate>
      <guid>https://karbalayghareh.github.io/slides/example/</guid>
      <description>&lt;h1 id=&#34;create-slides-in-markdown-with-wowchemy&#34;&gt;Create slides in Markdown with Wowchemy&lt;/h1&gt;
&lt;p&gt;&lt;a href=&#34;https://wowchemy.com/&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;Wowchemy&lt;/a&gt; | &lt;a href=&#34;https://owchemy.com/docs/managing-content/#create-slides&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;Documentation&lt;/a&gt;&lt;/p&gt;
&lt;hr&gt;
&lt;h2 id=&#34;features&#34;&gt;Features&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Efficiently write slides in Markdown&lt;/li&gt;
&lt;li&gt;3-in-1: Create, Present, and Publish your slides&lt;/li&gt;
&lt;li&gt;Supports speaker notes&lt;/li&gt;
&lt;li&gt;Mobile friendly slides&lt;/li&gt;
&lt;/ul&gt;
&lt;hr&gt;
&lt;h2 id=&#34;controls&#34;&gt;Controls&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Next: &lt;code&gt;Right Arrow&lt;/code&gt; or &lt;code&gt;Space&lt;/code&gt;&lt;/li&gt;
&lt;li&gt;Previous: &lt;code&gt;Left Arrow&lt;/code&gt;&lt;/li&gt;
&lt;li&gt;Start: &lt;code&gt;Home&lt;/code&gt;&lt;/li&gt;
&lt;li&gt;Finish: &lt;code&gt;End&lt;/code&gt;&lt;/li&gt;
&lt;li&gt;Overview: &lt;code&gt;Esc&lt;/code&gt;&lt;/li&gt;
&lt;li&gt;Speaker notes: &lt;code&gt;S&lt;/code&gt;&lt;/li&gt;
&lt;li&gt;Fullscreen: &lt;code&gt;F&lt;/code&gt;&lt;/li&gt;
&lt;li&gt;Zoom: &lt;code&gt;Alt + Click&lt;/code&gt;&lt;/li&gt;
&lt;li&gt;&lt;a href=&#34;https://github.com/hakimel/reveal.js#pdf-export&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;PDF Export&lt;/a&gt;: &lt;code&gt;E&lt;/code&gt;&lt;/li&gt;
&lt;/ul&gt;
&lt;hr&gt;
&lt;h2 id=&#34;code-highlighting&#34;&gt;Code Highlighting&lt;/h2&gt;
&lt;p&gt;Inline code: &lt;code&gt;variable&lt;/code&gt;&lt;/p&gt;
&lt;p&gt;Code block:&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-python&#34;&gt;porridge = &amp;quot;blueberry&amp;quot;
if porridge == &amp;quot;blueberry&amp;quot;:
    print(&amp;quot;Eating...&amp;quot;)
&lt;/code&gt;&lt;/pre&gt;
&lt;hr&gt;
&lt;h2 id=&#34;math&#34;&gt;Math&lt;/h2&gt;
&lt;p&gt;In-line math: $x + y = z$&lt;/p&gt;
&lt;p&gt;Block math:&lt;/p&gt;
&lt;p&gt;$$
f\left( x \right) = ;\frac{{2\left( {x + 4} \right)\left( {x - 4} \right)}}{{\left( {x + 4} \right)\left( {x + 1} \right)}}
$$&lt;/p&gt;
&lt;hr&gt;
&lt;h2 id=&#34;fragments&#34;&gt;Fragments&lt;/h2&gt;
&lt;p&gt;Make content appear incrementally&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;{{% fragment %}} One {{% /fragment %}}
{{% fragment %}} **Two** {{% /fragment %}}
{{% fragment %}} Three {{% /fragment %}}
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;Press &lt;code&gt;Space&lt;/code&gt; to play!&lt;/p&gt;
&lt;p&gt;&lt;span class=&#34;fragment &#34; &gt;
One
&lt;/span&gt;
&lt;span class=&#34;fragment &#34; &gt;
&lt;strong&gt;Two&lt;/strong&gt;
&lt;/span&gt;
&lt;span class=&#34;fragment &#34; &gt;
Three
&lt;/span&gt;&lt;/p&gt;
&lt;hr&gt;
&lt;p&gt;A fragment can accept two optional parameters:&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;&lt;code&gt;class&lt;/code&gt;: use a custom style (requires definition in custom CSS)&lt;/li&gt;
&lt;li&gt;&lt;code&gt;weight&lt;/code&gt;: sets the order in which a fragment appears&lt;/li&gt;
&lt;/ul&gt;
&lt;hr&gt;
&lt;h2 id=&#34;speaker-notes&#34;&gt;Speaker Notes&lt;/h2&gt;
&lt;p&gt;Add speaker notes to your presentation&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-markdown&#34;&gt;{{% speaker_note %}}
- Only the speaker can read these notes
- Press `S` key to view
{{% /speaker_note %}}
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;Press the &lt;code&gt;S&lt;/code&gt; key to view the speaker notes!&lt;/p&gt;
&lt;aside class=&#34;notes&#34;&gt;
  &lt;ul&gt;
&lt;li&gt;Only the speaker can read these notes&lt;/li&gt;
&lt;li&gt;Press &lt;code&gt;S&lt;/code&gt; key to view&lt;/li&gt;
&lt;/ul&gt;

&lt;/aside&gt;
&lt;hr&gt;
&lt;h2 id=&#34;themes&#34;&gt;Themes&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;black: Black background, white text, blue links (default)&lt;/li&gt;
&lt;li&gt;white: White background, black text, blue links&lt;/li&gt;
&lt;li&gt;league: Gray background, white text, blue links&lt;/li&gt;
&lt;li&gt;beige: Beige background, dark text, brown links&lt;/li&gt;
&lt;li&gt;sky: Blue background, thin dark text, blue links&lt;/li&gt;
&lt;/ul&gt;
&lt;hr&gt;
&lt;ul&gt;
&lt;li&gt;night: Black background, thick white text, orange links&lt;/li&gt;
&lt;li&gt;serif: Cappuccino background, gray text, brown links&lt;/li&gt;
&lt;li&gt;simple: White background, black text, blue links&lt;/li&gt;
&lt;li&gt;solarized: Cream-colored background, dark green text, blue links&lt;/li&gt;
&lt;/ul&gt;
&lt;hr&gt;

&lt;section data-noprocess data-shortcode-slide
  
      
      data-background-image=&#34;/media/boards.jpg&#34;
  &gt;

&lt;h2 id=&#34;custom-slide&#34;&gt;Custom Slide&lt;/h2&gt;
&lt;p&gt;Customize the slide style and background&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-markdown&#34;&gt;{{&amp;lt; slide background-image=&amp;quot;/media/boards.jpg&amp;quot; &amp;gt;}}
{{&amp;lt; slide background-color=&amp;quot;#0000FF&amp;quot; &amp;gt;}}
{{&amp;lt; slide class=&amp;quot;my-style&amp;quot; &amp;gt;}}
&lt;/code&gt;&lt;/pre&gt;
&lt;hr&gt;
&lt;h2 id=&#34;custom-css-example&#34;&gt;Custom CSS Example&lt;/h2&gt;
&lt;p&gt;Let&amp;rsquo;s make headers navy colored.&lt;/p&gt;
&lt;p&gt;Create &lt;code&gt;assets/css/reveal_custom.css&lt;/code&gt; with:&lt;/p&gt;
&lt;pre&gt;&lt;code class=&#34;language-css&#34;&gt;.reveal section h1,
.reveal section h2,
.reveal section h3 {
  color: navy;
}
&lt;/code&gt;&lt;/pre&gt;
&lt;hr&gt;
&lt;h1 id=&#34;questions&#34;&gt;Questions?&lt;/h1&gt;
&lt;p&gt;&lt;a href=&#34;https://github.com/wowchemy/wowchemy-hugo-modules/discussions&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;Ask&lt;/a&gt;&lt;/p&gt;
&lt;p&gt;&lt;a href=&#34;https://wowchemy.com/docs/managing-content/#create-slides&#34; target=&#34;_blank&#34; rel=&#34;noopener&#34;&gt;Documentation&lt;/a&gt;&lt;/p&gt;
</description>
    </item>
    
    <item>
      <title>OBTL</title>
      <link>https://karbalayghareh.github.io/project/internal-project-2/</link>
      <pubDate>Sun, 15 Jul 2018 00:00:00 +0000</pubDate>
      <guid>https://karbalayghareh.github.io/project/internal-project-2/</guid>
      <description>&lt;p&gt;Transfer learning has recently attracted significant research attention, as it simultaneously learns from different source domains, which have plenty of labeled data, and transfers the relevant knowledge to the target domain with limited labeled data to improve the prediction performance. We propose a Bayesian transfer learning framework, in the homogeneous transfer learning scenario, where the source and target domains are related through the joint prior density of the model parameters. The modeling of joint prior densities enables better understanding of the “transferability” between domains. We define a joint Wishart distribution for the precision matrices of the Gaussian feature-label distributions in the source and target domains to act like a bridge that transfers the useful information of the source domain to help classification in the target domain by improving the target posteriors. Using several theorems in multivariate statistics, the posteriors and posterior predictive densities are derived in closed forms with hypergeometric functions of matrix argument, leading to our novel closed-form and fast Optimal Bayesian Transfer Learning (OBTL) classifier. Experimental results on both synthetic and real-world benchmark data confirm the superb performance of the OBTL compared to the other state-of-the-art transfer learning and domain adaptation methods.&lt;/p&gt;
</description>
    </item>
    
    <item>
      <title>Optimal Bayesian transfer learning</title>
      <link>https://karbalayghareh.github.io/publication/journal-article/</link>
      <pubDate>Sun, 15 Jul 2018 00:00:00 +0000</pubDate>
      <guid>https://karbalayghareh.github.io/publication/journal-article/</guid>
      <description></description>
    </item>
    
    <item>
      <title>Classification of Gaussian trajectories with missing data in Boolean gene regulatory networks</title>
      <link>https://karbalayghareh.github.io/publication/conference-paper/</link>
      <pubDate>Sun, 05 Mar 2017 00:00:00 +0000</pubDate>
      <guid>https://karbalayghareh.github.io/publication/conference-paper/</guid>
      <description></description>
    </item>
    
    <item>
      <title></title>
      <link>https://karbalayghareh.github.io/admin/config.yml</link>
      <pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
      <guid>https://karbalayghareh.github.io/admin/config.yml</guid>
      <description></description>
    </item>
    
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