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blog/2016-10-30-farthest-points/index.html

@@ -312,7 +312,7 @@ <h1 class="title">Finding the Farthest Points in a Point Cloud</h1>
 <span id="cb2-17"><a href="#cb2-17" aria-hidden="true" tabindex="-1"></a><span class="fu">plot</span>(mat, <span class="at">asp =</span> <span class="dv">1</span>, <span class="at">xlab =</span> <span class="st">""</span>, <span class="at">ylab =</span> <span class="st">""</span>)</span>
 <span id="cb2-18"><a href="#cb2-18" aria-hidden="true" tabindex="-1"></a><span class="fu">points</span>(mat[ind, ], <span class="at">pch =</span> <span class="dv">19</span>)</span>
 <span id="cb2-19"><a href="#cb2-19" aria-hidden="true" tabindex="-1"></a><span class="fu">text</span>(mat[ind, ], <span class="at">adj =</span> <span class="fu">c</span>(<span class="dv">0</span>, <span class="sc">-</span><span class="fl">1.5</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
-<div class="cell quarto-layout-panel" data-fig-lab="greedy-approach" data-layout-ncol="2">
+<div class="cell quarto-layout-panel" data-layout-ncol="2" data-fig-lab="greedy-approach">
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 <div class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: flex-start;">
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@@ -358,7 +358,7 @@ <h1 class="title">Finding the Farthest Points in a Point Cloud</h1>
 <span id="cb4-14"><a href="#cb4-14" aria-hidden="true" tabindex="-1"></a><span class="fu">plot</span>(mat, <span class="at">asp =</span> <span class="dv">1</span>, <span class="at">xlab =</span> <span class="st">""</span>, <span class="at">ylab =</span> <span class="st">""</span>)</span>
 <span id="cb4-15"><a href="#cb4-15" aria-hidden="true" tabindex="-1"></a><span class="fu">points</span>(mat[r, ], <span class="at">pch =</span> <span class="dv">19</span>)</span>
 <span id="cb4-16"><a href="#cb4-16" aria-hidden="true" tabindex="-1"></a><span class="fu">text</span>(mat[r, ], <span class="at">adj =</span> <span class="fu">c</span>(<span class="dv">0</span>, <span class="sc">-</span><span class="fl">1.5</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
-<div class="cell quarto-layout-panel" data-fig-lab="new-approach" data-layout-ncol="2">
+<div class="cell quarto-layout-panel" data-layout-ncol="2" data-fig-lab="new-approach">
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 <div class="quarto-layout-cell" style="flex-basis: 50.0%;justify-content: flex-start;">
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blog/2024-05-22-phd-thesis/index.html

@@ -290,7 +290,7 @@ <h1 class="title">PhD Thesis</h1>
 <div id="fig-cover" class="lightbox quarto-figure quarto-figure-center quarto-float anchored page-columns page-full">
 <figure class="quarto-float quarto-float-fig figure page-columns page-full">
 <div aria-describedby="fig-cover-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
-<a href="front-cover.png" class="lightbox" data-glightbox="description: .lightbox-desc-1" data-gallery="quarto-lightbox-gallery-1"><img src="front-cover.png" class="border img-fluid figure-img" width="300"></a>
+<a href="front-cover.png" class="lightbox" data-gallery="quarto-lightbox-gallery-1" data-glightbox="description: .lightbox-desc-1"><img src="front-cover.png" class="border img-fluid figure-img" width="300"></a>
 </div>
 <figcaption class="quarto-float-caption-margin quarto-float-caption quarto-float-fig margin-caption" id="fig-cover-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
 Figure&nbsp;1: The cover of my thesis. The image features a subset of the elastic net path for the famous diabetes data set.
@@ -382,7 +382,7 @@ <h2 class="anchored" data-anchor-id="paper-2">Paper 2</h2>
 <div id="fig-paper2" class="lightbox quarto-figure quarto-figure-center quarto-float anchored page-columns page-full">
 <figure class="quarto-float quarto-float-fig figure page-columns page-full">
 <div aria-describedby="fig-paper2-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
-<a href="paper2-highlight.png" class="lightbox" data-glightbox="description: .lightbox-desc-2" data-gallery="quarto-lightbox-gallery-2"><img src="paper2-highlight.png" class="img-fluid figure-img"></a>
+<a href="paper2-highlight.png" class="lightbox" data-gallery="quarto-lightbox-gallery-2" data-glightbox="description: .lightbox-desc-2"><img src="paper2-highlight.png" class="img-fluid figure-img"></a>
 </div>
 <figcaption class="quarto-float-caption-margin quarto-float-caption quarto-float-fig margin-caption" id="fig-paper2-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
 Figure&nbsp;2: Look-ahead screening for 20 randomly selected features from the <em>leukemia</em> data set. Blue squares indicate that the respective feature can be discarded from the problem for that step of the regularization path.
@@ -403,7 +403,7 @@ <h2 class="anchored" data-anchor-id="paper-4">Paper 4</h2>
 <div id="fig-paper4" class="lightbox fig-cap-location-bottom quarto-figure quarto-figure-center quarto-float anchored page-columns page-full">
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-<a href="paper4-highlight.svg" class="lightbox" data-glightbox="description: .lightbox-desc-3" data-gallery="quarto-lightbox-gallery-3"><img src="paper4-highlight.svg" class="fig-cap-location-bottom img-fluid figure-img"></a>
+<a href="paper4-highlight.svg" class="lightbox" data-gallery="quarto-lightbox-gallery-3" data-glightbox="description: .lightbox-desc-3"><img src="paper4-highlight.svg" class="fig-cap-location-bottom img-fluid figure-img"></a>
 </div>
 <figcaption class="quarto-float-caption-margin quarto-float-caption quarto-float-fig margin-caption" id="fig-paper4-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
 Figure&nbsp;3: A schematic over how a benchmark is set up and run using benchopt. The benchmark consists of a set of files that define objectives, datasets, and solvers. When the user runs benchopt, the package combines all of the possible combinations of objectives, datasets, and solvers and outputs a neatly formatted database of the results.
@@ -419,7 +419,7 @@ <h2 class="anchored" data-anchor-id="paper-5">Paper 5</h2>
 <div id="fig-paper5" class="lightbox quarto-figure quarto-figure-center quarto-float anchored page-columns page-full">
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 <div aria-describedby="fig-paper5-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
-<a href="paper5-highlight.svg" class="lightbox" data-glightbox="description: .lightbox-desc-4" data-gallery="quarto-lightbox-gallery-4"><img src="paper5-highlight.svg" class="img-fluid figure-img" width="700"></a>
+<a href="paper5-highlight.svg" class="lightbox" data-gallery="quarto-lightbox-gallery-4" data-glightbox="description: .lightbox-desc-4"><img src="paper5-highlight.svg" class="img-fluid figure-img" width="700"></a>
 </div>
 <figcaption class="quarto-float-caption-margin quarto-float-caption quarto-float-fig margin-caption" id="fig-paper5-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
 Figure&nbsp;4: An illustration of the hybrid coordinate descent solver we developed for SLOPE, showing progress until convergence for the coordinate descent solver (CD) that we use as part of the hybrid method, our hybrid method, and proximal gradient descent (PGD).
@@ -434,7 +434,7 @@ <h2 class="anchored" data-anchor-id="paper-6">Paper 6</h2>
 <div id="fig-paper6" class="lightbox quarto-figure quarto-figure-center quarto-float anchored page-columns page-full">
 <figure class="quarto-float quarto-float-fig figure page-columns page-full">
 <div aria-describedby="fig-paper6-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
-<a href="paper6-highlight.svg" class="lightbox" data-glightbox="description: .lightbox-desc-5" data-gallery="quarto-lightbox-gallery-5"><img src="paper6-highlight.svg" class="img-fluid figure-img" width="700"></a>
+<a href="paper6-highlight.svg" class="lightbox" data-gallery="quarto-lightbox-gallery-5" data-glightbox="description: .lightbox-desc-5"><img src="paper6-highlight.svg" class="img-fluid figure-img" width="700"></a>
 </div>
 <figcaption class="quarto-float-caption-margin quarto-float-caption quarto-float-fig margin-caption" id="fig-paper6-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
 Figure&nbsp;5: Estimated coefficients from lasso and ridge regression for a two-feature problem where one of the features has a quasi-normal distribution (values deterministically set via the quantile function), with standard deviation 1/2, and the other is a binary (quasi-Bernoulli) feature with class-balance <span class="math inline">\(q\)</span>. The normal feature is standardized in every case, whereas the binary feature is scaled with <span class="math inline">\((q - q^2)^\delta\)</span>—its variance to the power of <span class="math inline">\(\delta\)</span>. In other words, we have no scaling for <span class="math inline">\(\delta=0\)</span>, standard deviation scaling when <span class="math inline">\(\delta=1/2\)</span>, and variance-scaling when <span class="math inline">\(\delta = 1\)</span>.
@@ -937,7 +937,7 @@ <h2 class="anchored" data-anchor-id="defense">Defense</h2>
     </div>
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+<script>var lightboxQuarto = GLightbox({"descPosition":"bottom","loop":false,"selector":".lightbox","openEffect":"zoom","closeEffect":"zoom"});
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blog/2024-05-30-moloch/index.html

@@ -285,7 +285,7 @@ <h1 class="title">Moloch: A Revival of the Metropolis LaTeX Beamer Theme</h1>
 
 
 <p>My beamer configuration for LaTeX presentations has been in a state of flux for as long as I can remember. I have tried many different themes and configurations, and have typically tried to keep the theme minimalisic but at the same time functional and visually appealing. Nevertheless, I have frequently found myself scrapping my custom modifications and returning to the <a href="https://github.com/matze/mtheme">Metropolis theme</a>, which I think is the most well-designed theme that I have so far encountered for beamer.</p>
-<p>The only problem is that Metropolis is no longer actively maintained. The latest update (at the time of writing) was six years ago and since then a number of issues have cropped up. Most of them are not major and can be circumvented through various hacks and workarounds, but I have grown increasingly frustrated with the separate file of Metropolis patches that I’ve had to keep around to fix these issues. Beamer tself in fact even includes several patches now in order to stop the theme from breaking (see <a href="https://github.com/josephwright/beamer/blob/c0d91f15165421646b5383546e6195187b7f97c9/base/beamerbasecompatibility.sty#L253">here</a>, <a href="https://github.com/josephwright/beamer/blob/c0d91f15165421646b5383546e6195187b7f97c9/base/beamerbasesection.sty#L209">here</a>, and <a href="https://github.com/josephwright/beamer/blob/c0d91f15165421646b5383546e6195187b7f97c9/base/beamerbaselocalstructure.sty#L29">here</a>.)</p>
+<p>The only problem is that Metropolis is no longer actively maintained. The latest update (at the time of writing) was six years ago and since then a number of issues have cropped up. Most of them are not major and can be circumvented through various hacks and workarounds, but I have grown increasingly frustrated with the separate file of Metropolis patches that I’ve had to keep around to fix these issues. Beamer itself in fact even includes several patches now in order to stop the theme from breaking (see <a href="https://github.com/josephwright/beamer/blob/c0d91f15165421646b5383546e6195187b7f97c9/base/beamerbasecompatibility.sty#L253">here</a>, <a href="https://github.com/josephwright/beamer/blob/c0d91f15165421646b5383546e6195187b7f97c9/base/beamerbasesection.sty#L209">here</a>, and <a href="https://github.com/josephwright/beamer/blob/c0d91f15165421646b5383546e6195187b7f97c9/base/beamerbaselocalstructure.sty#L29">here</a>.)</p>
 <section id="moloch" class="level2">
 <h2 class="anchored" data-anchor-id="moloch">Moloch</h2>
 <p>This has now (since some months back actually) led me to fork Metropolis to try to fix these outstanding issues. I call the new theme <em>Moloch</em> (which is likely familiar to you if you know your Metropolis). The original design is still pretty much intact save for a few tweaks that I will summarize in <a href="#sec-changes" class="quarto-xref">Section&nbsp;3</a>, which overall bring the theme closer to normal beamer behavior. The code for the theme has also been simplified and made more robust. Metropolis, for instance, made much use of <code>\patchcmd</code> from the etoolbox package to patch beamer theme internals in order to support modifications to, for instance, frame titles. This was what lead the theme to break in the first place as beamer introduced changes in these commands and I have thus opted to remove all this kind of patching in favor of relying on standard functionality from the beamer theme instead.</p>
@@ -399,17 +399,20 @@ <h3 class="anchored" data-anchor-id="title-page-redesign">Title Page Redesign</h
 <h3 class="anchored" data-anchor-id="font-settings">Font Settings</h3>
 <p>Metropolis includes special handling of font settings. If you use LuaTeX or XeTeX, then Metropolis automatically checks if the Fira Sans font is available and sets it up for you. I like the Fira fonts myself and think that they are a nice choice for presentations, but I do not think that they should be set as part of the theme, especially since this means that you get different output by default if you run your document through pdfTeX instead, which I think is undesireable.</p>
 <p>I’ve therefore disabled these font settings, but if you want to replicate the look of Metropolis when it comes to the fonts as well, then all you need is you use XeTeX or LuaTeX and set your font options according to the following example (or something similar).</p>
-<div class="sourceCode" id="cb5"><pre class="sourceCode latex code-with-copy"><code class="sourceCode latex"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="bu">\usepackage</span>{<span class="ex">mathspec</span>}</span>
-<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a><span class="fu">\setsansfont</span>[</span>
-<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a>  ItalicFont={Fira Sans Light Italic},</span>
-<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a>  BoldFont={Fira Sans},</span>
-<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a>  BoldItalicFont={Fira Sans Italic}</span>
-<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a>]{Fira Sans Light}</span>
-<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a><span class="fu">\setmonofont</span>[BoldFont={Fira Mono Medium}]{Fira Mono}</span>
-<span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a><span class="fu">\setmathfont</span>{Fira Math Light}</span>
-<span id="cb5-9"><a href="#cb5-9" aria-hidden="true" tabindex="-1"></a><span class="fu">\AtBeginEnvironment</span>{tabular}{<span class="co">%</span></span>
-<span id="cb5-10"><a href="#cb5-10" aria-hidden="true" tabindex="-1"></a>  <span class="fu">\addfontfeature</span>{Numbers={Monospaced}}</span>
-<span id="cb5-11"><a href="#cb5-11" aria-hidden="true" tabindex="-1"></a>}</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode" id="cb5"><pre class="sourceCode latex code-with-copy"><code class="sourceCode latex"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="bu">\usepackage</span>{<span class="ex">fontspec</span>}</span>
+<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a><span class="fu">\setsansfont</span>[</span>
+<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a>  ItalicFont={Fira Sans Light Italic},</span>
+<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a>  BoldFont={Fira Sans},</span>
+<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a>  BoldItalicFont={Fira Sans Italic}</span>
+<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a>]{Fira Sans Light}</span>
+<span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a><span class="fu">\setmonofont</span>[BoldFont={Fira Mono Medium}]{Fira Mono}</span>
+<span id="cb5-9"><a href="#cb5-9" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb5-10"><a href="#cb5-10" aria-hidden="true" tabindex="-1"></a><span class="fu">\AtBeginEnvironment</span>{tabular}{<span class="co">%</span></span>
+<span id="cb5-11"><a href="#cb5-11" aria-hidden="true" tabindex="-1"></a>  <span class="fu">\addfontfeature</span>{Numbers={Monospaced}}</span>
+<span id="cb5-12"><a href="#cb5-12" aria-hidden="true" tabindex="-1"></a>}</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<p>If you want to have <code>\operatorname</code>, <code>\mathrm</code>, and company in the Fira font as well, then you’ll need to set <code>\setmainfont</code> as well.</p>
+<p>Note that there is only a beta version of the Fira Math Light font available and that it is not at all complete, so unfortunately there is no good way to get a matching math font for Fira Sans Light at the moment. (Otherwise we could use <strong>unicode-maths</strong> and <code>Fira Math Light</code>). This I think is another good argument for why Fira should not be set as the default font for the theme.</p>
 </section>
 <section id="no-more-automatic-paragraph-spacing" class="level3">
 <h3 class="anchored" data-anchor-id="no-more-automatic-paragraph-spacing">No More Automatic Paragraph Spacing</h3>
@@ -920,7 +923,7 @@ <h3 class="anchored" data-anchor-id="acknowledgements">Acknowledgements</h3>
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