From 547fb99ab2835e567d7b82ee6a533e7645adcf6d Mon Sep 17 00:00:00 2001
From: Dimitri Lozeve <dimitri@lozeve.com>
Date: Tue, 14 Apr 2020 12:51:55 +0200
Subject: [PATCH] Update header and styling

---
 _site/archive.html                            |  47 +---
 _site/atom.xml                                |  14 +-
 _site/contact.html                            |  29 +--
 _site/css/default.css                         |   2 +-
 _site/cv.html                                 | 122 +---------
 _site/index.html                              | 102 +--------
 _site/posts/ginibre-ensemble.html             |  44 +---
 ...transport-for-document-classification.html | 103 +--------
 _site/posts/ising-apl.html                    | 208 +-----------------
 _site/posts/ising-model.html                  | 124 +----------
 _site/posts/lsystems.html                     | 138 +-----------
 _site/posts/peano.html                        | 115 +---------
 _site/posts/reinforcement-learning-1.html     |  72 +-----
 .../posts/self-learning-chatbots-destygo.html |  25 +--
 _site/projects.html                           |  57 +----
 _site/projects/adsb.html                      |  19 +-
 _site/projects/civilisation.html              |  19 +-
 _site/projects/community-detection.html       |  19 +-
 _site/projects/ising-model.html               |  19 +-
 _site/projects/lsystems.html                  |  19 +-
 _site/projects/orbit.html                     |  19 +-
 _site/projects/satrap.html                    |  19 +-
 _site/projects/tda.html                       |  19 +-
 _site/projects/ww2-bombings.html              |  19 +-
 _site/rss.xml                                 |  14 +-
 _site/skills.html                             |  63 +-----
 css/default.css                               |  66 ++----
 ...-transport-for-document-classification.org |   6 +-
 templates/default.html                        |  10 +-
 templates/post.html                           |   1 -
 30 files changed, 57 insertions(+), 1476 deletions(-)

diff --git a/_site/archive.html b/_site/archive.html
index 25bcf2f..cdb6910 100644
--- a/_site/archive.html
+++ b/_site/archive.html
@@ -9,6 +9,7 @@
     <title>Dimitri Lozeve - Archives</title>
     <link rel="stylesheet" href="./css/tufte.css" />
     <link rel="stylesheet" href="./css/pandoc.css" />
+    <link rel="stylesheet" href="./css/default.css" />
     <link rel="stylesheet" href="./css/syntax.css" />
 
     <!-- KaTeX CSS styles -->
@@ -25,9 +26,6 @@
     <article>
       
       <header>
-	<div class="logo">
-          <a href="./">Dimitri Lozeve</a>
-	</div>
 	<nav>
           <a href="./">Home</a>
 	  <a href="./projects.html">Projects</a>
@@ -43,9 +41,6 @@
       </header>
       
 
-      <!-- <header> -->
-	<!-- </header> -->
-
       
     </article>
 
@@ -87,46 +82,6 @@
 </ul>
 
 
-    <!-- <main role="main"> -->
-      <!-- 	Here you can find all my previous posts:
-<ul>
-    
-        <li>
-            <a href="/posts/hierarchical-optimal-transport-for-document-classification.html">Reading notes: Hierarchical Optimal Transport for Document Representation</a> - April  5, 2020
-        </li>
-    
-        <li>
-            <a href="/posts/self-learning-chatbots-destygo.html">Mindsay: Towards Self-Learning Chatbots</a> - April  6, 2019
-        </li>
-    
-        <li>
-            <a href="/posts/ginibre-ensemble.html">Random matrices from the Ginibre ensemble</a> - March 20, 2019
-        </li>
-    
-        <li>
-            <a href="/posts/peano.html">Peano Axioms</a> - March 18, 2019
-        </li>
-    
-        <li>
-            <a href="/posts/reinforcement-learning-1.html">Quick Notes on Reinforcement Learning</a> - November 21, 2018
-        </li>
-    
-        <li>
-            <a href="/posts/ising-apl.html">Ising model simulation in APL</a> - March  5, 2018
-        </li>
-    
-        <li>
-            <a href="/posts/ising-model.html">Ising model simulation</a> - February  5, 2018
-        </li>
-    
-        <li>
-            <a href="/posts/lsystems.html">Generating and representing L-systems</a> - January 18, 2018
-        </li>
-    
-</ul>
-
- -->
-      <!-- </main> -->
 
     <footer>
       Site proudly generated by
diff --git a/_site/atom.xml b/_site/atom.xml
index 9b6b16b..c20090d 100644
--- a/_site/atom.xml
+++ b/_site/atom.xml
@@ -17,7 +17,6 @@
     <updated>2020-04-05T00:00:00Z</updated>
     <summary type="html"><![CDATA[<article>
     <section class="header">
-        Posted on April  5, 2020
         
     </section>
     <section>
@@ -67,9 +66,9 @@ W_1(p, q) = \min_{P \in \mathbb{R}_+^{n\times m}} \sum_{i,j} C_{i,j} P_{i,j}
 </ul>
 <p>The first one can be precomputed once for all subsequent distances, so it is invariable in the number of documents we have to process. The second one only operates on <span class="math inline">\(\lvert T \rvert\)</span> topics instead of the full vocabulary: the resulting optimisation problem is much smaller! This is great for performance, as it should be easy now to compute all pairwise distances in a large set of documents.</p>
 <p>Another interesting insight is that topics are represented as collections of words (we can keep the top 20 as a visual representations), and documents as collections of topics with weights. Both of these representations are highly interpretable for a human being who wants to understand what’s going on. I think this is one of the strongest aspects of these approaches: both the various representations and the algorithms are fully interpretable. Compared to a deep learning approach, we can make sense of every intermediate step, from the representations of topics to the weights in the optimisation algorithm to compute higher-level distances.</p>
-<figure>
-<img src="/images/hott_fig1.jpg" alt="Representation of two documents in topic space, along with how the distance was computed between them. Everything is interpretable: from the documents as collections of topics, to the matchings between topics determining the overall distance between the books (Yurochkin et al. 2019)." /><figcaption>Representation of two documents in topic space, along with how the distance was computed between them. Everything is interpretable: from the documents as collections of topics, to the matchings between topics determining the overall distance between the books <span class="citation" data-cites="yurochkin2019_hierar_optim_trans_docum_repres">(Yurochkin et al. <a href="#ref-yurochkin2019_hierar_optim_trans_docum_repres">2019</a>)</span>.</figcaption>
-</figure>
+<p><img src="/images/hott_fig1.jpg" /><span><label for="sn-2" class="margin-toggle">&#8853;</label><input type="checkbox" id="sn-2" class="margin-toggle"/><span class="marginnote"> Representation of two documents in topic space, along with how the distance was computed between them. Everything is interpretable: from the documents as collections of topics, to the matchings between topics determining the overall distance between the books <span class="citation" data-cites="yurochkin2019_hierar_optim_trans_docum_repres">(Yurochkin et al. <a href="#ref-yurochkin2019_hierar_optim_trans_docum_repres">2019</a>)</span>.<br />
+<br />
+</span></span></p>
 <h1 id="experiments">Experiments</h1>
 <p>The paper is very complete regarding experiments, providing a full evaluation of the method on one particular application: document clustering. They use <a href="https://scikit-learn.org/stable/modules/decomposition.html#latentdirichletallocation">Latent Dirichlet Allocation</a> to compute topics and GloVe for pretrained word embeddings <span class="citation" data-cites="pennington2014_glove">(Pennington, Socher, and Manning <a href="#ref-pennington2014_glove">2014</a>)</span>, and <a href="https://www.gurobi.com/">Gurobi</a> to solve the optimisation problems. Their code is available <a href="https://github.com/IBM/HOTT">on GitHub</a>.</p>
 <p>If you want the details, I encourage you to read the full paper, they tested the methods on a wide variety of datasets, with datasets containing very short documents (like Twitter), and long documents with a large vocabulary (books). With a simple <span class="math inline">\(k\)</span>-NN classification, they establish that HOTT performs best on average, especially on large vocabularies (books, the “gutenberg” dataset). It also has a much better computational performance than alternative methods based on regularisation of the optimal transport problem directly on words. So the hierarchical nature of the approach allows to gain considerably in performance, along with improvements in interpretability.</p>
@@ -111,7 +110,6 @@ W_1(p, q) = \min_{P \in \mathbb{R}_+^{n\times m}} \sum_{i,j} C_{i,j} P_{i,j}
     <updated>2019-04-06T00:00:00Z</updated>
     <summary type="html"><![CDATA[<article>
     <section class="header">
-        Posted on April  6, 2019
         
     </section>
     <section>
@@ -133,7 +131,6 @@ W_1(p, q) = \min_{P \in \mathbb{R}_+^{n\times m}} \sum_{i,j} C_{i,j} P_{i,j}
     <updated>2019-03-20T00:00:00Z</updated>
     <summary type="html"><![CDATA[<article>
     <section class="header">
-        Posted on March 20, 2019
         
     </section>
     <section>
@@ -174,7 +171,6 @@ W_1(p, q) = \min_{P \in \mathbb{R}_+^{n\times m}} \sum_{i,j} C_{i,j} P_{i,j}
     <updated>2019-03-18T00:00:00Z</updated>
     <summary type="html"><![CDATA[<article>
     <section class="header">
-        Posted on March 18, 2019
         
     </section>
     <section>
@@ -286,7 +282,6 @@ then <span class="math inline">\(\varphi(n)\)</span> is true for every natural n
     <updated>2018-11-21T00:00:00Z</updated>
     <summary type="html"><![CDATA[<article>
     <section class="header">
-        Posted on November 21, 2018
         
     </section>
     <section>
@@ -355,7 +350,6 @@ then <span class="math inline">\(\varphi(n)\)</span> is true for every natural n
     <updated>2018-03-05T00:00:00Z</updated>
     <summary type="html"><![CDATA[<article>
     <section class="header">
-        Posted on March  5, 2018
         
     </section>
     <section>
@@ -560,7 +554,6 @@ then <span class="math inline">\(\varphi(n)\)</span> is true for every natural n
     <updated>2018-02-05T00:00:00Z</updated>
     <summary type="html"><![CDATA[<article>
     <section class="header">
-        Posted on February  5, 2018
         
             by Dimitri Lozeve
         
@@ -681,7 +674,6 @@ J\sigma_i \sum_{j\sim i} \sigma_j.  \]</span></p>
     <updated>2018-01-18T00:00:00Z</updated>
     <summary type="html"><![CDATA[<article>
     <section class="header">
-        Posted on January 18, 2018
         
             by Dimitri Lozeve
         
diff --git a/_site/contact.html b/_site/contact.html
index a68d1e5..7ef3c64 100644
--- a/_site/contact.html
+++ b/_site/contact.html
@@ -9,6 +9,7 @@
     <title>Dimitri Lozeve - Contact</title>
     <link rel="stylesheet" href="./css/tufte.css" />
     <link rel="stylesheet" href="./css/pandoc.css" />
+    <link rel="stylesheet" href="./css/default.css" />
     <link rel="stylesheet" href="./css/syntax.css" />
 
     <!-- KaTeX CSS styles -->
@@ -25,9 +26,6 @@
     <article>
       
       <header>
-	<div class="logo">
-          <a href="./">Dimitri Lozeve</a>
-	</div>
 	<nav>
           <a href="./">Home</a>
 	  <a href="./projects.html">Projects</a>
@@ -43,9 +41,6 @@
       </header>
       
 
-      <!-- <header> -->
-	<!-- </header> -->
-
       
     </article>
 
@@ -69,28 +64,6 @@
 <dd><a href="https://twitter.com/DimitriLozeve">DimitriLozeve</a>
 </dd>
 </dl>
-    <!-- <main role="main"> -->
-      <!-- 	<dl>
-<dt><strong><a href="https://jedisct1.github.io/minisign/">minisign</a> public key</strong></dt>
-<dd>RWQ6uexORp8f7USHA7nX9lFfltaCA9x6aBV06MvgiGjUt6BVf6McyD26
-</dd>
-<dt><strong>E-mail</strong></dt>
-<dd>dimitri+web [at] lozeve [dot] com
-</dd>
-<dt><strong>GitHub</strong></dt>
-<dd><a href="https://github.com/dlozeve/">dlozeve</a>
-</dd>
-<dt><strong>LinkedIn</strong></dt>
-<dd><a href="https://www.linkedin.com/in/dimitrilozeve">Dimitri Lozeve</a>
-</dd>
-<dt><strong>StackOverflow</strong></dt>
-<dd><a href="https://stackoverflow.com/story/dimitrilozeve">dimitrilozeve</a>
-</dd>
-<dt><strong>Twitter</strong></dt>
-<dd><a href="https://twitter.com/DimitriLozeve">DimitriLozeve</a>
-</dd>
-</dl> -->
-      <!-- </main> -->
 
     <footer>
       Site proudly generated by
diff --git a/_site/css/default.css b/_site/css/default.css
index e078463..5cd7836 100644
--- a/_site/css/default.css
+++ b/_site/css/default.css
@@ -1 +1 @@
-body{font-family:Helvetica,Arial,sans-serif;line-height:1.5;color:#111;max-width:50rem;padding:2rem;margin:auto;background:#fafafa;counter-reset:theorem;counter-reset:definition}img{max-width:100%}a{color:#0B0080}h1{font-size:1.6rem}h2{font-size:1.2rem}header{border-bottom:0.15rem solid #000;margin-bottom:2rem}nav{text-align:right}nav a{font-size:1.2rem;font-weight:bold;color:#000;text-decoration:none;padding:.5rem}.logo a{float:left;font-size:1.2rem;font-weight:bold;color:#000;text-decoration:none}footer{margin-top:3rem;padding:.5rem 0;border-top:0.1rem solid #000;color:#555}article .header{font-style:italic;color:#555}.sourceCode{display:block;padding-left:1rem;margin-top:1rem;margin-bottom:1rem;background:#eee}.definition,.proposition,.theorem{display:block;border-left:2px solid #808080;padding-left:1rem;margin-top:1rem;margin-bottom:1rem}.proposition,.theorem{counter-increment:theorem;font-style:italic}.definition p:first-child,.proposition p:first-child,.theorem p:first-child,.proof p:first-child{display:inline}.definition p,.proposition p,.theorem p,.proof p{margin-top:0.4rem;margin-bottom:0.4rem;padding-left:1rem}.theorem:before{content:"Theorem " counter(theorem) ".";font-weight:bold;font-style:normal}.proposition:before{content:"Proposition " counter(theorem) ".";font-weight:bold;font-style:normal}.definition:before{counter-increment:definition;content:"Definition " counter(definition) ".";font-weight:bold;font-style:normal}.proof:before{content:"Proof.";font-style:italic}.proof:after{content:"\220E";float:right}
\ No newline at end of file
+body{background:#fafafa;counter-reset:theorem;counter-reset:definition}header{margin:1em 0 2em 0}header nav{width:87.5%}header nav a{display:inline-block;font-size:1.4rem;font-weight:bold;text-decoration:none!important;margin:0 0.5rem;padding:0 0}header nav a:first-child{margin-left:0}header nav a:last-child{margin-right:0}footer{margin-top:3rem;padding:.5rem 0;border-top:0.1rem solid #000;color:#555}article .header{font-style:italic;color:#555}.definition,.proposition,.theorem{display:block;border-left:2px solid #808080;padding-left:1rem;margin-top:1rem;margin-bottom:1rem}.proposition,.theorem{counter-increment:theorem;font-style:italic}.definition p:first-child,.proposition p:first-child,.theorem p:first-child,.proof p:first-child{display:inline}.definition p,.proposition p,.theorem p,.proof p{margin-top:0.4rem;margin-bottom:0.4rem;padding-left:1rem}.theorem:before{content:"Theorem " counter(theorem) ".";font-weight:bold;font-style:normal}.proposition:before{content:"Proposition " counter(theorem) ".";font-weight:bold;font-style:normal}.definition:before{counter-increment:definition;content:"Definition " counter(definition) ".";font-weight:bold;font-style:normal}.proof:before{content:"Proof.";font-style:italic}.proof:after{content:"\220E";float:right}
\ No newline at end of file
diff --git a/_site/cv.html b/_site/cv.html
index b4b4521..5262f71 100644
--- a/_site/cv.html
+++ b/_site/cv.html
@@ -9,6 +9,7 @@
     <title>Dimitri Lozeve - Curriculum Vitæ</title>
     <link rel="stylesheet" href="./css/tufte.css" />
     <link rel="stylesheet" href="./css/pandoc.css" />
+    <link rel="stylesheet" href="./css/default.css" />
     <link rel="stylesheet" href="./css/syntax.css" />
 
     <!-- KaTeX CSS styles -->
@@ -25,9 +26,6 @@
     <article>
       
       <header>
-	<div class="logo">
-          <a href="./">Dimitri Lozeve</a>
-	</div>
 	<nav>
           <a href="./">Home</a>
 	  <a href="./projects.html">Projects</a>
@@ -43,9 +41,6 @@
       </header>
       
 
-      <!-- <header> -->
-	<!-- </header> -->
-
       
     </article>
 
@@ -162,121 +157,6 @@
 <h3 id="sports">Sports</h3>
 <p><strong>Fencing:</strong> vice-president of the 2016 <a href="http://x-systra.com/">X-SYSTRA International Fencing Challenge</a>; 29th in the 2016 sabre French Student Championships</p>
 <p><strong>Scuba-diving:</strong> CMAS ★ ★ ★, 170+ dives</p>
-    <!-- <main role="main"> -->
-      <!-- 	<p><a href="./files/cv.pdf">(PDF version)</a></p>
-<h1 id="work-experience">Work experience</h1>
-<h3 id="mindsay-rd-data-scientist-and-engineering-manager"><a href="https://www.mindsay.com/">Mindsay</a>: R&amp;D Data Scientist and Engineering Manager</h3>
-<p>October 2018–present</p>
-<ul>
-<li>Natural Language Processing and Reinforcement Learning for Chatbots</li>
-<li>Management of the R&amp;D team (3 data scientists) and of all research projects</li>
-<li>Entirely responsible with the CTO for the patents strategy in Europe and abroad</li>
-<li>Attended a 6-day training programme for young managers (<a href="https://ignition-program.com/formations/spineup-mars-2020">SpineUp</a> by Ignition Program)</li>
-</ul>
-<h3 id="sysnav-real-time-geolocalization-algorithm-on-an-embedded-device"><a href="http://www.sysnav.fr/">Sysnav</a>: Real-time geolocalization algorithm on an embedded device</h3>
-<p>March–August 2017</p>
-<ul>
-<li>Mathematical modelling of the human walk</li>
-<li>Step detection using artificial intelligence on inertial sensors data</li>
-<li>Statistical methods for trajectory reconstruction</li>
-<li><em>Award:</em> <a href="http://www.sysnav.fr/dimitri-lozeve-etudiant-sysnav-obtient-le-prix-du-meilleur-stage-de-recherche-2017-de-lecole-polytechnique/">Best Research Internship 2017, from École polytechnique</a></li>
-<li><a href="./files/sysnav_internship.pdf">Outline of the confidential report (PDF, in French)</a> (<a href="./files/sysnav_internship.pdf.minisig">sig</a>) and <a href="https://dlozeve.github.io/stage3a/">slides</a></li>
-</ul>
-<h3 id="natixis-london-branch-global-infrastructure-and-projects-intern-analyst"><a href="https://www.natixis.com/">Natixis</a> London Branch, Global Infrastructure and Projects: Intern Analyst</h3>
-<p>June–August 2016</p>
-<p>Origination and execution of project finance transactions: offshore windfarms, hydroelectric dams, and a biomass power plant now under construction in northeastern England. Long-term projections of energy and financial time series data.</p>
-<h3 id="french-engineering-corps-army-officer">French Engineering Corps: Army officer</h3>
-<p>2014–2015</p>
-<p>Operation Sangaris: Military intervention in the Central African Republic.</p>
-<ul>
-<li>Instructor for new recruits for 4 months (around 30 soldiers)</li>
-<li>Security Officer during the building of a Bailey bridge in Bangui</li>
-<li>Participation in an intelligence gathering mission in the Northeastern part of the country</li>
-<li><em>French Republic Distinctions:</em> Overseas Medal, National Defence Medal</li>
-</ul>
-<h1 id="education">Education</h1>
-<h3 id="university-of-oxford-msc-in-statistical-science">University of Oxford: <a href="https://www.ox.ac.uk/admissions/graduate/courses/msc-statistical-science">MSc in Statistical Science</a></h3>
-<p>2017–2018</p>
-<ul>
-<li>Applied and computational statistics, statistical machine learning and statistical inference</li>
-</ul>
-<h3 id="école-polytechnique"><a href="https://www.polytechnique.edu/">École polytechnique</a></h3>
-<p>2014–2017</p>
-<ul>
-<li>Majors in Majors in Applied Mathematics, Operations Research, Data Science, and Computer Science</li>
-<li><em>Distinctions:</em> Outstanding Investment, Outstanding Leadership</li>
-</ul>
-<h3 id="lycée-privé-sainte-geneviève-versailles-preparatory-classes-to-french-grandes-écoles">Lycée Privé Sainte-Geneviève, Versailles: Preparatory classes to French <em>Grandes Écoles</em></h3>
-<p>2012–2014</p>
-<ul>
-<li>Majors in Mathematics and Physics</li>
-</ul>
-<h1 id="scientific-projects">Scientific projects</h1>
-<h3 id="topological-data-analysis-of-time-dependent-networks">Topological Data Analysis of time-dependent networks</h3>
-<p>2018</p>
-<ul>
-<li>Master’s thesis, joint work with Oxford’s Department of Statistics and Mathematical Institute, with Prof. Heather Harrington (Oxford), Prof. Mason Porter (UCLA), and Prof. Renaud Lambiotte (Oxford)</li>
-<li>Application of the recent advances in Topological Data Analysis (TDA) and Persistent Homology to periodicity detection in temporal networks</li>
-<li><a href="./files/tdanetworks.pdf">Dissertation (PDF)</a> (<a href="./files/tdanetworks.pdf.minisig">sig</a>)</li>
-</ul>
-<h3 id="research-work-on-community-detection-in-social-networks">Research work on Community Detection in Social Networks</h3>
-<p>2016–2017</p>
-<ul>
-<li>Research project with the Microsoft-INRIA joint center, with Prof. Laurent Massoulié</li>
-<li>Comparison of the performance of state-of-the-art algorithms (theory and implementations)</li>
-<li>Application to large-scale, real-world social networks</li>
-<li><a href="./files/communitydetection.pdf">Dissertation (PDF, in French)</a> (<a href="./files/communitydetection.pdf.minisig">sig</a>) and <a href="https://dlozeve.github.io/reveal_CommunityDetection/">slides</a></li>
-</ul>
-<h3 id="serb-x-cubesat-ii-program-a-nano-satellite-dedicated-to-sun-earth-relationship">SERB X-CubeSat II program: a nano-satellite dedicated to Sun-Earth relationship</h3>
-<p>2015–2016</p>
-<ul>
-<li>Solar Irradiance and Earth Radiation Budget: Payload preliminary design</li>
-<li>Co-authored <a href="http://dx.doi.org/10.1117/12.2222660">SPIE Proceedings article</a> on the project’s technical specifications</li>
-<li><a href="./files/serb.pdf">Dissertation (PDF, in French)</a> (<a href="./files/serb.pdf.minisig">sig</a>)</li>
-</ul>
-<h3 id="research-work-on-markov-chains-and-queuing-theory">Research work on Markov Chains and Queuing Theory</h3>
-<p>2013–2014</p>
-<ul>
-<li>Study on the convergence of queues through algebra and numerical simulations</li>
-<li><a href="./files/filesdattente.pdf">Dissertation (PDF, in French)</a> (<a href="./files/filesdattente.pdf.minisig">sig</a>)</li>
-</ul>
-<h1 id="languages-and-skills">Languages and skills</h1>
-<h3 id="computer-science">Computer science</h3>
-<p><strong>Python:</strong></p>
-<ul>
-<li>Numerical computing: <a href="http://www.numpy.org/">Numpy</a>, <a href="https://www.scipy.org/">Scipy</a></li>
-<li>Data analysis: <a href="https://pandas.pydata.org/">Pandas</a></li>
-<li>Machine Learning: <a href="http://scikit-learn.org/">Scikit-Learn</a></li>
-<li>Deep Learning: <a href="https://www.tensorflow.org/">TensorFlow</a>, <a href="http://pytorch.org/">PyTorch</a></li>
-<li>Network analysis: <a href="https://networkx.github.io/">NetworkX</a>, <a href="https://graph-tool.skewed.de/">graph-tool</a></li>
-<li>Research projects and hackathons: <a href="https://github.com/dlozeve/community-detection">community detection</a> and <a href="https://github.com/dlozeve/DocAssist">DocAssist</a></li>
-</ul>
-<p><strong>Julia:</strong></p>
-<ul>
-<li>Numerical computing, machine learning</li>
-<li>Optimisation and Operations Research: <a href="https://github.com/JuliaOpt/JuMP.jl">JuMP</a></li>
-<li>Projects: <a href="https://github.com/dlozeve/GardenOptim">Garden optimisation</a> using Markov Chain Monte Carlo and integer programming</li>
-</ul>
-<p><strong>R:</strong></p>
-<ul>
-<li>Statistical modelling and inference (generalised linear models, bayesian analysis)</li>
-<li>Data analysis: <a href="https://www.tidyverse.org/">Tidyverse</a></li>
-<li>Network analysis: <a href="http://igraph.org/">igraph</a></li>
-</ul>
-<p><strong>C, Java:</strong> Embedded and <a href="https://github.com/dlozeve/Satrap">network</a> programming, <a href="https://github.com/dlozeve/topological-persistence">scientific computing</a></p>
-<p><strong>SQL:</strong> Basics</p>
-<p><strong>Haskell, Lisp (Scheme):</strong> Hobby projects (<a href="https://github.com/dlozeve/orbit">N-body simulation</a>, <a href="https://github.com/dlozeve/Civilisation-hs">SAT solver</a>, <a href="https://github.com/dlozeve/aoc2017">Advent of Code 2017</a>)</p>
-<p><strong>Software:</strong> Git, GNU/Linux, LaTeX, <a href="https://aws.amazon.com/">Amazon AWS</a>, <a href="https://www.mongodb.com/">MongoDB</a>, <a href="https://www.wolfram.com/mathematica/">Wolfram Mathematica</a>, Microsoft Office</p>
-<p>See also <a href="./skills.html">a complete list of my skills in Statistics, Data Science and Machine Learning</a>.</p>
-<h3 id="languages">Languages</h3>
-<ul>
-<li>French</li>
-<li>English</li>
-</ul>
-<h3 id="sports">Sports</h3>
-<p><strong>Fencing:</strong> vice-president of the 2016 <a href="http://x-systra.com/">X-SYSTRA International Fencing Challenge</a>; 29th in the 2016 sabre French Student Championships</p>
-<p><strong>Scuba-diving:</strong> CMAS ★ ★ ★, 170+ dives</p> -->
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     <title>Dimitri Lozeve - Home</title>
     <link rel="stylesheet" href="./css/tufte.css" />
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@@ -142,101 +137,6 @@ public key: RWQ6uexORp8f7USHA7nX9lFfltaCA9x6aBV06MvgiGjUt6BVf6McyD26
 
 <p>Find more in the <a href="./archive.html">archives</a>.</p>
 
-    <!-- <main role="main"> -->
-      <!-- 	<img src="/images/portrait_small.jpg" style="width: 30%; float: right; margin: 10px;" alt="Dimitri Lozeve portrait"/>
-
-<h2>Welcome</h2>
-
-<p>Hi! I am a Data Scientist
-  at <a href="https://www.mindsay.com/">Mindsay</a> (formerly called
-  Destygo), working on making chatbots smarter through Machine
-  Learning.</p>
-
-<p>During my free time, I love tinkering with functional programming
-  languages for scientific simulations and with embedded development
-  and electronics.</p>
-
-<p>See my <a href="/cv.html">full CV</a>, or
-a <a href="/files/cv.pdf">PDF version</a><!-- (<a href="/files/cv.pdf.minisig">signature</a>) -->.</p>
-
-<a href="mailto:dimitri+web@lozeve.com" class="icon">
-  <img src="./images/icons/email.svg" style="width: 40px;" alt="email" />
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-<a href="https://github.com/dlozeve/" class="icon">
-  <img src="./images/icons/github.svg" style="width: 40px;" alt="github" />
-</a>
-<a href="https://www.linkedin.com/in/dimitrilozeve" class="icon">
-  <img src="./images/icons/linkedin.svg" style="width: 40px;" alt="linkedin" />
-</a>
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-<p><a href="https://jedisct1.github.io/minisign/">minisign</a>/<a href="https://man.openbsd.org/signify.1">signify(1)</a>
-public key: RWQ6uexORp8f7USHA7nX9lFfltaCA9x6aBV06MvgiGjUt6BVf6McyD26
-(<a href="./files/minisign.pub">download</a>)</p>
-
-<h2>Some Projects</h2>
-<ul>
-  <li>
-    <a href="./files/tdanetworks.pdf">Topological Data Analysis of
-    time-dependent networks</a>
-    (<a href="./files/tdanetworks.pdf.minisig">sig</a>)<br> Application
-    of the recent advances in Topological Data Analysis (TDA) and
-    Persistent Homology to periodicity detection in temporal networks.
-  </li>
-  <li>
-    <a href="https://dlozeve.github.io/reveal_CommunityDetection/#/">Community
-    Detection</a><br> Community detection algorithms and applications
-    to a large social network obtained from Prestashop data.
-  </li>
-  <li>
-    <a href="./posts/ising-model.html">Ising model simulation</a><br>
-    Monte Carlo simulation of the Ising model using
-    Metropolis-Hastings.
-  </li>
-</ul>
-
-<h2>Recent Posts</h2>
-<p>Get notified of new posts via <a href="./rss.xml">RSS</a> or <a href="./atom.xml">Atom</a> feeds!</p>
-
-<ul>
-    
-        <li>
-            <a href="./posts/hierarchical-optimal-transport-for-document-classification.html">Reading notes: Hierarchical Optimal Transport for Document Representation</a> - April  5, 2020
-        </li>
-    
-        <li>
-            <a href="./posts/self-learning-chatbots-destygo.html">Mindsay: Towards Self-Learning Chatbots</a> - April  6, 2019
-        </li>
-    
-        <li>
-            <a href="./posts/ginibre-ensemble.html">Random matrices from the Ginibre ensemble</a> - March 20, 2019
-        </li>
-    
-        <li>
-            <a href="./posts/peano.html">Peano Axioms</a> - March 18, 2019
-        </li>
-    
-        <li>
-            <a href="./posts/reinforcement-learning-1.html">Quick Notes on Reinforcement Learning</a> - November 21, 2018
-        </li>
-    
-        <li>
-            <a href="./posts/ising-apl.html">Ising model simulation in APL</a> - March  5, 2018
-        </li>
-    
-        <li>
-            <a href="./posts/ising-model.html">Ising model simulation</a> - February  5, 2018
-        </li>
-    
-        <li>
-            <a href="./posts/lsystems.html">Generating and representing L-systems</a> - January 18, 2018
-        </li>
-    
-</ul>
-
-
-<p>Find more in the <a href="./archive.html">archives</a>.</p>
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diff --git a/_site/posts/ginibre-ensemble.html b/_site/posts/ginibre-ensemble.html
index 9bf641b..b2061db 100644
--- a/_site/posts/ginibre-ensemble.html
+++ b/_site/posts/ginibre-ensemble.html
@@ -9,6 +9,7 @@
     <title>Dimitri Lozeve - Random matrices from the Ginibre ensemble</title>
     <link rel="stylesheet" href="../css/tufte.css" />
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     <article>
       
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-          <a href="../">Dimitri Lozeve</a>
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@@ -43,15 +41,11 @@
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     </article>
 
     <article>
     <section class="header">
-        Posted on March 20, 2019
         
     </section>
     <section>
@@ -83,42 +77,6 @@
     </section>
 </article>
 
-    <!-- <main role="main"> -->
-      <!-- 	<article>
-    <section class="header">
-        Posted on March 20, 2019
-        
-    </section>
-    <section>
-        <h2 id="ginibre-ensemble-and-its-properties">Ginibre ensemble and its properties</h2>
-<p>The <em>Ginibre ensemble</em> is a set of random matrices with the entries chosen independently. Each entry of a <span class="math inline">\(n \times n\)</span> matrix is a complex number, with both the real and imaginary part sampled from a normal distribution of mean zero and variance <span class="math inline">\(1/2n\)</span>.</p>
-<p>Random matrices distributions are very complex and are a very active subject of research. I stumbled on this example while reading an article in <em>Notices of the AMS</em> by Brian C. Hall <a href="#ref-1">(1)</a>.</p>
-<p>Now what is interesting about these random matrices is the distribution of their <span class="math inline">\(n\)</span> eigenvalues in the complex plane.</p>
-<p>The <a href="https://en.wikipedia.org/wiki/Circular_law">circular law</a> (first established by Jean Ginibre in 1965 <a href="#ref-2">(2)</a>) states that when <span class="math inline">\(n\)</span> is large, with high probability, almost all the eigenvalues lie in the unit disk. Moreover, they tend to be nearly uniformly distributed there.</p>
-<p>I find this mildly fascinating that such a straightforward definition of a random matrix can exhibit such non-random properties in their spectrum.</p>
-<h2 id="simulation">Simulation</h2>
-<p>I ran a quick simulation, thanks to <a href="https://julialang.org/">Julia</a>’s great ecosystem for linear algebra and statistical distributions:</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode julia"><code class="sourceCode julia"><a class="sourceLine" id="cb1-1" title="1">using LinearAlgebra</a>
-<a class="sourceLine" id="cb1-2" title="2">using UnicodePlots</a>
-<a class="sourceLine" id="cb1-3" title="3"></a>
-<a class="sourceLine" id="cb1-4" title="4"><span class="kw">function</span> ginibre(n)</a>
-<a class="sourceLine" id="cb1-5" title="5">    <span class="kw">return</span> randn((n, n)) * sqrt(<span class="fl">1</span>/<span class="fl">2</span>n) + im * randn((n, n)) * sqrt(<span class="fl">1</span>/<span class="fl">2</span>n)</a>
-<a class="sourceLine" id="cb1-6" title="6"><span class="kw">end</span></a>
-<a class="sourceLine" id="cb1-7" title="7"></a>
-<a class="sourceLine" id="cb1-8" title="8">v = eigvals(ginibre(<span class="fl">2000</span>))</a>
-<a class="sourceLine" id="cb1-9" title="9"></a>
-<a class="sourceLine" id="cb1-10" title="10">scatterplot(real(v), imag(v), xlim=[-<span class="fl">1.5</span>,<span class="fl">1.5</span>], ylim=[-<span class="fl">1.5</span>,<span class="fl">1.5</span>])</a></code></pre></div>
-<p>I like using <code>UnicodePlots</code> for this kind of quick-and-dirty plots, directly in the terminal. Here is the output:</p>
-<p><img src="../images/ginibre.png" /></p>
-<h2 id="references">References</h2>
-<ol>
-<li><span id="ref-1"></span>Hall, Brian C. 2019. “Eigenvalues of Random Matrices in the General Linear Group in the Large-<span class="math inline">\(N\)</span> Limit.” <em>Notices of the American Mathematical Society</em> 66, no. 4 (Spring): 568-569. <a href="https://www.ams.org/journals/notices/201904/201904FullIssue.pdf" class="uri">https://www.ams.org/journals/notices/201904/201904FullIssue.pdf</a></li>
-<li><span id="ref-2"></span>Ginibre, Jean. “Statistical ensembles of complex, quaternion, and real matrices.” Journal of Mathematical Physics 6.3 (1965): 440-449. <a href="https://doi.org/10.1063/1.1704292" class="uri">https://doi.org/10.1063/1.1704292</a></li>
-</ol>
-    </section>
-</article>
- -->
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diff --git a/_site/posts/hierarchical-optimal-transport-for-document-classification.html b/_site/posts/hierarchical-optimal-transport-for-document-classification.html
index a02c5d3..05afb17 100644
--- a/_site/posts/hierarchical-optimal-transport-for-document-classification.html
+++ b/_site/posts/hierarchical-optimal-transport-for-document-classification.html
@@ -9,6 +9,7 @@
     <title>Dimitri Lozeve - Reading notes: Hierarchical Optimal Transport for Document Representation</title>
     <link rel="stylesheet" href="../css/tufte.css" />
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@@ -43,15 +41,11 @@
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     <article>
     <section class="header">
-        Posted on April  5, 2020
         
     </section>
     <section>
@@ -101,9 +95,9 @@ W_1(p, q) = \min_{P \in \mathbb{R}_+^{n\times m}} \sum_{i,j} C_{i,j} P_{i,j}
 </ul>
 <p>The first one can be precomputed once for all subsequent distances, so it is invariable in the number of documents we have to process. The second one only operates on <span class="math inline">\(\lvert T \rvert\)</span> topics instead of the full vocabulary: the resulting optimisation problem is much smaller! This is great for performance, as it should be easy now to compute all pairwise distances in a large set of documents.</p>
 <p>Another interesting insight is that topics are represented as collections of words (we can keep the top 20 as a visual representations), and documents as collections of topics with weights. Both of these representations are highly interpretable for a human being who wants to understand what’s going on. I think this is one of the strongest aspects of these approaches: both the various representations and the algorithms are fully interpretable. Compared to a deep learning approach, we can make sense of every intermediate step, from the representations of topics to the weights in the optimisation algorithm to compute higher-level distances.</p>
-<figure>
-<img src="../images/hott_fig1.jpg" alt="Representation of two documents in topic space, along with how the distance was computed between them. Everything is interpretable: from the documents as collections of topics, to the matchings between topics determining the overall distance between the books (Yurochkin et al. 2019)." /><figcaption>Representation of two documents in topic space, along with how the distance was computed between them. Everything is interpretable: from the documents as collections of topics, to the matchings between topics determining the overall distance between the books <span class="citation" data-cites="yurochkin2019_hierar_optim_trans_docum_repres">(Yurochkin et al. <a href="#ref-yurochkin2019_hierar_optim_trans_docum_repres">2019</a>)</span>.</figcaption>
-</figure>
+<p><img src="../images/hott_fig1.jpg" /><span><label for="sn-2" class="margin-toggle">⊕</label><input type="checkbox" id="sn-2" class="margin-toggle" /><span class="marginnote"> Representation of two documents in topic space, along with how the distance was computed between them. Everything is interpretable: from the documents as collections of topics, to the matchings between topics determining the overall distance between the books <span class="citation" data-cites="yurochkin2019_hierar_optim_trans_docum_repres">(Yurochkin et al. <a href="#ref-yurochkin2019_hierar_optim_trans_docum_repres">2019</a>)</span>.<br />
+<br />
+</span></span></p>
 <h1 id="experiments">Experiments</h1>
 <p>The paper is very complete regarding experiments, providing a full evaluation of the method on one particular application: document clustering. They use <a href="https://scikit-learn.org/stable/modules/decomposition.html#latentdirichletallocation">Latent Dirichlet Allocation</a> to compute topics and GloVe for pretrained word embeddings <span class="citation" data-cites="pennington2014_glove">(Pennington, Socher, and Manning <a href="#ref-pennington2014_glove">2014</a>)</span>, and <a href="https://www.gurobi.com/">Gurobi</a> to solve the optimisation problems. Their code is available <a href="https://github.com/IBM/HOTT">on GitHub</a>.</p>
 <p>If you want the details, I encourage you to read the full paper, they tested the methods on a wide variety of datasets, with datasets containing very short documents (like Twitter), and long documents with a large vocabulary (books). With a simple <span class="math inline">\(k\)</span>-NN classification, they establish that HOTT performs best on average, especially on large vocabularies (books, the “gutenberg” dataset). It also has a much better computational performance than alternative methods based on regularisation of the optimal transport problem directly on words. So the hierarchical nature of the approach allows to gain considerably in performance, along with improvements in interpretability.</p>
@@ -136,95 +130,6 @@ W_1(p, q) = \min_{P \in \mathbb{R}_+^{n\times m}} \sum_{i,j} C_{i,j} P_{i,j}
     </section>
 </article>
 
-    <!-- <main role="main"> -->
-      <!-- 	<article>
-    <section class="header">
-        Posted on April  5, 2020
-        
-    </section>
-    <section>
-        <p>Two weeks ago, I did a presentation for my colleagues of the paper from <span class="citation" data-cites="yurochkin2019_hierar_optim_trans_docum_repres">Yurochkin et al. (<a href="#ref-yurochkin2019_hierar_optim_trans_docum_repres">2019</a>)</span>, from <a href="https://papers.nips.cc/book/advances-in-neural-information-processing-systems-32-2019">NeurIPS 2019</a>. It contains an interesting approach to document classification leading to strong performance, and, most importantly, excellent interpretability.</p>
-<p>This paper seems interesting to me because of it uses two methods with strong theoretical guarantees: optimal transport and topic modelling. Optimal transport looks very promising to me in NLP, and has seen a lot of interest in recent years due to advances in approximation algorithms, such as entropy regularisation. It is also quite refreshing to see approaches using solid results in optimisation, compared to purely experimental deep learning methods.</p>
-<h1 id="introduction-and-motivation">Introduction and motivation</h1>
-<p>The problem of the paper is to measure similarity (i.e. a distance) between pairs of documents, by incorporating <em>semantic</em> similarities (and not only syntactic artefacts), without encountering scalability issues.</p>
-<p>They propose a “meta-distance” between documents, called the hierarchical optimal topic transport (HOTT), providing a scalable metric incorporating topic information between documents. As such, they try to combine two different levels of analysis:</p>
-<ul>
-<li>word embeddings data, to embed language knowledge (via pre-trained embeddings for instance),</li>
-<li>topic modelling methods (e.g. <a href="https://scikit-learn.org/stable/modules/decomposition.html#latentdirichletallocation">Latent Dirichlet Allocation</a>), to represent semantically-meaningful groups of words.</li>
-</ul>
-<h1 id="background-optimal-transport">Background: optimal transport</h1>
-<p>The essential backbone of the method is the Wasserstein distance, derived from optimal transport theory. Optimal transport is a fascinating and deep subject, so I won’t enter into the details here. For an introduction to the theory and its applications, check out the excellent book from <span class="citation" data-cites="peyreComputationalOptimalTransport2019">Peyré and Cuturi (<a href="#ref-peyreComputationalOptimalTransport2019">2019</a>)</span>, (<a href="https://arxiv.org/abs/1803.00567">available on ArXiv</a> as well). There are also <a href="https://images.math.cnrs.fr/Le-transport-optimal-numerique-et-ses-applications-Partie-1.html?lang=fr">very nice posts</a> (in French) by Gabriel Peyré on the <a href="https://images.math.cnrs.fr/">CNRS maths blog</a>. Many more resources (including slides for presentations) are available at <a href="https://optimaltransport.github.io" class="uri">https://optimaltransport.github.io</a>. For a more complete theoretical treatment of the subject, check out <span class="citation" data-cites="santambrogioOptimalTransportApplied2015">Santambrogio (<a href="#ref-santambrogioOptimalTransportApplied2015">2015</a>)</span>, or, if you’re feeling particularly adventurous, <span class="citation" data-cites="villaniOptimalTransportOld2009">Villani (<a href="#ref-villaniOptimalTransportOld2009">2009</a>)</span>.</p>
-<p>For this paper, only a superficial understanding of how the <a href="https://en.wikipedia.org/wiki/Wasserstein_metric">Wasserstein distance</a> works is necessary. Optimal transport is an optimisation technique to lift a distance between points in a given metric space, to a distance between probability <em>distributions</em> over this metric space. The historical example is to move piles of dirt around: you know the distance between any two points, and you have piles of dirt lying around<span><label for="sn-1" class="margin-toggle">&#8853;</label><input type="checkbox" id="sn-1" class="margin-toggle"/><span class="marginnote"> Optimal transport originated with Monge, and then Kantorovich, both of whom had very clear military applications in mind (either in Revolutionary France, or during WWII). A lot of historical examples move cannon balls, or other military equipment, along a front line.<br />
-<br />
-</span></span>. Now, if you want to move these piles to another configuration (fewer piles, say, or a different repartition of dirt a few metres away), you need to find the most efficient way to move them. The total cost you obtain will define a distance between the two configurations of dirt, and is usually called the <a href="https://en.wikipedia.org/wiki/Earth_mover%27s_distance">earth mover’s distance</a>, which is just an instance of the general Wasserstein metric.</p>
-<p>More formally, we start with two sets of points <span class="math inline">\(x = (x_1, x_2, \ldots,
-      x_n)\)</span>, and <span class="math inline">\(y = (y_1, y_2, \ldots, y_n)\)</span>, along with probability distributions <span class="math inline">\(p \in \Delta^n\)</span>, <span class="math inline">\(q \in \Delta^m\)</span> over <span class="math inline">\(x\)</span> and <span class="math inline">\(y\)</span> (<span class="math inline">\(\Delta^n\)</span> is the probability simplex of dimension <span class="math inline">\(n\)</span>, i.e. the set of vectors of size <span class="math inline">\(n\)</span> summing to 1). We can then define the Wasserstein distance as <span class="math display">\[
-W_1(p, q) = \min_{P \in \mathbb{R}_+^{n\times m}} \sum_{i,j} C_{i,j} P_{i,j}
-\]</span> <span class="math display">\[
-\text{\small subject to } \sum_j P_{i,j} = p_i \text{ \small and } \sum_i P_{i,j} = q_j,
-\]</span> where <span class="math inline">\(C_{i,j} = d(x_i, x_j)\)</span> are the costs computed from the original distance between points, and <span class="math inline">\(P_{i,j}\)</span> represent the amount we are moving from pile <span class="math inline">\(i\)</span> to pile <span class="math inline">\(j\)</span>.</p>
-<p>Now, how can this be applied to a natural language setting? Once we have word embeddings, we can consider that the vocabulary forms a metric space (we can compute a distance, for instance the euclidean or the <a href="https://en.wikipedia.org/wiki/Cosine_similarity">cosine distance</a>, between two word embeddings). The key is to define documents as <em>distributions</em> over words.</p>
-<p>Given a vocabulary <span class="math inline">\(V \subset \mathbb{R}^n\)</span> and a corpus <span class="math inline">\(D = (d^1, d^2, \ldots, d^{\lvert D \rvert})\)</span>, we represent a document as <span class="math inline">\(d^i \in \Delta^{l_i}\)</span> where <span class="math inline">\(l_i\)</span> is the number of unique words in <span class="math inline">\(d^i\)</span>, and <span class="math inline">\(d^i_j\)</span> is the proportion of word <span class="math inline">\(v_j\)</span> in the document <span class="math inline">\(d^i\)</span>. The word mover’s distance (WMD) is then defined simply as <span class="math display">\[ \operatorname{WMD}(d^1, d^2) = W_1(d^1, d^2). \]</span></p>
-<p>If you didn’t follow all of this, don’t worry! The gist is: if you have a distance between points, you can solve an optimisation problem to obtain a distance between <em>distributions</em> over these points! This is especially useful when you consider that each word embedding is a point, and a document is just a set of words, along with the number of times they appear.</p>
-<h1 id="hierarchical-optimal-transport">Hierarchical optimal transport</h1>
-<p>Using optimal transport, we can use the word mover’s distance to define a metric between documents. However, this suffers from two drawbacks:</p>
-<ul>
-<li>Documents represented as distributions over words are not easily interpretable. For long documents, the vocabulary is huge and word frequencies are not easily understandable for humans.</li>
-<li>Large vocabularies mean that the space on which we have to find an optimal matching is huge. The <a href="https://en.wikipedia.org/wiki/Hungarian_algorithm">Hungarian algorithm</a> used to compute the optimal transport distance runs in <span class="math inline">\(O(l^3 \log l)\)</span>, where <span class="math inline">\(l\)</span> is the maximum number of unique words in each documents. This quickly becomes intractable as the size of documents become larger, or if you have to compute all pairwise distances between a large number of documents (e.g. for clustering purposes).</li>
-</ul>
-<p>To escape these issues, we will add an intermediary step using <a href="https://en.wikipedia.org/wiki/Topic_model">topic modelling</a>. Once we have topics <span class="math inline">\(T = (t_1, t_2, \ldots, t_{\lvert T
-\rvert}) \subset \Delta^{\lvert V \rvert}\)</span>, we get two kinds of representations:</p>
-<ul>
-<li>representations of topics as distributions over words,</li>
-<li>representations of documents as distributions over topics <span class="math inline">\(\bar{d^i} \in \Delta^{\lvert T \rvert}\)</span>.</li>
-</ul>
-<p>Since they are distributions over words, the word mover’s distance defines a metric over topics. As such, the topics with the WMD become a metric space.</p>
-<p>We can now define the hierarchical optimal topic transport (HOTT), as the optimal transport distance between documents, represented as distributions over topics. For two documents <span class="math inline">\(d^1\)</span>, <span class="math inline">\(d^2\)</span>, <span class="math display">\[
-\operatorname{HOTT}(d^1, d^2) = W_1\left( \sum_{k=1}^{\lvert T \rvert} \bar{d^1_k} \delta_{t_k}, \sum_{k=1}^{\lvert T \rvert} \bar{d^2_k} \delta_{t_k} \right).
-\]</span> where <span class="math inline">\(\delta_{t_k}\)</span> is a distribution supported on topic <span class="math inline">\(t_k\)</span>.</p>
-<p>Note that in this case, we used optimal transport <em>twice</em>:</p>
-<ul>
-<li>once to find distances between topics (WMD),</li>
-<li>once to find distances between documents, where the distance between topics became the costs in the new optimal transport problem.</li>
-</ul>
-<p>The first one can be precomputed once for all subsequent distances, so it is invariable in the number of documents we have to process. The second one only operates on <span class="math inline">\(\lvert T \rvert\)</span> topics instead of the full vocabulary: the resulting optimisation problem is much smaller! This is great for performance, as it should be easy now to compute all pairwise distances in a large set of documents.</p>
-<p>Another interesting insight is that topics are represented as collections of words (we can keep the top 20 as a visual representations), and documents as collections of topics with weights. Both of these representations are highly interpretable for a human being who wants to understand what’s going on. I think this is one of the strongest aspects of these approaches: both the various representations and the algorithms are fully interpretable. Compared to a deep learning approach, we can make sense of every intermediate step, from the representations of topics to the weights in the optimisation algorithm to compute higher-level distances.</p>
-<figure>
-<img src="/images/hott_fig1.jpg" alt="Representation of two documents in topic space, along with how the distance was computed between them. Everything is interpretable: from the documents as collections of topics, to the matchings between topics determining the overall distance between the books (Yurochkin et al. 2019)." /><figcaption>Representation of two documents in topic space, along with how the distance was computed between them. Everything is interpretable: from the documents as collections of topics, to the matchings between topics determining the overall distance between the books <span class="citation" data-cites="yurochkin2019_hierar_optim_trans_docum_repres">(Yurochkin et al. <a href="#ref-yurochkin2019_hierar_optim_trans_docum_repres">2019</a>)</span>.</figcaption>
-</figure>
-<h1 id="experiments">Experiments</h1>
-<p>The paper is very complete regarding experiments, providing a full evaluation of the method on one particular application: document clustering. They use <a href="https://scikit-learn.org/stable/modules/decomposition.html#latentdirichletallocation">Latent Dirichlet Allocation</a> to compute topics and GloVe for pretrained word embeddings <span class="citation" data-cites="pennington2014_glove">(Pennington, Socher, and Manning <a href="#ref-pennington2014_glove">2014</a>)</span>, and <a href="https://www.gurobi.com/">Gurobi</a> to solve the optimisation problems. Their code is available <a href="https://github.com/IBM/HOTT">on GitHub</a>.</p>
-<p>If you want the details, I encourage you to read the full paper, they tested the methods on a wide variety of datasets, with datasets containing very short documents (like Twitter), and long documents with a large vocabulary (books). With a simple <span class="math inline">\(k\)</span>-NN classification, they establish that HOTT performs best on average, especially on large vocabularies (books, the “gutenberg” dataset). It also has a much better computational performance than alternative methods based on regularisation of the optimal transport problem directly on words. So the hierarchical nature of the approach allows to gain considerably in performance, along with improvements in interpretability.</p>
-<p>What’s really interesting in the paper is the sensitivity analysis: they ran experiments with different word embeddings methods (word2vec, <span class="citation" data-cites="mikolovDistributedRepresentationsWords2013">(Mikolov et al. <a href="#ref-mikolovDistributedRepresentationsWords2013">2013</a>)</span>), and with different parameters for the topic modelling (topic truncation, number of topics, etc). All of these reveal that changes in hyperparameters do not impact the performance of HOTT significantly. This is extremely important in a field like NLP where most of the times small variations in approach lead to drastically different results.</p>
-<h1 id="conclusion">Conclusion</h1>
-<p>All in all, this paper present a very interesting approach to compute distance between natural-language documents. It is no secret that I like methods with strong theoretical background (in this case optimisation and optimal transport), guaranteeing a stability and benefiting from decades of research in a well-established domain.</p>
-<p>Most importantly, this paper allows for future exploration in document representation with <em>interpretability</em> in mind. This is often added as an afterthought in academic research but is one of the most important topics for the industry, as a system must be understood by end users, often not trained in ML, before being deployed. The notion of topic, and distances as weights, can be understood easily by anyone without significant background in ML or in maths.</p>
-<p>Finally, I feel like they did not stop at a simple theoretical argument, but carefully checked on real-world datasets, measuring sensitivity to all the arbitrary choices they had to take. Again, from an industry perspective, this allows to implement the new approach quickly and easily, being confident that it won’t break unexpectedly without extensive testing.</p>
-<h1 id="references" class="unnumbered">References</h1>
-<div id="refs" class="references">
-<div id="ref-mikolovDistributedRepresentationsWords2013">
-<p>Mikolov, Tomas, Ilya Sutskever, Kai Chen, Greg S Corrado, and Jeff Dean. 2013. “Distributed Representations of Words and Phrases and Their Compositionality.” In <em>Advances in Neural Information Processing Systems 26</em>, 3111–9. <a href="http://papers.nips.cc/paper/5021-distributed-representations-of-words-and-phrases-and-their-compositionality.pdf" class="uri">http://papers.nips.cc/paper/5021-distributed-representations-of-words-and-phrases-and-their-compositionality.pdf</a>.</p>
-</div>
-<div id="ref-pennington2014_glove">
-<p>Pennington, Jeffrey, Richard Socher, and Christopher Manning. 2014. “Glove: Global Vectors for Word Representation.” In <em>Proceedings of the 2014 Conference on Empirical Methods in Natural Language Processing (EMNLP)</em>, 1532–43. Doha, Qatar: Association for Computational Linguistics. <a href="https://doi.org/10.3115/v1/D14-1162" class="uri">https://doi.org/10.3115/v1/D14-1162</a>.</p>
-</div>
-<div id="ref-peyreComputationalOptimalTransport2019">
-<p>Peyré, Gabriel, and Marco Cuturi. 2019. “Computational Optimal Transport.” <em>Foundations and Trends in Machine Learning</em> 11 (5-6): 355–206. <a href="https://doi.org/10.1561/2200000073" class="uri">https://doi.org/10.1561/2200000073</a>.</p>
-</div>
-<div id="ref-santambrogioOptimalTransportApplied2015">
-<p>Santambrogio, Filippo. 2015. <em>Optimal Transport for Applied Mathematicians</em>. Vol. 87. Progress in Nonlinear Differential Equations and Their Applications. Cham: Springer International Publishing. <a href="https://doi.org/10.1007/978-3-319-20828-2" class="uri">https://doi.org/10.1007/978-3-319-20828-2</a>.</p>
-</div>
-<div id="ref-villaniOptimalTransportOld2009">
-<p>Villani, Cédric. 2009. <em>Optimal Transport: Old and New</em>. Grundlehren Der Mathematischen Wissenschaften 338. Berlin: Springer.</p>
-</div>
-<div id="ref-yurochkin2019_hierar_optim_trans_docum_repres">
-<p>Yurochkin, Mikhail, Sebastian Claici, Edward Chien, Farzaneh Mirzazadeh, and Justin M Solomon. 2019. “Hierarchical Optimal Transport for Document Representation.” In <em>Advances in Neural Information Processing Systems 32</em>, 1599–1609. <a href="http://papers.nips.cc/paper/8438-hierarchical-optimal-transport-for-document-representation.pdf" class="uri">http://papers.nips.cc/paper/8438-hierarchical-optimal-transport-for-document-representation.pdf</a>.</p>
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-    <section>
-        <h1 id="the-apl-family-of-languages">The APL family of languages</h1>
-<h2 id="why-apl">Why APL?</h2>
-<p>I recently got interested in <a href="https://en.wikipedia.org/wiki/APL_(programming_language)">APL</a>, an <em>array-based</em> programming language. In APL (and derivatives), we try to reason about programs as series of transformations of multi-dimensional arrays. This is exactly the kind of style I like in Haskell and other functional languages, where I also try to use higher-order functions (map, fold, etc) on lists or arrays. A developer only needs to understand these abstractions once, instead of deconstructing each loop or each recursive function encountered in a program.</p>
-<p>APL also tries to be a really simple and <em>terse</em> language. This combined with strange Unicode characters for primitive functions and operators, gives it a reputation of unreadability. However, there is only a small number of functions to learn, and you get used really quickly to read them and understand what they do. Some combinations also occur so frequently that you can recognize them instantly (APL programmers call them <em>idioms</em>).</p>
-<h2 id="implementations">Implementations</h2>
-<p>APL is actually a family of languages. The classic APL, as created by Ken Iverson, with strange symbols, has many implementations. I initially tried <a href="https://www.gnu.org/software/apl/">GNU APL</a>, but due to the lack of documentation and proper tooling, I went to <a href="https://www.dyalog.com/">Dyalog APL</a> (which is proprietary, but free for personal use). There are also APL derivatives, that often use ASCII symbols: <a href="http://www.jsoftware.com/">J</a> (free) and <a href="https://code.kx.com/q/">Q/kdb+</a> (proprietary, but free for personal use).</p>
-<p>The advantage of Dyalog is that it comes with good tooling (which is necessary for inserting all the symbols!), a large ecosystem, and pretty good <a href="http://docs.dyalog.com/">documentation</a>. If you want to start, look at <a href="http://www.dyalog.com/mastering-dyalog-apl.htm"><em>Mastering Dyalog APL</em></a> by Bernard Legrand, freely available online.</p>
-<h1 id="the-ising-model-in-apl">The Ising model in APL</h1>
-<p>I needed a small project to try APL while I was learning. Something array-based, obviously. Since I already implemented a Metropolis-Hastings simulation of the <a href="./ising-model.html">Ising model</a>, which is based on a regular lattice, I decided to reimplement it in Dyalog APL.</p>
-<p>It is only a few lines long, but I will try to explain what it does step by step.</p>
-<p>The first function simply generates a random lattice filled by elements of <span class="math inline">\(\{-1,+1\}\)</span>.</p>
-<pre class="apl"><code>L←{(2×?⍵ ⍵⍴2)-3}
-</code></pre>
-<p>Let’s deconstruct what is done here:</p>
-<ul>
-<li>⍵ is the argument of our function.</li>
-<li>We generate a ⍵×⍵ matrix filled with 2, using the <code>⍴</code> function: <code>⍵ ⍵⍴2</code></li>
-<li><code>?</code> draws a random number between 1 and its argument. We give it our matrix to generate a random matrix of 1 and 2.</li>
-<li>We multiply everything by 2 and subtract 3, so that the result is in <span class="math inline">\(\{-1,+1\}\)</span>.</li>
-<li>Finally, we assign the result to the name <code>L</code>.</li>
-</ul>
-<p>Sample output:</p>
-<pre class="apl"><code>      ising.L 5
- 1 ¯1  1 ¯1  1
- 1  1  1 ¯1 ¯1
- 1 ¯1 ¯1 ¯1 ¯1
- 1  1  1 ¯1 ¯1
-¯1 ¯1  1  1  1
-</code></pre>
-<p>Next, we compute the energy variation (for details on the Ising model, see <a href="./ising-model.html">my previous post</a>).</p>
-<pre class="apl"><code>∆E←{
-    ⎕IO←0
-    (x y)←⍺
-    N←⊃⍴⍵
-    xn←N|((x-1)y)((x+1)y)
-    yn←N|(x(y-1))(x(y+1))
-    ⍵[x;y]×+/⍵[xn,yn]
-}
-</code></pre>
-<ul>
-<li>⍺ is the left argument (coordinates of the site), ⍵ is the right argument (lattice).</li>
-<li>We extract the x and y coordinates of the site.</li>
-<li><code>N</code> is the size of the lattice.</li>
-<li><code>xn</code> and <code>yn</code> are respectively the vertical and lateral neighbours of the site. <code>N|</code> takes the coordinates modulo <code>N</code> (so the lattice is actually a torus). (Note: we used <code>⎕IO←0</code> to use 0-based array indexing.)</li>
-<li><code>+/</code> sums over all neighbours of the site, and then we multiply by the value of the site itself to get <span class="math inline">\(\Delta E\)</span>.</li>
-</ul>
-<p>Sample output, for site <span class="math inline">\((3, 3)\)</span> in a random <span class="math inline">\(5\times 5\)</span> lattice:</p>
-<pre class="apl"><code>      3 3ising.∆E ising.L 5
-¯4
-</code></pre>
-<p>Then comes the actual Metropolis-Hastings part:</p>
-<pre class="apl"><code>U←{
-    ⎕IO←0
-    N←⊃⍴⍵
-    (x y)←?N N
-    new←⍵
-    new[x;y]×←(2×(?0)&gt;*-⍺×x y ∆E ⍵)-1
-    new
-}
-</code></pre>
-<ul>
-<li>⍺ is the <span class="math inline">\(\beta\)</span> parameter of the Ising model, ⍵ is the lattice.</li>
-<li>We draw a random site <span class="math inline">\((x,y)\)</span> with the <code>?</code> function.</li>
-<li><code>new</code> is the lattice but with the <span class="math inline">\((x,y)\)</span> site flipped.</li>
-<li>We compute the probability <span class="math inline">\(\alpha = \exp(-\beta\Delta E)\)</span> using the <code>*</code> function (exponential) and our previous <code>∆E</code> function.</li>
-<li><code>?0</code> returns a uniform random number in <span class="math inline">\([0,1)\)</span>. Based on this value, we decide whether to update the lattice, and we return it.</li>
-</ul>
-<p>We can now bring everything together for display:</p>
-<pre class="apl"><code>Ising←{&#39; ⌹&#39;[1+1=({10 U ⍵}⍣⍵)L ⍺]}
-</code></pre>
-<ul>
-<li>We draw a random lattice of size ⍺ with <code>L ⍺</code>.</li>
-<li>We apply to it our update function, with $<em>β</em>$=10, ⍵ times (using the <code>⍣</code> function, which applies a function <span class="math inline">\(n\)</span> times.</li>
-<li>Finally, we display -1 as a space and 1 as a domino ⌹.</li>
-</ul>
-<p>Final output, with a <span class="math inline">\(80\times 80\)</span> random lattice, after 50000 update steps:</p>
-<pre class="apl"><code>      80ising.Ising 50000
-   ⌹⌹⌹⌹ ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹      ⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹          
-   ⌹⌹⌹⌹      ⌹⌹⌹⌹⌹⌹     ⌹⌹⌹⌹⌹        ⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹⌹ ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹           
-⌹⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹⌹       ⌹⌹⌹     ⌹⌹⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹            ⌹
-⌹⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹⌹       ⌹⌹⌹  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹         ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹            ⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹            ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹     ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹             ⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹            ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹   ⌹⌹⌹     ⌹⌹⌹⌹⌹⌹             ⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹ ⌹⌹⌹            ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹   ⌹⌹       ⌹⌹⌹⌹⌹      ⌹       
-  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹          ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹   ⌹        ⌹⌹⌹⌹      ⌹⌹⌹      
- ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹  ⌹⌹⌹⌹⌹⌹⌹            ⌹⌹⌹       ⌹⌹⌹      
- ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹         ⌹⌹⌹    ⌹⌹⌹⌹⌹⌹      
-⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹        ⌹⌹⌹⌹              ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹        ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹         ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹           ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹    ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹         ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹           ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹            ⌹⌹⌹          ⌹⌹⌹⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹            ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹            ⌹⌹⌹           ⌹⌹⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹           ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹            ⌹⌹⌹⌹           ⌹⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹⌹⌹  ⌹⌹⌹⌹⌹
-⌹⌹⌹⌹ ⌹⌹⌹⌹⌹     ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹            ⌹⌹⌹            ⌹⌹⌹⌹⌹⌹⌹     ⌹⌹⌹⌹⌹⌹⌹⌹  ⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹   ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹           ⌹⌹⌹⌹                ⌹⌹⌹     ⌹⌹⌹⌹⌹⌹⌹    ⌹⌹⌹⌹
-  ⌹ ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹ ⌹⌹⌹⌹           ⌹⌹⌹⌹                ⌹⌹⌹      ⌹⌹⌹⌹⌹         
-  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹    ⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹                ⌹⌹        ⌹           
-  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹    ⌹⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹⌹⌹⌹                                     
-  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹    ⌹⌹⌹⌹⌹⌹⌹⌹     ⌹⌹⌹⌹⌹⌹⌹⌹⌹                                    
-  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹  ⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹           ⌹                         
- ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹  ⌹⌹⌹⌹⌹⌹        ⌹⌹⌹⌹⌹⌹⌹          ⌹                          
-⌹⌹⌹⌹⌹⌹  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹     ⌹⌹⌹          ⌹⌹⌹⌹⌹⌹                          ⌹⌹     ⌹⌹⌹
-⌹⌹⌹⌹⌹⌹  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹                  ⌹⌹⌹⌹⌹⌹         ⌹               ⌹⌹⌹     ⌹⌹⌹
-⌹⌹⌹⌹⌹⌹  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹                   ⌹⌹⌹⌹⌹⌹                     ⌹⌹⌹⌹⌹⌹     ⌹⌹⌹
-⌹⌹⌹⌹⌹⌹  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹            ⌹⌹⌹⌹⌹⌹    ⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹     ⌹⌹⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹            ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹    ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹             ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹    ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹     ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹                ⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹    ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹    ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹                 ⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹       ⌹              ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹ ⌹⌹⌹⌹⌹⌹⌹⌹⌹              ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹                            ⌹⌹⌹⌹⌹⌹⌹    ⌹⌹⌹⌹⌹⌹⌹⌹⌹          ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹                               ⌹⌹⌹⌹      ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹                                ⌹⌹⌹        ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹    ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹                   ⌹⌹⌹⌹             ⌹⌹        ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹   ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹                   ⌹⌹⌹⌹                           ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹                  ⌹⌹⌹⌹⌹⌹⌹                ⌹⌹            ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹ 
-  ⌹⌹⌹⌹                  ⌹⌹⌹⌹⌹⌹⌹              ⌹⌹⌹⌹              ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹  
-  ⌹⌹⌹⌹                 ⌹⌹⌹⌹⌹⌹⌹⌹⌹             ⌹⌹⌹⌹              ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹  
-  ⌹⌹⌹⌹   ⌹         ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹         ⌹⌹⌹⌹⌹⌹              ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹  
- ⌹⌹⌹⌹⌹   ⌹ ⌹       ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹⌹⌹⌹           ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹  
- ⌹⌹⌹⌹⌹   ⌹         ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹⌹⌹⌹           ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹  
- ⌹⌹⌹⌹⌹             ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹        ⌹⌹⌹⌹⌹           ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹  
-⌹⌹⌹⌹⌹              ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹        ⌹⌹⌹⌹⌹⌹⌹          ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹   ⌹⌹⌹⌹⌹
-⌹⌹⌹⌹              ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹⌹        ⌹⌹⌹⌹⌹⌹⌹⌹⌹    ⌹⌹⌹⌹⌹
-⌹⌹⌹⌹              ⌹⌹⌹⌹⌹⌹⌹  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹        ⌹⌹⌹⌹⌹⌹⌹⌹        ⌹⌹⌹⌹⌹⌹⌹⌹⌹ ⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹           ⌹⌹⌹⌹⌹⌹⌹⌹⌹    ⌹⌹⌹⌹⌹⌹⌹⌹⌹          ⌹⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹   ⌹⌹⌹⌹⌹⌹⌹⌹⌹           ⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹   ⌹⌹⌹⌹⌹⌹⌹⌹⌹            ⌹⌹⌹         ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹     ⌹⌹⌹⌹⌹⌹⌹⌹   ⌹⌹⌹⌹⌹⌹⌹⌹             ⌹          ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹  ⌹⌹⌹⌹⌹⌹⌹⌹                       ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹⌹            ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹         ⌹⌹            ⌹⌹⌹⌹⌹⌹⌹   ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹              ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹         ⌹⌹⌹⌹⌹⌹⌹⌹     ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-                    ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹⌹     ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹
-                       ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹⌹    ⌹⌹⌹⌹⌹⌹⌹⌹⌹  
-            ⌹⌹⌹⌹⌹⌹        ⌹⌹⌹⌹⌹⌹⌹⌹          ⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹  
-           ⌹⌹⌹⌹⌹⌹⌹⌹        ⌹⌹⌹⌹⌹⌹⌹          ⌹⌹⌹⌹⌹  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹     ⌹⌹⌹⌹⌹⌹  
-   ⌹⌹⌹ ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹        ⌹⌹⌹⌹⌹          ⌹⌹⌹⌹⌹  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹   ⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹        ⌹⌹⌹⌹           ⌹⌹⌹⌹⌹  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹   ⌹⌹⌹⌹⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹        ⌹⌹⌹             ⌹⌹⌹      ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹  ⌹⌹⌹⌹   ⌹⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹         ⌹⌹⌹        ⌹⌹⌹                       ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹    ⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹         ⌹⌹⌹         ⌹⌹⌹                          ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹     ⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹       ⌹⌹⌹         ⌹⌹⌹    ⌹⌹                      ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹     ⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹      ⌹⌹⌹         ⌹⌹⌹⌹⌹⌹⌹⌹⌹                      ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹       
-  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹   ⌹⌹          ⌹⌹⌹⌹⌹⌹⌹⌹                      ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹       
-  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹   ⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹                         ⌹⌹⌹⌹⌹⌹⌹⌹       
-  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹   ⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹⌹⌹⌹                          ⌹⌹⌹⌹⌹⌹⌹       
-  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹    ⌹⌹⌹⌹⌹         ⌹⌹⌹⌹⌹⌹                          ⌹⌹⌹          
- ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹    ⌹⌹⌹⌹⌹⌹        ⌹⌹⌹⌹⌹⌹⌹⌹                        ⌹⌹⌹          
- ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹                        ⌹⌹⌹          
-⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹         ⌹⌹⌹⌹⌹        ⌹⌹⌹⌹⌹⌹⌹⌹                      ⌹⌹⌹⌹          
-⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹            ⌹⌹⌹⌹        ⌹⌹⌹⌹⌹⌹⌹⌹       ⌹             ⌹⌹⌹⌹⌹       ⌹⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹ ⌹             ⌹⌹⌹⌹        ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹   ⌹⌹⌹            ⌹⌹⌹⌹⌹⌹     ⌹⌹⌹⌹⌹
-⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹             ⌹⌹⌹⌹        ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹           ⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹
-   ⌹⌹⌹⌹⌹⌹⌹⌹             ⌹⌹⌹⌹        ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹        ⌹⌹⌹⌹⌹⌹⌹⌹        ⌹⌹ 
-   ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹         ⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹         ⌹⌹⌹⌹⌹⌹⌹⌹           
-   ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹        ⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹   ⌹⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹         
-   ⌹⌹⌹  ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹      ⌹⌹⌹⌹⌹        ⌹⌹⌹⌹⌹⌹⌹    ⌹⌹⌹⌹       ⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹⌹         
-</code></pre>
-<p>Complete code, with the namespace:</p>
-<pre class="apl"><code>:Namespace ising
-
-        L←{(2×?⍵ ⍵⍴2)-3}
-
-        ∆E←{
-                ⎕IO←0
-                (x y)←⍺
-                N←⊃⍴⍵
-                xn←N|((x-1)y)((x+1)y)
-                yn←N|(x(y-1))(x(y+1))
-                ⍵[x;y]×+/⍵[xn,yn]
-        }
-
-        U←{
-                ⎕IO←0
-                N←⊃⍴⍵
-                (x y)←?N N
-                new←⍵
-                new[x;y]×←(2×(?0)&gt;*-⍺×x y ∆E ⍵)-1
-                new
-        }
-
-        Ising←{&#39; ⌹&#39;[1+1=({10 U ⍵}⍣⍵)L ⍺]}
-
-:EndNamespace
-</code></pre>
-<h1 id="conclusion">Conclusion</h1>
-<p>The algorithm is very fast (I think it can be optimized by the interpreter because there is no branching), and is easy to reason about. The whole program fits in a few lines, and you clearly see what each function and each line does. It could probably be optimized further (I don’t know every APL function yet…), and also could probably be golfed to a few lines (at the cost of readability?).</p>
-<p>It took me some time to write this, but Dyalog’s tools make it really easy to insert symbols and to look up what they do. Next time, I will look into some ASCII-based APL descendants. J seems to have a <a href="http://code.jsoftware.com/wiki/NuVoc">good documentation</a> and a tradition of <em>tacit definitions</em>, similar to the point-free style in Haskell. Overall, J seems well-suited to modern functional programming, while APL is still under the influence of its early days when it was more procedural. Another interesting area is K, Q, and their database engine kdb+, which seems to be extremely performant and actually used in production.</p>
-<p>Still, Unicode symbols make the code much more readable, mainly because there is a one-to-one link between symbols and functions, which cannot be maintained with only a few ASCII characters.</p>
-    </section>
-</article>
- -->
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diff --git a/_site/posts/ising-model.html b/_site/posts/ising-model.html
index a6406ac..8f50293 100644
--- a/_site/posts/ising-model.html
+++ b/_site/posts/ising-model.html
@@ -9,6 +9,7 @@
     <title>Dimitri Lozeve - Ising model simulation</title>
     <link rel="stylesheet" href="../css/tufte.css" />
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+    <link rel="stylesheet" href="../css/default.css" />
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@@ -25,9 +26,6 @@
     <article>
       
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-          <a href="../">Dimitri Lozeve</a>
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       </header>
       
 
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-
       
     </article>
 
     <article>
     <section class="header">
-        Posted on February  5, 2018
         
             by Dimitri Lozeve
         
@@ -163,122 +157,6 @@ J\sigma_i \sum_{j\sim i} \sigma_j.  \]</span></p>
     </section>
 </article>
 
-    <!-- <main role="main"> -->
-      <!-- 	<article>
-    <section class="header">
-        Posted on February  5, 2018
-        
-            by Dimitri Lozeve
-        
-    </section>
-    <section>
-        <p>The <a href="https://en.wikipedia.org/wiki/Ising_model">Ising model</a> is a model used to represent magnetic dipole moments in statistical physics. Physical details are on the Wikipedia page, but what is interesting is that it follows a complex probability distribution on a lattice, where each site can take the value +1 or -1.</p>
-<p><img src="../images/ising.gif" /></p>
-<h1 id="mathematical-definition">Mathematical definition</h1>
-<p>We have a lattice <span class="math inline">\(\Lambda\)</span> consisting of sites <span class="math inline">\(k\)</span>. For each site, there is a moment <span class="math inline">\(\sigma_k \in \{ -1, +1 \}\)</span>. <span class="math inline">\(\sigma =
-(\sigma_k)_{k\in\Lambda}\)</span> is called the <em>configuration</em> of the lattice.</p>
-<p>The total energy of the configuration is given by the <em>Hamiltonian</em> <span class="math display">\[
-H(\sigma) = -\sum_{i\sim j} J_{ij}\, \sigma_i\, \sigma_j,
-\]</span> where <span class="math inline">\(i\sim j\)</span> denotes <em>neighbours</em>, and <span class="math inline">\(J\)</span> is the <em>interaction matrix</em>.</p>
-<p>The <em>configuration probability</em> is given by: <span class="math display">\[
-\pi_\beta(\sigma) = \frac{e^{-\beta H(\sigma)}}{Z_\beta}
-\]</span> where <span class="math inline">\(\beta = (k_B T)^{-1}\)</span> is the inverse temperature, and <span class="math inline">\(Z_\beta\)</span> the normalisation constant.</p>
-<p>For our simulation, we will use a constant interaction term <span class="math inline">\(J &gt; 0\)</span>. If <span class="math inline">\(\sigma_i = \sigma_j\)</span>, the probability will be proportional to <span class="math inline">\(\exp(\beta J)\)</span>, otherwise it would be <span class="math inline">\(\exp(\beta J)\)</span>. Thus, adjacent spins will try to align themselves.</p>
-<h1 id="simulation">Simulation</h1>
-<p>The Ising model is generally simulated using Markov Chain Monte Carlo (MCMC), with the <a href="https://en.wikipedia.org/wiki/Metropolis%E2%80%93Hastings_algorithm">Metropolis-Hastings</a> algorithm.</p>
-<p>The algorithm starts from a random configuration and runs as follows:</p>
-<ol>
-<li>Select a site <span class="math inline">\(i\)</span> at random and reverse its spin: <span class="math inline">\(\sigma&#39;_i = -\sigma_i\)</span></li>
-<li>Compute the variation in energy (hamiltonian) <span class="math inline">\(\Delta E = H(\sigma&#39;) - H(\sigma)\)</span></li>
-<li>If the energy is lower, accept the new configuration</li>
-<li>Otherwise, draw a uniform random number <span class="math inline">\(u \in ]0,1[\)</span> and accept the new configuration if <span class="math inline">\(u &lt; \min(1, e^{-\beta \Delta E})\)</span>.</li>
-</ol>
-<h1 id="implementation">Implementation</h1>
-<p>The simulation is in Clojure, using the <a href="http://quil.info/">Quil library</a> (a <a href="https://processing.org/">Processing</a> library for Clojure) to display the state of the system.</p>
-<p>This post is “literate Clojure”, and contains <a href="https://github.com/dlozeve/ising-model/blob/master/src/ising_model/core.clj"><code>core.clj</code></a>. The complete project can be found on <a href="https://github.com/dlozeve/ising-model">GitHub</a>.</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode clojure"><code class="sourceCode clojure"><a class="sourceLine" id="cb1-1" title="1">(<span class="kw">ns</span> ising-model.core</a>
-<a class="sourceLine" id="cb1-2" title="2">  (<span class="at">:require</span> [quil.core <span class="at">:as</span> q]</a>
-<a class="sourceLine" id="cb1-3" title="3">        [quil.middleware <span class="at">:as</span> m]))</a></code></pre></div>
-<p>The application works with Quil’s <a href="https://github.com/quil/quil/wiki/Functional-mode-(fun-mode)">functional mode</a>, with each function taking a state and returning an updated state at each time step.</p>
-<p>The <code>setup</code> function generates the initial state, with random initial spins. It also sets the frame rate. The matrix is a single vector in row-major mode. The state also holds relevant parameters for the simulation: <span class="math inline">\(\beta\)</span>, <span class="math inline">\(J\)</span>, and the iteration step.</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode clojure"><code class="sourceCode clojure"><a class="sourceLine" id="cb2-1" title="1">(<span class="bu">defn</span><span class="fu"> setup </span>[size]</a>
-<a class="sourceLine" id="cb2-2" title="2">  <span class="st">&quot;Setup the display parameters and the initial state&quot;</span></a>
-<a class="sourceLine" id="cb2-3" title="3">  (q/frame-rate <span class="dv">300</span>)</a>
-<a class="sourceLine" id="cb2-4" title="4">  (q/color-mode <span class="at">:hsb</span>)</a>
-<a class="sourceLine" id="cb2-5" title="5">  (<span class="kw">let</span> [matrix (<span class="kw">vec</span> (<span class="kw">repeatedly</span> (<span class="kw">*</span> size size) #(<span class="kw">-</span> (<span class="kw">*</span> <span class="dv">2</span> (<span class="kw">rand-int</span> <span class="dv">2</span>)) <span class="dv">1</span>)))]</a>
-<a class="sourceLine" id="cb2-6" title="6">    {<span class="at">:grid-size</span> size</a>
-<a class="sourceLine" id="cb2-7" title="7">     <span class="at">:matrix</span> matrix</a>
-<a class="sourceLine" id="cb2-8" title="8">     <span class="at">:beta</span> <span class="dv">10</span></a>
-<a class="sourceLine" id="cb2-9" title="9">     <span class="at">:intensity</span> <span class="dv">10</span></a>
-<a class="sourceLine" id="cb2-10" title="10">     <span class="at">:iteration</span> <span class="dv">0</span>}))</a></code></pre></div>
-<p>Given a site <span class="math inline">\(i\)</span>, we reverse its spin to generate a new configuration state.</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode clojure"><code class="sourceCode clojure"><a class="sourceLine" id="cb3-1" title="1">(<span class="bu">defn</span><span class="fu"> toggle-state </span>[state i]</a>
-<a class="sourceLine" id="cb3-2" title="2">  <span class="st">&quot;Compute the new state when we toggle a cell&#39;s value&quot;</span></a>
-<a class="sourceLine" id="cb3-3" title="3">  (<span class="kw">let</span> [matrix (<span class="at">:matrix</span> state)]</a>
-<a class="sourceLine" id="cb3-4" title="4">    (<span class="kw">assoc</span> state <span class="at">:matrix</span> (<span class="kw">assoc</span> matrix i (<span class="kw">*</span> <span class="dv">-1</span> (matrix i))))))</a></code></pre></div>
-<p>In order to decide whether to accept this new state, we compute the difference in energy introduced by reversing site <span class="math inline">\(i\)</span>: <span class="math display">\[ \Delta E =
-J\sigma_i \sum_{j\sim i} \sigma_j.  \]</span></p>
-<p>The <code>filter some?</code> is required to eliminate sites outside of the boundaries of the lattice.</p>
-<div class="sourceCode" id="cb4"><pre class="sourceCode clojure"><code class="sourceCode clojure"><a class="sourceLine" id="cb4-1" title="1">(<span class="bu">defn</span><span class="fu"> get-neighbours </span>[state idx]</a>
-<a class="sourceLine" id="cb4-2" title="2">  <span class="st">&quot;Return the values of a cell&#39;s neighbours&quot;</span></a>
-<a class="sourceLine" id="cb4-3" title="3">  [(<span class="kw">get</span> (<span class="at">:matrix</span> state) (<span class="kw">-</span> idx (<span class="at">:grid-size</span> state)))</a>
-<a class="sourceLine" id="cb4-4" title="4">   (<span class="kw">get</span> (<span class="at">:matrix</span> state) (<span class="kw">dec</span> idx))</a>
-<a class="sourceLine" id="cb4-5" title="5">   (<span class="kw">get</span> (<span class="at">:matrix</span> state) (<span class="kw">inc</span> idx))</a>
-<a class="sourceLine" id="cb4-6" title="6">   (<span class="kw">get</span> (<span class="at">:matrix</span> state) (<span class="kw">+</span> (<span class="at">:grid-size</span> state) idx))])</a>
-<a class="sourceLine" id="cb4-7" title="7"></a>
-<a class="sourceLine" id="cb4-8" title="8">(<span class="bu">defn</span><span class="fu"> delta-e </span>[state i]</a>
-<a class="sourceLine" id="cb4-9" title="9">  <span class="st">&quot;Compute the energy difference introduced by a particular cell&quot;</span></a>
-<a class="sourceLine" id="cb4-10" title="10">  (<span class="kw">*</span> (<span class="at">:intensity</span> state) ((<span class="at">:matrix</span> state) i)</a>
-<a class="sourceLine" id="cb4-11" title="11">     (<span class="kw">reduce</span> <span class="kw">+</span> (<span class="kw">filter</span> some? (get-neighbours state i)))))</a></code></pre></div>
-<p>We also add a function to compute directly the hamiltonian for the entire configuration state. We can use it later to log its values across iterations.</p>
-<div class="sourceCode" id="cb5"><pre class="sourceCode clojure"><code class="sourceCode clojure"><a class="sourceLine" id="cb5-1" title="1">(<span class="bu">defn</span><span class="fu"> hamiltonian </span>[state]</a>
-<a class="sourceLine" id="cb5-2" title="2">  <span class="st">&quot;Compute the Hamiltonian of a configuration state&quot;</span></a>
-<a class="sourceLine" id="cb5-3" title="3">  (<span class="kw">-</span> (<span class="kw">reduce</span> <span class="kw">+</span> (<span class="kw">for</span> [i (<span class="kw">range</span> (<span class="kw">count</span> (<span class="at">:matrix</span> state)))</a>
-<a class="sourceLine" id="cb5-4" title="4">             j (<span class="kw">filter</span> some? (get-neighbours state i))]</a>
-<a class="sourceLine" id="cb5-5" title="5">         (<span class="kw">*</span> (<span class="at">:intensity</span> state) ((<span class="at">:matrix</span> state) i) j)))))</a></code></pre></div>
-<p>Finally, we put everything together in the <code>update-state</code> function, which will decide whether to accept or reject the new configuration.</p>
-<div class="sourceCode" id="cb6"><pre class="sourceCode clojure"><code class="sourceCode clojure"><a class="sourceLine" id="cb6-1" title="1">(<span class="bu">defn</span><span class="fu"> update-state </span>[state]</a>
-<a class="sourceLine" id="cb6-2" title="2">  <span class="st">&quot;Accept or reject a new state based on energy</span></a>
-<a class="sourceLine" id="cb6-3" title="3"><span class="st">  difference (Metropolis-Hastings)&quot;</span></a>
-<a class="sourceLine" id="cb6-4" title="4">  (<span class="kw">let</span> [i (<span class="kw">rand-int</span> (<span class="kw">count</span> (<span class="at">:matrix</span> state)))</a>
-<a class="sourceLine" id="cb6-5" title="5">    new-state (toggle-state state i)</a>
-<a class="sourceLine" id="cb6-6" title="6">    alpha (q/exp (<span class="kw">-</span> (<span class="kw">*</span> (<span class="at">:beta</span> state) (delta-e state i))))]</a>
-<a class="sourceLine" id="cb6-7" title="7">    <span class="co">;;(println (hamiltonian new-state))</span></a>
-<a class="sourceLine" id="cb6-8" title="8">    (<span class="kw">update</span> (<span class="kw">if</span> (<span class="kw">&lt;</span> (<span class="kw">rand</span>) alpha) new-state state)</a>
-<a class="sourceLine" id="cb6-9" title="9">        <span class="at">:iteration</span> <span class="kw">inc</span>)))</a></code></pre></div>
-<p>The last thing to do is to draw the new configuration:</p>
-<div class="sourceCode" id="cb7"><pre class="sourceCode clojure"><code class="sourceCode clojure"><a class="sourceLine" id="cb7-1" title="1">(<span class="bu">defn</span><span class="fu"> draw-state </span>[state]</a>
-<a class="sourceLine" id="cb7-2" title="2">  <span class="st">&quot;Draw a configuration state as a grid&quot;</span></a>
-<a class="sourceLine" id="cb7-3" title="3">  (q/background <span class="dv">255</span>)</a>
-<a class="sourceLine" id="cb7-4" title="4">  (<span class="kw">let</span> [cell-size (<span class="kw">quot</span> (q/width) (<span class="at">:grid-size</span> state))]</a>
-<a class="sourceLine" id="cb7-5" title="5">    (<span class="kw">doseq</span> [[i v] (map-indexed <span class="kw">vector</span> (<span class="at">:matrix</span> state))]</a>
-<a class="sourceLine" id="cb7-6" title="6">  (<span class="kw">let</span> [x (<span class="kw">*</span> cell-size (<span class="kw">rem</span> i (<span class="at">:grid-size</span> state)))</a>
-<a class="sourceLine" id="cb7-7" title="7">        y (<span class="kw">*</span> cell-size  (<span class="kw">quot</span> i (<span class="at">:grid-size</span> state)))]</a>
-<a class="sourceLine" id="cb7-8" title="8">    (q/no-stroke)</a>
-<a class="sourceLine" id="cb7-9" title="9">    (q/fill</a>
-<a class="sourceLine" id="cb7-10" title="10">     (<span class="kw">if</span> (<span class="kw">=</span> <span class="dv">1</span> v) <span class="dv">0</span> <span class="dv">255</span>))</a>
-<a class="sourceLine" id="cb7-11" title="11">    (q/rect x y cell-size cell-size))))</a>
-<a class="sourceLine" id="cb7-12" title="12">  <span class="co">;;(when (zero? (mod (:iteration state) 50)) (q/save-frame &quot;img/ising-######.jpg&quot;))</span></a>
-<a class="sourceLine" id="cb7-13" title="13">  )</a></code></pre></div>
-<p>And to reset the simulation when the user clicks anywhere on the screen:</p>
-<div class="sourceCode" id="cb8"><pre class="sourceCode clojure"><code class="sourceCode clojure"><a class="sourceLine" id="cb8-1" title="1">(<span class="bu">defn</span><span class="fu"> mouse-clicked </span>[state event]</a>
-<a class="sourceLine" id="cb8-2" title="2">  <span class="st">&quot;When the mouse is clicked, reset the configuration to a random one&quot;</span></a>
-<a class="sourceLine" id="cb8-3" title="3">  (setup <span class="dv">100</span>))</a></code></pre></div>
-<div class="sourceCode" id="cb9"><pre class="sourceCode clojure"><code class="sourceCode clojure"><a class="sourceLine" id="cb9-1" title="1">(q/defsketch ising-model</a>
-<a class="sourceLine" id="cb9-2" title="2">  <span class="at">:title</span> <span class="st">&quot;Ising model&quot;</span></a>
-<a class="sourceLine" id="cb9-3" title="3">  <span class="at">:size</span> [<span class="dv">300</span> <span class="dv">300</span>]</a>
-<a class="sourceLine" id="cb9-4" title="4">  <span class="at">:setup</span> #(setup <span class="dv">100</span>)</a>
-<a class="sourceLine" id="cb9-5" title="5">  <span class="at">:update</span> update-state</a>
-<a class="sourceLine" id="cb9-6" title="6">  <span class="at">:draw</span> draw-state</a>
-<a class="sourceLine" id="cb9-7" title="7">  <span class="at">:mouse-clicked</span> mouse-clicked</a>
-<a class="sourceLine" id="cb9-8" title="8">  <span class="at">:features</span> [<span class="at">:keep-on-top</span> <span class="at">:no-bind-output</span>]</a>
-<a class="sourceLine" id="cb9-9" title="9">  <span class="at">:middleware</span> [m/fun-mode])</a></code></pre></div>
-<h1 id="conclusion">Conclusion</h1>
-<p>The Ising model is a really easy (and common) example use of MCMC and Metropolis-Hastings. It allows to easily and intuitively understand how the algorithm works, and to make nice visualizations!</p>
-    </section>
-</article>
- -->
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diff --git a/_site/posts/lsystems.html b/_site/posts/lsystems.html
index 58a0947..c6ea7a1 100644
--- a/_site/posts/lsystems.html
+++ b/_site/posts/lsystems.html
@@ -9,6 +9,7 @@
     <title>Dimitri Lozeve - Generating and representing L-systems</title>
     <link rel="stylesheet" href="../css/tufte.css" />
     <link rel="stylesheet" href="../css/pandoc.css" />
+    <link rel="stylesheet" href="../css/default.css" />
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@@ -25,9 +26,6 @@
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-          <a href="../">Dimitri Lozeve</a>
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@@ -43,15 +41,11 @@
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     <article>
     <section class="header">
-        Posted on January 18, 2018
         
             by Dimitri Lozeve
         
@@ -177,136 +171,6 @@ Available options:
     </section>
 </article>
 
-    <!-- <main role="main"> -->
-      <!-- 	<article>
-    <section class="header">
-        Posted on January 18, 2018
-        
-            by Dimitri Lozeve
-        
-    </section>
-    <section>
-        <p>L-systems are a formal way to make interesting visualisations. You can use them to model a wide variety of objects: space-filling curves, fractals, biological systems, tilings, etc.</p>
-<p>See the Github repo: <a href="https://github.com/dlozeve/lsystems" class="uri">https://github.com/dlozeve/lsystems</a></p>
-<h1 id="what-is-an-l-system">What is an L-system?</h1>
-<h2 id="a-few-examples-to-get-started">A few examples to get started</h2>
-<p><img src="../images/lsystems/dragon.png" /></p>
-<p><img src="../images/lsystems/gosper.png" /></p>
-<p><img src="../images/lsystems/plant.png" /></p>
-<p><img src="../images/lsystems/penroseP3.png" /></p>
-<h2 id="definition">Definition</h2>
-<p>An <a href="https://en.wikipedia.org/wiki/L-system">L-system</a> is a set of rewriting rules generating sequences of symbols. Formally, an L-system is a triplet of:</p>
-<ul>
-<li>an <em>alphabet</em> <span class="math inline">\(V\)</span> (an arbitrary set of symbols)</li>
-<li>an <em>axiom</em> <span class="math inline">\(\omega\)</span>, which is a non-empty word of the alphabet (<span class="math inline">\(\omega \in V^+\)</span>)</li>
-<li>a set of <em>rewriting rules</em> (or <em>productions</em>) <span class="math inline">\(P\)</span>, each mapping a symbol to a word: <span class="math inline">\(P \subset V \times V^*\)</span>. Symbols not present in <span class="math inline">\(P\)</span> are assumed to be mapped to themselves.</li>
-</ul>
-<p>During an iteration, the algorithm takes each symbol in the current word and replaces it by the value in its rewriting rule. Not that the output of the rewriting rule can be absolutely <em>anything</em> in <span class="math inline">\(V^*\)</span>, including the empty word! (So yes, you can generate symbols just to delete them afterwards.)</p>
-<p>At this point, an L-system is nothing more than a way to generate very long strings of characters. In order to get something useful out of this, we have to give them <em>meaning</em>.</p>
-<h2 id="drawing-instructions-and-representation">Drawing instructions and representation</h2>
-<p>Our objective is to draw the output of the L-system in order to visually inspect the output. The most common way is to interpret the output as a sequence of instruction for a LOGO-like drawing turtle. For instance, a simple alphabet consisting only in the symbols <span class="math inline">\(F\)</span>, <span class="math inline">\(+\)</span>, and <span class="math inline">\(-\)</span> could represent the instructions “move forward”, “turn right by 90°”, and “turn left by 90°” respectively.</p>
-<p>Thus, we add new components to our definition of L-systems:</p>
-<ul>
-<li>a set of <em>instructions</em>, <span class="math inline">\(I\)</span>. These are limited by the capabilities of our imagined turtle, so we can assume that they are the same for every L-system we will consider:
-<ul>
-<li><code>Forward</code> makes the turtle draw a straight segment.</li>
-<li><code>TurnLeft</code> and <code>TurnRight</code> makes the turtle turn on itself by a given angle.</li>
-<li><code>Push</code> and <code>Pop</code> allow the turtle to store and retrieve its position on a stack. This will allow for branching in the turtle’s path.</li>
-<li><code>Stay</code>, which orders the turtle to do nothing.</li>
-</ul></li>
-<li>a <em>distance</em> <span class="math inline">\(d \in \mathbb{R_+}\)</span>, i.e. how long should each forward segment should be.</li>
-<li>an <em>angle</em> <span class="math inline">\(\theta\)</span> used for rotation.</li>
-<li>a set of <em>representation rules</em> <span class="math inline">\(R \subset V \times I\)</span>. As before, they will match a symbol to an instruction. Symbols not matched by any rule will be associated to <code>Stay</code>.</li>
-</ul>
-<p>Finally, our complete L-system, representable by a turtle with capabilities <span class="math inline">\(I\)</span>, can be defined as <span class="math display">\[ L = (V, \omega, P, d, \theta,
-R). \]</span></p>
-<p>One could argue that the representation is not part of the L-system, and that the same L-system could be represented differently by changing the representation rules. However, in our setting, we won’t observe the L-system other than by displaying it, so we might as well consider that two systems differing only by their representation rules are different systems altogether.</p>
-<h1 id="implementation-details">Implementation details</h1>
-<h2 id="the-lsystem-data-type">The <code>LSystem</code> data type</h2>
-<p>The mathematical definition above translate almost immediately in a Haskell data type:</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode haskell"><code class="sourceCode haskell"><a class="sourceLine" id="cb1-1" title="1"><span class="co">-- | L-system data type</span></a>
-<a class="sourceLine" id="cb1-2" title="2"><span class="kw">data</span> <span class="dt">LSystem</span> a <span class="fu">=</span> <span class="dt">LSystem</span></a>
-<a class="sourceLine" id="cb1-3" title="3">  {<span class="ot"> name ::</span> <span class="dt">String</span></a>
-<a class="sourceLine" id="cb1-4" title="4">  ,<span class="ot"> alphabet ::</span> [a] <span class="co">-- ^ variables and constants used by the system</span></a>
-<a class="sourceLine" id="cb1-5" title="5">  ,<span class="ot"> axiom ::</span> [a] <span class="co">-- ^ initial state of the system</span></a>
-<a class="sourceLine" id="cb1-6" title="6">  ,<span class="ot"> rules ::</span> [(a, [a])] <span class="co">-- ^ production rules defining how each</span></a>
-<a class="sourceLine" id="cb1-7" title="7">            <span class="co">-- variable can be replaced by a sequence of</span></a>
-<a class="sourceLine" id="cb1-8" title="8">            <span class="co">-- variables and constants</span></a>
-<a class="sourceLine" id="cb1-9" title="9">  ,<span class="ot"> angle ::</span> <span class="dt">Float</span> <span class="co">-- ^ angle used for the representation</span></a>
-<a class="sourceLine" id="cb1-10" title="10">  ,<span class="ot"> distance ::</span> <span class="dt">Float</span> <span class="co">-- ^ distance of each segment in the representation</span></a>
-<a class="sourceLine" id="cb1-11" title="11">  ,<span class="ot"> representation ::</span> [(a, <span class="dt">Instruction</span>)] <span class="co">-- ^ representation rules</span></a>
-<a class="sourceLine" id="cb1-12" title="12">                     <span class="co">-- defining how each variable</span></a>
-<a class="sourceLine" id="cb1-13" title="13">                     <span class="co">-- and constant should be</span></a>
-<a class="sourceLine" id="cb1-14" title="14">                     <span class="co">-- represented</span></a>
-<a class="sourceLine" id="cb1-15" title="15">  } <span class="kw">deriving</span> (<span class="dt">Eq</span>, <span class="dt">Show</span>, <span class="dt">Generic</span>)</a></code></pre></div>
-<p>Here, <code>a</code> is the type of the literal in the alphabet. For all practical purposes, it will almost always be <code>Char</code>.</p>
-<p><code>Instruction</code> is just a sum type over all possible instructions listed above.</p>
-<h2 id="iterating-and-representing">Iterating and representing</h2>
-<p>From here, generating L-systems and iterating is straightforward. We iterate recursively by looking up each symbol in <code>rules</code> and replacing it by its expansion. We then transform the result to a list of <code>Instruction</code>.</p>
-<h2 id="drawing">Drawing</h2>
-<p>The only remaining thing is to implement the virtual turtle which will actually execute the instructions. It goes through the list of instructions, building a sequence of points and maintaining an internal state (position, angle, stack). The stack is used when <code>Push</code> and <code>Pop</code> operations are met. In this case, the turtle builds a separate line starting from its current position.</p>
-<p>The final output is a set of lines, each being a simple sequence of points. All relevant data types are provided by the <a href="https://hackage.haskell.org/package/gloss">Gloss</a> library, along with the function that can display the resulting <code>Picture</code>.</p>
-<h1 id="common-file-format-for-l-systems">Common file format for L-systems</h1>
-<p>In order to define new L-systems quickly and easily, it is necessary to encode them in some form. We chose to represent them as JSON values.</p>
-<p>Here is an example for the <a href="https://en.wikipedia.org/wiki/Gosper_curve">Gosper curve</a>:</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode json"><code class="sourceCode json"><a class="sourceLine" id="cb2-1" title="1"><span class="fu">{</span></a>
-<a class="sourceLine" id="cb2-2" title="2">  <span class="dt">&quot;name&quot;</span><span class="fu">:</span> <span class="st">&quot;gosper&quot;</span><span class="fu">,</span></a>
-<a class="sourceLine" id="cb2-3" title="3">  <span class="dt">&quot;alphabet&quot;</span><span class="fu">:</span> <span class="st">&quot;AB+-&quot;</span><span class="fu">,</span></a>
-<a class="sourceLine" id="cb2-4" title="4">  <span class="dt">&quot;axiom&quot;</span><span class="fu">:</span> <span class="st">&quot;A&quot;</span><span class="fu">,</span></a>
-<a class="sourceLine" id="cb2-5" title="5">  <span class="dt">&quot;rules&quot;</span><span class="fu">:</span> <span class="ot">[</span></a>
-<a class="sourceLine" id="cb2-6" title="6">    <span class="ot">[</span><span class="st">&quot;A&quot;</span><span class="ot">,</span> <span class="st">&quot;A-B--B+A++AA+B-&quot;</span><span class="ot">],</span></a>
-<a class="sourceLine" id="cb2-7" title="7">    <span class="ot">[</span><span class="st">&quot;B&quot;</span><span class="ot">,</span> <span class="st">&quot;+A-BB--B-A++A+B&quot;</span><span class="ot">]</span></a>
-<a class="sourceLine" id="cb2-8" title="8">  <span class="ot">]</span><span class="fu">,</span></a>
-<a class="sourceLine" id="cb2-9" title="9">  <span class="dt">&quot;angle&quot;</span><span class="fu">:</span> <span class="fl">60.0</span><span class="fu">,</span></a>
-<a class="sourceLine" id="cb2-10" title="10">  <span class="dt">&quot;distance&quot;</span><span class="fu">:</span> <span class="fl">10.0</span><span class="fu">,</span></a>
-<a class="sourceLine" id="cb2-11" title="11">  <span class="dt">&quot;representation&quot;</span><span class="fu">:</span> <span class="ot">[</span></a>
-<a class="sourceLine" id="cb2-12" title="12">    <span class="ot">[</span><span class="st">&quot;A&quot;</span><span class="ot">,</span> <span class="st">&quot;Forward&quot;</span><span class="ot">],</span></a>
-<a class="sourceLine" id="cb2-13" title="13">    <span class="ot">[</span><span class="st">&quot;B&quot;</span><span class="ot">,</span> <span class="st">&quot;Forward&quot;</span><span class="ot">],</span></a>
-<a class="sourceLine" id="cb2-14" title="14">    <span class="ot">[</span><span class="st">&quot;+&quot;</span><span class="ot">,</span> <span class="st">&quot;TurnRight&quot;</span><span class="ot">],</span></a>
-<a class="sourceLine" id="cb2-15" title="15">    <span class="ot">[</span><span class="st">&quot;-&quot;</span><span class="ot">,</span> <span class="st">&quot;TurnLeft&quot;</span><span class="ot">]</span></a>
-<a class="sourceLine" id="cb2-16" title="16">  <span class="ot">]</span></a>
-<a class="sourceLine" id="cb2-17" title="17"><span class="fu">}</span></a></code></pre></div>
-<p>Using this format, it is easy to define new L-systems (along with how they should be represented). This is translated nearly automatically to the <code>LSystem</code> data type using <a href="https://hackage.haskell.org/package/aeson">Aeson</a>.</p>
-<h1 id="variations-on-l-systems">Variations on L-systems</h1>
-<p>We can widen the possibilities of L-systems in various ways. L-systems are in effect deterministic context-free grammars.</p>
-<p>By allowing multiple rewriting rules for each symbol with probabilities, we can extend the model to <a href="https://en.wikipedia.org/wiki/Probabilistic_context-free_grammar">probabilistic context-free grammars</a>.</p>
-<p>We can also have replacement rules not for a single symbol, but for a subsequence of them, thus effectively taking into account their neighbours (context-sensitive grammars). This seems very close to 1D cellular automata.</p>
-<p>Finally, L-systems could also have a 3D representation (for instance space-filling curves in 3 dimensions).</p>
-<h1 id="usage-notes">Usage notes</h1>
-<ol>
-<li>Clone the repository: <code>git clone [[https://github.com/dlozeve/lsystems]]</code></li>
-<li>Build: <code>stack build</code></li>
-<li>Execute <code>stack exec lsystems-exe -- examples/penroseP3.json</code> to see the list of options</li>
-<li>(Optional) Run tests and build documentation: <code>stack test --haddock</code></li>
-</ol>
-<p>Usage: <code>stack exec lsystems-exe -- --help</code></p>
-<pre><code>lsystems -- Generate L-systems
-
-Usage: lsystems-exe FILENAME [-n|--iterations N] [-c|--color R,G,B]
-                    [-w|--white-background]
-  Generate and draw an L-system
-
-Available options:
-  FILENAME                 JSON file specifying an L-system
-  -n,--iterations N        Number of iterations (default: 5)
-  -c,--color R,G,B         Foreground color RGBA
-                           (0-255) (default: RGBA 1.0 1.0 1.0 1.0)
-  -w,--white-background    Use a white background
-  -h,--help                Show this help text
-</code></pre>
-<p>Apart from the selection of the input JSON file, you can adjust the number of iterations and the colors.</p>
-<p><code>stack exec lsystems-exe -- examples/levyC.json -n 12 -c 0,255,255</code></p>
-<p><img src="../images/lsystems/levyC.png" /></p>
-<h1 id="references">References</h1>
-<ol>
-<li>Prusinkiewicz, Przemyslaw; Lindenmayer, Aristid (1990). <em>The Algorithmic Beauty of Plants.</em> Springer-Verlag. ISBN 978-0-387-97297-8. <a href="http://algorithmicbotany.org/papers/#abop" class="uri">http://algorithmicbotany.org/papers/#abop</a></li>
-<li>Weisstein, Eric W. “Lindenmayer System.” From MathWorld–A Wolfram Web Resource. <a href="http://mathworld.wolfram.com/LindenmayerSystem.html" class="uri">http://mathworld.wolfram.com/LindenmayerSystem.html</a></li>
-<li>Corte, Leo. “L-systems and Penrose P3 in Inkscape.” <em>The Brick in the Sky.</em> <a href="https://thebrickinthesky.wordpress.com/2013/03/17/l-systems-and-penrose-p3-in-inkscape/" class="uri">https://thebrickinthesky.wordpress.com/2013/03/17/l-systems-and-penrose-p3-in-inkscape/</a></li>
-</ol>
-    </section>
-</article>
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-        Posted on March 18, 2019
         
     </section>
     <section>
@@ -154,113 +148,6 @@ then <span class="math inline">\(\varphi(n)\)</span> is true for every natural n
     </section>
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-    <!-- <main role="main"> -->
-      <!-- 	<article>
-    <section class="header">
-        Posted on March 18, 2019
-        
-    </section>
-    <section>
-        <h1 id="introduction">Introduction</h1>
-<p>I have recently bought the book <em>Category Theory</em> from Steve Awodey <span class="citation" data-cites="awodeyCategoryTheory2010">(Awodey <a href="#ref-awodeyCategoryTheory2010">2010</a>)</span> is awesome, but probably the topic for another post), and a particular passage excited my curiosity:</p>
-<blockquote>
-<p>Let us begin by distinguishing between the following things: i. categorical foundations for mathematics, ii. mathematical foundations for category theory.</p>
-<p>As for the first point, one sometimes hears it said that category theory can be used to provide “foundations for mathematics,” as an alternative to set theory. That is in fact the case, but it is not what we are doing here. In set theory, one often begins with existential axioms such as “there is an infinite set” and derives further sets by axioms like “every set has a powerset,” thus building up a universe of mathematical objects (namely sets), which in principle suffice for “all of mathematics.”</p>
-</blockquote>
-<p>This statement is interesting because one often considers category theory as pretty “fundamental”, in the sense that it has no issue with considering what I call “dangerous” notions, such as the category <span class="math inline">\(\mathbf{Set}\)</span> of all sets, and even the category <span class="math inline">\(\mathbf{Cat}\)</span> of all categories. Surely a theory this general, that can afford to study such objects, should provide suitable foundations for mathematics? Awodey addresses these issues very explicitly in the section following the quote above, and finds a good way of avoiding circular definitions.</p>
-<p>Now, I remember some basics from my undergrad studies about foundations of mathematics. I was told that if you could define arithmetic, you basically had everything else “for free” (as Kronecker famously said, “natural numbers were created by God, everything else is the work of men”). I was also told that two sets of axioms existed, the <a href="https://en.wikipedia.org/wiki/Peano_axioms">Peano axioms</a> and the <a href="https://en.wikipedia.org/wiki/Zermelo%E2%80%93Fraenkel_set_theory">Zermelo-Fraenkel</a> axioms. Also, I should steer clear of the axiom of choice if I could, because one can do <a href="https://en.wikipedia.org/wiki/Banach%E2%80%93Tarski_paradox">strange things</a> with it, and it is equivalent to many <a href="https://en.wikipedia.org/wiki/Zorn%27s_lemma">different statements</a>. Finally (and this I knew mainly from <em>Logicomix</em>, I must admit), it is <a href="https://en.wikipedia.org/wiki/G%C3%B6del%27s_incompleteness_theorems">impossible</a> for a set of axioms to be both complete and consistent.</p>
-<p>Given all this, I realised that my knowledge of foundational mathematics was pretty deficient. I do not believe that it is a very important topic that everyone should know about, even though Gödel’s incompleteness theorem is very interesting from a logical and philosophical standpoint. However, I wanted to go deeper on this subject.</p>
-<p>In this post, I will try to share my path through Peano’s axioms <span class="citation" data-cites="gowersPrincetonCompanionMathematics2010">(Gowers, Barrow-Green, and Leader <a href="#ref-gowersPrincetonCompanionMathematics2010">2010</a>)</span>, because they are very simple, and it is easy to uncover basic algebraic structure from them.</p>
-<h1 id="the-axioms">The Axioms</h1>
-<p>The purpose of the axioms is to define a collection of objects that we will call the <em>natural numbers</em>. Here, we place ourselves in the context of <a href="https://en.wikipedia.org/wiki/First-order_logic">first-order logic</a>. Logic is not the main topic here, so I will just assume that I have access to some quantifiers, to some predicates, to some variables, and, most importantly, to a relation <span class="math inline">\(=\)</span> which is reflexive, symmetric, transitive, and closed over the natural numbers.</p>
-<p>Without further digressions, let us define two symbols <span class="math inline">\(0\)</span> and <span class="math inline">\(s\)</span> (called <em>successor</em>) such that:</p>
-<ol>
-<li><span class="math inline">\(0\)</span> is a natural number.</li>
-<li>For every natural number <span class="math inline">\(n\)</span>, <span class="math inline">\(s(n)\)</span> is a natural number. (“The successor of a natural number is a natural number.”)</li>
-<li>For all natural number <span class="math inline">\(m\)</span> and <span class="math inline">\(n\)</span>, if <span class="math inline">\(s(m) = s(n)\)</span>, then <span class="math inline">\(m=n\)</span>. (“If two numbers have the same successor, they are equal.”)</li>
-<li>For every natural number <span class="math inline">\(n\)</span>, <span class="math inline">\(s(n) = 0\)</span> is false. (“<span class="math inline">\(0\)</span> is nobody’s successor.”)</li>
-<li>If <span class="math inline">\(A\)</span> is a set such that:
-<ul>
-<li><span class="math inline">\(0\)</span> is in <span class="math inline">\(A\)</span></li>
-<li>for every natural number <span class="math inline">\(n\)</span>, if <span class="math inline">\(n\)</span> is in <span class="math inline">\(A\)</span> then <span class="math inline">\(s(n)\)</span> is in <span class="math inline">\(A\)</span></li>
-</ul>
-then <span class="math inline">\(A\)</span> contains every natural number.</li>
-</ol>
-<p>Let’s break this down. Axioms 1–4 define a collection of objects, written <span class="math inline">\(0\)</span>, <span class="math inline">\(s(0)\)</span>, <span class="math inline">\(s(s(0))\)</span>, and so on, and ensure their basic properties. All of these are natural numbers by the first four axioms, but how can we be sure that <em>all</em> natural numbers are of the form <span class="math inline">\(s( \cdots s(0))\)</span>? This is where the <em>induction axiom</em> (Axiom 5) intervenes. It ensures that every natural number is “well-formed” according to the previous axioms.</p>
-<p>But Axiom 5 is slightly disturbing, because it mentions a “set” and a relation “is in”. This seems pretty straightforward at first sight, but these notions were never defined anywhere before that! Isn’t our goal to <em>define</em> all these notions in order to derive a foundation of mathematics? (I still don’t know the answer to that question.) I prefer the following alternative version of the induction axiom:</p>
-<ul>
-<li>If <span class="math inline">\(\varphi\)</span> is a <a href="https://en.wikipedia.org/wiki/Predicate_(mathematical_logic)">unary predicate</a> such that:
-<ul>
-<li><span class="math inline">\(\varphi(0)\)</span> is true</li>
-<li>for every natural number <span class="math inline">\(n\)</span>, if <span class="math inline">\(\varphi(n)\)</span> is true, then <span class="math inline">\(\varphi(s(n))\)</span> is also true</li>
-</ul>
-then <span class="math inline">\(\varphi(n)\)</span> is true for every natural number <span class="math inline">\(n\)</span>.</li>
-</ul>
-<p>The alternative formulation is much better in my opinion, as it obviously implies the first one (juste choose <span class="math inline">\(\varphi(n)\)</span> as “<span class="math inline">\(n\)</span> is a natural number”), and it only references predicates. It will also be much more useful afterwards, as we will see.</p>
-<h1 id="addition">Addition</h1>
-<p>What is needed afterwards? The most basic notion after the natural numbers themselves is the addition operator. We define an operator <span class="math inline">\(+\)</span> by the following (recursive) rules:</p>
-<ol>
-<li><span class="math inline">\(\forall a,\quad a+0 = a\)</span>.</li>
-<li><span class="math inline">\(\forall a, \forall b,\quad a + s(b) = s(a+b)\)</span>.</li>
-</ol>
-<p>Let us use these rules to prove the basic properties of <span class="math inline">\(+\)</span>.</p>
-<h2 id="commutativity">Commutativity</h2>
-<div class="proposition">
-<p><span class="math inline">\(\forall a, \forall b,\quad a+b = b+a\)</span>.</p>
-</div>
-<div class="proof">
-<p>First, we prove that every natural number commutes with <span class="math inline">\(0\)</span>.</p>
-<ul>
-<li><span class="math inline">\(0+0 = 0+0\)</span>.</li>
-<li><p>For every natural number <span class="math inline">\(a\)</span> such that <span class="math inline">\(0+a = a+0\)</span>, we have:</p></li>
-</ul>
-<p>By Axiom 5, every natural number commutes with <span class="math inline">\(0\)</span>.</p>
-<p>We can now prove the main proposition:</p>
-<ul>
-<li><span class="math inline">\(\forall a,\quad a+0=0+a\)</span>.</li>
-<li><p>For all <span class="math inline">\(a\)</span> and <span class="math inline">\(b\)</span> such that <span class="math inline">\(a+b=b+a\)</span>,</p></li>
-</ul>
-<p>We used the opposite of the second rule for <span class="math inline">\(+\)</span>, namely <span class="math inline">\(\forall a,
-\forall b,\quad s(a) + b = s(a+b)\)</span>. This can easily be proved by another induction.</p>
-</div>
-<h2 id="associativity">Associativity</h2>
-<div class="proposition">
-<p><span class="math inline">\(\forall a, \forall b, \forall c,\quad a+(b+c) = (a+b)+c\)</span>.</p>
-</div>
-<div class="proof">
-<p>Todo, left as an exercise to the reader 😉</p>
-</div>
-<h2 id="identity-element">Identity element</h2>
-<div class="proposition">
-<p><span class="math inline">\(\forall a,\quad a+0 = 0+a = a\)</span>.</p>
-</div>
-<div class="proof">
-<p>This follows directly from the definition of <span class="math inline">\(+\)</span> and commutativity.</p>
-</div>
-<p>From all these properties, it follows that the set of natural numbers with <span class="math inline">\(+\)</span> is a commutative <a href="https://en.wikipedia.org/wiki/Monoid">monoid</a>.</p>
-<h1 id="going-further">Going further</h1>
-<p>We have imbued our newly created set of natural numbers with a significant algebraic structure. From there, similar arguments will create more structure, notably by introducing another operation <span class="math inline">\(\times\)</span>, and an order <span class="math inline">\(\leq\)</span>.</p>
-<p>It is now a matter of conventional mathematics to construct the integers <span class="math inline">\(\mathbb{Z}\)</span> and the rationals <span class="math inline">\(\mathbb{Q}\)</span> (using equivalence classes), and eventually the real numbers <span class="math inline">\(\mathbb{R}\)</span>.</p>
-<p>It is remarkable how very few (and very simple, as far as you would consider the induction axiom “simple”) axioms are enough to build an entire theory of mathematics. This sort of things makes me agree with Eugene Wigner <span class="citation" data-cites="wignerUnreasonableEffectivenessMathematics1990">(Wigner <a href="#ref-wignerUnreasonableEffectivenessMathematics1990">1990</a>)</span> when he says that “mathematics is the science of skillful operations with concepts and rules invented just for this purpose”. We drew some arbitrary rules out of thin air, and derived countless properties and theorems from them, basically for our own enjoyment. (As Wigner would say, it is <em>incredible</em> that any of these fanciful inventions coming out of nowhere turned out to be even remotely useful.) Mathematics is done mainly for the mathematician’s own pleasure!</p>
-<blockquote>
-<p>Mathematics cannot be defined without acknowledging its most obvious feature: namely, that it is interesting — M. Polanyi <span class="citation" data-cites="wignerUnreasonableEffectivenessMathematics1990">(Wigner <a href="#ref-wignerUnreasonableEffectivenessMathematics1990">1990</a>)</span></p>
-</blockquote>
-<h1 id="references" class="unnumbered">References</h1>
-<div id="refs" class="references">
-<div id="ref-awodeyCategoryTheory2010">
-<p>Awodey, Steve. 2010. <em>Category Theory</em>. 2nd ed. Oxford Logic Guides 52. Oxford ; New York: Oxford University Press.</p>
-</div>
-<div id="ref-gowersPrincetonCompanionMathematics2010">
-<p>Gowers, Timothy, June Barrow-Green, and Imre Leader. 2010. <em>The Princeton Companion to Mathematics</em>. Princeton University Press.</p>
-</div>
-<div id="ref-wignerUnreasonableEffectivenessMathematics1990">
-<p>Wigner, Eugene P. 1990. “The Unreasonable Effectiveness of Mathematics in the Natural Sciences.” In <em>Mathematics and Science</em>, by Ronald E Mickens, 291–306. WORLD SCIENTIFIC. <a href="https://doi.org/10.1142/9789814503488_0018" class="uri">https://doi.org/10.1142/9789814503488_0018</a>.</p>
-</div>
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     <title>Dimitri Lozeve - Quick Notes on Reinforcement Learning</title>
     <link rel="stylesheet" href="../css/tufte.css" />
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-    </section>
-    <section>
-        <h1 id="introduction">Introduction</h1>
-<p>In this series of blog posts, I intend to write my notes as I go through Richard S. Sutton’s excellent <em>Reinforcement Learning: An Introduction</em> <a href="#ref-1">(1)</a>.</p>
-<p>I will try to formalise the maths behind it a little bit, mainly because I would like to use it as a useful personal reference to the main concepts in RL. I will probably add a few remarks about a possible implementation as I go on.</p>
-<h1 id="relationship-between-agent-and-environment">Relationship between agent and environment</h1>
-<h2 id="context-and-assumptions">Context and assumptions</h2>
-<p>The goal of reinforcement learning is to select the best actions availables to an agent as it goes through a series of states in an environment. In this post, we will only consider <em>discrete</em> time steps.</p>
-<p>The most important hypothesis we make is the <em>Markov property:</em></p>
-<blockquote>
-<p>At each time step, the next state of the agent depends only on the current state and the current action taken. It cannot depend on the history of the states visited by the agent.</p>
-</blockquote>
-<p>This property is essential to make our problems tractable, and often holds true in practice (to a reasonable approximation).</p>
-<p>With this assumption, we can define the relationship between agent and environment as a <em>Markov Decision Process</em> (MDP).</p>
-<div class="definition">
-<p>A <em>Markov Decision Process</em> is a tuple <span class="math inline">\((\mathcal{S}, \mathcal{A},
-\mathcal{R}, p)\)</span> where:</p>
-<ul>
-<li><span class="math inline">\(\mathcal{S}\)</span> is a set of <em>states</em>,</li>
-<li><span class="math inline">\(\mathcal{A}\)</span> is an application mapping each state <span class="math inline">\(s \in
- \mathcal{S}\)</span> to a set <span class="math inline">\(\mathcal{A}(s)\)</span> of possible <em>actions</em> for this state. In this post, we will often simplify by using <span class="math inline">\(\mathcal{A}\)</span> as a set, assuming that all actions are possible for each state,</li>
-<li><span class="math inline">\(\mathcal{R} \subset \mathbb{R}\)</span> is a set of <em>rewards</em>,</li>
-<li><p>and <span class="math inline">\(p\)</span> is a function representing the <em>dynamics</em> of the MDP:</p>
-<p>such that <span class="math display">\[ \forall s \in \mathcal{S}, \forall a \in \mathcal{A},\quad \sum_{s&#39;, r} p(s&#39;, r \;|\; s, a) = 1. \]</span></p></li>
-</ul>
-</div>
-<p>The function <span class="math inline">\(p\)</span> represents the probability of transitioning to the state <span class="math inline">\(s&#39;\)</span> and getting a reward <span class="math inline">\(r\)</span> when the agent is at state <span class="math inline">\(s\)</span> and chooses action <span class="math inline">\(a\)</span>.</p>
-<p>We will also use occasionally the <em>state-transition probabilities</em>:</p>
-
-<h2 id="rewarding-the-agent">Rewarding the agent</h2>
-<div class="definition">
-<p>The <em>expected reward</em> of a state-action pair is the function</p>
-</div>
-<div class="definition">
-<p>The <em>discounted return</em> is the sum of all future rewards, with a multiplicative factor to give more weights to more immediate rewards: <span class="math display">\[ G_t := \sum_{k=t+1}^T \gamma^{k-t-1} R_k, \]</span> where <span class="math inline">\(T\)</span> can be infinite or <span class="math inline">\(\gamma\)</span> can be 1, but not both.</p>
-</div>
-<h1 id="deciding-what-to-do-policies">Deciding what to do: policies</h1>
-<h2 id="defining-our-policy-and-its-value">Defining our policy and its value</h2>
-<p>A <em>policy</em> is a way for the agent to choose the next action to perform.</p>
-<div class="definition">
-<p>A <em>policy</em> is a function <span class="math inline">\(\pi\)</span> defined as</p>
-</div>
-<p>In order to compare policies, we need to associate values to them.</p>
-<div class="definition">
-<p>The <em>state-value function</em> of a policy <span class="math inline">\(\pi\)</span> is</p>
-</div>
-<p>We can also compute the value starting from a state <span class="math inline">\(s\)</span> by also taking into account the action taken <span class="math inline">\(a\)</span>.</p>
-<div class="definition">
-<p>The <em>action-value function</em> of a policy <span class="math inline">\(\pi\)</span> is</p>
-</div>
-<h2 id="the-quest-for-the-optimal-policy">The quest for the optimal policy</h2>
-<h1 id="references">References</h1>
-<ol>
-<li><span id="ref-1"></span>R. S. Sutton and A. G. Barto, Reinforcement learning: an introduction, Second edition. Cambridge, MA: The MIT Press, 2018.</li>
-</ol>
-    </section>
-</article>
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diff --git a/_site/posts/self-learning-chatbots-destygo.html b/_site/posts/self-learning-chatbots-destygo.html
index ee3246c..8f865b2 100644
--- a/_site/posts/self-learning-chatbots-destygo.html
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     <title>Dimitri Lozeve - Mindsay: Towards Self-Learning Chatbots</title>
     <link rel="stylesheet" href="../css/tufte.css" />
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-        Posted on April  6, 2019
         
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-        Posted on April  6, 2019
-        
-    </section>
-    <section>
-        <p>Last week I made a presentation at the <a href="https://www.meetup.com/Paris-NLP/">Paris NLP Meetup</a>, on how we implemented self-learning chatbots in production at Mindsay.</p>
-<p>It was fascinating to other people interested in NLP about the technologies and models we deploy at work! It’s always nice to have some feedback about our work, and preparing this talk forced me to take a step back about what we do and rethink it in new interesting ways.</p>
-<p>Also check out the <a href="https://nlpparis.wordpress.com/2019/03/29/paris-nlp-season-3-meetup-4-at-meilleursagents/">other presentations</a>, one about diachronic (i.e. time-dependent) word embeddings and the other about the different models and the use of Knowledge Bases for Information Retrieval. (This might even give us new ideas to explore…)</p>
-<p>If you’re interested about exciting applications at the confluence of Reinforcement Learning and NLP, the slides are available <a href="https://drive.google.com/file/d/1aS1NpPxRzsQCsAqoQIVZrdf8R1Y2VKrT/view">here</a>. It includes basic RL theory, how we transposed it to the specific case of conversational agents, the technical and mathematical challenges in implementing self-learning chatbots, and of course plenty of references for further reading if we piqued your interest!</p>
-<p><strong><strong>Update:</strong></strong> The videos are now available on the <a href="https://nlpparis.wordpress.com/2019/03/29/paris-nlp-season-3-meetup-4-at-meilleursagents/">NLP Meetup website</a>.</p>
-<p><strong><strong>Update 2:</strong></strong> Destygo changed its name to <a href="https://www.mindsay.com/">Mindsay</a>!</p>
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diff --git a/_site/projects.html b/_site/projects.html
index 10661e6..14173fd 100644
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     <title>Dimitri Lozeve - Projects</title>
     <link rel="stylesheet" href="./css/tufte.css" />
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-    <!-- <main role="main"> -->
-      <!-- 	
-<hr>
-<h2><a href="/files/tdanetworks.pdf">Topological Data Analysis of time-dependent networks</a></h2>
-<p>Application of the recent advances in Topological Data Analysis (TDA) and Persistent Homology to periodicity detection in temporal networks. <a href="/files/tdanetworks.pdf">Master's thesis dissertation.</a></p>
-<p><img src="/images/persistence_diagram.svg" style="max-width: 50%"/></p>
-
-<hr>
-<h2><a href="https://github.com/dlozeve/ising-model">Ising model simulation</a></h2>
-<p>Monte Carlo simulation of the <a href="https://en.wikipedia.org/wiki/Ising_model">Ising model</a> using Metropolis-Hastings.</p>
-<p><img src="/images/ising.gif" style="max-width: 50%"/></p>
-
-<hr>
-<h2><a href="https://github.com/dlozeve/lsystems">L-systems</a></h2>
-<p>Generate and draw L-systems.</p>
-<p><img src="/images/lsystems/levyC.png" style="max-width: 50%"/></p>
-
-<hr>
-<h2><a href="https://dlozeve.github.io/ww2-bombings">WWII bombings visualization</a></h2>
-<p>Every allied bombing during WWII, mapped over the whole world. The data has been released by the U.S. Department of Defense <a href="https://data.world/datamil/world-war-ii-thor-data">here.</a></p>
-<p><img src="/images/ww2-bombings.png" style="max-width: 50%"/></p>
-
-<hr>
-<h2><a href="https://github.com/dlozeve/Satrap">Satrap</a></h2>
-<p>Simple ARP spoofer, allowing for interception and modification of all communications between two targets. It sends ARP packets to perform a man-in-the-middle attack.</p>
-<p><img src="/images/satrap.png" style="max-width: 50%"/></p>
-
-<hr>
-<h2><a href="https://github.com/dlozeve/orbit">Orbit</a></h2>
-<p>N-body simulator.</p>
-<p><img src="/images/orbit.png" style="max-width: 50%"/></p>
-
-<hr>
-<h2><a href="https://github.com/dlozeve/community-detection">Community Detection</a></h2>
-<p>Community detection algorithms and applications to a large social network obtained from Prestashop data. <a href="https://dlozeve.github.io/reveal_CommunityDetection/#/">Slides (in French).</a></p>
-<p><img src="/images/communities.png" style="max-width: 50%"/></p>
-
-<hr>
-<h2><a href="https://github.com/dlozeve/Civilisation-hs">Civilisation</a></h2>
-<p>SAT solver, using the Davis-Putnam-Logemann-Loveland (DPLL) algorithm.</p>
-<p><img src="/images/dpll.png" style="max-width: 50%"/></p>
-
-<hr>
-<h2><a href="https://dlozeve.github.io/adsb">ADS-B data visualization</a></h2>
-<p>Visualization of plane trajectories over Northeastern France. The data was gathered using a Software Defined Radio to listen to aircrafts.</p>
-<p><img src="/images/adsb.png" style="max-width: 50%"/></p>
-
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index 236e0f5..c8f2533 100644
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     <title>Dimitri Lozeve - ADS-B data visualization</title>
     <link rel="stylesheet" href="../css/tufte.css" />
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 </article>
 
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index 57b511f..1e16ec1 100644
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@@ -9,6 +9,7 @@
     <title>Dimitri Lozeve - Civilisation</title>
     <link rel="stylesheet" href="../css/tufte.css" />
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index a1564cd..9358217 100644
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     <title>Dimitri Lozeve - Community Detection</title>
     <link rel="stylesheet" href="../css/tufte.css" />
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index c984508..00339a7 100644
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     <title>Dimitri Lozeve - Ising model simulation</title>
     <link rel="stylesheet" href="../css/tufte.css" />
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index 47a202f..da56900 100644
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@@ -9,6 +9,7 @@
     <title>Dimitri Lozeve - L-systems</title>
     <link rel="stylesheet" href="../css/tufte.css" />
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     <title>Dimitri Lozeve - Orbit</title>
     <link rel="stylesheet" href="../css/tufte.css" />
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     <title>Dimitri Lozeve - Satrap</title>
     <link rel="stylesheet" href="../css/tufte.css" />
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     <title>Dimitri Lozeve - Topological Data Analysis of time-dependent networks</title>
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     </article>
 
@@ -59,18 +54,6 @@
     </section>
 </article>
 
-    <!-- <main role="main"> -->
-      <!-- 	<article>
-    <section class="header">
-        Posted on September  1, 2018
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-</article>
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diff --git a/_site/projects/ww2-bombings.html b/_site/projects/ww2-bombings.html
index 4e215ef..ab5716f 100644
--- a/_site/projects/ww2-bombings.html
+++ b/_site/projects/ww2-bombings.html
@@ -9,6 +9,7 @@
     <title>Dimitri Lozeve - WWII bombings visualization</title>
     <link rel="stylesheet" href="../css/tufte.css" />
     <link rel="stylesheet" href="../css/pandoc.css" />
+    <link rel="stylesheet" href="../css/default.css" />
     <link rel="stylesheet" href="../css/syntax.css" />
 
     <!-- KaTeX CSS styles -->
@@ -25,9 +26,6 @@
     <article>
       
       <header>
-	<div class="logo">
-          <a href="../">Dimitri Lozeve</a>
-	</div>
 	<nav>
           <a href="../">Home</a>
 	  <a href="../projects.html">Projects</a>
@@ -43,9 +41,6 @@
       </header>
       
 
-      <!-- <header> -->
-	<!-- </header> -->
-
       
     </article>
 
@@ -59,18 +54,6 @@
     </section>
 </article>
 
-    <!-- <main role="main"> -->
-      <!-- 	<article>
-    <section class="header">
-        Posted on July 26, 2017
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-    <section>
-        
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-</article>
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     <footer>
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diff --git a/_site/rss.xml b/_site/rss.xml
index e41b2ba..d59e504 100644
--- a/_site/rss.xml
+++ b/_site/rss.xml
@@ -13,7 +13,6 @@
     <link>https://www.lozeve.com/posts/hierarchical-optimal-transport-for-document-classification.html</link>
     <description><![CDATA[<article>
     <section class="header">
-        Posted on April  5, 2020
         
     </section>
     <section>
@@ -63,9 +62,9 @@ W_1(p, q) = \min_{P \in \mathbb{R}_+^{n\times m}} \sum_{i,j} C_{i,j} P_{i,j}
 </ul>
 <p>The first one can be precomputed once for all subsequent distances, so it is invariable in the number of documents we have to process. The second one only operates on <span class="math inline">\(\lvert T \rvert\)</span> topics instead of the full vocabulary: the resulting optimisation problem is much smaller! This is great for performance, as it should be easy now to compute all pairwise distances in a large set of documents.</p>
 <p>Another interesting insight is that topics are represented as collections of words (we can keep the top 20 as a visual representations), and documents as collections of topics with weights. Both of these representations are highly interpretable for a human being who wants to understand what’s going on. I think this is one of the strongest aspects of these approaches: both the various representations and the algorithms are fully interpretable. Compared to a deep learning approach, we can make sense of every intermediate step, from the representations of topics to the weights in the optimisation algorithm to compute higher-level distances.</p>
-<figure>
-<img src="/images/hott_fig1.jpg" alt="Representation of two documents in topic space, along with how the distance was computed between them. Everything is interpretable: from the documents as collections of topics, to the matchings between topics determining the overall distance between the books (Yurochkin et al. 2019)." /><figcaption>Representation of two documents in topic space, along with how the distance was computed between them. Everything is interpretable: from the documents as collections of topics, to the matchings between topics determining the overall distance between the books <span class="citation" data-cites="yurochkin2019_hierar_optim_trans_docum_repres">(Yurochkin et al. <a href="#ref-yurochkin2019_hierar_optim_trans_docum_repres">2019</a>)</span>.</figcaption>
-</figure>
+<p><img src="/images/hott_fig1.jpg" /><span><label for="sn-2" class="margin-toggle">&#8853;</label><input type="checkbox" id="sn-2" class="margin-toggle"/><span class="marginnote"> Representation of two documents in topic space, along with how the distance was computed between them. Everything is interpretable: from the documents as collections of topics, to the matchings between topics determining the overall distance between the books <span class="citation" data-cites="yurochkin2019_hierar_optim_trans_docum_repres">(Yurochkin et al. <a href="#ref-yurochkin2019_hierar_optim_trans_docum_repres">2019</a>)</span>.<br />
+<br />
+</span></span></p>
 <h1 id="experiments">Experiments</h1>
 <p>The paper is very complete regarding experiments, providing a full evaluation of the method on one particular application: document clustering. They use <a href="https://scikit-learn.org/stable/modules/decomposition.html#latentdirichletallocation">Latent Dirichlet Allocation</a> to compute topics and GloVe for pretrained word embeddings <span class="citation" data-cites="pennington2014_glove">(Pennington, Socher, and Manning <a href="#ref-pennington2014_glove">2014</a>)</span>, and <a href="https://www.gurobi.com/">Gurobi</a> to solve the optimisation problems. Their code is available <a href="https://github.com/IBM/HOTT">on GitHub</a>.</p>
 <p>If you want the details, I encourage you to read the full paper, they tested the methods on a wide variety of datasets, with datasets containing very short documents (like Twitter), and long documents with a large vocabulary (books). With a simple <span class="math inline">\(k\)</span>-NN classification, they establish that HOTT performs best on average, especially on large vocabularies (books, the “gutenberg” dataset). It also has a much better computational performance than alternative methods based on regularisation of the optimal transport problem directly on words. So the hierarchical nature of the approach allows to gain considerably in performance, along with improvements in interpretability.</p>
@@ -107,7 +106,6 @@ W_1(p, q) = \min_{P \in \mathbb{R}_+^{n\times m}} \sum_{i,j} C_{i,j} P_{i,j}
     <link>https://www.lozeve.com/posts/self-learning-chatbots-destygo.html</link>
     <description><![CDATA[<article>
     <section class="header">
-        Posted on April  6, 2019
         
     </section>
     <section>
@@ -129,7 +127,6 @@ W_1(p, q) = \min_{P \in \mathbb{R}_+^{n\times m}} \sum_{i,j} C_{i,j} P_{i,j}
     <link>https://www.lozeve.com/posts/ginibre-ensemble.html</link>
     <description><![CDATA[<article>
     <section class="header">
-        Posted on March 20, 2019
         
     </section>
     <section>
@@ -170,7 +167,6 @@ W_1(p, q) = \min_{P \in \mathbb{R}_+^{n\times m}} \sum_{i,j} C_{i,j} P_{i,j}
     <link>https://www.lozeve.com/posts/peano.html</link>
     <description><![CDATA[<article>
     <section class="header">
-        Posted on March 18, 2019
         
     </section>
     <section>
@@ -282,7 +278,6 @@ then <span class="math inline">\(\varphi(n)\)</span> is true for every natural n
     <link>https://www.lozeve.com/posts/reinforcement-learning-1.html</link>
     <description><![CDATA[<article>
     <section class="header">
-        Posted on November 21, 2018
         
     </section>
     <section>
@@ -351,7 +346,6 @@ then <span class="math inline">\(\varphi(n)\)</span> is true for every natural n
     <link>https://www.lozeve.com/posts/ising-apl.html</link>
     <description><![CDATA[<article>
     <section class="header">
-        Posted on March  5, 2018
         
     </section>
     <section>
@@ -556,7 +550,6 @@ then <span class="math inline">\(\varphi(n)\)</span> is true for every natural n
     <link>https://www.lozeve.com/posts/ising-model.html</link>
     <description><![CDATA[<article>
     <section class="header">
-        Posted on February  5, 2018
         
             by Dimitri Lozeve
         
@@ -677,7 +670,6 @@ J\sigma_i \sum_{j\sim i} \sigma_j.  \]</span></p>
     <link>https://www.lozeve.com/posts/lsystems.html</link>
     <description><![CDATA[<article>
     <section class="header">
-        Posted on January 18, 2018
         
             by Dimitri Lozeve
         
diff --git a/_site/skills.html b/_site/skills.html
index 064e1be..b2a5cd3 100644
--- a/_site/skills.html
+++ b/_site/skills.html
@@ -9,6 +9,7 @@
     <title>Dimitri Lozeve - Skills in Statistics, Data Science and Machine Learning</title>
     <link rel="stylesheet" href="./css/tufte.css" />
     <link rel="stylesheet" href="./css/pandoc.css" />
+    <link rel="stylesheet" href="./css/default.css" />
     <link rel="stylesheet" href="./css/syntax.css" />
 
     <!-- KaTeX CSS styles -->
@@ -25,9 +26,6 @@
     <article>
       
       <header>
-	<div class="logo">
-          <a href="./">Dimitri Lozeve</a>
-	</div>
 	<nav>
           <a href="./">Home</a>
 	  <a href="./projects.html">Projects</a>
@@ -43,9 +41,6 @@
       </header>
       
 
-      <!-- <header> -->
-	<!-- </header> -->
-
       
     </article>
 
@@ -103,62 +98,6 @@
 <li>Reversible jump MCMC</li>
 <li>Hidden Markov Models and Sequential Monte Carlo Methods</li>
 </ul>
-    <!-- <main role="main"> -->
-      <!-- 	<h1 id="statistics">Statistics</h1>
-<ul>
-<li>Knowledge of Linear Models and Generalised Linear Models (including logistic regression), both in theory and in applications</li>
-<li>Classical Statistical inference (maximum likelihood estimation, method of moments, minimal variance unbiased estimators) and testing (including goodness of fit)</li>
-<li>Nonparametric statistics</li>
-<li>Bootstrap methods, hidden Markov models</li>
-<li>Knowledge of Bayesian Analysis techniques for inference and testing: Markov Chain Monte Carlo, Approximate Bayesian Computation, Reversible Jump MCMC</li>
-<li>Good knowledge of R for statistical modelling and plotting</li>
-</ul>
-<h1 id="data-analysis">Data Analysis</h1>
-<ul>
-<li>Experience with large datasets, for classification and regression</li>
-<li>Descriptive statistics, plotting (with dimensionality reduction)</li>
-<li>Data cleaning and formatting</li>
-<li>Experience with unstructured data coming directly from embedded sensors to a microcontroller</li>
-<li>Experience with large graph and network data</li>
-<li>Experience with live data from APIs</li>
-<li>Data analysis with Pandas, xarray (Python) and the tidyverse (R)</li>
-<li>Basic knowledge of SQL</li>
-</ul>
-<h1 id="graph-and-network-analysis">Graph and Network Analysis</h1>
-<ul>
-<li>Research project on community detection and graph clustering (theory and implementation)</li>
-<li>Research project on Topological Data Analysis for time-dependent networks</li>
-<li>Random graph models</li>
-<li>Estimation in networks (Stein’s method for Normal and Poisson estimation)</li>
-<li>Network Analysis with NetworkX, graph-tool (Python) and igraph (R and Python)</li>
-</ul>
-<h1 id="time-series-analysis">Time Series Analysis</h1>
-<ul>
-<li>experience in analysing inertial sensors data (accelerometer, gyroscope, magnetometer), both in real-time and in post-processing</li>
-<li>use of statistical method for step detection, gait detection, and trajectory reconstruction</li>
-<li>Kalman filtering, Fourier and wavelet analysis</li>
-<li>Machine Learning methods applied to time series (decision trees, SVMs and Recurrent Neural Networks in particular)</li>
-<li>Experience with signal processing functions in Numpy and Scipy (Python)</li>
-</ul>
-<h1 id="machine-learning">Machine Learning</h1>
-<ul>
-<li>Experience in Dimensionality Reduction (PCA, MDS, Kernel PCA, Isomap, spectral clustering)</li>
-<li>Experience with the most common methods and techniques</li>
-<li>Random forests, SVMs, Neural Networks (including CNNs and RNNs), both theoretical knowledge and practical experience</li>
-<li>Bagging and boosting estimators</li>
-<li>Cross-validation</li>
-<li>Kernel methods, reproducing kernel Hilbert spaces, collaborative filtering, variational Bayes, Gaussian processes</li>
-<li>Machine Learning libraries: Scikit-Learn, PyTorch, TensorFlow, Keras</li>
-</ul>
-<h1 id="simulation">Simulation</h1>
-<ul>
-<li>Inversion, Transformation, Rejection, and Importance sampling</li>
-<li>Gibbs sampling</li>
-<li>Metropolis-Hastings</li>
-<li>Reversible jump MCMC</li>
-<li>Hidden Markov Models and Sequential Monte Carlo Methods</li>
-</ul> -->
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diff --git a/css/default.css b/css/default.css
index 4671627..4b77227 100644
--- a/css/default.css
+++ b/css/default.css
@@ -1,55 +1,25 @@
 body {
-    font-family: Helvetica, Arial, sans-serif;
-    line-height: 1.5;
-    color: #111;
-    max-width: 50rem;
-    padding: 2rem;
-    margin: auto;
     background: #fafafa;
     counter-reset: theorem;
     counter-reset: definition;
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-img {
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-}
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-    font-size: 1.6rem;
-}
-
-h2 {
-    font-size: 1.2rem;
-}
-
 header {
-    border-bottom: 0.15rem solid #000;
-    margin-bottom: 2rem;
+    margin: 1em 0 2em 0;
 }
-
-nav {
-    text-align: right;
+header nav {
+    width: 87.5%;
 }
-
-nav a {
-    font-size: 1.2rem;
+header nav a {
+    display: inline-block;
+    font-size: 1.4rem;
     font-weight: bold;
-    color: #000;
-    text-decoration: none;
-    padding: .5rem;
-}
-
-.logo a {
-    float: left;
-    font-size: 1.2rem;
-    font-weight: bold;
-    color: #000;
-    text-decoration: none;
+    text-decoration: none !important;
+    margin: 0 0.5rem;
+    padding: 0 0;
 }
+header nav a:first-child { margin-left: 0; }
+header nav a:last-child { margin-right: 0; }
 
 footer {
     margin-top: 3rem;
@@ -63,13 +33,13 @@ article .header {
     color: #555;
 }
 
-.sourceCode {
-    display:block;
-    padding-left: 1rem;
-    margin-top: 1rem;
-    margin-bottom: 1rem;
-    background: #eee;
-}
+/* .sourceCode { */
+/*     display:block; */
+/*     padding-left: 1rem; */
+/*     margin-top: 1rem; */
+/*     margin-bottom: 1rem; */
+/*     background: #eee; */
+/* } */
 
 .definition, .proposition, .theorem {
     display: block;
diff --git a/posts/hierarchical-optimal-transport-for-document-classification.org b/posts/hierarchical-optimal-transport-for-document-classification.org
index 1d39f19..c713445 100644
--- a/posts/hierarchical-optimal-transport-for-document-classification.org
+++ b/posts/hierarchical-optimal-transport-for-document-classification.org
@@ -154,8 +154,12 @@ to a deep learning approach, we can make sense of every intermediate
 step, from the representations of topics to the weights in the
 optimisation algorithm to compute higher-level distances.
 
-#+caption: Representation of two documents in topic space, along with how the distance was computed between them. Everything is interpretable: from the documents as collections of topics, to the matchings between topics determining the overall distance between the books citep:yurochkin2019_hierar_optim_trans_docum_repres.
 [[file:/images/hott_fig1.jpg]]
+ [fn::{-} Representation of two documents in topic space, along with
+how the distance was computed between them. Everything is
+interpretable: from the documents as collections of topics, to the
+matchings between topics determining the overall distance between the
+books citep:yurochkin2019_hierar_optim_trans_docum_repres.]
 
 * Experiments
 
diff --git a/templates/default.html b/templates/default.html
index b2a99e0..52e6ac3 100644
--- a/templates/default.html
+++ b/templates/default.html
@@ -11,6 +11,7 @@
     <title>Dimitri Lozeve - $title$</title>
     <link rel="stylesheet" href="/css/tufte.css" />
     <link rel="stylesheet" href="/css/pandoc.css" />
+    <link rel="stylesheet" href="/css/default.css" />
     <link rel="stylesheet" href="/css/syntax.css" />
 
     <!-- KaTeX CSS styles -->
@@ -28,9 +29,6 @@
     <article>
       $if(title)$
       <header>
-	<div class="logo">
-          <a href="/">Dimitri Lozeve</a>
-	</div>
 	<nav>
           <a href="/">Home</a>
 	  <a href="/projects.html">Projects</a>
@@ -52,9 +50,6 @@
       </header>
       $endif$
 
-      <!-- <header> -->
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-
       $if(toc)$
       <nav id="$idprefix$TOC">
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@@ -63,9 +58,6 @@
     </article>
 
     $body$
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diff --git a/templates/post.html b/templates/post.html
index 732149b..acfc6fc 100644
--- a/templates/post.html
+++ b/templates/post.html
@@ -1,6 +1,5 @@
 <article>
     <section class="header">
-        Posted on $date$
         $if(author)$
             by $author$
         $endif$