From f2055d697a107f9f07f0d3f2871f8f42c83cea27 Mon Sep 17 00:00:00 2001
From: Aatish Pradhan <49292267+aatishpr@users.noreply.github.com>
Date: Tue, 5 Sep 2023 11:10:00 -0400
Subject: [PATCH] Updated documentation for AutoML

---
 chemml_library.html |  72 ++++++++++++++++++-------------
 chemml_wrapper.html |  63 ++++++++++++++++++---------
 genindex.html       |  31 ++++++--------
 index.html          | 102 +++++++++++++++++++++++++-------------------
 objects.inv         | Bin 18931 -> 16686 bytes
 py-modindex.html    |  17 +++-----
 search.html         |  17 +++-----
 searchindex.js      |   2 +-
 8 files changed, 171 insertions(+), 133 deletions(-)
diff --git a/chemml_library.html b/chemml_library.html
index 542c108f..1af85824 100644
--- a/chemml_library.html
+++ b/chemml_library.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" >
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Introduction to ChemML Library &mdash; ChemML  documentation</title>
@@ -12,8 +12,9 @@
   <![endif]-->
   
         <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
+        <script src="_static/jquery.js"></script>
+        <script src="_static/underscore.js"></script>
         <script src="_static/doctools.js"></script>
-        <script src="_static/sphinx_highlight.js"></script>
         <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
         <script src="https://unpkg.com/@jupyter-widgets/html-manager@^0.20.0/dist/embed-amd.js"></script>
     <script src="_static/js/theme.js"></script>
@@ -28,15 +29,11 @@
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search" >
-
-          
-          
-          <a href="index.html" class="icon icon-home">
-            ChemML
+            <a href="index.html" class="icon icon-home"> ChemML
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="text" name="q" placeholder="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
@@ -53,8 +50,8 @@
 <li class="toctree-l1"><a class="reference internal" href="prepare_task/index.html">Prepare</a></li>
 <li class="toctree-l1"><a class="reference internal" href="model_task/index.html">Model</a></li>
 <li class="toctree-l1"><a class="reference internal" href="optimize_task/index.html">Optimize</a></li>
-<li class="toctree-l1"><a class="reference internal" href="explain_task/index.html">Explain</a></li>
 <li class="toctree-l1"><a class="reference internal" href="visualize_task/index.html">Visualize</a></li>
+<li class="toctree-l1"><a class="reference internal" href="automl_task/index.html">AutoML</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">ChemML Wrapper</span></p>
 <ul>
@@ -83,8 +80,8 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
-      <li class="breadcrumb-item active">Introduction to ChemML Library</li>
+      <li><a href="index.html" class="icon icon-home"></a> &raquo;</li>
+      <li>Introduction to ChemML Library</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/chemml_library.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -94,8 +91,32 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
              
-  <section id="introduction-to-chemml-library">
-<h1>Introduction to ChemML Library<a class="headerlink" href="#introduction-to-chemml-library" title="Permalink to this heading"></a></h1>
+  
+<style>
+/* CSS overrides for sphinx_rtd_theme */
+
+/* 24px margin */
+.nbinput.nblast.container,
+.nboutput.nblast.container {
+    margin-bottom: 19px;  /* padding has already 5px */
+}
+
+/* ... except between code cells! */
+.nblast.container + .nbinput.container {
+    margin-top: -19px;
+}
+
+.admonition > p:before {
+    margin-right: 4px;  /* make room for the exclamation icon */
+}
+
+/* Fix math alignment, see https://github.com/rtfd/sphinx_rtd_theme/pull/686 */
+.math {
+    text-align: unset;
+}
+</style>
+<section id="introduction-to-chemml-library">
+<h1>Introduction to ChemML Library<a class="headerlink" href="#introduction-to-chemml-library" title="Permalink to this headline"></a></h1>
 <p>ChemML is an open machine learning (ML) and informatics program suite that is designed to support and advance the data-driven research paradigm that is currently emerging in the chemical and materials domain. ChemML allows its users to perform various data science tasks and execute ML workflows that are
 adapted specifically for the chemical and materials context. Key features are automation, general-purpose utility, versatility, and user-friendliness in order to make the application of modern data science a viable and widely accessible proposition in the broader chemistry and materials community. ChemML is also designed to facilitate methodological innovation, and it is one of the cornerstones of the software ecosystem for data-driven in silico research.</p>
 <a class="reference external image-reference" href="https://mojtabah.github.io/ChemML"><img alt="_images/chemml_tasks.png" src="_images/chemml_tasks.png" style="width: 540px;" /></a>
@@ -128,31 +149,24 @@ <h1>Introduction to ChemML Library<a class="headerlink" href="#introduction-to-c
 </dl>
 </li>
 <li><dl class="simple">
-<dt>Explain</dt><dd><p>This class provides explainations for deep neural networks using XAI three XAI methods. It supports intuitive vizualization methods which further illuminate the black-box of deep neural networks. The module provides a ranking of features based on their contribution towards the predictions of our deep neural network.</p>
-</dd>
-</dl>
-</li>
-<li><dl class="simple">
 <dt>Visualize</dt><dd><p>Data visualization methods that help facilitate a better comprehension of the modeling results are available via a separate module, which builds on the Matplotlib and Seaborn libraries for key visualization elements. These elements are accessible as part of any ML workflow.</p>
 </dd>
 </dl>
 </li>
 </ul>
 <section id="citation">
-<h2>Citation:<a class="headerlink" href="#citation" title="Permalink to this heading"></a></h2>
+<h2>Citation:<a class="headerlink" href="#citation" title="Permalink to this headline"></a></h2>
 <p>Please cite the use of ChemML as:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Main</span> <span class="n">citation</span><span class="p">:</span>
 
- <span class="nd">@article</span><span class="p">{</span><span class="n">haghighatlari2019chemml</span><span class="p">,</span>
-     <span class="n">title</span>        <span class="o">=</span> <span class="p">{{</span><span class="n">ChemML</span><span class="p">}:</span> <span class="n">A</span> <span class="n">machine</span> <span class="n">learning</span> <span class="ow">and</span> <span class="n">informatics</span> <span class="n">program</span> <span class="n">package</span> <span class="k">for</span> <span class="n">the</span> <span class="n">analysis</span><span class="p">,</span> <span class="n">mining</span><span class="p">,</span> <span class="ow">and</span> <span class="n">modeling</span> <span class="n">of</span> <span class="n">chemical</span> <span class="ow">and</span> <span class="n">materials</span> <span class="n">data</span><span class="p">},</span>
-     <span class="n">author</span>       <span class="o">=</span> <span class="p">{</span><span class="n">Haghighatlari</span><span class="p">,</span> <span class="n">Mojtaba</span> <span class="ow">and</span> <span class="n">Vishwakarma</span><span class="p">,</span> <span class="n">Gaurav</span> <span class="ow">and</span> <span class="n">Altarawy</span><span class="p">,</span> <span class="n">Doaa</span> <span class="ow">and</span> <span class="n">Subramanian</span><span class="p">,</span> <span class="n">Ramachandran</span> <span class="ow">and</span> <span class="n">Kota</span><span class="p">,</span> <span class="n">Bhargava</span> <span class="n">U</span> <span class="ow">and</span> <span class="n">Sonpal</span><span class="p">,</span> <span class="n">Aditya</span> <span class="ow">and</span> <span class="n">Setlur</span><span class="p">,</span> <span class="n">Srirangaraj</span> <span class="ow">and</span> <span class="n">Hachmann</span><span class="p">,</span> <span class="n">Johannes</span><span class="p">},</span>
-     <span class="n">year</span>         <span class="o">=</span> <span class="mi">2020</span><span class="p">,</span>
-     <span class="n">journal</span>      <span class="o">=</span> <span class="p">{</span><span class="n">Wiley</span> <span class="n">Interdisciplinary</span> <span class="n">Reviews</span><span class="p">:</span> <span class="n">Computational</span> <span class="n">Molecular</span> <span class="n">Science</span><span class="p">},</span>
-     <span class="n">publisher</span>    <span class="o">=</span> <span class="p">{</span><span class="n">Wiley</span> <span class="n">Online</span> <span class="n">Library</span><span class="p">},</span>
-     <span class="n">volume</span>       <span class="o">=</span> <span class="mi">10</span><span class="p">,</span>
-     <span class="n">doi</span>          <span class="o">=</span> <span class="p">{</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">doi</span><span class="o">.</span><span class="n">org</span><span class="o">/</span><span class="mf">10.1002</span><span class="o">/</span><span class="n">wcms</span><span class="mf">.1458</span><span class="p">},</span>
-     <span class="n">pages</span>        <span class="o">=</span> <span class="p">{</span><span class="n">e1458</span><span class="p">},</span>
- <span class="p">}</span>
+<span class="nd">@article</span><span class="p">{</span><span class="n">chemml2019</span><span class="p">,</span>
+<span class="n">author</span> <span class="o">=</span> <span class="p">{</span><span class="n">Haghighatlari</span><span class="p">,</span> <span class="n">Mojtaba</span> <span class="ow">and</span> <span class="n">Vishwakarma</span><span class="p">,</span> <span class="n">Gaurav</span> <span class="ow">and</span> <span class="n">Altarawy</span><span class="p">,</span> <span class="n">Doaa</span> <span class="ow">and</span> <span class="n">Subramanian</span><span class="p">,</span> <span class="n">Ramachandran</span> <span class="ow">and</span> <span class="n">Kota</span><span class="p">,</span> <span class="n">Bhargava</span> <span class="n">Urala</span> <span class="ow">and</span> <span class="n">Sonpal</span><span class="p">,</span> <span class="n">Aditya</span> <span class="ow">and</span> <span class="n">Setlur</span><span class="p">,</span> <span class="n">Srirangaraj</span> <span class="ow">and</span> <span class="n">Hachmann</span><span class="p">,</span> <span class="n">Johannes</span><span class="p">},</span>
+<span class="n">journal</span> <span class="o">=</span> <span class="p">{</span><span class="n">ChemRxiv</span><span class="p">},</span>
+<span class="n">pages</span> <span class="o">=</span> <span class="p">{</span><span class="mi">8323271</span><span class="p">},</span>
+<span class="n">title</span> <span class="o">=</span> <span class="p">{</span><span class="n">ChemML</span><span class="p">:</span> <span class="n">A</span> <span class="n">Machine</span> <span class="n">Learning</span> <span class="ow">and</span> <span class="n">Informatics</span> <span class="n">Program</span> <span class="n">Package</span> <span class="k">for</span> <span class="n">the</span> <span class="n">Analysis</span><span class="p">,</span> <span class="n">Mining</span><span class="p">,</span> <span class="ow">and</span> <span class="n">Modeling</span> <span class="n">of</span> <span class="n">Chemical</span> <span class="ow">and</span> <span class="n">Materials</span> <span class="n">Data</span><span class="p">},</span>
+<span class="n">doi</span> <span class="o">=</span> <span class="p">{</span><span class="mf">10.26434</span><span class="o">/</span><span class="n">chemrxiv</span><span class="mf">.8323271</span><span class="o">.</span><span class="n">v1</span><span class="p">},</span>
+<span class="n">year</span> <span class="o">=</span> <span class="p">{</span><span class="mi">2019</span><span class="p">}</span>
+<span class="p">}</span>
 </pre></div>
 </div>
 </section>
diff --git a/chemml_wrapper.html b/chemml_wrapper.html
index 65788099..a8652c3b 100644
--- a/chemml_wrapper.html
+++ b/chemml_wrapper.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" >
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Introduction to ChemML Wrapper &mdash; ChemML  documentation</title>
@@ -12,15 +12,16 @@
   <![endif]-->
   
         <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
+        <script src="_static/jquery.js"></script>
+        <script src="_static/underscore.js"></script>
         <script src="_static/doctools.js"></script>
-        <script src="_static/sphinx_highlight.js"></script>
         <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
         <script src="https://unpkg.com/@jupyter-widgets/html-manager@^0.20.0/dist/embed-amd.js"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="ChemML Wrapper Tutorial" href="wrapper/index.html" />
-    <link rel="prev" title="Visualize" href="ipython_notebooks/visualize.html" /> 
+    <link rel="prev" title="Load your data" href="ipython_notebooks/autoML_regression.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -28,15 +29,11 @@
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search" >
-
-          
-          
-          <a href="index.html" class="icon icon-home">
-            ChemML
+            <a href="index.html" class="icon icon-home"> ChemML
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="text" name="q" placeholder="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
@@ -50,8 +47,8 @@
 <li class="toctree-l1"><a class="reference internal" href="prepare_task/index.html">Prepare</a></li>
 <li class="toctree-l1"><a class="reference internal" href="model_task/index.html">Model</a></li>
 <li class="toctree-l1"><a class="reference internal" href="optimize_task/index.html">Optimize</a></li>
-<li class="toctree-l1"><a class="reference internal" href="explain_task/index.html">Explain</a></li>
 <li class="toctree-l1"><a class="reference internal" href="visualize_task/index.html">Visualize</a></li>
+<li class="toctree-l1"><a class="reference internal" href="automl_task/index.html">AutoML</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">ChemML Wrapper</span></p>
 <ul class="current">
@@ -89,8 +86,8 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
-      <li class="breadcrumb-item active">Introduction to ChemML Wrapper</li>
+      <li><a href="index.html" class="icon icon-home"></a> &raquo;</li>
+      <li>Introduction to ChemML Wrapper</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/chemml_wrapper.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -100,15 +97,39 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
              
-  <section id="introduction-to-chemml-wrapper">
-<h1>Introduction to ChemML Wrapper<a class="headerlink" href="#introduction-to-chemml-wrapper" title="Permalink to this heading"></a></h1>
+  
+<style>
+/* CSS overrides for sphinx_rtd_theme */
+
+/* 24px margin */
+.nbinput.nblast.container,
+.nboutput.nblast.container {
+    margin-bottom: 19px;  /* padding has already 5px */
+}
+
+/* ... except between code cells! */
+.nblast.container + .nbinput.container {
+    margin-top: -19px;
+}
+
+.admonition > p:before {
+    margin-right: 4px;  /* make room for the exclamation icon */
+}
+
+/* Fix math alignment, see https://github.com/rtfd/sphinx_rtd_theme/pull/686 */
+.math {
+    text-align: unset;
+}
+</style>
+<section id="introduction-to-chemml-wrapper">
+<h1>Introduction to ChemML Wrapper<a class="headerlink" href="#introduction-to-chemml-wrapper" title="Permalink to this headline"></a></h1>
 <p>ChemML Wrapper carry out a workflow of operations hosted by different
 open-source or commercial libraries/software.
 The workflow is similar to a directed graph and it can be designed in a text file.
 An input file (configuration file) is required to run the ChemML Wrapper.</p>
 <p>In this section we walk you through all the required steps to run an input file.</p>
 <section id="step-1-prepare-an-input-file">
-<h2>Step #1: prepare an input file<a class="headerlink" href="#step-1-prepare-an-input-file" title="Permalink to this heading"></a></h2>
+<h2>Step #1: prepare an input file<a class="headerlink" href="#step-1-prepare-an-input-file" title="Permalink to this headline"></a></h2>
 <p>ChemML Wrapper requires an input file to configure and run an arbitrary workflow.
 This file must be a text file in any arbitrary format.
 If you want to create or modify an input file manually,
@@ -183,10 +204,10 @@ <h2>Step #1: prepare an input file<a class="headerlink" href="#step-1-prepare-an
 <img alt="_images/tut_graph.png" src="_images/tut_graph.png" />
 </section>
 <section id="step-2-run-chemml-wrapper">
-<h2>Step #2: run ChemML Wrapper<a class="headerlink" href="#step-2-run-chemml-wrapper" title="Permalink to this heading"></a></h2>
+<h2>Step #2: run ChemML Wrapper<a class="headerlink" href="#step-2-run-chemml-wrapper" title="Permalink to this headline"></a></h2>
 <p>Now that we have prepared an input script/file, we can run it using any of the following ways.</p>
 <section id="method-one-running-in-the-terminal">
-<h3>method one: Running in the Terminal<a class="headerlink" href="#method-one-running-in-the-terminal" title="Permalink to this heading"></a></h3>
+<h3>method one: Running in the Terminal<a class="headerlink" href="#method-one-running-in-the-terminal" title="Permalink to this headline"></a></h3>
 <p>Let’s say you saved your script with the name ‘tutorial.config’ in your Desktop folder (name and format are both arbitrary).
 In the Terminal, navigate to the Desktop folder and enter the following command:</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>chemmlwrapper -i tutorial.config -o output_directory
@@ -194,7 +215,7 @@ <h3>method one: Running in the Terminal<a class="headerlink" href="#method-one-r
 </div>
 </section>
 <section id="method-two-running-in-any-python-interpreter">
-<h3>method two: Running in any Python Interpreter<a class="headerlink" href="#method-two-running-in-any-python-interpreter" title="Permalink to this heading"></a></h3>
+<h3>method two: Running in any Python Interpreter<a class="headerlink" href="#method-two-running-in-any-python-interpreter" title="Permalink to this headline"></a></h3>
 <p>You can also run your input script with python codes as a python script or interactively, using:</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># we assume you saved your script with the name &#39;tutorial.config&#39; in your Desktop folder</span>
 <span class="kn">from</span> <span class="nn">chemml.wrapper.engine</span> <span class="kn">import</span> <span class="n">run</span>
@@ -276,9 +297,9 @@ <h3>method two: Running in any Python Interpreter<a class="headerlink" href="#me
 </section>
 </section>
 <section id="step-3-check-the-output-directory">
-<h2>Step #3: check the output directory<a class="headerlink" href="#step-3-check-the-output-directory" title="Permalink to this heading"></a></h2>
+<h2>Step #3: check the output directory<a class="headerlink" href="#step-3-check-the-output-directory" title="Permalink to this headline"></a></h2>
 <p>After running ChemML Wrapper you can collect all your saved files by navigating to the output directory.
-These saved files can be any type of results and fugures from your workflow,
+These saved files can be any type of results and figures from your workflow,
 or default files, e.g. error file, log file, a copy of input file,
 and citation file.</p>
 </section>
@@ -288,7 +309,7 @@ <h2>Step #3: check the output directory<a class="headerlink" href="#step-3-check
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="ipython_notebooks/visualize.html" class="btn btn-neutral float-left" title="Visualize" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="ipython_notebooks/autoML_regression.html" class="btn btn-neutral float-left" title="Load your data" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <a href="wrapper/index.html" class="btn btn-neutral float-right" title="ChemML Wrapper Tutorial" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
diff --git a/genindex.html b/genindex.html
index 4695a22c..d5a0fdd4 100644
--- a/genindex.html
+++ b/genindex.html
@@ -11,8 +11,9 @@
   <![endif]-->
   
         <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
+        <script src="_static/jquery.js"></script>
+        <script src="_static/underscore.js"></script>
         <script src="_static/doctools.js"></script>
-        <script src="_static/sphinx_highlight.js"></script>
         <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
         <script src="https://unpkg.com/@jupyter-widgets/html-manager@^0.20.0/dist/embed-amd.js"></script>
     <script src="_static/js/theme.js"></script>
@@ -25,15 +26,11 @@
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search" >
-
-          
-          
-          <a href="index.html" class="icon icon-home">
-            ChemML
+            <a href="index.html" class="icon icon-home"> ChemML
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="text" name="q" placeholder="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
@@ -47,8 +44,8 @@
 <li class="toctree-l1"><a class="reference internal" href="prepare_task/index.html">Prepare</a></li>
 <li class="toctree-l1"><a class="reference internal" href="model_task/index.html">Model</a></li>
 <li class="toctree-l1"><a class="reference internal" href="optimize_task/index.html">Optimize</a></li>
-<li class="toctree-l1"><a class="reference internal" href="explain_task/index.html">Explain</a></li>
 <li class="toctree-l1"><a class="reference internal" href="visualize_task/index.html">Visualize</a></li>
+<li class="toctree-l1"><a class="reference internal" href="automl_task/index.html">AutoML</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">ChemML Wrapper</span></p>
 <ul>
@@ -77,8 +74,8 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
-      <li class="breadcrumb-item active">Index</li>
+      <li><a href="index.html" class="icon icon-home"></a> &raquo;</li>
+      <li>Index</li>
       <li class="wy-breadcrumbs-aside">
       </li>
   </ul>
@@ -334,18 +331,12 @@ <h2 id="F">F</h2>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="API/chemml.chem.magpie_python.html#chemml.chem.magpie_python.APEAttributeGenerator.find_efficiently_packed_clusters">find_efficiently_packed_clusters() (chemml.chem.magpie_python.APEAttributeGenerator class method)</a>
 </li>
-      <li><a href="API/chemml.initialization.html#chemml.initialization.Split.fit">fit() (chemml.initialization.Split method)</a>
+      <li><a href="API/chemml.initialization.html#chemml.initialization.SaveFile.fit">fit() (chemml.initialization.SaveFile method)</a>
 
       <ul>
-        <li><a href="API/chemml.visualization.html#chemml.visualization.decorator.fit">(chemml.visualization.decorator method)</a>
+        <li><a href="API/chemml.initialization.html#chemml.initialization.Split.fit">(chemml.initialization.Split method)</a>
 </li>
-      </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="API/chemml.models.html#chemml.models.NeuralGraphHidden.from_config">from_config() (chemml.models.NeuralGraphHidden class method)</a>
-
-      <ul>
-        <li><a href="API/chemml.models.html#chemml.models.NeuralGraphOutput.from_config">(chemml.models.NeuralGraphOutput class method)</a>
+        <li><a href="API/chemml.visualization.html#chemml.visualization.decorator.fit">(chemml.visualization.decorator method)</a>
 </li>
       </ul></li>
   </ul></td>
@@ -647,6 +638,8 @@ <h2 id="S">S</h2>
         <li><a href="API/chemml.visualization.html#chemml.visualization.SavePlot.save">(chemml.visualization.SavePlot method)</a>
 </li>
       </ul></li>
+      <li><a href="API/chemml.initialization.html#chemml.initialization.SaveFile">SaveFile (class in chemml.initialization)</a>
+</li>
       <li><a href="API/chemml.visualization.html#chemml.visualization.SavePlot">SavePlot (class in chemml.visualization)</a>
 </li>
       <li><a href="API/chemml.visualization.html#chemml.visualization.scatter2D">scatter2D (class in chemml.visualization)</a>
diff --git a/index.html b/index.html
index e13c1c9d..fdd3008d 100644
--- a/index.html
+++ b/index.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" >
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Welcome to the ChemML’s documentation! &mdash; ChemML  documentation</title>
@@ -12,8 +12,9 @@
   <![endif]-->
   
         <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
+        <script src="_static/jquery.js"></script>
+        <script src="_static/underscore.js"></script>
         <script src="_static/doctools.js"></script>
-        <script src="_static/sphinx_highlight.js"></script>
         <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
         <script src="https://unpkg.com/@jupyter-widgets/html-manager@^0.20.0/dist/embed-amd.js"></script>
     <script src="_static/js/theme.js"></script>
@@ -27,15 +28,11 @@
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search" >
-
-          
-          
-          <a href="#" class="icon icon-home">
-            ChemML
+            <a href="#" class="icon icon-home"> ChemML
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="text" name="q" placeholder="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
@@ -49,8 +46,8 @@
 <li class="toctree-l1"><a class="reference internal" href="prepare_task/index.html">Prepare</a></li>
 <li class="toctree-l1"><a class="reference internal" href="model_task/index.html">Model</a></li>
 <li class="toctree-l1"><a class="reference internal" href="optimize_task/index.html">Optimize</a></li>
-<li class="toctree-l1"><a class="reference internal" href="explain_task/index.html">Explain</a></li>
 <li class="toctree-l1"><a class="reference internal" href="visualize_task/index.html">Visualize</a></li>
+<li class="toctree-l1"><a class="reference internal" href="automl_task/index.html">AutoML</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">ChemML Wrapper</span></p>
 <ul>
@@ -79,8 +76,8 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="#" class="icon icon-home" aria-label="Home"></a></li>
-      <li class="breadcrumb-item active">Welcome to the ChemML’s documentation!</li>
+      <li><a href="#" class="icon icon-home"></a> &raquo;</li>
+      <li>Welcome to the ChemML’s documentation!</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/index.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -90,9 +87,33 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
              
-  <p><a class="reference external" href="https://mojtabah.github.io/ChemML"><img alt="logo" src="_images/logo.png" style="width: 540px;" /></a></p>
+  
+<style>
+/* CSS overrides for sphinx_rtd_theme */
+
+/* 24px margin */
+.nbinput.nblast.container,
+.nboutput.nblast.container {
+    margin-bottom: 19px;  /* padding has already 5px */
+}
+
+/* ... except between code cells! */
+.nblast.container + .nbinput.container {
+    margin-top: -19px;
+}
+
+.admonition > p:before {
+    margin-right: 4px;  /* make room for the exclamation icon */
+}
+
+/* Fix math alignment, see https://github.com/rtfd/sphinx_rtd_theme/pull/686 */
+.math {
+    text-align: unset;
+}
+</style>
+<p><a class="reference external" href="https://mojtabah.github.io/ChemML"><img alt="logo" src="_images/logo.png" style="width: 540px;" /></a></p>
 <section id="welcome-to-the-chemml-s-documentation">
-<h1>Welcome to the ChemML’s documentation!<a class="headerlink" href="#welcome-to-the-chemml-s-documentation" title="Permalink to this heading"></a></h1>
+<h1>Welcome to the ChemML’s documentation!<a class="headerlink" href="#welcome-to-the-chemml-s-documentation" title="Permalink to this headline"></a></h1>
 <p>ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data.</p>
 <blockquote>
 <div><ul class="simple">
@@ -100,13 +121,13 @@ <h1>Welcome to the ChemML’s documentation!<a class="headerlink" href="#welcome
 </ul>
 </div></blockquote>
 <section id="code-design">
-<h2>Code Design:<a class="headerlink" href="#code-design" title="Permalink to this heading"></a></h2>
+<h2>Code Design:<a class="headerlink" href="#code-design" title="Permalink to this headline"></a></h2>
 <p>ChemML is developed in the Python 3 programming language and makes use of a host of data analysis and ML libraries(accessible through the Anaconda distribution), as well as domain-specific libraries.
 The development follows a strictly modular and object-oriented design to make the overall code as flexible and versatile as possible.</p>
 <p>The format of library is similar to the well known libraries like Scikit-learn.</p>
 </section>
 <section id="latest-version">
-<h2>Latest Version:<a class="headerlink" href="#latest-version" title="Permalink to this heading"></a></h2>
+<h2>Latest Version:<a class="headerlink" href="#latest-version" title="Permalink to this headline"></a></h2>
 <blockquote>
 <div><ul class="simple">
 <li><p>to find out about the latest version and release history, click here: <a class="reference external" href="https://pypi.org/project/chemml/#history">https://pypi.org/project/chemml/#history</a></p></li>
@@ -114,7 +135,7 @@ <h2>Latest Version:<a class="headerlink" href="#latest-version" title="Permalink
 </div></blockquote>
 </section>
 <section id="installation-and-dependencies">
-<h2>Installation and Dependencies:<a class="headerlink" href="#installation-and-dependencies" title="Permalink to this heading"></a></h2>
+<h2>Installation and Dependencies:<a class="headerlink" href="#installation-and-dependencies" title="Permalink to this headline"></a></h2>
 <p>We strongly recommend you to install ChemML in an Anaconda environment. The instructions to create the environment, install ChemML’s dependencies, and subsequently install Chemml using the Python Package Index (PyPI) via pip are as follows:</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>conda create --name chemml_env <span class="nv">python</span><span class="o">=</span><span class="m">3</span>.8
 <span class="nb">source</span> activate chemml_env
@@ -139,19 +160,17 @@ <h2>Installation and Dependencies:<a class="headerlink" href="#installation-and-
 </dl>
 </section>
 <section id="citation">
-<h2>Citation:<a class="headerlink" href="#citation" title="Permalink to this heading"></a></h2>
+<h2>Citation:<a class="headerlink" href="#citation" title="Permalink to this headline"></a></h2>
 <p>Please cite the use of ChemML as:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Main</span> <span class="n">citation</span><span class="p">:</span>
 
-<span class="nd">@article</span><span class="p">{</span><span class="n">haghighatlari2019chemml</span><span class="p">,</span>
-    <span class="n">title</span>        <span class="o">=</span> <span class="p">{{</span><span class="n">ChemML</span><span class="p">}:</span> <span class="n">A</span> <span class="n">machine</span> <span class="n">learning</span> <span class="ow">and</span> <span class="n">informatics</span> <span class="n">program</span> <span class="n">package</span> <span class="k">for</span> <span class="n">the</span> <span class="n">analysis</span><span class="p">,</span> <span class="n">mining</span><span class="p">,</span> <span class="ow">and</span> <span class="n">modeling</span> <span class="n">of</span> <span class="n">chemical</span> <span class="ow">and</span> <span class="n">materials</span> <span class="n">data</span><span class="p">},</span>
-    <span class="n">author</span>       <span class="o">=</span> <span class="p">{</span><span class="n">Haghighatlari</span><span class="p">,</span> <span class="n">Mojtaba</span> <span class="ow">and</span> <span class="n">Vishwakarma</span><span class="p">,</span> <span class="n">Gaurav</span> <span class="ow">and</span> <span class="n">Altarawy</span><span class="p">,</span> <span class="n">Doaa</span> <span class="ow">and</span> <span class="n">Subramanian</span><span class="p">,</span> <span class="n">Ramachandran</span> <span class="ow">and</span> <span class="n">Kota</span><span class="p">,</span> <span class="n">Bhargava</span> <span class="n">U</span> <span class="ow">and</span> <span class="n">Sonpal</span><span class="p">,</span> <span class="n">Aditya</span> <span class="ow">and</span> <span class="n">Setlur</span><span class="p">,</span> <span class="n">Srirangaraj</span> <span class="ow">and</span> <span class="n">Hachmann</span><span class="p">,</span> <span class="n">Johannes</span><span class="p">},</span>
-    <span class="n">year</span>         <span class="o">=</span> <span class="mi">2020</span><span class="p">,</span>
-    <span class="n">journal</span>      <span class="o">=</span> <span class="p">{</span><span class="n">Wiley</span> <span class="n">Interdisciplinary</span> <span class="n">Reviews</span><span class="p">:</span> <span class="n">Computational</span> <span class="n">Molecular</span> <span class="n">Science</span><span class="p">},</span>
-    <span class="n">publisher</span>    <span class="o">=</span> <span class="p">{</span><span class="n">Wiley</span> <span class="n">Online</span> <span class="n">Library</span><span class="p">},</span>
-    <span class="n">volume</span>       <span class="o">=</span> <span class="mi">10</span><span class="p">,</span>
-    <span class="n">doi</span>          <span class="o">=</span> <span class="p">{</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">doi</span><span class="o">.</span><span class="n">org</span><span class="o">/</span><span class="mf">10.1002</span><span class="o">/</span><span class="n">wcms</span><span class="mf">.1458</span><span class="p">},</span>
-    <span class="n">pages</span>        <span class="o">=</span> <span class="p">{</span><span class="n">e1458</span><span class="p">},</span>
+<span class="nd">@article</span><span class="p">{</span><span class="n">chemml2019</span><span class="p">,</span>
+<span class="n">author</span> <span class="o">=</span> <span class="p">{</span><span class="n">Haghighatlari</span><span class="p">,</span> <span class="n">Mojtaba</span> <span class="ow">and</span> <span class="n">Vishwakarma</span><span class="p">,</span> <span class="n">Gaurav</span> <span class="ow">and</span> <span class="n">Altarawy</span><span class="p">,</span> <span class="n">Doaa</span> <span class="ow">and</span> <span class="n">Subramanian</span><span class="p">,</span> <span class="n">Ramachandran</span> <span class="ow">and</span> <span class="n">Kota</span><span class="p">,</span> <span class="n">Bhargava</span> <span class="n">Urala</span> <span class="ow">and</span> <span class="n">Sonpal</span><span class="p">,</span> <span class="n">Aditya</span> <span class="ow">and</span> <span class="n">Setlur</span><span class="p">,</span> <span class="n">Srirangaraj</span> <span class="ow">and</span> <span class="n">Hachmann</span><span class="p">,</span> <span class="n">Johannes</span><span class="p">},</span>
+<span class="n">journal</span> <span class="o">=</span> <span class="p">{</span><span class="n">ChemRxiv</span><span class="p">},</span>
+<span class="n">pages</span> <span class="o">=</span> <span class="p">{</span><span class="mi">8323271</span><span class="p">},</span>
+<span class="n">title</span> <span class="o">=</span> <span class="p">{</span><span class="n">ChemML</span><span class="p">:</span> <span class="n">A</span> <span class="n">Machine</span> <span class="n">Learning</span> <span class="ow">and</span> <span class="n">Informatics</span> <span class="n">Program</span> <span class="n">Package</span> <span class="k">for</span> <span class="n">the</span> <span class="n">Analysis</span><span class="p">,</span> <span class="n">Mining</span><span class="p">,</span> <span class="ow">and</span> <span class="n">Modeling</span> <span class="n">of</span> <span class="n">Chemical</span> <span class="ow">and</span> <span class="n">Materials</span> <span class="n">Data</span><span class="p">},</span>
+<span class="n">doi</span> <span class="o">=</span> <span class="p">{</span><span class="mf">10.26434</span><span class="o">/</span><span class="n">chemrxiv</span><span class="mf">.8323271</span><span class="o">.</span><span class="n">v1</span><span class="p">},</span>
+<span class="n">year</span> <span class="o">=</span> <span class="p">{</span><span class="mi">2019</span><span class="p">}</span>
 <span class="p">}</span>
 
 
@@ -240,8 +259,8 @@ <h2>Citation:<a class="headerlink" href="#citation" title="Permalink to this hea
 <li class="toctree-l3"><a class="reference internal" href="ipython_notebooks/ml_model.html#Loading-the-saved-ChemML-model">Loading the saved ChemML model</a></li>
 <li class="toctree-l3"><a class="reference internal" href="ipython_notebooks/ml_model.html#Predict-the-densities-for-the-test-data">Predict the densities for the test data</a></li>
 <li class="toctree-l3"><a class="reference internal" href="ipython_notebooks/ml_model.html#Evaluate-model-performance-using-chemml.utils.regression_metrics">Evaluate model performance using <code class="docutils literal notranslate"><span class="pre">chemml.utils.regression_metrics</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="ipython_notebooks/ml_model.html#Plot-actual-vs.-predicted-values">Plot actual vs. predicted values</a></li>
-<li class="toctree-l3"><a class="reference internal" href="ipython_notebooks/ml_model.html#If-the-Underlying-(TensorFlow/PyTorch)-model-is-required-...">If the Underlying (TensorFlow/PyTorch) model is required …</a></li>
+<li class="toctree-l3"><a class="reference internal" href="ipython_notebooks/ml_model.html#Plot-actual-vs. predicted-values">Plot actual vs. predicted values</a></li>
+<li class="toctree-l3"><a class="reference internal" href="ipython_notebooks/ml_model.html#If-the-Underlying-(TensorFlow/PyTorch)-model-is-required-…">If the Underlying (TensorFlow/PyTorch) model is required …</a></li>
 <li class="toctree-l3"><a class="reference internal" href="ipython_notebooks/ml_model.html#Sometimes-you-may-need-the-keras-model-without-the-output-layer-(for-e.g.,-for-transfer-learning)">Sometimes you may need the keras model without the output layer (for e.g., for transfer learning)</a></li>
 </ul>
 </li>
@@ -279,19 +298,16 @@ <h2>Citation:<a class="headerlink" href="#citation" title="Permalink to this hea
 </li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="explain_task/index.html">Explain</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="ipython_notebooks/Explain_visualizations.html">Generating Deep Neural Network Model Explanations via ChemML’s Explain Module</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="ipython_notebooks/Explain_visualizations.html#The-chemml.explain-module-has-three-eXplainable-AI-(XAI)-methods---DeepSHAP,-LRP,-and-LIME.-It-allows-both-local-(for-a-single-instance)-and-global-(aggregated-for-multiple-instances)-explanations.-The-explainations-are-in-the-form-of-a-relevance-score-attributed-to-each-feature-used-to-build-the-DNN-model.">The <code class="docutils literal notranslate"><span class="pre">chemml.explain</span></code> module has three eXplainable AI (XAI) methods - DeepSHAP, LRP, and LIME. It allows both local (for a single instance) and global (aggregated for multiple instances) explanations. The explainations are in the form of a relevance score attributed to each feature used to build the DNN model.</a></li>
-<li class="toctree-l3"><a class="reference internal" href="ipython_notebooks/Explain_visualizations.html#DeepSHAP-Explanations">DeepSHAP Explanations</a></li>
-<li class="toctree-l3"><a class="reference internal" href="ipython_notebooks/Explain_visualizations.html#Visualizing-local-DeepSHAP-explanations-using-a-waterfall-plot-adapted-from-the-shap-library.">Visualizing local DeepSHAP explanations using a waterfall plot adapted from the shap library.</a></li>
-</ul>
-</li>
-</ul>
-</li>
 <li class="toctree-l1"><a class="reference internal" href="visualize_task/index.html">Visualize</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="ipython_notebooks/visualize.html">Visualize</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="automl_task/index.html">AutoML</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="ipython_notebooks/autoML_regression.html">Load your data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="ipython_notebooks/autoML_regression.html#Run-autoML-for-a-regression-task">Run autoML for a regression task</a></li>
+<li class="toctree-l2"><a class="reference internal" href="ipython_notebooks/autoML_regression.html#Save-scores-to-csv">Save scores to csv</a></li>
+</ul>
+</li>
 </ul>
 </div>
 <div class="toctree-wrapper compound">
@@ -315,6 +331,7 @@ <h2>Citation:<a class="headerlink" href="#citation" title="Permalink to this hea
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="wrapper/CMLWInputFileGenerator.html">Input File GUI</a></li>
+<li class="toctree-l2"><a class="reference internal" href="ipython_notebooks/read_excel.html">Generate Morgan fingerprints from SMILES codes</a></li>
 <li class="toctree-l2"><a class="reference internal" href="ipython_notebooks/pyscript_usage.html">Pyscript Usage</a></li>
 <li class="toctree-l2"><a class="reference internal" href="ipython_notebooks/simple_ml_model.html">Build a simple ML model</a></li>
 <li class="toctree-l2"><a class="reference internal" href="ipython_notebooks/GA_tutorial.html">Genetic Algorithm GUI tutorial</a><ul>
@@ -356,7 +373,6 @@ <h2>Citation:<a class="headerlink" href="#citation" title="Permalink to this hea
 <li class="toctree-l3"><a class="reference internal" href="API/chemml.preprocessing.html">Preprocessing module</a></li>
 <li class="toctree-l3"><a class="reference internal" href="API/chemml.models.html">Models module</a></li>
 <li class="toctree-l3"><a class="reference internal" href="API/chemml.optimization.html">Optimization module</a></li>
-<li class="toctree-l3"><a class="reference internal" href="API/chemml.explain.html">Explain module</a></li>
 <li class="toctree-l3"><a class="reference internal" href="API/chemml.visualization.html">Visualization module</a></li>
 </ul>
 </li>
@@ -371,14 +387,14 @@ <h2>Citation:<a class="headerlink" href="#citation" title="Permalink to this hea
 </div>
 </section>
 <section id="license">
-<h2>License:<a class="headerlink" href="#license" title="Permalink to this heading"></a></h2>
+<h2>License:<a class="headerlink" href="#license" title="Permalink to this headline"></a></h2>
 <p>ChemML is copyright (C) 2014-2022 Johannes Hachmann, Mojtaba Haghighatlari, Aditya Sonpal, Gaurav Vishwakarma and Aatish Pradhan all rights reserved.
 ChemML is distributed under 3-Clause BSD License (<a class="reference external" href="https://opensource.org/licenses/BSD-3-Clause">https://opensource.org/licenses/BSD-3-Clause</a>).</p>
 </section>
 <section id="about-us">
-<h2>About us:<a class="headerlink" href="#about-us" title="Permalink to this heading"></a></h2>
+<h2>About us:<a class="headerlink" href="#about-us" title="Permalink to this headline"></a></h2>
 <dl class="field-list">
-<dt class="field-odd">Maintainers<span class="colon">:</span></dt>
+<dt class="field-odd">Maintainers</dt>
 <dd class="field-odd"><ul class="simple">
 <li><p>Johannes Hachmann, <a class="reference external" href="mailto:hachmann&#37;&#52;&#48;buffalo&#46;edu">hachmann<span>&#64;</span>buffalo<span>&#46;</span>edu</a></p></li>
 <li><p>Mojtaba Haghighatlari</p></li>
@@ -388,7 +404,7 @@ <h2>About us:<a class="headerlink" href="#about-us" title="Permalink to this hea
 </ul>
 <p>University at Buffalo - The State University of New York (UB)</p>
 </dd>
-<dt class="field-even">Contributors<span class="colon">:</span></dt>
+<dt class="field-even">Contributors</dt>
 <dd class="field-even"><ul class="simple">
 <li><p>Doaa Altarawy (MolSSI): scientific advice and software mentor</p></li>
 <li><p>Gaurav Vishwakarma (UB): automated model optimization</p></li>
@@ -402,7 +418,7 @@ <h2>About us:<a class="headerlink" href="#about-us" title="Permalink to this hea
 <li><p>We encourage any contributions and feedback. Feel free to fork and make pull-request to the “development” branch.</p></li>
 </ul>
 </dd>
-<dt class="field-odd">Acknowledgements<span class="colon">:</span></dt>
+<dt class="field-odd">Acknowledgements</dt>
 <dd class="field-odd"><ul class="simple">
 <li><p>ChemML is based upon work supported by the U.S. National Science Foundation under grant #OAC-1751161 and in part by #OAC-1640867.</p></li>
 <li><p>ChemML was also supported by start-up funds provided by UB’s School of Engineering and Applied Science and UB’s Department of Chemical and Biological Engineering, the New York State Center of Excellence in Materials Informatics through seed grant #1140384-8-75163, and the U.S. Department of Energy under grant #DE-SC0017193.</p></li>
diff --git a/objects.inv b/objects.inv
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diff --git a/py-modindex.html b/py-modindex.html
index a63cfc28..3002bdb7 100644
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"introduction-to-chemml-wrapper"]], "Step #1: prepare an input file": [[116, "step-1-prepare-an-input-file"]], "Step #2: run ChemML Wrapper": [[116, "step-2-run-chemml-wrapper"]], "method one: Running in the Terminal": [[116, "method-one-running-in-the-terminal"]], "method two: Running in any Python Interpreter": [[116, "method-two-running-in-any-python-interpreter"]], "Step #3: check the output directory": [[116, "step-3-check-the-output-directory"]], "Explain": [[117, "explain"], [117, null]], "Welcome to the ChemML\u2019s documentation!": [[118, "welcome-to-the-chemml-s-documentation"]], "Code Design:": [[118, "code-design"]], "Latest Version:": [[118, "latest-version"]], "Installation and Dependencies:": [[118, "installation-and-dependencies"]], "ChemML Library": [[118, null]], "ChemML Wrapper": [[118, null], [144, null]], "Published Models": [[118, null]], "License:": [[118, "license"]], "About us:": [[118, "about-us"]], "Neural Fingerprints": [[120, "Neural-Fingerprints"]], "Splitting and preprocessing the data": [[120, "Splitting-and-preprocessing-the-data"]], "Building the Neural Fingerprints": [[120, "Building-the-Neural-Fingerprints"]], "Building and training the neural network": [[120, "Building-and-training-the-neural-network"]], "Generating Deep Neural Network Model Explanations via ChemML\u2019s Explain Module": [[121, "Generating-Deep-Neural-Network-Model-Explanations-via-ChemML's-Explain-Module"]], "The chemml.explain module has three eXplainable AI (XAI) methods - DeepSHAP, LRP, and LIME. It allows both local (for a single instance) and global (aggregated for multiple instances) explanations. The explainations are in the form of a relevance score attributed to each feature used to build the DNN model.": [[121, "The-chemml.explain-module-has-three-eXplainable-AI-(XAI)-methods---DeepSHAP,-LRP,-and-LIME.-It-allows-both-local-(for-a-single-instance)-and-global-(aggregated-for-multiple-instances)-explanations.-The-explainations-are-in-the-form-of-a-relevance-score-attributed-to-each-feature-used-to-build-the-DNN-model."]], "DeepSHAP Explanations": [[121, "DeepSHAP-Explanations"]], "Visualizing local DeepSHAP explanations using a waterfall plot adapted from the shap library.": [[121, "Visualizing-local-DeepSHAP-explanations-using-a-waterfall-plot-adapted-from-the-shap-library."]], "Genetic Algorithm GUI tutorial": [[122, "Genetic-Algorithm-GUI-tutorial"]], "evaluate": [[122, "evaluate"]], "error_metric": [[122, "error_metric"]], "single_obj": [[122, "single_obj"]], "space": [[122, "space"]], "test_hyperparameters": [[122, "test_hyperparameters"]], "Molecule": [[123, "Molecule"]], "Construct a molecule using SMILES": [[123, "Construct-a-molecule-using-SMILES"]], "Construct a molecule using 3D atomic coordinates": [[123, "Construct-a-molecule-using-3D-atomic-coordinates"]], "Construct a molecule using InChi": [[123, "Construct-a-molecule-using-InChi"]], "Visualize the molecule": [[123, "Visualize-the-molecule"]], "Add or remove hydrogens": [[123, "Add-or-remove-hydrogens"]], "Convert chemical formats": [[123, "Convert-chemical-formats"]], "Optimize XYZ geometry": [[123, "Optimize-XYZ-geometry"]], "Active Learning": [[124, "Active-Learning"]], "Keras model example": [[124, "Keras-model-example"]], "Initialize active learning: EMC": [[124, "Initialize-active-learning:-EMC"]], "Start the active search": [[124, "Start-the-active-search"]], "Get a baseline: random sampling": [[124, "Get-a-baseline:-random-sampling"]], "Visualize distributions": [[124, "Visualize-distributions"]], "Search in a loop": [[124, "Search-in-a-loop"]], "Create a video": [[124, "Create-a-video"]], "Feature Representation Methods in ChemML": [[126, "Feature-Representation-Methods-in-ChemML"]], "Creating chemml.chem.Molecule object from molecule SMILES": [[126, "Creating-chemml.chem.Molecule-object-from-molecule-SMILES"]], "Coulomb Matrix": [[126, "Coulomb-Matrix"]], "Fingerprints from RDKit": [[126, "Fingerprints-from-RDKit"]], "Molecule tensors from chemml.chem.Molecule objects": [[126, "Molecule-tensors-from-chemml.chem.Molecule-objects"]], "Feature Selection using chemml.optimization.GeneticAlgorithm": [[127, "Feature-Selection-using-chemml.optimization.GeneticAlgorithm"]], "Defining hyperparameter space": [[127, "Defining-hyperparameter-space"], [128, "Defining-hyperparameter-space"]], "Defining objective function": [[127, "Defining-objective-function"], [128, "Defining-objective-function"]], "Optimize the feature space": [[127, "Optimize-the-feature-space"]], "Hyperparameter Optimization using chemml.optimization.GeneticAlgorithm": [[128, "Hyperparameter-Optimization-using-chemml.optimization.GeneticAlgorithm"]], "Optimize the model": [[128, "Optimize-the-model"]], "Resume optimization": [[128, "Resume-optimization"]], "Prepare: Handling Missing Values": [[129, "Prepare:-Handling-Missing-Values"]], "ChemML implements 4 strategies to handle missing values and interpolate, replace or remove them.": [[129, "ChemML-implements-4-strategies-to-handle-missing-values-and-interpolate,-replace-or-remove-them."]], "Strategy 1: Ignoring Rows": [[129, "Strategy-1:-Ignoring-Rows"]], "Strategy 2: Replacing With Zeros": [[129, "Strategy-2:-Replacing-With-Zeros"]], "Strategy 3: Interpolate": [[129, "Strategy-3:-Interpolate"]], "Strategy 3: Ignore Columns": [[129, "Strategy-3:-Ignore-Columns"]], "Build a Neural Network using ChemML": [[130, "Build-a-Neural-Network-using-ChemML"]], "Fit the chemml.model.MLP model to the training data": [[130, "Fit-the-chemml.model.MLP-model-to-the-training-data"]], "Saving the ChemML model": [[130, "Saving-the-ChemML-model"]], "Loading the saved ChemML model": [[130, "Loading-the-saved-ChemML-model"]], "Predict the densities for the test data": [[130, "Predict-the-densities-for-the-test-data"]], "Evaluate model performance using chemml.utils.regression_metrics": [[130, "Evaluate-model-performance-using-chemml.utils.regression_metrics"]], "Plot actual vs. predicted values": [[130, "Plot-actual-vs.-predicted-values"]], "If the Underlying (TensorFlow/PyTorch) model is required \u2026": [[130, "If-the-Underlying-(TensorFlow/PyTorch)-model-is-required-..."]], "Sometimes you may need the keras model without the output layer (for e.g., for transfer learning)": [[130, "Sometimes-you-may-need-the-keras-model-without-the-output-layer-(for-e.g.,-for-transfer-learning)"]], "Prepare: Remove Constant Columns and Outliers": [[131, "Prepare:-Remove-Constant-Columns-and-Outliers"]], "Removing Constant Columns": [[131, "Removing-Constant-Columns"]], "Removing oultiers based on mean": [[131, 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