deploy: 6986e38

.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 93e6fb10c299a3ad3e0432b95cd7a644
+config: dadd8496dfdb231bc7c0ab9ba3b7fe51
 tags: 645f666f9bcd5a90fca523b33c5a78b7

01_0_transform_data_to_wide_format.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Transfer data for NAGuideR format &#8212; pimms_workflow 0.1.dev1+g3810eb9 documentation</title>
+    <title>Transfer data for NAGuideR format &#8212; pimms_workflow 0.1.dev1+g6986e38 documentation</title>
 
 
 
@@ -40,7 +40,7 @@
   <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549" />
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549" />
 
-    <script src="_static/documentation_options.js?v=acfa9e01"></script>
+    <script src="_static/documentation_options.js?v=6e42c05d"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
@@ -52,7 +52,7 @@
     <link rel="prev" title="Experiment 03 - Data" href="01_0_split_data.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.1.dev1+g3810eb9" />
+  <meta name="docsearch:version" content="0.1.dev1+g6986e38" />
   </head>
 
 
@@ -127,7 +127,7 @@
 
 
 
-    <p class="title logo__title">pimms_workflow 0.1.dev1+g3810eb9 documentation</p>
+    <p class="title logo__title">pimms_workflow 0.1.dev1+g6986e38 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item">

01_1_train_CF.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Collaborative Filtering &#8212; pimms_workflow 0.1.dev1+g3810eb9 documentation</title>
+    <title>Collaborative Filtering &#8212; pimms_workflow 0.1.dev1+g6986e38 documentation</title>
 
 
 
@@ -40,7 +40,7 @@
   <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549" />
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549" />
 
-    <script src="_static/documentation_options.js?v=acfa9e01"></script>
+    <script src="_static/documentation_options.js?v=6e42c05d"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
@@ -52,7 +52,7 @@
     <link rel="prev" title="K- Nearest Neighbors (KNN)" href="01_1_train_KNN.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
-  <meta name="docsearch:version" content="0.1.dev1+g3810eb9" />
+  <meta name="docsearch:version" content="0.1.dev1+g6986e38" />
   </head>
 
 
@@ -127,7 +127,7 @@
 
 
 
-    <p class="title logo__title">pimms_workflow 0.1.dev1+g3810eb9 documentation</p>
+    <p class="title logo__title">pimms_workflow 0.1.dev1+g6986e38 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item">
@@ -995,8 +995,8 @@ <h3>Training<a class="headerlink" href="#training" title="Link to this heading">
         background: #F44336;
     }
 </style>
-</div><div class="output text_html"></div><div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>suggested_lr.valley = 0.00631
-No improvement since epoch 11: early stopping
+</div><div class="output text_html"></div><div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>suggested_lr.valley = 0.00759
+No improvement since epoch 10: early stopping
 pimmslearn.plotting - INFO     Saved Figures to runs/alzheimer_study/figures/collab_training
 </pre></div>
 </div>
@@ -1032,85 +1032,79 @@ <h3>Training<a class="headerlink" href="#training" title="Link to this heading">
   <tbody>
     <tr>
       <td>0</td>
-      <td>7.884120</td>
-      <td>11.135465</td>
+      <td>7.365228</td>
+      <td>10.037841</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>1</td>
-      <td>3.075876</td>
-      <td>3.893917</td>
+      <td>2.032692</td>
+      <td>2.401942</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>2</td>
-      <td>0.880193</td>
-      <td>1.124664</td>
+      <td>0.711758</td>
+      <td>0.873825</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>3</td>
-      <td>0.588416</td>
-      <td>0.758478</td>
+      <td>0.566351</td>
+      <td>0.741343</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>4</td>
-      <td>0.531779</td>
-      <td>0.713435</td>
+      <td>0.545464</td>
+      <td>0.724314</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>5</td>
-      <td>0.488391</td>
-      <td>0.665009</td>
+      <td>0.489364</td>
+      <td>0.649803</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>6</td>
-      <td>0.437718</td>
-      <td>0.603302</td>
+      <td>0.413048</td>
+      <td>0.561579</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>7</td>
-      <td>0.403666</td>
-      <td>0.555058</td>
+      <td>0.382740</td>
+      <td>0.530915</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>8</td>
-      <td>0.366097</td>
-      <td>0.531438</td>
+      <td>0.343510</td>
+      <td>0.504798</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>9</td>
-      <td>0.333807</td>
-      <td>0.502692</td>
+      <td>0.305056</td>
+      <td>0.478460</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>10</td>
-      <td>0.290191</td>
-      <td>0.481388</td>
+      <td>0.271160</td>
+      <td>0.463562</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>11</td>
-      <td>0.254149</td>
-      <td>0.472110</td>
-      <td>00:01</td>
-    </tr>
-    <tr>
-      <td>12</td>
-      <td>0.233288</td>
-      <td>0.473117</td>
+      <td>0.239125</td>
+      <td>0.484891</td>
       <td>00:01</td>
     </tr>
   </tbody>
-</table></div><img alt="_images/de6d97bd5ffefedfaa2cb53d40bff4e066dee45d985bc6363b53a14a1c208dae.png" src="_images/de6d97bd5ffefedfaa2cb53d40bff4e066dee45d985bc6363b53a14a1c208dae.png" />
-<img alt="_images/7300e2cd6522ea286427e7acdd198bdc90b5f961f63ac6b00d984620525a41a8.png" src="_images/7300e2cd6522ea286427e7acdd198bdc90b5f961f63ac6b00d984620525a41a8.png" />
+</table></div><img alt="_images/d66125edd6b5af11510ef584142ea086f3f6b554670e4ed7559c574e3beaad0d.png" src="_images/d66125edd6b5af11510ef584142ea086f3f6b554670e4ed7559c574e3beaad0d.png" />
+<img alt="_images/98f358eff0f75d1115807834727a3fbba438128c36e5dcc957d3000b9bb7af61.png" src="_images/98f358eff0f75d1115807834727a3fbba438128c36e5dcc957d3000b9bb7af61.png" />
 </div>
 </div>
 </section>
@@ -1185,31 +1179,31 @@ <h3>Predictions<a class="headerlink" href="#predictions" title="Link to this hea
       <th>Sample_158</th>
       <th>Q9UN70;Q9UN70-2</th>
       <td>14.630</td>
-      <td>15.901</td>
+      <td>15.688</td>
     </tr>
     <tr>
       <th>Sample_050</th>
       <th>Q9Y287</th>
       <td>15.755</td>
-      <td>16.853</td>
+      <td>16.321</td>
     </tr>
     <tr>
       <th>Sample_107</th>
       <th>Q8N475;Q8N475-2</th>
       <td>15.029</td>
-      <td>14.730</td>
+      <td>14.681</td>
     </tr>
     <tr>
       <th>Sample_199</th>
       <th>P06307</th>
       <td>19.376</td>
-      <td>19.901</td>
+      <td>19.612</td>
     </tr>
     <tr>
       <th>Sample_067</th>
       <th>Q5VUB5</th>
       <td>15.309</td>
-      <td>15.921</td>
+      <td>15.382</td>
     </tr>
     <tr>
       <th>...</th>
@@ -1221,31 +1215,31 @@ <h3>Predictions<a class="headerlink" href="#predictions" title="Link to this hea
       <th>Sample_111</th>
       <th>F6SYF8;Q9UBP4</th>
       <td>22.822</td>
-      <td>23.032</td>
+      <td>23.062</td>
     </tr>
     <tr>
       <th>Sample_002</th>
       <th>A0A0A0MT36</th>
       <td>18.165</td>
-      <td>16.772</td>
+      <td>15.780</td>
     </tr>
     <tr>
       <th>Sample_049</th>
       <th>Q8WY21;Q8WY21-2;Q8WY21-3;Q8WY21-4</th>
       <td>15.525</td>
-      <td>15.471</td>
+      <td>15.189</td>
     </tr>
     <tr>
       <th>Sample_182</th>
       <th>Q8NFT8</th>
       <td>14.379</td>
-      <td>14.137</td>
+      <td>13.638</td>
     </tr>
     <tr>
       <th>Sample_123</th>
       <th>Q16853;Q16853-2</th>
       <td>14.504</td>
-      <td>14.582</td>
+      <td>14.396</td>
     </tr>
   </tbody>
 </table>
@@ -1318,27 +1312,27 @@ <h3>Predictions<a class="headerlink" href="#predictions" title="Link to this hea
       <th rowspan="5" valign="top">Sample_000</th>
       <th>A0A075B6P5;P01615</th>
       <td>17.016</td>
-      <td>17.506</td>
+      <td>17.538</td>
     </tr>
     <tr>
       <th>A0A087X089;Q16627;Q16627-2</th>
       <td>18.280</td>
-      <td>18.354</td>
+      <td>17.803</td>
     </tr>
     <tr>
       <th>A0A0B4J2B5;S4R460</th>
       <td>21.735</td>
-      <td>22.773</td>
+      <td>22.921</td>
     </tr>
     <tr>
       <th>A0A140T971;O95865;Q5SRR8;Q5SSV3</th>
       <td>14.603</td>
-      <td>15.511</td>
+      <td>15.239</td>
     </tr>
     <tr>
       <th>A0A140TA33;A0A140TA41;A0A140TA52;P22105;P22105-3;P22105-4</th>
       <td>16.143</td>
-      <td>16.724</td>
+      <td>16.048</td>
     </tr>
     <tr>
       <th>...</th>
@@ -1350,27 +1344,27 @@ <h3>Predictions<a class="headerlink" href="#predictions" title="Link to this hea
       <th rowspan="5" valign="top">Sample_209</th>
       <th>Q96ID5</th>
       <td>16.074</td>
-      <td>15.732</td>
+      <td>16.052</td>
     </tr>
     <tr>
       <th>Q9H492;Q9H492-2</th>
       <td>13.173</td>
-      <td>13.282</td>
+      <td>13.225</td>
     </tr>
     <tr>
       <th>Q9HC57</th>
       <td>14.207</td>
-      <td>13.931</td>
+      <td>14.390</td>
     </tr>
     <tr>
       <th>Q9NPH3;Q9NPH3-2;Q9NPH3-5</th>
       <td>14.962</td>
-      <td>15.100</td>
+      <td>15.381</td>
     </tr>
     <tr>
       <th>Q9UGM5;Q9UGM5-2</th>
       <td>16.871</td>
-      <td>16.176</td>
+      <td>16.136</td>
     </tr>
   </tbody>
 </table>
@@ -1662,8 +1656,8 @@ <h3>Validation data<a class="headerlink" href="#validation-data" title="Link to
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Selected as truth to compare to: observed
 </pre></div>
 </div>
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;CF&#39;: {&#39;MSE&#39;: 0.4731172653694631,
-  &#39;MAE&#39;: 0.4683235744722517,
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;CF&#39;: {&#39;MSE&#39;: 0.4848906868950271,
+  &#39;MAE&#39;: 0.4732235899731502,
   &#39;N&#39;: 12600,
   &#39;prop&#39;: 1.0}}
 </pre></div>
@@ -1687,8 +1681,8 @@ <h3>Test Datasplit<a class="headerlink" href="#test-datasplit" title="Link to th
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Selected as truth to compare to: observed
 </pre></div>
 </div>
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;CF&#39;: {&#39;MSE&#39;: 0.48344993352087207,
-  &#39;MAE&#39;: 0.470247366612567,
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;CF&#39;: {&#39;MSE&#39;: 0.5095124560652031,
+  &#39;MAE&#39;: 0.4802188171423251,
   &#39;N&#39;: 12600,
   &#39;prop&#39;: 1.0}}
 </pre></div>
@@ -1746,13 +1740,13 @@ <h3>Test Datasplit<a class="headerlink" href="#test-datasplit" title="Link to th
     <tr>
       <th rowspan="4" valign="top">CF</th>
       <th>MSE</th>
-      <td>0.473</td>
-      <td>0.483</td>
+      <td>0.485</td>
+      <td>0.510</td>
     </tr>
     <tr>
       <th>MAE</th>
-      <td>0.468</td>
-      <td>0.470</td>
+      <td>0.473</td>
+      <td>0.480</td>
     </tr>
     <tr>
       <th>N</th>
@@ -1808,7 +1802,7 @@ <h2>Config<a class="headerlink" href="#config" title="Link to this heading">#</a
  &#39;batch_size&#39;: 1024,
  &#39;cuda&#39;: False,
  &#39;data&#39;: Path(&#39;runs/alzheimer_study/data&#39;),
- &#39;epoch_trained&#39;: 13,
+ &#39;epoch_trained&#39;: 12,
  &#39;epochs_max&#39;: 100,
  &#39;file_format&#39;: &#39;csv&#39;,
  &#39;fn_rawfile_metadata&#39;: &#39;https://raw.githubusercontent.com/RasmussenLab/njab/HEAD/docs/tutorial/data/alzheimer/meta.csv&#39;,