deploy: 8543be3

.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: 44f7f4aa3f917f86db52f95e79f02ca2
+config: 4150f2a854ee5c65b1de2e560fea7fcb
 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+g7c122b1 documentation</title>
+    <title>Transfer data for NAGuideR format &#8212; pimms_workflow 0.1.dev1+g8543be3 documentation</title>
 
 
 
@@ -37,7 +37,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=ab9e9613"></script>
+    <script src="_static/documentation_options.js?v=db877691"></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>
@@ -134,7 +134,7 @@
 
 
 
-    <p class="title logo__title">pimms_workflow 0.1.dev1+g7c122b1 documentation</p>
+    <p class="title logo__title">pimms_workflow 0.1.dev1+g8543be3 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+g7c122b1 documentation</title>
+    <title>Collaborative Filtering &#8212; pimms_workflow 0.1.dev1+g8543be3 documentation</title>
 
 
 
@@ -37,7 +37,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=ab9e9613"></script>
+    <script src="_static/documentation_options.js?v=db877691"></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>
@@ -134,7 +134,7 @@
 
 
 
-    <p class="title logo__title">pimms_workflow 0.1.dev1+g7c122b1 documentation</p>
+    <p class="title logo__title">pimms_workflow 0.1.dev1+g8543be3 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item">
@@ -1014,8 +1014,8 @@ <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 = 0.00437
-No improvement since epoch 13: 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 = 0.00631
+No improvement since epoch 11: early stopping
 pimmslearn.plotting - INFO     Saved Figures to runs/alzheimer_study/figures/collab_training
 </pre></div>
 </div>
@@ -1051,97 +1051,85 @@ <h3>Training<a class="headerlink" href="#training" title="Link to this heading">
   <tbody>
     <tr>
       <td>0</td>
-      <td>8.500570</td>
-      <td>12.473230</td>
+      <td>7.892747</td>
+      <td>11.195817</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>1</td>
-      <td>5.442508</td>
-      <td>7.572977</td>
+      <td>3.086744</td>
+      <td>3.923189</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>2</td>
-      <td>1.881536</td>
-      <td>2.482819</td>
+      <td>0.883860</td>
+      <td>1.122097</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>3</td>
-      <td>0.758629</td>
-      <td>0.980508</td>
+      <td>0.591659</td>
+      <td>0.758595</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>4</td>
-      <td>0.587375</td>
-      <td>0.754108</td>
+      <td>0.549168</td>
+      <td>0.732440</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>5</td>
-      <td>0.552653</td>
-      <td>0.731532</td>
+      <td>0.512251</td>
+      <td>0.680737</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>6</td>
-      <td>0.545145</td>
-      <td>0.714668</td>
+      <td>0.441552</td>
+      <td>0.599838</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>7</td>
-      <td>0.482015</td>
-      <td>0.652523</td>
+      <td>0.382136</td>
+      <td>0.555003</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>8</td>
-      <td>0.419034</td>
-      <td>0.572415</td>
+      <td>0.366594</td>
+      <td>0.522107</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>9</td>
-      <td>0.383625</td>
-      <td>0.538009</td>
+      <td>0.333798</td>
+      <td>0.498097</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>10</td>
-      <td>0.351312</td>
-      <td>0.511087</td>
+      <td>0.294033</td>
+      <td>0.484798</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>11</td>
-      <td>0.319665</td>
-      <td>0.479390</td>
+      <td>0.251572</td>
+      <td>0.465343</td>
       <td>00:01</td>
     </tr>
     <tr>
       <td>12</td>
-      <td>0.288079</td>
-      <td>0.471856</td>
-      <td>00:01</td>
-    </tr>
-    <tr>
-      <td>13</td>
-      <td>0.244357</td>
-      <td>0.452568</td>
-      <td>00:01</td>
-    </tr>
-    <tr>
-      <td>14</td>
-      <td>0.224256</td>
-      <td>0.460775</td>
+      <td>0.230376</td>
+      <td>0.482688</td>
       <td>00:01</td>
     </tr>
   </tbody>
-</table></div><img alt="_images/086602f77d35caeff6b7d714f1f7326990eb0bf44633d9eca0a32d6ae5c26cc2.png" src="_images/086602f77d35caeff6b7d714f1f7326990eb0bf44633d9eca0a32d6ae5c26cc2.png" />
-<img alt="_images/d94876a9ab96cd423fa1d279adabe1f3b7a1fdc58d68b064841a44fe19802c2d.png" src="_images/d94876a9ab96cd423fa1d279adabe1f3b7a1fdc58d68b064841a44fe19802c2d.png" />
+</table></div><img alt="_images/477dabc2e8bf60860fa87fc0afac10c22f96b434bcbb0f23ad262352ca112d20.png" src="_images/477dabc2e8bf60860fa87fc0afac10c22f96b434bcbb0f23ad262352ca112d20.png" />
+<img alt="_images/5af39401c77b6157dbab0d460d3da219ecfb741832aab2dfec73cd72fd280cf0.png" src="_images/5af39401c77b6157dbab0d460d3da219ecfb741832aab2dfec73cd72fd280cf0.png" />
 </div>
 </div>
 </section>
@@ -1216,31 +1204,31 @@ <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>15.490</td>
+      <td>16.290</td>
     </tr>
     <tr>
       <th>Sample_050</th>
       <th>Q9Y287</th>
       <td>15.755</td>
-      <td>16.438</td>
+      <td>16.487</td>
     </tr>
     <tr>
       <th>Sample_107</th>
       <th>Q8N475;Q8N475-2</th>
       <td>15.029</td>
-      <td>14.493</td>
+      <td>14.177</td>
     </tr>
     <tr>
       <th>Sample_199</th>
       <th>P06307</th>
       <td>19.376</td>
-      <td>19.467</td>
+      <td>19.634</td>
     </tr>
     <tr>
       <th>Sample_067</th>
       <th>Q5VUB5</th>
       <td>15.309</td>
-      <td>15.567</td>
+      <td>15.151</td>
     </tr>
     <tr>
       <th>...</th>
@@ -1252,31 +1240,31 @@ <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>22.991</td>
+      <td>23.101</td>
     </tr>
     <tr>
       <th>Sample_002</th>
       <th>A0A0A0MT36</th>
       <td>18.165</td>
-      <td>15.640</td>
+      <td>16.130</td>
     </tr>
     <tr>
       <th>Sample_049</th>
       <th>Q8WY21;Q8WY21-2;Q8WY21-3;Q8WY21-4</th>
       <td>15.525</td>
-      <td>15.645</td>
+      <td>15.241</td>
     </tr>
     <tr>
       <th>Sample_182</th>
       <th>Q8NFT8</th>
       <td>14.379</td>
-      <td>14.102</td>
+      <td>14.105</td>
     </tr>
     <tr>
       <th>Sample_123</th>
       <th>Q16853;Q16853-2</th>
       <td>14.504</td>
-      <td>14.774</td>
+      <td>14.618</td>
     </tr>
   </tbody>
 </table>
@@ -1349,27 +1337,27 @@ <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>17.186</td>
+      <td>17.713</td>
     </tr>
     <tr>
       <th>A0A087X089;Q16627;Q16627-2</th>
       <td>18.280</td>
-      <td>17.528</td>
+      <td>17.847</td>
     </tr>
     <tr>
       <th>A0A0B4J2B5;S4R460</th>
       <td>21.735</td>
-      <td>22.508</td>
+      <td>22.369</td>
     </tr>
     <tr>
       <th>A0A140T971;O95865;Q5SRR8;Q5SSV3</th>
       <td>14.603</td>
-      <td>15.304</td>
+      <td>15.149</td>
     </tr>
     <tr>
       <th>A0A140TA33;A0A140TA41;A0A140TA52;P22105;P22105-3;P22105-4</th>
       <td>16.143</td>
-      <td>16.649</td>
+      <td>16.554</td>
     </tr>
     <tr>
       <th>...</th>
@@ -1381,27 +1369,27 @@ <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>16.029</td>
+      <td>15.962</td>
     </tr>
     <tr>
       <th>Q9H492;Q9H492-2</th>
       <td>13.173</td>
-      <td>13.291</td>
+      <td>13.211</td>
     </tr>
     <tr>
       <th>Q9HC57</th>
       <td>14.207</td>
-      <td>13.456</td>
+      <td>13.364</td>
     </tr>
     <tr>
       <th>Q9NPH3;Q9NPH3-2;Q9NPH3-5</th>
       <td>14.962</td>
-      <td>14.875</td>
+      <td>15.052</td>
     </tr>
     <tr>
       <th>Q9UGM5;Q9UGM5-2</th>
       <td>16.871</td>
-      <td>16.226</td>
+      <td>16.318</td>
     </tr>
   </tbody>
 </table>
@@ -1693,8 +1681,8 @@ <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;: 0.46077456020729163,
-  &#39;MAE&#39;: 0.459358426930181,
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;CF&#39;: {&#39;MSE&#39;: 0.48268840318008593,
+  &#39;MAE&#39;: 0.4696153842871417,
   &#39;N&#39;: 12600,
   &#39;prop&#39;: 1.0}}
 </pre></div>
@@ -1718,8 +1706,8 @@ <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;: 0.4888552605449465,
-  &#39;MAE&#39;: 0.4675777042638178,
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;CF&#39;: {&#39;MSE&#39;: 0.4968121130332079,
+  &#39;MAE&#39;: 0.475317514461773,
   &#39;N&#39;: 12600,
   &#39;prop&#39;: 1.0}}
 </pre></div>
@@ -1777,13 +1765,13 @@ <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>0.461</td>
-      <td>0.489</td>
+      <td>0.483</td>
+      <td>0.497</td>
     </tr>
     <tr>
       <th>MAE</th>
-      <td>0.459</td>
-      <td>0.468</td>
+      <td>0.470</td>
+      <td>0.475</td>
     </tr>
     <tr>
       <th>N</th>
@@ -1839,7 +1827,7 @@ <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;: 15,
+ &#39;epoch_trained&#39;: 13,
  &#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;,