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CU-8694vxcyx MedCAT 1.12 support #22

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Jun 25, 2024
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CU-8694vxcyx MedCAT 1.12 support #22

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eb5f785
CU-8693v4mx1: Update ICD10 and OPCS4 mappings in SNOMED CDB preproces…
mart-r Feb 16, 2024
7b7ff33
CU-8694vxcyx: Remove deprecated method usage and reference
mart-r Jun 19, 2024
b9b4ac5
CU-8694vxcyx: Bump medcat requirement to 1.12
mart-r Jun 20, 2024
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50 changes: 25 additions & 25 deletions notebooks/introductory/Part_4_2_Supervised_Training_and_Meta_annotations.html
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Expand Up @@ -13799,7 +13799,7 @@ <h2 id="Fine-tuning-the-NER+L&#160;model">Fine-tuning the NER+L&#160;model<a cla
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<p>To fine-tune the existing models we use the <code>train_supervised()</code> method from MedCAT. The method has the following options:</p>
<p>To fine-tune the existing models we use the <code>train_supervised_from_json()</code> method from MedCAT. The method has the following options:</p>
<hr>
<p><code>data_path</code> - Path to the JSON file exported from MedCATtrainer</p>
<p><code>reset_cui_count</code> - Each cui has an internal counter that is used for weight decay, this will reset it.</p>
Expand All @@ -13823,11 +13823,11 @@ <h2 id="Fine-tuning-the-NER+L&#160;model">Fine-tuning the NER+L&#160;model<a cla
<div class="prompt input_prompt">In&nbsp;[11]:</div>
<div class="inner_cell">
<div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">cat</span><span class="o">.</span><span class="n">train_supervised</span><span class="p">(</span><span class="n">data_path</span><span class="o">=</span><span class="n">DATA_DIR</span> <span class="o">+</span> <span class="s2">&quot;MedCAT_Export.json&quot;</span><span class="p">,</span>
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<div class=" highlight hl-ipython3"><pre><span></span><span class="n">cat</span><span class="o">.</span><span class="n">train_supervised_from_json</span><span class="p">(</span><span class="n">data_path</span><span class="o">=</span><span class="n">DATA_DIR</span> <span class="o">+</span> <span class="s2">&quot;MedCAT_Export.json&quot;</span><span class="p">,</span>
<span class="n">nepochs</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">reset_cui_count</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
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<span class="n">use_filters</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
</pre></div>

</div>
Expand Down Expand Up @@ -13859,10 +13859,10 @@ <h2 id="Fine-tuning-the-NER+L&#160;model">Fine-tuning the NER+L&#160;model<a cla



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Expand All @@ -13881,10 +13881,10 @@ <h2 id="Fine-tuning-the-NER+L&#160;model">Fine-tuning the NER+L&#160;model<a cla



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Expand Down Expand Up @@ -13963,10 +13963,10 @@ <h2 id="Fine-tuning-the-NER+L&#160;model">Fine-tuning the NER+L&#160;model<a cla



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Expand All @@ -13985,10 +13985,10 @@ <h2 id="Fine-tuning-the-NER+L&#160;model">Fine-tuning the NER+L&#160;model<a cla



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Expand Down Expand Up @@ -17926,7 +17926,7 @@ <h3 id="Train-MetaCAT">Train MetaCAT<a class="anchor-link" href="#Train-MetaCAT"
<div class="prompt input_prompt">In&nbsp;[19]:</div>
<div class="inner_cell">
<div class="input_area">
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">mc</span><span class="o">.</span><span class="n">train</span><span class="p">(</span><span class="n">json_path</span><span class="o">=</span> <span class="n">DATA_DIR</span><span class="o">+</span><span class="s2">&quot;MedCAT_Export.json&quot;</span><span class="p">,</span> <span class="n">save_dir_path</span><span class="o">=</span><span class="s1">&#39;status&#39;</span><span class="p">)</span>
<div class=" highlight hl-ipython3"><pre><span></span><span class="n">mc</span><span class="o">.</span><span class="n">train_from_json</span><span class="p">(</span><span class="n">json_path</span><span class="o">=</span> <span class="n">DATA_DIR</span><span class="o">+</span><span class="s2">&quot;MedCAT_Export.json&quot;</span><span class="p">,</span> <span class="n">save_dir_path</span><span class="o">=</span><span class="s1">&#39;status&#39;</span><span class="p">)</span>
<span class="c1"># Saving the model this way will only save the model epoch with the best performance</span>
</pre></div>

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14 changes: 7 additions & 7 deletions notebooks/introductory/Part_4_2_Supervised_Training_and_Meta_annotations.ipynb
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Expand Up @@ -664,7 +664,7 @@
"id": "OTR2bcSZDP5V"
},
"source": [
"To fine-tune the existing models we use the `train_supervised()` method from MedCAT. The method has the following options:\n",
"To fine-tune the existing models we use the `train_supervised_from_json()` method from MedCAT. The method has the following options:\n",
"\n",
"\n",
"---\n",
Expand Down Expand Up @@ -4353,11 +4353,11 @@
}
],
"source": [
"cat.train_supervised(data_path=DATA_DIR + \"MedCAT_Export.json\", \n",
" nepochs=1,\n",
" reset_cui_count=False,\n",
" print_stats=True, \n",
" use_filters=True) "
"cat.train_supervised_from_json(data_path=DATA_DIR + \"MedCAT_Export.json\", \n",
" nepochs=1,\n",
" reset_cui_count=False,\n",
" print_stats=True, \n",
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{
Expand Down Expand Up @@ -6001,7 +6001,7 @@
}
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"mc.train(json_path= DATA_DIR+\"MedCAT_Export.json\", save_dir_path='status')\n",
"mc.train_from_json(json_path= DATA_DIR+\"MedCAT_Export.json\", save_dir_path='status')\n",
"# Saving the model this way will only save the model epoch with the best performance"
]
},
Expand Down
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