Note about modifying the SHAP lib

explainability/shap_plots.ipynb

@@ -17,7 +17,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -38,9 +38,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "FileNotFoundError",
+     "evalue": "[Errno 2] No such file or directory: '../EDA/output/feature_names/all_features.npy'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mFileNotFoundError\u001b[0m                         Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[3], line 2\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[38;5;66;03m# Retrieve attribute names in order\u001b[39;00m\n\u001b[0;32m----> 2\u001b[0m attribute_names \u001b[38;5;241m=\u001b[39m attribute_names \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(\u001b[43mnp\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mload\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43m../EDA/output/feature_names/all_features.npy\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mallow_pickle\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m)\n\u001b[1;32m      4\u001b[0m \u001b[38;5;66;03m# Load test data\u001b[39;00m\n\u001b[1;32m      5\u001b[0m X_test_pre \u001b[38;5;241m=\u001b[39m np\u001b[38;5;241m.\u001b[39mload(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m../gen_train_data/output/pre/X_test_pre.npy\u001b[39m\u001b[38;5;124m'\u001b[39m, allow_pickle\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n",
+      "File \u001b[0;32m~/covid_analysis/.venv/lib/python3.9/site-packages/numpy/lib/npyio.py:427\u001b[0m, in \u001b[0;36mload\u001b[0;34m(file, mmap_mode, allow_pickle, fix_imports, encoding, max_header_size)\u001b[0m\n\u001b[1;32m    425\u001b[0m     own_fid \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n\u001b[1;32m    426\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 427\u001b[0m     fid \u001b[38;5;241m=\u001b[39m stack\u001b[38;5;241m.\u001b[39menter_context(\u001b[38;5;28;43mopen\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mos_fspath\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfile\u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mrb\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m)\n\u001b[1;32m    428\u001b[0m     own_fid \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m\n\u001b[1;32m    430\u001b[0m \u001b[38;5;66;03m# Code to distinguish from NumPy binary files and pickles.\u001b[39;00m\n",
+      "\u001b[0;31mFileNotFoundError\u001b[0m: [Errno 2] No such file or directory: '../EDA/output/feature_names/all_features.npy'"
+     ]
+    }
+   ],
    "source": [
     "# Retrieve attribute names in order\n",
     "attribute_names = attribute_names = list(np.load('../EDA/output/feature_names/all_features.npy', allow_pickle=True))\n",
@@ -133,9 +146,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "NameError",
+     "evalue": "name 'plt' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[1], line 2\u001b[0m\n\u001b[1;32m      1\u001b[0m method_name \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mORIG_CW\u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[0;32m----> 2\u001b[0m \u001b[43mplt\u001b[49m\u001b[38;5;241m.\u001b[39mfigure(figsize\u001b[38;5;241m=\u001b[39m(\u001b[38;5;241m35\u001b[39m, \u001b[38;5;241m75\u001b[39m))\n\u001b[1;32m      3\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m i, group \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28menumerate\u001b[39m([\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mpre\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mpost\u001b[39m\u001b[38;5;124m'\u001b[39m]):\n\u001b[1;32m      4\u001b[0m             X_test \u001b[38;5;241m=\u001b[39m data_dic[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mX_test_\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;241m+\u001b[39m group]\n",
+      "\u001b[0;31mNameError\u001b[0m: name 'plt' is not defined"
+     ]
+    }
+   ],
    "source": [
     "method_name = 'ORIG_CW'\n",
     "plt.figure(figsize=(35, 75))\n",
@@ -182,8 +207,13 @@
     "**IMPORTANT NOTE**\n",
     "For the code to work as intended, the SHAP source code had to be modified:\n",
     "* **File**: shap/plots/_beeswarm.py\n",
-    "* **Line**: 591\n",
-    "* **Modification**: "
+    "* **Modification**: .venv/lib/python3.9/site-packages/shap/plots/_beeswarm.py \\\n",
+    "\n",
+    "sort_inds = np.argsort(-np.abs(shap_values.sum(1)).sum(0)) \\\n",
+    "**replaced by** \\\n",
+    "sort_inds = np.arange(39)\n",
+    "\n",
+    "The idea is to display the features in the original order instead of sorting them according to their absolute SHAP impact, as the library originally does\n"
    ]
   },
   {
@@ -476,7 +506,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.2"
+   "version": "3.9.5"
   }
  },
  "nbformat": 4,