Fixed a bug in a deprecated import

EBjerrum · Mar 18, 2024 · 2973f70 · 2973f70
1 parent c6c1003
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diff --git a/notebooks/06_hyperparameter_tuning.ipynb b/notebooks/06_hyperparameter_tuning.ipynb
@@ -16,10 +16,10 @@
    "id": "7df4793c",
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-     "shell.execute_reply": "2023-03-19T08:54:37.013259Z"
+     "iopub.execute_input": "2024-03-18T13:17:06.835155Z",
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@@ -53,10 +53,10 @@
    "id": "45a8ebf1",
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-     "shell.execute_reply": "2023-03-19T08:54:37.022080Z"
+     "iopub.execute_input": "2024-03-18T13:17:07.941632Z",
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+     "shell.execute_reply": "2024-03-18T13:17:07.944438Z"
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@@ -87,10 +87,10 @@
    "id": "08c233a7",
    "metadata": {
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+     "shell.execute_reply": "2024-03-18T13:17:07.985938Z"
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    "outputs": [
@@ -124,17 +124,17 @@
    "id": "5363d05a",
    "metadata": {
     "execution": {
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-     "iopub.status.idle": "2023-03-19T08:54:37.084574Z",
-     "shell.execute_reply": "2023-03-19T08:54:37.084021Z"
+     "iopub.execute_input": "2024-03-18T13:17:07.989052Z",
+     "iopub.status.busy": "2024-03-18T13:17:07.988851Z",
+     "iopub.status.idle": "2024-03-18T13:17:07.993705Z",
+     "shell.execute_reply": "2024-03-18T13:17:07.993138Z"
     },
     "lines_to_next_cell": 2
    },
    "outputs": [],
    "source": [
     "\n",
-    "mol_list_train, mol_list_test, y_train, y_test = train_test_split(data.ROMol, data.pXC50, random_state=0)"
+    "mol_list_train, mol_list_test, y_train, y_test = train_test_split(data.ROMol, data.pXC50, random_state=42)"
    ]
   },
   {
@@ -151,10 +151,10 @@
    "id": "885daf12",
    "metadata": {
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-     "shell.execute_reply": "2023-03-19T08:54:37.454153Z"
+     "iopub.execute_input": "2024-03-18T13:17:07.996298Z",
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+     "shell.execute_reply": "2024-03-18T13:17:08.360550Z"
     }
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    "outputs": [],
@@ -182,10 +182,10 @@
    "id": "8fd14250",
    "metadata": {
     "execution": {
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-     "iopub.status.idle": "2023-03-19T08:54:37.461663Z",
-     "shell.execute_reply": "2023-03-19T08:54:37.461052Z"
+     "iopub.execute_input": "2024-03-18T13:17:08.364585Z",
+     "iopub.status.busy": "2024-03-18T13:17:08.364029Z",
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+     "shell.execute_reply": "2024-03-18T13:17:08.366933Z"
     }
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    "outputs": [],
@@ -212,17 +212,18 @@
    "id": "fa082078",
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2023-03-19T08:54:37.464188Z",
-     "iopub.status.busy": "2023-03-19T08:54:37.463905Z",
-     "iopub.status.idle": "2023-03-19T08:54:37.467187Z",
-     "shell.execute_reply": "2023-03-19T08:54:37.466548Z"
+     "iopub.execute_input": "2024-03-18T13:17:08.369937Z",
+     "iopub.status.busy": "2024-03-18T13:17:08.369731Z",
+     "iopub.status.idle": "2024-03-18T13:17:08.372598Z",
+     "shell.execute_reply": "2024-03-18T13:17:08.372103Z"
     },
     "title": "Now hyperparameter tuning"
    },
    "outputs": [],
    "source": [
     "from sklearn.model_selection import RandomizedSearchCV\n",
-    "from sklearn.utils.fixes import loguniform"
+    "#from sklearn.utils.fixes import loguniform\n",
+    "from scipy.stats import loguniform"
    ]
   },
   {
@@ -239,18 +240,18 @@
    "id": "046e24d3",
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2023-03-19T08:54:37.470133Z",
-     "iopub.status.busy": "2023-03-19T08:54:37.469879Z",
-     "iopub.status.idle": "2023-03-19T08:54:37.476370Z",
-     "shell.execute_reply": "2023-03-19T08:54:37.475763Z"
+     "iopub.execute_input": "2024-03-18T13:17:08.374931Z",
+     "iopub.status.busy": "2024-03-18T13:17:08.374724Z",
+     "iopub.status.idle": "2024-03-18T13:17:08.380663Z",
+     "shell.execute_reply": "2024-03-18T13:17:08.380185Z"
     },
     "title": "Which keys do we have?"
    },
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "dict_keys(['memory', 'steps', 'verbose', 'morgantransformer', 'ridge', 'morgantransformer__nBits', 'morgantransformer__parallel', 'morgantransformer__radius', 'morgantransformer__useBondTypes', 'morgantransformer__useChirality', 'morgantransformer__useCounts', 'morgantransformer__useFeatures', 'ridge__alpha', 'ridge__copy_X', 'ridge__fit_intercept', 'ridge__max_iter', 'ridge__positive', 'ridge__random_state', 'ridge__solver', 'ridge__tol'])"
+       "dict_keys(['memory', 'steps', 'verbose', 'morganfingerprinttransformer', 'ridge', 'morganfingerprinttransformer__nBits', 'morganfingerprinttransformer__parallel', 'morganfingerprinttransformer__radius', 'morganfingerprinttransformer__useBondTypes', 'morganfingerprinttransformer__useChirality', 'morganfingerprinttransformer__useCounts', 'morganfingerprinttransformer__useFeatures', 'ridge__alpha', 'ridge__copy_X', 'ridge__fit_intercept', 'ridge__max_iter', 'ridge__positive', 'ridge__random_state', 'ridge__solver', 'ridge__tol'])"
       ]
      },
      "execution_count": 8,
@@ -277,21 +278,21 @@
    "id": "cf2c45d7",
    "metadata": {
     "execution": {
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-     "shell.execute_reply": "2023-03-19T08:54:37.482688Z"
+     "iopub.execute_input": "2024-03-18T13:17:08.383218Z",
+     "iopub.status.busy": "2024-03-18T13:17:08.382844Z",
+     "iopub.status.idle": "2024-03-18T13:17:08.387097Z",
+     "shell.execute_reply": "2024-03-18T13:17:08.386532Z"
     },
     "lines_to_next_cell": 1
    },
    "outputs": [],
    "source": [
     "\n",
     "param_dist = {'ridge__alpha': loguniform(1e-2, 1e3),\n",
-    "            \"morgantransformer__nBits\": [256,512,1024,2048,4096],\n",
-    "            'morgantransformer__radius':[1,2,3,4],\n",
-    "            'morgantransformer__useCounts': [True,False],\n",
-    "            'morgantransformer__useFeatures':[True,False]}"
+    "            \"morganfingerprinttransformer__nBits\": [256,512,1024,2048,4096],\n",
+    "            'morganfingerprinttransformer__radius':[1,2,3,4],\n",
+    "            'morganfingerprinttransformer__useCounts': [True,False],\n",
+    "            'morganfingerprinttransformer__useFeatures':[True,False]}"
    ]
   },
   {
@@ -308,10 +309,10 @@
    "id": "fbb2cacd",
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2023-03-19T08:54:37.485906Z",
-     "iopub.status.busy": "2023-03-19T08:54:37.485645Z",
-     "iopub.status.idle": "2023-03-19T08:54:37.489973Z",
-     "shell.execute_reply": "2023-03-19T08:54:37.489382Z"
+     "iopub.execute_input": "2024-03-18T13:17:08.389557Z",
+     "iopub.status.busy": "2024-03-18T13:17:08.389341Z",
+     "iopub.status.idle": "2024-03-18T13:17:08.393214Z",
+     "shell.execute_reply": "2024-03-18T13:17:08.392741Z"
     },
     "title": "From https://scikit-learn.org/stable/auto_examples/model_selection/plot_randomized_search.html#sphx-glr-auto-examples-model-selection-plot-randomized-search-py"
    },
@@ -347,18 +348,18 @@
    "id": "bc66efa3",
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2023-03-19T08:54:37.492677Z",
-     "iopub.status.busy": "2023-03-19T08:54:37.492327Z",
-     "iopub.status.idle": "2023-03-19T08:54:44.019837Z",
-     "shell.execute_reply": "2023-03-19T08:54:44.018820Z"
+     "iopub.execute_input": "2024-03-18T13:17:08.395641Z",
+     "iopub.status.busy": "2024-03-18T13:17:08.395386Z",
+     "iopub.status.idle": "2024-03-18T13:17:12.986572Z",
+     "shell.execute_reply": "2024-03-18T13:17:12.986010Z"
     }
    },
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Runtime: 6.52 for 25 iterations)\n"
+      "Runtime: 4.59 for 25 iterations)\n"
      ]
     }
    ],
@@ -380,10 +381,10 @@
    "id": "b2b3d623",
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2023-03-19T08:54:44.026632Z",
-     "iopub.status.busy": "2023-03-19T08:54:44.024799Z",
-     "iopub.status.idle": "2023-03-19T08:54:44.034480Z",
-     "shell.execute_reply": "2023-03-19T08:54:44.033518Z"
+     "iopub.execute_input": "2024-03-18T13:17:12.989282Z",
+     "iopub.status.busy": "2024-03-18T13:17:12.988845Z",
+     "iopub.status.idle": "2024-03-18T13:17:12.992724Z",
+     "shell.execute_reply": "2024-03-18T13:17:12.992202Z"
     },
     "lines_to_next_cell": 0
    },
@@ -393,16 +394,16 @@
      "output_type": "stream",
      "text": [
       "Model with rank: 1\n",
-      "Mean validation score: 0.492 (std: 0.048)\n",
-      "Parameters: {'morgantransformer__nBits': 2048, 'morgantransformer__radius': 4, 'morgantransformer__useCounts': False, 'morgantransformer__useFeatures': False, 'ridge__alpha': 18.49687467370123}\n",
+      "Mean validation score: 0.526 (std: 0.183)\n",
+      "Parameters: {'morganfingerprinttransformer__nBits': 4096, 'morganfingerprinttransformer__radius': 2, 'morganfingerprinttransformer__useCounts': False, 'morganfingerprinttransformer__useFeatures': False, 'ridge__alpha': 0.03506956723396942}\n",
       "\n",
       "Model with rank: 2\n",
-      "Mean validation score: 0.446 (std: 0.188)\n",
-      "Parameters: {'morgantransformer__nBits': 256, 'morgantransformer__radius': 2, 'morgantransformer__useCounts': False, 'morgantransformer__useFeatures': False, 'ridge__alpha': 0.22311472368521185}\n",
+      "Mean validation score: 0.523 (std: 0.127)\n",
+      "Parameters: {'morganfingerprinttransformer__nBits': 4096, 'morganfingerprinttransformer__radius': 4, 'morganfingerprinttransformer__useCounts': False, 'morganfingerprinttransformer__useFeatures': False, 'ridge__alpha': 7.715592595566691}\n",
       "\n",
       "Model with rank: 3\n",
-      "Mean validation score: 0.440 (std: 0.025)\n",
-      "Parameters: {'morgantransformer__nBits': 4096, 'morgantransformer__radius': 3, 'morgantransformer__useCounts': False, 'morgantransformer__useFeatures': True, 'ridge__alpha': 6.023414585108017}\n",
+      "Mean validation score: 0.495 (std: 0.096)\n",
+      "Parameters: {'morganfingerprinttransformer__nBits': 2048, 'morganfingerprinttransformer__radius': 3, 'morganfingerprinttransformer__useCounts': False, 'morganfingerprinttransformer__useFeatures': False, 'ridge__alpha': 28.390132035436164}\n",
       "\n"
      ]
     }
@@ -433,19 +434,19 @@
    "id": "cb369a0e",
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2023-03-19T08:54:44.041562Z",
-     "iopub.status.busy": "2023-03-19T08:54:44.039729Z",
-     "iopub.status.idle": "2023-03-19T08:54:44.258048Z",
-     "shell.execute_reply": "2023-03-19T08:54:44.256978Z"
+     "iopub.execute_input": "2024-03-18T13:17:12.995596Z",
+     "iopub.status.busy": "2024-03-18T13:17:12.995274Z",
+     "iopub.status.idle": "2024-03-18T13:17:13.177121Z",
+     "shell.execute_reply": "2024-03-18T13:17:13.176195Z"
     }
    },
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "No Standardization 0.5222\n",
-      "With Standardization 0.5222\n"
+      "No Standardization 0.6791\n",
+      "With Standardization 0.6791\n"
      ]
     }
    ],
@@ -477,19 +478,25 @@
    "id": "f6426b23",
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2023-03-19T08:54:44.264895Z",
-     "iopub.status.busy": "2023-03-19T08:54:44.264460Z",
-     "iopub.status.idle": "2023-03-19T08:54:44.295917Z",
-     "shell.execute_reply": "2023-03-19T08:54:44.294841Z"
+     "iopub.execute_input": "2024-03-18T13:17:13.180039Z",
+     "iopub.status.busy": "2024-03-18T13:17:13.179823Z",
+     "iopub.status.idle": "2024-03-18T13:17:13.196436Z",
+     "shell.execute_reply": "2024-03-18T13:17:13.195835Z"
     }
    },
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Predictions with no standardization: [6.29056823 6.31806374 6.34706809 6.44119607 6.41499794]\n",
-      "Predictions with standardization:    [6.29056823 6.29056823 6.29056823 6.29056823 6.29056823]\n"
+      "Predictions with no standardization: [5.77626555 5.94364787 5.94364787 6.13649679 6.04966392]\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Predictions with standardization:    [5.77626555 5.77626555 5.77626555 5.77626555 5.77626555]\n"
      ]
     }
    ],
@@ -539,7 +546,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.9"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/06_hyperparameter_tuning.py b/notebooks/06_hyperparameter_tuning.py
@@ -7,7 +7,7 @@
 #       extension: .py
 #       format_name: percent
 #       format_version: '1.3'
-#       jupytext_version: 1.14.5
+#       jupytext_version: 1.16.1
 #   kernelspec:
 #     display_name: Python 3.9.4 ('rdkit')
 #     language: python
@@ -96,7 +96,8 @@
 
 # %% Now hyperparameter tuning
 from sklearn.model_selection import RandomizedSearchCV
-from sklearn.utils.fixes import loguniform
+#from sklearn.utils.fixes import loguniform
+from scipy.stats import loguniform
 
 # %% [markdown]
 # With the pipelines, getting the names of the parameters to tune is a bit more tricky, as they are concatenations of the name of the step and the parameter with double underscores in between. We can get the available parameters from the pipeline with the get_params() method, and select the parameters we want to change from there.