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b/readmission_risk_prediction.ipynb |
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{ |
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"cells": [ |
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{ |
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"cell_type": "code", |
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"execution_count": 8, |
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"id": "ec2980fa-e433-4924-bf8e-ae890c9352f2", |
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"metadata": {}, |
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"outputs": [ |
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{ |
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"name": "stdout", |
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"output_type": "stream", |
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"text": [ |
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"Fitting 5 folds for each of 90 candidates, totalling 450 fits\n", |
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"Best parameters: {'classifier__criterion': 'entropy', 'classifier__max_depth': None, 'classifier__min_samples_leaf': 1, 'classifier__min_samples_split': 2}\n", |
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"Decision Tree Model:\n", |
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"Accuracy: 0.508\n", |
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"Classification Report:\n", |
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" precision recall f1-score support\n", |
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"\n", |
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" 0 0.51 0.52 0.51 1000\n", |
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" 1 0.51 0.50 0.50 1000\n", |
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"\n", |
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" accuracy 0.51 2000\n", |
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" macro avg 0.51 0.51 0.51 2000\n", |
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"weighted avg 0.51 0.51 0.51 2000\n", |
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"\n", |
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"Confusion Matrix:\n", |
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"[[517 483]\n", |
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" [501 499]]\n", |
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"\n", |
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"Top 10 Most Important Features:\n", |
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" feature importance\n", |
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"4 result 0.409878\n", |
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"6 duration_result_ratio 0.279102\n", |
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"0 age 0.120918\n", |
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"5 age_comorbidity_interaction 0.106891\n", |
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"1 gender 0.042323\n", |
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"3 duration 0.016378\n", |
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"9 age_group_2 0.006668\n", |
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"10 age_group_3 0.005753\n", |
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"11 age_group_4 0.004192\n", |
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"8 age_group_1 0.003047\n" |
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] |
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} |
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], |
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"source": [ |
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"import mysql.connector\n", |
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"import pandas as pd\n", |
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"import numpy as np\n", |
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"from sklearn.model_selection import train_test_split, GridSearchCV\n", |
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"from sklearn.tree import DecisionTreeClassifier\n", |
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"from sklearn.preprocessing import StandardScaler\n", |
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"from sklearn.impute import SimpleImputer\n", |
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"from sklearn.pipeline import Pipeline\n", |
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"from sklearn.metrics import accuracy_score, classification_report, confusion_matrix\n", |
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"from imblearn.over_sampling import SMOTE\n", |
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"\n", |
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"# Database connection\n", |
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"db = mysql.connector.connect(\n", |
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" host=\"localhost\",\n", |
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" user=\"root\",\n", |
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" password=\"HunnyS@1511\",\n", |
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" database=\"patient_readmission\"\n", |
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")\n", |
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"\n", |
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"# Create a cursor object to execute SQL queries\n", |
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"cursor = db.cursor()\n", |
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"\n", |
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"# SQL query to retrieve patient features data\n", |
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"query = \"\"\"\n", |
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" WITH patient_medications AS (\n", |
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" SELECT \n", |
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" patient_id,\n", |
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" medication_name,\n", |
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" start_date,\n", |
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" end_date,\n", |
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" DATEDIFF(end_date, start_date) AS duration\n", |
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" FROM \n", |
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" medications\n", |
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" ),\n", |
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" lab_result_averages AS (\n", |
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" SELECT \n", |
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" patient_id,\n", |
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" AVG(result_value) AS result\n", |
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" FROM \n", |
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" lab_results\n", |
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" GROUP BY \n", |
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" patient_id\n", |
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" ),\n", |
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" comorbidity_index AS (\n", |
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" SELECT \n", |
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" patient_id,\n", |
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" COUNT(icd_code) AS comorbidity_index\n", |
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" FROM \n", |
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" diagnoses\n", |
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" GROUP BY \n", |
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" patient_id\n", |
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" )\n", |
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" SELECT \n", |
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" p.patient_id,\n", |
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" p.age,\n", |
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" p.gender,\n", |
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" ci.comorbidity_index,\n", |
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" pm.duration,\n", |
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" lra.result,\n", |
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" r.readmission_risk\n", |
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" FROM \n", |
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" patients p\n", |
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" JOIN \n", |
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" comorbidity_index ci ON p.patient_id = ci.patient_id\n", |
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" JOIN \n", |
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" patient_medications pm ON p.patient_id = pm.patient_id\n", |
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" JOIN \n", |
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" lab_result_averages lra ON p.patient_id = lra.patient_id\n", |
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" JOIN \n", |
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" readmission_risk r ON p.patient_id = r.patient_id;\n", |
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"\"\"\"\n", |
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"\n", |
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"# Execute the SQL query\n", |
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"cursor.execute(query)\n", |
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"\n", |
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"# Fetch all the rows from the query result\n", |
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"data = cursor.fetchall()\n", |
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"\n", |
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"# Create pandas dataframe from the retrieved data\n", |
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"df = pd.DataFrame(data, columns=['patient_id', 'age', 'gender', 'comorbidity_count', 'duration', 'result', 'readmission_risk'])\n", |
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"\n", |
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"# Convert gender to numerical value\n", |
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"df['gender'] = df['gender'].map({'Male': 0, 'Female': 1})\n", |
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"\n", |
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"# Feature engineering\n", |
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"df['age_group'] = pd.cut(df['age'], bins=[0, 18, 35, 50, 65, 100], labels=[0, 1, 2, 3, 4])\n", |
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"df['comorbidity_group'] = pd.cut(df['comorbidity_count'], bins=[0, 1, 3, 5, np.inf], labels=[0, 1, 2, 3])\n", |
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"df['duration_group'] = pd.cut(df['duration'], bins=[-np.inf, 7, 14, 30, np.inf], labels=[0, 1, 2, 3])\n", |
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"\n", |
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"# Additional feature engineering\n", |
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"df['age_comorbidity_interaction'] = df['age'] * df['comorbidity_count']\n", |
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"df['duration_result_ratio'] = df['duration'] / (df['result'] + 1) # Adding 1 to avoid division by zero\n", |
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"\n", |
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"# One-hot encode categorical variables\n", |
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"df = pd.get_dummies(df, columns=['age_group', 'comorbidity_group', 'duration_group'])\n", |
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"\n", |
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"# Split data into features and target\n", |
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"X = df.drop(['patient_id', 'readmission_risk'], axis=1)\n", |
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"y = df['readmission_risk']\n", |
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"\n", |
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"# Split data into training and testing sets\n", |
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"X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, random_state=42)\n", |
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"\n", |
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"# Create a pipeline\n", |
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"pipeline = Pipeline([\n", |
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" ('imputer', SimpleImputer(strategy='median')),\n", |
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" ('scaler', StandardScaler()),\n", |
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" ('classifier', DecisionTreeClassifier(random_state=42))\n", |
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"])\n", |
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"\n", |
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"# Define the parameter grid for GridSearchCV\n", |
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"param_grid = {\n", |
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" 'classifier__max_depth': [5, 10, 15, 20, None],\n", |
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" 'classifier__min_samples_split': [2, 5, 10],\n", |
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" 'classifier__min_samples_leaf': [1, 2, 4],\n", |
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" 'classifier__criterion': ['gini', 'entropy']\n", |
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"}\n", |
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"\n", |
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"# Perform GridSearchCV\n", |
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"grid_search = GridSearchCV(pipeline, param_grid, cv=5, n_jobs=-1, verbose=2)\n", |
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"\n", |
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"# Handle class imbalance with SMOTE\n", |
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"smote = SMOTE(random_state=42)\n", |
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"X_train_resampled, y_train_resampled = smote.fit_resample(X_train, y_train)\n", |
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"\n", |
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"# Fit the model\n", |
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"grid_search.fit(X_train_resampled, y_train_resampled)\n", |
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"\n", |
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"# Print the best parameters\n", |
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"print(\"Best parameters:\", grid_search.best_params_)\n", |
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"\n", |
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"# Make predictions\n", |
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"y_pred = grid_search.predict(X_test)\n", |
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"\n", |
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"# Evaluate the model\n", |
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"print('Decision Tree Model:')\n", |
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"print('Accuracy:', accuracy_score(y_test, y_pred))\n", |
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"print('Classification Report:')\n", |
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"print(classification_report(y_test, y_pred))\n", |
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"print('Confusion Matrix:')\n", |
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"print(confusion_matrix(y_test, y_pred))\n", |
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"\n", |
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"# Feature importance\n", |
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"feature_importance = grid_search.best_estimator_.named_steps['classifier'].feature_importances_\n", |
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"feature_names = X.columns\n", |
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"feature_importance_df = pd.DataFrame({'feature': feature_names, 'importance': feature_importance})\n", |
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"feature_importance_df = feature_importance_df.sort_values('importance', ascending=False)\n", |
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"print(\"\\nTop 10 Most Important Features:\")\n", |
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"print(feature_importance_df.head(10))\n", |
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"\n", |
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"# Close the cursor and connection\n", |
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"cursor.close()\n", |
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"db.close()" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": null, |
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"id": "98c9f03e-5fc1-45cd-9173-925b70df4956", |
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"metadata": {}, |
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"outputs": [], |
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"source": [] |
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} |
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], |
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"metadata": { |
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"kernelspec": { |
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"display_name": "Python 3 (ipykernel)", |
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"language": "python", |
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"name": "python3" |
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}, |
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"language_info": { |
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"codemirror_mode": { |
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"name": "ipython", |
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"version": 3 |
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}, |
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"file_extension": ".py", |
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"mimetype": "text/x-python", |
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"name": "python", |
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"nbconvert_exporter": "python", |
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"pygments_lexer": "ipython3", |
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"version": "3.9.18" |
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} |
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"nbformat": 4, |
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"nbformat_minor": 5 |
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} |