--- a +++ b/readmission_risk_prediction.ipynb @@ -0,0 +1,232 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 8, + "id": "ec2980fa-e433-4924-bf8e-ae890c9352f2", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Fitting 5 folds for each of 90 candidates, totalling 450 fits\n", + "Best parameters: {'classifier__criterion': 'entropy', 'classifier__max_depth': None, 'classifier__min_samples_leaf': 1, 'classifier__min_samples_split': 2}\n", + "Decision Tree Model:\n", + "Accuracy: 0.508\n", + "Classification Report:\n", + " precision recall f1-score support\n", + "\n", + " 0 0.51 0.52 0.51 1000\n", + " 1 0.51 0.50 0.50 1000\n", + "\n", + " accuracy 0.51 2000\n", + " macro avg 0.51 0.51 0.51 2000\n", + "weighted avg 0.51 0.51 0.51 2000\n", + "\n", + "Confusion Matrix:\n", + "[[517 483]\n", + " [501 499]]\n", + "\n", + "Top 10 Most Important Features:\n", + " feature importance\n", + "4 result 0.409878\n", + "6 duration_result_ratio 0.279102\n", + "0 age 0.120918\n", + "5 age_comorbidity_interaction 0.106891\n", + "1 gender 0.042323\n", + "3 duration 0.016378\n", + "9 age_group_2 0.006668\n", + "10 age_group_3 0.005753\n", + "11 age_group_4 0.004192\n", + "8 age_group_1 0.003047\n" + ] + } + ], + "source": [ + "import mysql.connector\n", + "import pandas as pd\n", + "import numpy as np\n", + "from sklearn.model_selection import train_test_split, GridSearchCV\n", + "from sklearn.tree import DecisionTreeClassifier\n", + "from sklearn.preprocessing import StandardScaler\n", + "from sklearn.impute import SimpleImputer\n", + "from sklearn.pipeline import Pipeline\n", + "from sklearn.metrics import accuracy_score, classification_report, confusion_matrix\n", + "from imblearn.over_sampling import SMOTE\n", + "\n", + "# Database connection\n", + "db = mysql.connector.connect(\n", + " host=\"localhost\",\n", + " user=\"root\",\n", + " password=\"HunnyS@1511\",\n", + " database=\"patient_readmission\"\n", + ")\n", + "\n", + "# Create a cursor object to execute SQL queries\n", + "cursor = db.cursor()\n", + "\n", + "# SQL query to retrieve patient features data\n", + "query = \"\"\"\n", + " WITH patient_medications AS (\n", + " SELECT \n", + " patient_id,\n", + " medication_name,\n", + " start_date,\n", + " end_date,\n", + " DATEDIFF(end_date, start_date) AS duration\n", + " FROM \n", + " medications\n", + " ),\n", + " lab_result_averages AS (\n", + " SELECT \n", + " patient_id,\n", + " AVG(result_value) AS result\n", + " FROM \n", + " lab_results\n", + " GROUP BY \n", + " patient_id\n", + " ),\n", + " comorbidity_index AS (\n", + " SELECT \n", + " patient_id,\n", + " COUNT(icd_code) AS comorbidity_index\n", + " FROM \n", + " diagnoses\n", + " GROUP BY \n", + " patient_id\n", + " )\n", + " SELECT \n", + " p.patient_id,\n", + " p.age,\n", + " p.gender,\n", + " ci.comorbidity_index,\n", + " pm.duration,\n", + " lra.result,\n", + " r.readmission_risk\n", + " FROM \n", + " patients p\n", + " JOIN \n", + " comorbidity_index ci ON p.patient_id = ci.patient_id\n", + " JOIN \n", + " patient_medications pm ON p.patient_id = pm.patient_id\n", + " JOIN \n", + " lab_result_averages lra ON p.patient_id = lra.patient_id\n", + " JOIN \n", + " readmission_risk r ON p.patient_id = r.patient_id;\n", + "\"\"\"\n", + "\n", + "# Execute the SQL query\n", + "cursor.execute(query)\n", + "\n", + "# Fetch all the rows from the query result\n", + "data = cursor.fetchall()\n", + "\n", + "# Create pandas dataframe from the retrieved data\n", + "df = pd.DataFrame(data, columns=['patient_id', 'age', 'gender', 'comorbidity_count', 'duration', 'result', 'readmission_risk'])\n", + "\n", + "# Convert gender to numerical value\n", + "df['gender'] = df['gender'].map({'Male': 0, 'Female': 1})\n", + "\n", + "# Feature engineering\n", + "df['age_group'] = pd.cut(df['age'], bins=[0, 18, 35, 50, 65, 100], labels=[0, 1, 2, 3, 4])\n", + "df['comorbidity_group'] = pd.cut(df['comorbidity_count'], bins=[0, 1, 3, 5, np.inf], labels=[0, 1, 2, 3])\n", + "df['duration_group'] = pd.cut(df['duration'], bins=[-np.inf, 7, 14, 30, np.inf], labels=[0, 1, 2, 3])\n", + "\n", + "# Additional feature engineering\n", + "df['age_comorbidity_interaction'] = df['age'] * df['comorbidity_count']\n", + "df['duration_result_ratio'] = df['duration'] / (df['result'] + 1) # Adding 1 to avoid division by zero\n", + "\n", + "# One-hot encode categorical variables\n", + "df = pd.get_dummies(df, columns=['age_group', 'comorbidity_group', 'duration_group'])\n", + "\n", + "# Split data into features and target\n", + "X = df.drop(['patient_id', 'readmission_risk'], axis=1)\n", + "y = df['readmission_risk']\n", + "\n", + "# Split data into training and testing sets\n", + "X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, random_state=42)\n", + "\n", + "# Create a pipeline\n", + "pipeline = Pipeline([\n", + " ('imputer', SimpleImputer(strategy='median')),\n", + " ('scaler', StandardScaler()),\n", + " ('classifier', DecisionTreeClassifier(random_state=42))\n", + "])\n", + "\n", + "# Define the parameter grid for GridSearchCV\n", + "param_grid = {\n", + " 'classifier__max_depth': [5, 10, 15, 20, None],\n", + " 'classifier__min_samples_split': [2, 5, 10],\n", + " 'classifier__min_samples_leaf': [1, 2, 4],\n", + " 'classifier__criterion': ['gini', 'entropy']\n", + "}\n", + "\n", + "# Perform GridSearchCV\n", + "grid_search = GridSearchCV(pipeline, param_grid, cv=5, n_jobs=-1, verbose=2)\n", + "\n", + "# Handle class imbalance with SMOTE\n", + "smote = SMOTE(random_state=42)\n", + "X_train_resampled, y_train_resampled = smote.fit_resample(X_train, y_train)\n", + "\n", + "# Fit the model\n", + "grid_search.fit(X_train_resampled, y_train_resampled)\n", + "\n", + "# Print the best parameters\n", + "print(\"Best parameters:\", grid_search.best_params_)\n", + "\n", + "# Make predictions\n", + "y_pred = grid_search.predict(X_test)\n", + "\n", + "# Evaluate the model\n", + "print('Decision Tree Model:')\n", + "print('Accuracy:', accuracy_score(y_test, y_pred))\n", + "print('Classification Report:')\n", + "print(classification_report(y_test, y_pred))\n", + "print('Confusion Matrix:')\n", + "print(confusion_matrix(y_test, y_pred))\n", + "\n", + "# Feature importance\n", + "feature_importance = grid_search.best_estimator_.named_steps['classifier'].feature_importances_\n", + "feature_names = X.columns\n", + "feature_importance_df = pd.DataFrame({'feature': feature_names, 'importance': feature_importance})\n", + "feature_importance_df = feature_importance_df.sort_values('importance', ascending=False)\n", + "print(\"\\nTop 10 Most Important Features:\")\n", + "print(feature_importance_df.head(10))\n", + "\n", + "# Close the cursor and connection\n", + "cursor.close()\n", + "db.close()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "98c9f03e-5fc1-45cd-9173-925b70df4956", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.9.18" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +}