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\ No newline at end of file diff --git a/notebooks/features.db b/notebooks/features.db new file mode 100644 index 0000000..e69de29 diff --git a/notebooks/ml_xgboost.ipynb b/notebooks/ml_xgboost.ipynb new file mode 100644 index 0000000..530c14f --- /dev/null +++ b/notebooks/ml_xgboost.ipynb @@ -0,0 +1,696 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "import sqlite3\n", + "import os\n", + "from datetime import datetime\n", + "import pandas as pd\n", + "import matplotlib.pyplot as plt\n", + "import xgboost as xgb\n", + "from sklearn.model_selection import GridSearchCV\n", + "from sklearn.metrics import confusion_matrix\n", + "import seaborn as sns" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Import Data from Database" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [], + "source": [ + "# connect to the database\n", + "conn = sqlite3.connect('../features.db')\n", + "c = conn.cursor()\n", + "# get training, validation and test data\n", + "train = pd.read_sql_query(\"SELECT * FROM train\", conn)\n", + "valid = pd.read_sql_query(\"SELECT * FROM validation\", conn)\n", + "test = pd.read_sql_query(\"SELECT * FROM test\", conn)\n", + "# close the connection\n", + "conn.close()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Format Data for Machine Learning" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "train_x shape: (3502, 10)\n", + "test_x shape: (438, 10)\n", + "valid_x shape: (438, 10)\n", + "features: ['age', 'gender', 'artial_rate', 'ventricular_rate', 'qrs_duration', 'qt_length', 'qrs_count', 'q_peak', 'r_axis', 't_axis']\n", + "number of classes: 4\n" + ] + } + ], + "source": [ + "# get the target and features\n", + "train_y = train['y']\n", + "train_y = train_y.map({'GSVT': 0, 'AFIB': 1, 'SR': 2, 'SB': 3})\n", + "train_x = train.drop(columns=['y'])\n", + "\n", + "valid_y = valid['y']\n", + "valid_y = valid_y.map({'GSVT': 0, 'AFIB': 1, 'SR': 2, 'SB': 3})\n", + "valid_x = valid.drop(columns=['y'])\n", + "\n", + "test_y = test['y']\n", + "test_y = test_y.map({'GSVT': 0, 'AFIB': 1, 'SR': 2, 'SB': 3})\n", + "test_x = test.drop(columns=['y'])\n", + "\n", + "# drop id column\n", + "train_x = train_x.drop(columns=['id'])\n", + "valid_x = valid_x.drop(columns=['id'])\n", + "test_x = test_x.drop(columns=['id'])\n", + "\n", + "print('train_x shape:', train_x.shape)\n", + "print('test_x shape:', test_x.shape)\n", + "print('valid_x shape:', valid_x.shape)\n", + "\n", + "# print column names\n", + "print('features:', train_x.columns.to_list())\n", + "\n", + "# use xgboost\n", + "dtrain = xgb.DMatrix(train_x, label=train_y)\n", + "dvalid = xgb.DMatrix(valid_x, label=valid_y)\n", + "dtest = xgb.DMatrix(test_x, label=test_y)\n", + "\n", + "num_classes= len(set(valid_y.to_list()))\n", + "print('number of classes:', num_classes)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Test Grid for Hyperparameter Analysis" + ] + }, + { + "cell_type": "code", + "execution_count": 47, + "metadata": {}, + "outputs": [], + "source": [ + "param_grid = {\n", + " 'max_depth': [3, 4, 5],\n", + " 'min_child_weight': [1, 2, 3],\n", + " 'eta': [0.1, 0.2, 0.3],\n", + " 'learning_rate': [0.1, 0.2, 0.3],\n", + " 'n_estimators': [100, 200, 300]\n", + "}" + ] + }, + { + "cell_type": "code", + "execution_count": 39, + "metadata": {}, + "outputs": [], + "source": [ + "# Create a XGBClassifier object\n", + "model = xgb.XGBClassifier(objective='multi:softmax', num_class=num_classes, eval_metric='merror')\n", + "\n", + "# Create the grid search object\n", + "grid_search = GridSearchCV(model, param_grid, cv=3, scoring='accuracy')\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Training" + ] + }, + { + "cell_type": "code", + "execution_count": 40, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "CPU times: total: 2h 15min 58s\n", + "Wall time: 10min\n" + ] + }, + { + "data": { + "text/html": [ + "
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