{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"%config InlineBackend.figure_formats = ['svg']"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"import random\n",
"import numpy as np\n",
"import pandas as pd\n",
"from joblib import dump, load\n",
"np.random.seed(42)\n",
"random.seed(42)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"data_dir = './data/'\n",
"with np.load('data/Xy.npz') as f:\n",
" X = f['X']\n",
" y = f['y']\n",
" y34 = f['y34']"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"# Perform temporal split of data into train/test sets\n",
"pop = pd.read_csv(data_dir + 'population/d10_with_vitals.csv').set_index('BMT_ID')\n",
"\n",
"split_date = 201701001\n",
"split_idx = -85\n",
"\n",
"assert (pop[:split_idx].index < split_date).all()\n",
"assert (pop[split_idx:].index >= split_date).all()"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"from sklearn import preprocessing, model_selection, metrics, utils\n",
"from sklearn.linear_model import LogisticRegression\n",
"from tqdm import tqdm\n",
"from joblib import Parallel, delayed\n",
"from sklearn.base import clone"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"# Specify hyperparameters and cv parameters\n",
"base_estimator = LogisticRegression(penalty='l2', class_weight='balanced', solver='liblinear')\n",
"param_grid = {\n",
" 'C': [10. ** n for n in range(-6, 7)],\n",
" 'penalty': ['l2'],\n",
"}"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Alternative label definition\n",
"{0,1,2} -> negative, {3,4} -> positive"
]
},
{
"cell_type": "code",
"execution_count": 472,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(0.31790123456790126, 0.13580246913580246)"
]
},
"execution_count": 472,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"y.mean(), y34.mean()"
]
},
{
"cell_type": "code",
"execution_count": 376,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/data4/tangsp/venv/lib/python3.7/site-packages/sklearn/model_selection/_search.py:814: DeprecationWarning: The default of the `iid` parameter will change from True to False in version 0.22 and will be removed in 0.24. This will change numeric results when test-set sizes are unequal.\n",
" DeprecationWarning)\n"
]
}
],
"source": [
"Xtr, Xte = X[:split_idx], X[split_idx:]\n",
"ytr, yte = y34[:split_idx], y34[split_idx:]\n",
"\n",
"cv_splits, cv_repeat = 5, 20\n",
"cv = model_selection.RepeatedStratifiedKFold(cv_splits, cv_repeat, random_state=0)\n",
"clf = model_selection.GridSearchCV(\n",
" clone(base_estimator), param_grid, \n",
" cv=cv, scoring='roc_auc', n_jobs=5,\n",
")\n",
"clf.fit(Xtr, ytr)\n",
"test_score = metrics.roc_auc_score(yte, clf.decision_function(Xte))"
]
},
{
"cell_type": "code",
"execution_count": 377,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
" \r"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Test AUC: 0.596 (0.423, 0.761)\n"
]
}
],
"source": [
"y_true = yte\n",
"y_score = clf.decision_function(Xte)\n",
"\n",
"def boostrap_func(i, y_true, y_score):\n",
" yte_true_b, yte_pred_b = utils.resample(y_true, y_score, replace=True, random_state=i)\n",
" return metrics.roc_curve(yte_true_b, yte_pred_b), metrics.roc_auc_score(yte_true_b, yte_pred_b)\n",
"\n",
"roc_curves, auc_scores = zip(*Parallel(n_jobs=4)(delayed(boostrap_func)(i, y_true, y_score) for i in tqdm(range(1000), leave=False)))\n",
"print('Test AUC: {:.3f} ({:.3f}, {:.3f})'.format(np.median(auc_scores), np.percentile(auc_scores, 2.5), np.percentile(auc_scores, 97.5)))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Random Forest model"
]
},
{
"cell_type": "code",
"execution_count": 378,
"metadata": {},
"outputs": [],
"source": [
"from sklearn.model_selection import RandomizedSearchCV\n",
"from sklearn.ensemble import RandomForestClassifier\n",
"import scipy"
]
},
{
"cell_type": "code",
"execution_count": 379,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"RandomizedSearchCV(cv=<sklearn.model_selection._split.RepeatedStratifiedKFold object at 0x7f9b8ffacc50>,\n",
" error_score='raise-deprecating',\n",
" estimator=RandomForestClassifier(bootstrap=True,\n",
" class_weight=None,\n",
" criterion='gini',\n",
" max_depth=None,\n",
" max_features='auto',\n",
" max_leaf_nodes=None,\n",
" min_impurity_decrease=0.0,\n",
" min_impurity_split=None,\n",
" min_samples_leaf=1,\n",
" min_sample...\n",
" 'min_samples_leaf': <scipy.stats._distn_infrastructure.rv_frozen object at 0x7f9b8ffad050>,\n",
" 'min_samples_split': <scipy.stats._distn_infrastructure.rv_frozen object at 0x7f9b8ffadc10>,\n",
" 'n_estimators': <scipy.stats._distn_infrastructure.rv_frozen object at 0x7f9b8ffad490>},\n",
" pre_dispatch='2*n_jobs', random_state=None, refit=True,\n",
" return_train_score=False, scoring='roc_auc', verbose=0)"
]
},
"execution_count": 379,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Xtr, Xte = X[:split_idx], X[split_idx:]\n",
"ytr, yte = y[:split_idx], y[split_idx:]\n",
"\n",
"cv_splits, cv_repeat = 5, 20\n",
"cv = model_selection.RepeatedStratifiedKFold(cv_splits, cv_repeat, random_state=0)\n",
"clf = RandomizedSearchCV(\n",
" RandomForestClassifier(), \n",
" {\n",
" \"criterion\": [\"gini\", \"entropy\"],\n",
" \"max_depth\": [4, 8, 16, 32, None],\n",
" \"max_features\": scipy.stats.randint(1, 100),\n",
" \"min_samples_split\": scipy.stats.randint(2, 11),\n",
" \"min_samples_leaf\": scipy.stats.randint(1, 11),\n",
" \"n_estimators\": scipy.stats.randint(50,500),\n",
" \"bootstrap\": [True],\n",
" },\n",
" n_iter=10,\n",
" cv=cv,\n",
" scoring='roc_auc',\n",
" n_jobs=5,\n",
" )\n",
"\n",
"clf.fit(Xtr, ytr)"
]
},
{
"cell_type": "code",
"execution_count": 380,
"metadata": {},
"outputs": [],
"source": [
"test_score = metrics.roc_auc_score(yte, clf.predict_proba(Xte)[:,1])"
]
},
{
"cell_type": "code",
"execution_count": 381,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
" \r"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Test AUC: 0.651 (0.525, 0.768)\n"
]
}
],
"source": [
"y_true = yte\n",
"y_score = clf.predict_proba(Xte)[:,1]\n",
"\n",
"def boostrap_func(i, y_true, y_score):\n",
" yte_true_b, yte_pred_b = utils.resample(y_true, y_score, replace=True, random_state=i)\n",
" return metrics.roc_curve(yte_true_b, yte_pred_b), metrics.roc_auc_score(yte_true_b, yte_pred_b)\n",
"\n",
"_, auc_scores_rf = zip(*Parallel(n_jobs=4)(delayed(boostrap_func)(i, y_true, y_score) for i in tqdm(range(1000), leave=False)))\n",
"print('Test AUC: {:.3f} ({:.3f}, {:.3f})'.format(np.median(auc_scores_rf), np.percentile(auc_scores_rf, 2.5), np.percentile(auc_scores_rf, 97.5)))"
]
},
{
"cell_type": "code",
"execution_count": 382,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
" \r"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Test AUC: 0.658 (0.536, 0.784)\n"
]
}
],
"source": [
"clf_main = load('data/model_combined.joblib')\n",
"y_score = clf_main.predict_proba(Xte)[:,1]\n",
"_, auc_scores_main = zip(*Parallel(n_jobs=4)(delayed(boostrap_func)(i, y_true, y_score) for i in tqdm(range(1000), leave=False)))\n",
"print('Test AUC: {:.3f} ({:.3f}, {:.3f})'.format(\n",
" np.median(auc_scores_main), np.percentile(auc_scores_main, 2.5), np.percentile(auc_scores_main, 97.5)))"
]
},
{
"cell_type": "code",
"execution_count": 383,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0.782"
]
},
"execution_count": 383,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# H0: proposed == baseline\n",
"# H1: proposed != baseline\n",
"# resampling test, two-sided p-value\n",
"2 * min(\n",
" (np.array(auc_scores_main) < np.array(auc_scores_rf)).mean(),\n",
" (np.array(auc_scores_main) > np.array(auc_scores_rf)).mean()\n",
")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Kaplan Meier plot"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"import matplotlib.pyplot as plt\n",
"from sklearn import utils"
]
},
{
"cell_type": "code",
"execution_count": 482,
"metadata": {},
"outputs": [],
"source": [
"Xtr, Xte = X[:split_idx], X[split_idx:]\n",
"ytr, yte = y[:split_idx], y[split_idx:]"
]
},
{
"cell_type": "code",
"execution_count": 483,
"metadata": {},
"outputs": [],
"source": [
"pop = pd.read_csv(data_dir + 'population/d10_with_vitals.csv').set_index('BMT_ID')\n",
"labels = pd.read_csv(data_dir + 'prep/label.csv').set_index('BMT_ID')\n",
"IDs = pop.index[split_idx:]\n",
"onset = labels.loc[IDs, 'GVHD_onset_day'].replace(np.nan, np.inf)"
]
},
{
"cell_type": "code",
"execution_count": 484,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"IntervalIndex([(0.234, 0.539], (0.539, 0.74]],\n",
" closed='right',\n",
" dtype='interval[float64]')\n"
]
}
],
"source": [
"clf = load('data/model_combined.joblib')\n",
"threshold = np.percentile(clf.predict_proba(Xtr)[:,1], [0, 70, 100])\n",
"y_prob = clf.predict_proba(Xte)[:,1]\n",
"y_group = pd.cut(y_prob, threshold)\n",
"print(y_group.categories)\n",
"y_group = y_group.codes"
]
},
{
"cell_type": "code",
"execution_count": 485,
"metadata": {},
"outputs": [],
"source": [
"# Standard errors calculated via the Greenwood's formula\n",
"# http://sphweb.bumc.bu.edu/otlt/MPH-Modules/BS/BS704_Survival/BS704_Survival4.html\n",
"def calculate_survival_curve_se(onset_m, times):\n",
" surv_probs = [(onset_m > 0).mean()]\n",
" stderrs = [0]\n",
" quotients = []\n",
" for day in sorted(times):\n",
" if np.isfinite(day):\n",
" Nt, Dt = (onset_m >= day).sum(), (onset_m == day).sum()\n",
" St = (onset_m > day).mean()\n",
" quotients.append(Dt / (Nt * (Nt - Dt)))\n",
" surv_probs.append(St)\n",
" stderrs.append(St * np.sqrt(np.sum(quotients)))\n",
" return np.array(surv_probs), np.array(stderrs)"
]
},
{
"cell_type": "code",
"execution_count": 486,
"metadata": {},
"outputs": [
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"text/plain": [
"<Figure size 432x288 with 1 Axes>"
]
},
"metadata": {
"needs_background": "light"
},
"output_type": "display_data"
}
],
"source": [
"times = onset.unique()\n",
"times = times[times <= 105]\n",
"times = sorted(times)\n",
"\n",
"for group in [0,1]:\n",
" m = (y_group == group)\n",
" o_m = onset[m]\n",
" surv_probs, stderrs = calculate_survival_curve_se(o_m, times)\n",
" CI = [\n",
" np.clip(surv_probs - 1.96 * stderrs, 0, 1), \n",
" np.clip(surv_probs + 1.96 * stderrs, 0, 1),\n",
" ]\n",
" plt.plot([0] + times, surv_probs)\n",
" plt.fill_between([0] + times, CI[0], CI[1], alpha=0.12)\n",
"\n",
"plt.xlim(0,100)\n",
"plt.legend(labels=['low risk', 'high risk'])\n",
"plt.xlabel('Days post-transplant')\n",
"plt.ylabel('Grade II-IV aGVHD-free probability')\n",
"plt.savefig('fig/kaplan_meier.svg')\n",
"plt.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Clustering results\n",
"\n",
"`'Temp-slope', 'Temp-abs(A1)', 'Temp-angle(A1)', 'SBP-abs(A1)'`"
]
},
{
"cell_type": "code",
"execution_count": 119,
"metadata": {},
"outputs": [],
"source": [
"from sklearn import preprocessing\n",
"from sklearn.cluster import KMeans, SpectralClustering\n",
"from sklearn.decomposition import PCA"
]
},
{
"cell_type": "code",
"execution_count": 86,
"metadata": {},
"outputs": [],
"source": [
"extracted_features = pd.read_csv('data/ts_features.csv', index_col='id')"
]
},
{
"cell_type": "code",
"execution_count": 100,
"metadata": {},
"outputs": [
{
"data": {
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" <th></th>\n",
" <th>DiaBP_dt=1_max__fft_coefficient__coeff_1__attr_\"abs\"</th>\n",
" <th>DiaBP_dt=1_max__fft_coefficient__coeff_1__attr_\"angle\"</th>\n",
" <th>DiaBP_dt=1_max__linear_trend__attr_\"slope\"</th>\n",
" <th>DiaBP_dt=1_max__mean</th>\n",
" <th>DiaBP_dt=1_max__sample_entropy</th>\n",
" <th>DiaBP_dt=1_mean__fft_coefficient__coeff_1__attr_\"abs\"</th>\n",
" <th>DiaBP_dt=1_mean__fft_coefficient__coeff_1__attr_\"angle\"</th>\n",
" <th>DiaBP_dt=1_mean__linear_trend__attr_\"slope\"</th>\n",
" <th>DiaBP_dt=1_mean__mean</th>\n",
" <th>DiaBP_dt=1_mean__sample_entropy</th>\n",
" <th>...</th>\n",
" <th>Temp_dt=1_min__fft_coefficient__coeff_1__attr_\"abs\"</th>\n",
" <th>Temp_dt=1_min__fft_coefficient__coeff_1__attr_\"angle\"</th>\n",
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" <td>201406001</td>\n",
" <td>13.711126</td>\n",
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" <td>80.8</td>\n",
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" <td>-0.939394</td>\n",
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" <td>2.014903</td>\n",
" <td>21.591328</td>\n",
" <td>-62.275730</td>\n",
" <td>-0.655020</td>\n",
" <td>67.781822</td>\n",
" <td>1.504077</td>\n",
" <td>...</td>\n",
" <td>1.444653</td>\n",
" <td>145.906924</td>\n",
" <td>0.045118</td>\n",
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" <td>2.181057</td>\n",
" <td>78.501122</td>\n",
" <td>0.113805</td>\n",
" <td>36.288889</td>\n",
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" DiaBP_dt=1_max__fft_coefficient__coeff_1__attr_\"abs\" \\\n",
"id \n",
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"201406002 3.452240 \n",
"201406003 14.437545 \n",
"201406004 39.672864 \n",
"201406005 46.236218 \n",
"\n",
" DiaBP_dt=1_max__fft_coefficient__coeff_1__attr_\"angle\" \\\n",
"id \n",
"201406001 -39.840250 \n",
"201406002 42.925589 \n",
"201406003 161.710499 \n",
"201406004 -56.532935 \n",
"201406005 -83.519009 \n",
"\n",
" DiaBP_dt=1_max__linear_trend__attr_\"slope\" DiaBP_dt=1_max__mean \\\n",
"id \n",
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"201406002 -0.066667 77.5 \n",
"201406003 -0.151515 86.9 \n",
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"201406005 -2.454545 77.7 \n",
"\n",
" DiaBP_dt=1_max__sample_entropy \\\n",
"id \n",
"201406001 1.504077 \n",
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"201406003 2.708050 \n",
"201406004 2.014903 \n",
"201406005 2.014903 \n",
"\n",
" DiaBP_dt=1_mean__fft_coefficient__coeff_1__attr_\"abs\" \\\n",
"id \n",
"201406001 12.511950 \n",
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"201406004 21.591328 \n",
"201406005 45.041080 \n",
"\n",
" DiaBP_dt=1_mean__fft_coefficient__coeff_1__attr_\"angle\" \\\n",
"id \n",
"201406001 -60.302991 \n",
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"201406004 -62.275730 \n",
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"\n",
" DiaBP_dt=1_mean__linear_trend__attr_\"slope\" DiaBP_dt=1_mean__mean \\\n",
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"201406003 0.150459 76.578379 \n",
"201406004 -0.655020 67.781822 \n",
"201406005 -1.821655 69.535720 \n",
"\n",
" DiaBP_dt=1_mean__sample_entropy ... \\\n",
"id ... \n",
"201406001 2.420368 ... \n",
"201406002 2.014903 ... \n",
"201406003 1.860752 ... \n",
"201406004 1.504077 ... \n",
"201406005 2.708050 ... \n",
"\n",
" Temp_dt=1_min__fft_coefficient__coeff_1__attr_\"abs\" \\\n",
"id \n",
"201406001 0.567878 \n",
"201406002 0.164019 \n",
"201406003 0.501112 \n",
"201406004 1.444653 \n",
"201406005 2.181057 \n",
"\n",
" Temp_dt=1_min__fft_coefficient__coeff_1__attr_\"angle\" \\\n",
"id \n",
"201406001 73.555730 \n",
"201406002 -59.464582 \n",
"201406003 -73.426276 \n",
"201406004 145.906924 \n",
"201406005 78.501122 \n",
"\n",
" Temp_dt=1_min__linear_trend__attr_\"slope\" Temp_dt=1_min__mean \\\n",
"id \n",
"201406001 0.021481 36.518889 \n",
"201406002 0.009091 36.316667 \n",
"201406003 -0.042088 36.172222 \n",
"201406004 0.045118 35.911111 \n",
"201406005 0.113805 36.288889 \n",
"\n",
" Temp_dt=1_min__sample_entropy \\\n",
"id \n",
"201406001 1.860752 \n",
"201406002 2.420368 \n",
"201406003 2.420368 \n",
"201406004 2.197225 \n",
"201406005 2.420368 \n",
"\n",
" Temp_dt=1_std__fft_coefficient__coeff_1__attr_\"abs\" \\\n",
"id \n",
"201406001 0.263259 \n",
"201406002 0.265981 \n",
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"\n",
" Temp_dt=1_std__fft_coefficient__coeff_1__attr_\"angle\" \\\n",
"id \n",
"201406001 69.530757 \n",
"201406002 100.908363 \n",
"201406003 -149.344978 \n",
"201406004 -3.505990 \n",
"201406005 118.454862 \n",
"\n",
" Temp_dt=1_std__linear_trend__attr_\"slope\" Temp_dt=1_std__mean \\\n",
"id \n",
"201406001 0.018092 0.220617 \n",
"201406002 0.004882 0.268865 \n",
"201406003 -0.000899 0.284152 \n",
"201406004 -0.006831 0.225669 \n",
"201406005 0.030110 0.271239 \n",
"\n",
" Temp_dt=1_std__sample_entropy \n",
"id \n",
"201406001 2.420368 \n",
"201406002 2.708050 \n",
"201406003 2.197225 \n",
"201406004 1.727221 \n",
"201406005 2.014903 \n",
"\n",
"[5 rows x 120 columns]"
]
},
"execution_count": 100,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"extracted_features.head()"
]
},
{
"cell_type": "code",
"execution_count": 89,
"metadata": {},
"outputs": [],
"source": [
"cols = [\n",
" c for c in extracted_features.columns\n",
" if c.startswith('Temp') or c.startswith('SysBP')\n",
"]\n",
"cols = [\n",
" c for c in cols\n",
" if \\\n",
" ('Temp' in c and 'slope' in c) or \\\n",
" ('Temp' in c and 'fft_coefficient__coeff_1__attr_\"abs\"' in c) or \\\n",
" ('Temp' in c and 'fft_coefficient__coeff_1__attr_\"angle\"' in c) or \\\n",
" ('SysBP' in c and 'fft_coefficient__coeff_1__attr_\"abs\"' in c)\n",
"]"
]
},
{
"cell_type": "code",
"execution_count": 96,
"metadata": {},
"outputs": [],
"source": [
"XX = extracted_features[cols].values\n",
"scaler = preprocessing.StandardScaler()\n",
"XX = scaler.fit_transform(XX)"
]
},
{
"cell_type": "code",
"execution_count": 97,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(324, 16)"
]
},
"execution_count": 97,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"XX.shape"
]
},
{
"cell_type": "code",
"execution_count": 104,
"metadata": {},
"outputs": [],
"source": [
"pca = PCA(2, random_state=0).fit(XX)"
]
},
{
"cell_type": "code",
"execution_count": 176,
"metadata": {},
"outputs": [],
"source": [
"clusterings = [np.nan, np.nan]\n",
"scores = [np.nan, np.nan]\n",
"for k in range(2,11):\n",
" cluster = KMeans(k, random_state=0, n_init=20, n_jobs=-1).fit(XX)\n",
" clusterings.append(cluster)\n",
" scores.append(cluster.inertia_)\n",
"# purities, sizes = [], []\n",
"# for c in range(k):\n",
"# m = (cluster.labels_ == c)\n",
"# yc = y[m].mean()\n",
"# purities.append(max(yc, 1-yc))\n",
"# sizes.append(sum(m) / len(y))\n",
"# purity = np.array(purities) @ np.array(sizes)\n",
"# scores.append(purity)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"plt.plot(scores)"
]
},
{
"cell_type": "code",
"execution_count": 220,
"metadata": {},
"outputs": [],
"source": [
"k = 3\n",
"cluster = clusterings[k]\n",
"pred = cluster.fit_predict(XX)"
]
},
{
"cell_type": "code",
"execution_count": 221,
"metadata": {},
"outputs": [],
"source": [
"purities, majority = [], []\n",
"for c in range(k):\n",
" m = (cluster.labels_ == c)\n",
" yc = y[m].mean()\n",
" purities.append(max(yc, 1-yc))"
]
},
{
"cell_type": "code",
"execution_count": 363,
"metadata": {},
"outputs": [
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"text/plain": [
"<Figure size 432x288 with 1 Axes>"
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},
"metadata": {
"needs_background": "light"
},
"output_type": "display_data"
}
],
"source": [
"# plt.scatter(*pca.transform(XX).T, c=y, s=5, cmap='bwr')\n",
"X_pca = pca.transform(XX)\n",
"for i in range(k):\n",
" plt.scatter(*X_pca[pred == i].T, c=[plt.get_cmap(\"tab10\")(i)], s=5, \n",
" label='Cluster {}, negative cases: {:.1%}'.format(i+1, purities[i]))\n",
"\n",
"# plt.scatter(*X_pca.T, c=[plt.get_cmap(\"tab10\")(ci) for ci in pred], s=5)\n",
"\n",
"# Mark negative cases with lighter color\n",
"plt.scatter(*X_pca.T, c=[{0: '#ffffff88', 1: '#00000000'}[yi] for yi in y], s=5)\n",
"\n",
"plt.xlabel('First principle component')\n",
"plt.ylabel('Second principle component')\n",
"plt.legend(fontsize=8)\n",
"plt.axis('square')\n",
"plt.savefig('fig/cluster.svg', bbox_inches='tight')\n",
"plt.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Visualize time series"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [],
"source": [
"Xtr, Xte = X[:split_idx], X[split_idx:]\n",
"ytr, yte = y[:split_idx], y[split_idx:]"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
"import pickle\n",
"ts_vitals_by_bmt = pickle.load(open(data_dir + 'features/ts_vitals_by_bmt_2014_2017_MiChart.p', 'rb'))\n",
"ts_vitals_by_bmt = {ID: ts_vitals_by_bmt[ID] for ID in list(pop.index)}\n",
"split_idx = len(ts_vitals_by_bmt)-85\n",
"\n",
"clf = load('data/model_combined.joblib')\n",
"y_prob = clf.predict_proba(Xte)[:,1]"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
"imax, imin = y_prob.argmax(), y_prob.argmin()"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [],
"source": [
"ID_max = pop.index[split_idx+imax]\n",
"ts_imax = ts_vitals_by_bmt[ID_max]\n",
"ID_min = pop.index[split_idx+imin]\n",
"ts_imin = ts_vitals_by_bmt[ID_min]"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(201708006, 201711007)"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ID_max, ID_min"
]
},
{
"cell_type": "code",
"execution_count": 41,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(0.21920581756972551, 0.7284919042899778)"
]
},
"execution_count": 41,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"y_prob[imin], y_prob[imax]"
]
},
{
"cell_type": "code",
"execution_count": 46,
"metadata": {},
"outputs": [
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"text/plain": [
"<Figure size 576x576 with 4 Axes>"
]
},
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],
"source": [
"fig, axes = plt.subplots(2, 2, figsize=(8,8), sharex=True, gridspec_kw={'hspace': 0.1, 'wspace': 0.1})\n",
"\n",
"plt.sca(axes[0,0])\n",
"ts_plot = ts_imax[(ts_imax['t'] >= -10) & (ts_imax['t'] < 15)][['t', 'Temp']].dropna()\n",
"ts_plot = ts_plot.set_index('t')\n",
"ts_plot['Temp_MA'] = np.nan\n",
"wsize = 0.1\n",
"for t in ts_plot.index:\n",
" ts_plot.loc[t, 'Temp_MA'] = np.mean(ts_plot.loc[\n",
" (t-wsize < ts_plot.index) & (ts_plot.index < t+wsize), 'Temp'\n",
" ])\n",
"ts_plot = ts_plot.reset_index()\n",
"x = ts_plot['t']\n",
"y = ts_plot['Temp_MA']\n",
"x_new = np.linspace(x.min(), x.max(), 1000)\n",
"f = interp1d(x, y, kind='quadratic')\n",
"y_smooth = f(x_new)\n",
"plt.plot(x_new, y_smooth, '--', lw=0.75, label=' positive example\\npredicted risk: {:.3f}'.format(y_prob[imax]))\n",
"# plt.plot(ts_plot['t'], ts_plot['Temp_MA'], '-', lw=1, label='positive example')\n",
"plt.scatter(ts_plot['t'], ts_plot['Temp_MA'], s=5)\n",
"\n",
"plt.xlim(-10, 15)\n",
"plt.ylim(36, 39)\n",
"# plt.xlabel('Days relative to transplant')\n",
"plt.ylabel('Temperature (Celsius)')\n",
"plt.legend()\n",
"\n",
"plt.sca(axes[0,1])\n",
"ts_plot = ts_imin[(ts_imin['t'] >= -10) & (ts_imin['t'] < 15)][['t', 'Temp']].dropna()\n",
"ts_plot = ts_plot.set_index('t')\n",
"ts_plot['Temp_MA'] = np.nan\n",
"wsize = 0.1\n",
"for t in ts_plot.index:\n",
" ts_plot.loc[t, 'Temp_MA'] = np.mean(ts_plot.loc[\n",
" (t-wsize < ts_plot.index) & (ts_plot.index < t+wsize), 'Temp'\n",
" ])\n",
"ts_plot = ts_plot.reset_index()\n",
"x = ts_plot['t']\n",
"y = ts_plot['Temp_MA']\n",
"x_new = np.linspace(x.min(), x.max(), 1000)\n",
"f = interp1d(x, y, kind='quadratic')\n",
"y_smooth = f(x_new)\n",
"plt.plot(x_new, y_smooth, '--', lw=0.75, label=' negative example\\npredicted risk: {:.3f}'.format(y_prob[imin]), c='tab:orange')\n",
"# plt.plot(ts_plot['t'], ts_plot['Temp_MA'], '-', lw=1, label='negative example')\n",
"plt.scatter(ts_plot['t'], ts_plot['Temp_MA'], s=5, c='tab:orange')\n",
"\n",
"plt.xlim(-10, 15)\n",
"plt.ylim(36, 39)\n",
"# plt.xlabel('Days relative to transplant')\n",
"# plt.ylabel('Temperature (Celsius)')\n",
"plt.legend()\n",
"\n",
"plt.sca(axes[1,0])\n",
"ts_plot = ts_imax[(ts_imax['t'] >= -10) & (ts_imax['t'] < 15)][['t', 'SysBP']].dropna()\n",
"ts_plot = ts_plot.set_index('t')\n",
"ts_plot['SysBP_MA'] = np.nan\n",
"wsize = 0.1\n",
"for t in ts_plot.index:\n",
" ts_plot.loc[t, 'SysBP_MA'] = np.mean(ts_plot.loc[\n",
" (t-wsize < ts_plot.index) & (ts_plot.index < t+wsize), 'SysBP'\n",
" ])\n",
"ts_plot = ts_plot.reset_index()\n",
"ts_plot = ts_plot.sort_values(by=['t'])\n",
"ts_plot = ts_plot.drop_duplicates(subset=['t'])\n",
"x = ts_plot['t']\n",
"y = ts_plot['SysBP_MA']\n",
"x_new = np.linspace(x.min(), x.max(), 1000)\n",
"f = interp1d(x, y, kind='quadratic')\n",
"y_smooth = f(x_new)\n",
"plt.plot(x_new, y_smooth, '--', lw=0.75, label='positive example')\n",
"plt.scatter(ts_plot['t'], ts_plot['SysBP_MA'], s=5)\n",
"\n",
"plt.xlim(-10, 15)\n",
"# plt.ylim(85, 101)\n",
"plt.xlabel('Days relative to transplant')\n",
"plt.ylabel('SysBP (mmHg)')\n",
"# plt.legend()\n",
"\n",
"plt.sca(axes[1,1])\n",
"ts_plot = ts_imin[(ts_imin['t'] >= -10) & (ts_imin['t'] < 15)][['t', 'SysBP']].dropna()\n",
"ts_plot = ts_plot.set_index('t')\n",
"ts_plot['SysBP_MA'] = np.nan\n",
"wsize = 0.1\n",
"for t in ts_plot.index:\n",
" ts_plot.loc[t, 'SysBP_MA'] = np.mean(ts_plot.loc[\n",
" (t-wsize < ts_plot.index) & (ts_plot.index < t+wsize), 'SysBP'\n",
" ])\n",
"ts_plot = ts_plot.reset_index()\n",
"ts_plot = ts_plot.sort_values(by=['t'])\n",
"ts_plot = ts_plot.drop_duplicates(subset=['t'])\n",
"x = ts_plot['t']\n",
"y = ts_plot['SysBP_MA']\n",
"x_new = np.linspace(x.min(), x.max(), 1000)\n",
"f = interp1d(x, y, kind='quadratic')\n",
"y_smooth = f(x_new)\n",
"plt.plot(x_new, y_smooth, '--', lw=0.75, label='negative example', c='tab:orange')\n",
"plt.scatter(ts_plot['t'], ts_plot['SysBP_MA'], s=5, c='tab:orange')\n",
"\n",
"plt.xlim(-10, 15)\n",
"# plt.ylim(85, 101)\n",
"plt.xlabel('Days relative to transplant')\n",
"# plt.ylabel('SysBP (mmHg)')\n",
"# plt.legend()\n",
"\n",
"for ax in axes.flat:\n",
" ax.label_outer()\n",
"\n",
"plt.savefig('fig/timeseries_Temp_SBP.svg')\n",
"plt.show()"
]
},
{
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