def fit(self, X, y, **fit_params):
X_ = X.copy()
X_[self.duration_column]=y[self.duration_column]
if self.event_col is not None:
X_[self.event_col] = y[self.event_col]
params = self.get_params()
est = CoxPHFitter(**params)
est.fit(X_, duration_col=self.duration_column, event_col=self.event_col, initial_beta=self.initial_beta, include_likelihood=self.include_likelihood, strata=self.strata, **fit_params)
self.estimator = est
return self
def cox_regression(clean_df):
cf = CoxPHFitter()
cf.fit(clean_df, 'time', event_col='event')
summary_df = cf.summary
#decimals = pd.Series([2, 2, 2], index=['exp(coef)', 'lower 0.95', 'upper 0.95'])
#summary_df = summary_df.round(decimals)
ori_dic = summary_df.to_dict()
res_dic= {}
for stat_of_interest in stats_of_interest:
if stat_of_interest != 'p':
res_dic[stat_of_interest] = round_dic(ori_dic[stat_of_interest])
else:
res_dic[stat_of_interest] = round_dic_eng(ori_dic[stat_of_interest])
return res_dic
def estCoxPHTE(df, treatment_col='treated', duration_col='dx', event_col='disease', covars=[]):
"""Estimates treatment efficacy using proportional hazards (Cox model).
Parameters
----------
df : pandas.DataFrame
treatment_col : string
Column in df indicating treatment.
duration_col : string
Column in df indicating survival times.
event_col : string
Column in df indicating events (censored data are 0)
covars : list
List of other columns to include in Cox model as covariates.
Returns
-------
est : float
Estimate of vaccine efficacy
ci : vector, length 2
95% confidence interval, [LL, UL]
pvalue : float
P-value for H0: VE=0"""
coxphf = CoxPHFitter()
coxphf.fit(df[[treatment_col, duration_col, event_col]+covars], duration_col=duration_col, event_col=event_col)
te = 1 - np.exp(coxphf.hazards_.loc['coef', treatment_col])
ci = 1 - np.exp(coxphf.confidence_intervals_[treatment_col].loc[['upper-bound', 'lower-bound']])
pvalue = coxphf._compute_p_values()[0]
ind1 = df[treatment_col] == 0
ind2 = df[treatment_col] == 1
results = logrank_test(df[duration_col].loc[ind1], df[duration_col].loc[ind2], event_observed_A=df[event_col].loc[ind1], event_observed_B=df[event_col].loc[ind2])
index = ['TE', 'UB', 'LB', 'pvalue', 'logrank_pvalue', 'model']
return pd.Series([te, ci['upper-bound'], ci['lower-bound'], pvalue, results.p_value, coxphf], index=index)
def test_coxph_plot_partial_effects_on_outcome_with_multiple_variables(
self, block):
df = load_rossi()
cp = CoxPHFitter()
cp.fit(df, "week", "arrest")
cp.plot_partial_effects_on_outcome(["age", "prio"],
[[10, 0], [50, 10], [80, 90]])
self.plt.title(
"test_coxph_plot_partial_effects_on_outcome_with_multiple_variables"
)
self.plt.show(block=block)
def _train_cph(x, t, e, folds, params):
if params is None:
l2 = 1e-3
else:
l2 = params['l2']
fold_model = {}
for f in set(folds):
df = convert_to_data_frame(x[folds != f], t[folds != f], e[folds != f])
cph = CoxPHFitter(penalizer=l2).fit(df,
duration_col='T',
event_col='E')
fold_model[f] = copy.deepcopy(cph)
return fold_model
def do_baseline(foldnum, train, valid, exp_code, model_str):
cph = CoxPHFitter()
df = pd.DataFrame(train.x)
print(df.shape)
df['duration'] = train.y
df['event'] = [1 if v == 0 else 0 for v in train.c]
df = df.fillna(df.mean())
cph.fit(df, 'duration', event_col="event")
cph.print_summary()
valid_df = pd.DataFrame(valid.x)
valid_df = valid_df.fillna(valid_df.mean())
print(cph.predict_log_partial_hazard(valid_df))
def test_coxph_plot_covariate_groups_with_multiple_variables_and_strata(
self, block):
df = load_rossi()
df["strata"] = np.random.choice(["A", "B"], size=df.shape[0])
cp = CoxPHFitter()
cp.fit(df, "week", "arrest", strata="strata")
cp.plot_covariate_groups(["age", "prio"],
[[10, 0], [50, 10], [80, 90]])
self.plt.title(
"test_coxph_plot_covariate_groups_with_multiple_variables_and_strata"
)
self.plt.show(block=block)
def test_cross_validator_returns_fitters_k_results():
cf = CoxPHFitter()
fitters = [cf, cf]
results = utils.k_fold_cross_validation(fitters,
load_regression_dataset(),
duration_col="T",
event_col="E",
k=3)
assert len(results) == 2
assert len(results[0]) == len(results[1]) == 3
results = utils.k_fold_cross_validation(fitters,
load_regression_dataset(),
duration_col="T",
event_col="E",
k=5)
assert len(results) == 2
assert len(results[0]) == len(results[1]) == 5
def CoxAnalysis(pd_data, pd_surval, tp):
cph = CoxPHFitter(penalizer=0.1)
if tp == 'univariate':
pd_out = ''
for i in range(pd_data.shape[1]):
df = pd_surval.T.append(pd_data.iloc[:, i].T).T
cph.fit(df, 'OS', event_col='status')
if type(pd_out) == str:
pd_out = cph.summary
else:
pd_out = pd_out.append(cph.summary)
elif tp == 'multivariable':
df = pd_data.T.append(pd_surval.T).T
df = df.dropna(axis=0, how='any')
cph.fit(df, 'OS', event_col='status', step_size=0.1)
pd_out = cph.summary
pd_out.to_csv('CoxRegress.txt', sep='\t', header=True, index=True)
plt.style.use('my-paper')
fig, axe = plt.subplots(figsize=(25, 8))
cph.plot(ax=axe)
axe.set_ylim(-0.2, 3.2)
axe.set_xlim(-2.5, 2.1)
plt.savefig('CoxRegress.pdf')
def COXPH_backward_elimination(COX_dataset,penalizer=0):
cph = CoxPHFitter(penalizer=penalizer)
cph.fit(COX_dataset , duration_col='Days', event_col='Vitality')
for i in range(COX_dataset.shape[1]-2):
current_ps = cph.summary['p']
highest_factor = current_ps.idxmax()
highest_p = current_ps.max()
if highest_p<0.05:
break
COX_dataset = COX_dataset.drop(highest_factor,axis=1)
cph.fit(COX_dataset, duration_col='Days', event_col='Vitality')
return cph
def cox(d_male, d_female):
df_male = pd.DataFrame({
"time":d_male,
"event":1,
"sex": 0
})
df_female = pd.DataFrame({
"time":d_female,
"event":1,
"sex": 1
})
df = pd.concat([df_male, df_female])
print(len(d_male), len(d_female))
cph = CoxPHFitter()
cph.fit(df, duration_col="time", event_col="event")
cph.print_summary()
def _compute_likelihood_ratio_test(self):
"""
This function computes the likelihood ratio test for the Cox model. We
compare the existing model (with all the covariates) to the trivial model
of no covariates.
Conveniently, we can actually use CoxPHFitter class to do most of the work.
"""
trivial_dataset = self.start_stop_and_events.groupby(level=0).last()[["event", "stop"]]
weights = self.weights.groupby(level=0).last()
trivial_dataset = trivial_dataset.join(weights)
ll_null = CoxPHFitter._trivial_log_likelihood(
trivial_dataset["stop"].values, trivial_dataset["event"].values, trivial_dataset["__weights"].values
)
ll_alt = self._log_likelihood
test_stat = 2 * (ll_alt - ll_null)
degrees_freedom = self.hazards_.shape[1]
_, p_value = chisq_test(test_stat, degrees_freedom=degrees_freedom, alpha=0.0)
return test_stat, degrees_freedom, np.log(p_value)
def survival_analyze(dataframe,
lifetime_col,
dead_col,
strata_cols,
covariate_col=None):
# Based on notebook here. https://github.com/CamDavidsonPilon/lifelines/tree/master/examples
import pandas as pd
from matplotlib import pyplot as plt
from lifelines import CoxPHFitter
cph = CoxPHFitter().fit(dataframe,
lifetime_col,
dead_col,
strata=strata_cols)
cph.plot(ax=ax[1])
if covariate_col:
cph.plot_covariate_groups(covariate_col, values=[0, 1])
pass
def Cox_Model(train, test):
'''
train: train_data
test: test_data
vars_list: variables list
'''
cph = CoxPHFitter(penalizer=15)
cph.fit(train,
duration_col='生存时间(天)',
event_col='是否死亡',
show_progress=True,
step_size=1)
Cox_train_Cindex = concordance_index(train['生存时间(天)'],
-cph.predict_partial_hazard(train),
train['是否死亡'])
Cox_test_Cindex = concordance_index(test['生存时间(天)'],
-cph.predict_partial_hazard(test),
test['是否死亡'])
return Cox_train_Cindex, Cox_test_Cindex, cph
def fitcoxmodel(classification, T, E, pid, verbose=True):
# Convert the inputs to PD dataframe
data = dict()
data['T'] = T
data['E'] = E
data['Cov'] = classification
data = pd.DataFrame(data=data, index=pid)
# Create the COX fitter
cph = CoxPHFitter()
cph.fit(data, duration_col='T', event_col='E')
if verbose:
cph.print_summary()
# Retreive the coefficient
s = cph.summary
coef = s['coef']['Cov']
CI = [s['lower 0.95']['Cov'], s['upper 0.95']['Cov']]
p = s['p']['Cov']
return coef, CI, p
def main():
# get command line arguments
cmd_args = commandLineParser()
# import data (mother/rain)
rainfall_df = pd.read_csv(cmd_args.rainfall_data)
mother_df = pd.read_csv(cmd_args.DHS_data)
# get relevant data from rain data
merged = pd.merge(mother_df, rainfall_df, on=['DHSID', 'Year'], how='left')
merged.set_index('IDHSPID', inplace=True)
# drop unneeded columns
drop_columns = ['DHSID', 'Year', r'%-ile', 'Total Rainfall (mm)']
for column in merged.columns:
if column in drop_columns:
merged.drop(column, axis=1, inplace=True)
# change Bools into ones or zeros
for column in [r'<5%-ile', r'<10%-ile', r'<15%-ile']:
merged[column] = (merged[column] == True).astype(int)
# regressions
cph = CoxPHFitter()
cph.fit(merged, 'Event Time', event_col='Event Occured')
# display results
cph.print_summary()
def coxph_smoke():
rossi = load_rossi()
cph = CoxPHFitter()
cph.fit(rossi, duration_col='week', event_col='arrest')
cph.print_summary()
rossiH2O = h2o.H2OFrame(rossi)
cphH2O = H2OCoxProportionalHazardsEstimator(stop_column="week")
cphH2O.train(x=["age", "fin", "race", "wexp", "mar", "paro", "prio"], y="arrest", training_frame=rossiH2O)
assert cphH2O.model_id != ""
assert cphH2O.formula() == "Surv(week, arrest) ~ fin + age + race + wexp + mar + paro + prio", \
"Expected formula to be 'Surv(week, arrest) ~ fin + age + race + wexp + mar + paro + prio' but it was " + cphH2O.formula()
predH2O = cphH2O.predict(test_data=rossiH2O)
assert len(predH2O) == len(rossi)
metricsH2O = cphH2O.model_performance(rossiH2O)
py_concordance = concordance_for_lifelines(cph)
assert abs(py_concordance - metricsH2O.concordance()) < 0.001
def cox_regression_experiment():
dynamic_features = np.load('pick_5_visit_features_merge_1.npy')[
0:2100, :, :-2]
dynamic_features.astype(np.int32)
labels = np.load('pick_5_visit_labels_merge_1.npy')[:, :, -4].reshape(
-1, dynamic_features.shape[1], 1)
data = np.concatenate((dynamic_features, labels), axis=2).reshape(-1, 94)
data_set = pd.DataFrame(data)
col_list = list(data_set.columns.values)
new_col = [str(x) for x in col_list]
data_set.columns = new_col
np.savetxt('allPatient_now.csv', data_set, delimiter=',')
print(list(data_set.columns.values))
cph = CoxPHFitter(penalizer=100)
cph.fit(data_set, duration_col='0', event_col='93', show_progress=True)
cph.print_summary()
# cph.plot(columns=['15','20','21','25'])
# plt.savefig('cox model' + '.png', format='png')
scores = k_fold_cross_validation(cph, data_set, '0', event_col='93', k=5)
print(scores)
print(np.mean(scores))
print(np.std(scores))
def cox_Proportional_hazard_model():
##################################################################
print('---------------------------------------')
print('Standard Cox proportional hazards model')
print('---------------------------------------')
'''
Standard Cox proportional hazards model
'''
cph = CoxPHFitter()
cph.fit(data_train,
duration_col='duration_d',
event_col='CVD',
show_progress=True)
# cph.print_summary()
# Cox model discrimination train set
prediction = cph.predict_partial_hazard(data_train)
print("\ntrain data c-index = " + str(
concordance_index(data_train.duration_d, -prediction, data_train.CVD)))
# Cox model discrimination test set
prediction = cph.predict_partial_hazard(data_test)
print("\ntest data c-index = " + str(
concordance_index(data_test.duration_d, -prediction, data_test.CVD)))
def create_data_df(self):
row_names_index = [(names, index) for v_conf in self.v_stack.configs
for (names, index) in v_conf.list_index.items()]
col_names = self.header + ["hr", "lcl", "ucl", "p_value"]
output_df = pd.DataFrame(columns=col_names,
data=0,
index=range(len(row_names_index)))
# loop over vconf
# create sub df with cols as [1:] of rows in vconf + time value + other value
# apply methods
# get results
# use results to populate outputs
i = -1
for v_conf in self.v_stack.configs:
col_names = set([x for x in v_conf.args])
name_df_dict = {}
for col_name in col_names:
one_hot = pd.get_dummies(self.df[col_name], drop_first=True)
non_dropped = [x for x in one_hot.columns]
dropped = [
x for x in self.df[col_name].unique()
if x not in non_dropped and not pd.isnull(x)
]
assert len(dropped) == 1
dropped = dropped[0]
one_hot["_observed"] = self.df["_observed"]
one_hot["_time_to_observation"] = self.df[
"_time_to_observation"]
cph = CoxPHFitter()
cph.fit(
one_hot,
duration_col="_time_to_observation",
event_col="_observed",
show_progress=False,
)
res = cph.confidence_intervals_
res["hr"] = cph.params_
res["lcl"] = res["95% lower-bound"]
res["ucl"] = res["95% upper-bound"]
res["p_value"] = cph._compute_p_values()
res = res.drop(columns=["95% lower-bound", "95% upper-bound"])
res = res.apply(lambda x: np.exp(x))
old_index = res.index
res.at[dropped, :] = 1
res = res.reindex(index=[dropped] + list(old_index))
name_df_dict[col_name] = res
for (names, index) in v_conf.list_index.items():
i += 1
# join on names
res_df = name_df_dict[names[0]]
line = [x for x in names] + [x for x in res_df.loc[names[1]]]
output_df.at[i, :] = line
# for (names, index) in v_conf.list_index.items():
# (cat, group, sample_size, label) = names
# if group in non_dropped:
# cph[group] =
# output.append([])
for header in self.header:
output_df[header] = output_df[header].astype(str)
for i, (row_names, row_index) in enumerate(row_names_index):
# set the header shit
for header, name in zip(self.header, row_names):
output_df.at[i, header] = name
for h_conf in self.h_stack.configs:
if h_conf.kind == "space":
name = list(h_conf.name_index.keys())[0]
output_df[name] = output_df[name].astype(str)
output_df[name] = ""
else:
for col_name, col_index in h_conf.name_index.items():
idx = row_index & col_index
new_df = self.df.iloc[idx]
series_reducer = h_conf.reducer
reducer = getattr(Reducers(), series_reducer)
if h_conf.kind == "space":
output_df[name] = output_df[name].astype(str)
try:
out_val = reducer(new_df[h_conf.name])
output_df.at[i, col_name] = out_val
except KeyError:
output_df[col_name] = output_df[col_name].astype(
object)
print(h_conf.name)
output_df.at[i, col_name] = "ERROR"
return output_df
# -*- coding: utf-8 -*-
# cox regression
if __name__ == "__main__":
import pandas as pd
import time
import numpy as np
from lifelines import CoxPHFitter
from lifelines.datasets import load_rossi, load_regression_dataset
reps = 1
df = load_rossi()
# df['s'] = "a"
df = pd.concat([df] * reps)
print(df.shape)
cph = CoxPHFitter(baseline_estimation_method="spline",
n_baseline_knots=3,
strata=["wexp"])
start_time = time.time()
cph.fit(df,
duration_col="week",
event_col="arrest",
show_progress=True,
timeline=np.linspace(1, 60, 100))
print(cph.score(df))
print("--- %s seconds ---" % (time.time() - start_time))
# -*- coding: utf-8 -*-
# cox regression
if __name__ == "__main__":
import pandas as pd
import time
import numpy as np
from lifelines import CoxPHFitter
from lifelines.datasets import load_rossi
df = load_rossi()
df = pd.concat([df] * 16)
# df = df.reset_index()
# df['week'] = np.random.exponential(1, size=df.shape[0])
cp = CoxPHFitter()
start_time = time.time()
cp.fit(df, duration_col="week", event_col="arrest", batch_mode=True)
print("--- %s seconds ---" % (time.time() - start_time))
cp.print_summary()
ts = ts[ np.random.choice(N, set_size, replace=True) ]
es = np.random.binomial(1, (1-censor_rate), set_size)
# Create a data-frame for R:
df = pd.DataFrame({
'time' : ts,
'status' : es,
'x1' : np.random.uniform(-1.0, 1.0, set_size)})
# Normalize:
df['x1'] = (df['x1'] - df['x1'].mean()) / df['x1'].std()
# Compute likelihood with R:
r_out = rfunc( df )
preds, r_lik = np.asarray(r_out[0]), np.negative(np.round(r_out[1][0],4))
tf_lik_r = K.eval( efron_estimator_tf(K.variable(ts), K.variable(es), K.variable(preds)) )
# Compute ll with Lifelines:
cp = CoxPHFitter()
cp.fit(df, 'time', 'status', initial_beta=np.ones((1,1))*0.543, step_size=0.0)
preds = cp.predict_log_partial_hazard(df.drop(['time', 'status'], axis=1)).values[:, 0]
tf_lik_lifelines = K.eval( efron_estimator_tf(K.variable(ts), K.variable(es), K.variable(preds)) )
print( 'TensorFlow w/ R: ', tf_lik_r )
print( 'R-survival : ', r_lik )
print( 'TensorFlow w/ lifelines: ', tf_lik_lifelines )
print( 'Lifelines : ', np.negative(cp._log_likelihood), end='\n\n')
# done.
name.append("zhongliu__f," + zhongliu_3DT1[0][id % 1781])
# print("name:",name[0],"\n",name[1],"\n",name[2],"\n",name[3],"\n",name[4],"\n")
# COX
data = {
'T': y_train[:, 0],
'E': y_train[:, 1],
'%s' % name[0]: X_selected[:, 0],
'%s' % name[1]: X_selected[:, 1],
'%s' % name[2]: X_selected[:, 2],
'%s' % name[3]: X_selected[:, 3],
'%s' % name[4]: X_selected[:, 4],
}
df = pd.DataFrame(data)
# cph = CoxPHFitter(penalizer=0.1, l1_ratio=1.0)
cph = CoxPHFitter()
cph.fit(df, duration_col='T', event_col='E')
# c_index = COX(X_selected,y_train,name)
train_c_index.append(cph.concordance_index_)
print("Train_c_index:", cph.concordance_index_)
# 预测c_index
# data_test
data_test = {
'T': y_test[:, 0],
'E': y_test[:, 1],
'%s' % name[0]: X_test[:, ID[0] - 1],
'%s' % name[1]: X_test[:, ID[1] - 1],
'%s' % name[2]: X_test[:, ID[2] - 1],
'%s' % name[3]: X_test[:, ID[3] - 1],
'%s' % name[4]: X_test[:, ID[4] - 1],
# '%s' % name[0]: X_test[:, ID[0]+1],
def test_cross_validator_with_stratified_cox_model():
cf = CoxPHFitter(strata=["race"])
utils.k_fold_cross_validation(cf, load_rossi(), duration_col="week", event_col="arrest")
from lifelines.datasets import generate_regression_dataset regression_dataset = generate_regression_dataset() from lifelines import AalenAdditiveFitter, CoxPHFitter cf = CoxPHFitter() cf.fit(regression_dataset, duration_col='T', event_col='E') aaf = AalenAdditiveFitter(fit_intercept=False) aaf.fit(regression_dataset, duration_col='T', event_col='E') x = regression_dataset[regression_dataset.columns - ['E','T']] aaf.predict_survival_function(x.ix[10:12]).plot() aaf.plot()
import pandas as pd
from lifelines import WeibullAFTFitter, CoxPHFitter
# This is an implementation of https://uwspace.uwaterloo.ca/bitstream/handle/10012/10265/Cook_Richard-10265.pdf
N = 50000
p = 0.5
bX = np.log(0.5)
bZ = np.log(4)
Z = np.random.binomial(1, p, size=N)
X = np.random.binomial(1, 0.5, size=N)
X_ = 20000 + 10 * np.random.randn(N)
W = weibull_min.rvs(1, scale=1, loc=0, size=N)
Y = bX * X + bZ * Z + np.log(W)
T = np.exp(Y)
#######################################
df = pd.DataFrame({"T": T, "x": X, "x_": X_})
wf = WeibullAFTFitter().fit(df, "T")
wf.print_summary(4)
cph = CoxPHFitter().fit(df, "T", show_progress=True, step_size=1.0)
cph.print_summary(4)
# Convert to data frame
data = pd.DataFrame({'duration': duration, 'event': not_censor, 'age': age, 'college': college})
# Plot observations with censoring
# plot_lifetimes(duration, event_observed = not_censor)
# Kaplan Meier Summary for Simulated Data
from lifelines import KaplanMeierFitter
kmf = KaplanMeierFitter()
kmf.fit(duration, event_observed = not_censor)
kmf.survival_function_.plot()
# Cox-PH Model Regression
from lifelines import CoxPHFitter
cf = CoxPHFitter()
cf.fit(data, 'duration', event_col = 'event')
cf.print_summary()
## Get Predictions from Model ##
# 24 year old college grad
#college_24 = pd.DataFrame({'age':[24], 'college':[1]})
#cf.predict_survival_function(college_24).plot()
# 65 year old high school grad
#hs_65 = pd.DataFrame({'age':[65], 'college':[0]})
#cf.predict_survival_function(hs_65).plot()
# Predicted Survival for 24yr-old College Grad and 65yr-old HS Grad
mixed = pd.DataFrame({'age':[24, 65,42], 'college':[1,0,.4], 'index': ['24yr old College Grad','65yr old HS Grad','Average']})
tx = df['history_of_neoadjuvant_treatment']=='Yes'
ax = plt.subplot(111)
kmf1 = KaplanMeierFitter(alpha=0.95)
kmf1.fit(durations=df.ix[tx, survival_col], event_observed=df.ix[tx, censor_col], label=['Tx==Yes'])
kmf1.plot(ax=ax, show_censors=True, ci_show=False)
kmf2 = KaplanMeierFitter(alpha=0.95)
kmf2.fit(durations=df.ix[~tx, survival_col], event_observed=df.ix[~tx, censor_col], label=['Tx==No'])
kmf2.plot(ax=ax, show_censors=True, ci_show=False )
add_at_risk_counts(kmf1, kmf2, ax=ax)
plt.title ('Acute myeloid leukemia survival analysis with Tx and without Tx')
plt.xlabel(survival_col)
plt.savefig('km.png')
results = logrank_test(df.ix[tx, survival_col], df.ix[~tx, survival_col], df.ix[tx, censor_col], df.ix[~tx, censor_col], alpha=.99 )
results.print_summary()
cox = CoxPHFitter(normalize=False)
df_age = df[[survival_col, censor_col, 'age_at_initial_pathologic_diagnosis']]
df_age = df_age[pd.notnull(df_age['age_at_initial_pathologic_diagnosis'])]
cox = cox.fit(df_age, survival_col, event_col=censor_col, include_likelihood=True)
cox.print_summary()
scores = k_fold_cross_validation(cox, df_age, survival_col, event_col=censor_col, k=10)
print scores
print 'Mean score', np.mean(scores)
print 'Std', np.std(scores)
def multivariate(df):
from lifelines import CoxPHFitter
cph = CoxPHFitter()
cph.fit(df, duration_col='time', event_col='status',
show_progress=True)
cph.print_summary() # access the results using cph.summary
#Survival Regression from lifelines.datasets import load_regression_dataset regression_dataset = load_regression_dataset() regression_dataset.head() from lifelines import AalenAdditiveFitter, CoxPHFitter # Using Cox Proportional Hazards model cf = CoxPHFitter() cf.fit(regression_dataset, 'T', event_col='E') cf.print_summary() # Using Aalen's Additive model aaf = AalenAdditiveFitter(fit_intercept=False) aaf.fit(regression_dataset, 'T', event_col='E') x = regression_dataset[regression_dataset.columns - ['E','T']] aaf.predict_survival_function(x.ix[10:12]).plot() #get the unique survival functions of the first two subjects
viz.plot_survival_curves(experiment_name = 'RSF', output_file=output_file, **rec_dict)
if __name__ == '__main__':
logger = logging.getLogger(__name__)
logger.setLevel(logging.DEBUG)
args = parse_args()
print("Arguments:",args)
# Load Dataset
print("Loading datasets: " + args.dataset)
datasets = utils.load_datasets(args.dataset)
# Train CPH model
print("Training CPH Model")
train_df = utils.format_dataset_to_df(datasets['train'], DURATION_COL, EVENT_COL)
cf = CoxPHFitter()
results = cf.fit(train_df, duration_col=DURATION_COL, event_col=EVENT_COL,
include_likelihood=True)
cf.print_summary()
print("Train Likelihood: " + str(cf._log_likelihood))
if 'valid' in datasets:
metrics = evaluate_model(cf, datasets['valid'])
print("Valid metrics: " + str(metrics))
if 'test' in datasets:
metrics = evaluate_model(cf, datasets['test'], bootstrap=True)
print("Test metrics: " + str(metrics))
print("Saving Visualizations")
if 'test' in datasets and args.treatment_idx is not None:
def __init__(self):
random.seed(0)
super(CoxPH, self).__init__(CoxPHFitter(), self.__class__.__name__)
def _plot_kmf_single(df,
condition_col,
survival_col,
censor_col,
threshold,
title,
xlabel,
ylabel,
ax,
with_condition_color,
no_condition_color,
with_condition_label,
no_condition_label,
color_map,
label_map,
color_palette,
ci_show,
print_as_title):
"""
Helper function to produce a single KM survival plot, among observations in df by groups defined by condition_col.
All inputs are required - this function is intended to be called by `plot_kmf`.
"""
# make color inputs consistent hex format
if colors.is_color_like(with_condition_color):
with_condition_color = colors.to_hex(with_condition_color)
if colors.is_color_like(no_condition_color):
no_condition_color = colors.to_hex(no_condition_color)
## prepare data to be plotted; producing 3 outputs:
# - `condition`, series containing category labels to be plotted
# - `label_map` (mapping condition values to plot labels)
# - `color_map` (mapping condition values to plotted colors)
if threshold is not None:
is_median = threshold == "median"
if is_median:
threshold = df[condition_col].median()
label_suffix = float_str(threshold)
condition = df[condition_col] > threshold
default_label_no_condition = "%s ≤ %s" % (condition_col, label_suffix)
if is_median:
label_suffix += " (median)"
default_label_with_condition = "%s > %s" % (condition_col, label_suffix)
with_condition_label = with_condition_label or default_label_with_condition
no_condition_label = no_condition_label or default_label_no_condition
if not label_map:
label_map = {False: no_condition_label,
True: with_condition_label}
if not color_map:
color_map = {False: no_condition_color,
True: with_condition_color}
elif df[condition_col].dtype == 'O' or df[condition_col].dtype.name == "category":
condition = df[condition_col].astype("category")
if not label_map:
label_map = dict()
[label_map.update({condition_value: '{} = {}'.format(condition_col,
condition_value)})
for condition_value in condition.unique()]
if not color_map:
rgb_values = sb.color_palette(color_palette, len(label_map.keys()))
hex_values = [colors.to_hex(col) for col in rgb_values]
color_map = dict(zip(label_map.keys(), hex_values))
elif df[condition_col].dtype == 'bool':
condition = df[condition_col]
default_label_with_condition = "= {}".format(condition_col)
default_label_no_condition = "¬ {}".format(condition_col)
with_condition_label = with_condition_label or default_label_with_condition
no_condition_label = no_condition_label or default_label_no_condition
if not label_map:
label_map = {False: no_condition_label,
True: with_condition_label}
if not color_map:
color_map = {False: no_condition_color,
True: with_condition_color}
else:
raise ValueError('Don\'t know how to plot data of type\
{}'.format(df[condition_col].dtype))
# produce kmf plot for each category (group) identified above
kmf = KaplanMeierFitter()
grp_desc = list()
grp_survival_data = dict()
grp_event_data = dict()
grp_names = list(condition.unique())
for grp_name, grp_df in df.groupby(condition):
grp_survival = grp_df[survival_col]
grp_event = (grp_df[censor_col].astype(bool))
grp_label = label_map[grp_name]
grp_color = color_map[grp_name]
kmf.fit(grp_survival, grp_event, label=grp_label)
desc_str = "# {}: {}".format(grp_label, len(grp_survival))
grp_desc.append(desc_str)
grp_survival_data[grp_name] = grp_survival
grp_event_data[grp_name] = grp_event
if ax:
ax = kmf.plot(ax=ax, show_censors=True, ci_show=ci_show, color=grp_color)
else:
ax = kmf.plot(show_censors=True, ci_show=ci_show, color=grp_color)
## format the plot
# Set the y-axis to range 0 to 1
ax.set_ylim(0, 1)
y_tick_vals = ax.get_yticks()
ax.set_yticklabels(["%d" % int(y_tick_val * 100) for y_tick_val in y_tick_vals])
# plot title
if title:
ax.set_title(title)
elif print_as_title:
ax.set_title(' | '.join(grp_desc))
else:
[print(desc) for desc in grp_desc]
# axis labels
if xlabel:
ax.set_xlabel(xlabel)
if ylabel:
ax.set_ylabel(ylabel)
## summarize analytical version of results
## again using same groups as are plotted
if len(grp_names) == 2:
# use log-rank test for 2 groups
results = logrank_test(grp_survival_data[grp_names[0]],
grp_survival_data[grp_names[1]],
event_observed_A=grp_event_data[grp_names[0]],
event_observed_B=grp_event_data[grp_names[1]])
elif len(grp_names) == 1:
# no analytical result for 1 or 0 groups
results = NullSurvivalResults()
else:
# cox PH fitter for >2 groups
cf = CoxPHFitter()
cox_df = patsy.dmatrix('+'.join([condition_col, survival_col,
censor_col]),
df, return_type='dataframe')
del cox_df['Intercept']
results = cf.fit(cox_df, survival_col, event_col=censor_col)
results.print_summary()
# add metadata to results object so caller can print them
results.survival_data_series = grp_survival_data
results.event_data_series = grp_event_data
results.desc = grp_desc
return results
def main(filter_gap_days, rp_vs_radiation):
# get RP procedure date
with open('../data/empi_to_rp_date_dic.pkl', 'rb') as handle:
empi_to_rp_date_dic = pickle.load(handle)
# if rp_vs_radiation:
# get biopsy date
with open('../data/empi_to_date_oi_dic.pkl', 'rb') as handle:
empi_to_date_oi_dic = pickle.load(handle)
# rp date min : 1992-8-5, rp date max : 2020-7-29
# rp_date_range = [np.arange(1992, 1998), np.arange(1998, 2004), np.arange(2004, 2009), np.arange(2009, 2015), np.arange(2015, 2021)]
# pre-process the data using radiation only patients / multiple RP patients
df_first_date_rads = pd.read_csv(
'../data/processed_data/first_date_rads.csv')
df_first_date_rads.set_index('EMPI', inplace=True)
for empi, pr_date in zip(df_first_date_rads.index,
df_first_date_rads.prdate_parsed.values):
if empi in empi_to_date_oi_dic.keys():
df_first_date_rads.at[empi, 'pr_date_minus_biopsy_date'] = (
pd.to_datetime(pr_date) - empi_to_date_oi_dic[empi]).days
df_first_date_rads_filtered = df_first_date_rads.loc[
df_first_date_rads.pr_date_minus_biopsy_date > 0]
df_first_date_rads_filtered = df_first_date_rads_filtered.loc[
df_first_date_rads_filtered.pr_date_minus_biopsy_date <=
filter_gap_days]
radiation_empis = set(df_first_date_rads_filtered.index)
df_multirp = pd.read_csv('../data/processed_data/multirp.csv')
df_multirp.set_index('EMPI', inplace=True)
multirp_empis = set(df_multirp.index)
# breakpoint()
# get relevant data
df_merged_comorb = pd.read_csv(
'../data/merged/df_merged_biopsy_based_C.csv')
df_merged_comorb.set_index(df_merged_comorb.columns[0], inplace=True)
df_merged_comorb.index.name = 'EMPI'
df_merged_psa_prior = pd.read_csv(
'../data/merged/df_merged_biopsy_based_E.csv')
df_merged_psa_prior.set_index(df_merged_psa_prior.columns[0], inplace=True)
df_merged_psa_prior.index.name = 'EMPI'
df_outcome_oi = pd.read_csv(
'../data/df_outcome_final_biopsy_based_clean.csv')
df_outcome_oi.set_index('EMPI', inplace=True)
# filter_gap_days = 60
df_outcome_oi_filtered_rp_postive = df_outcome_oi.loc[
df_outcome_oi.rp_date_minus_biopsy_date_in_days <= filter_gap_days]
df_outcome_oi_rp_negative = df_outcome_oi.loc[
df_outcome_oi.rp_date.isnull()]
if rp_vs_radiation:
# exclude both RP and Radiation
both_rp_radiation_empis = set(
df_outcome_oi_filtered_rp_postive.index) & radiation_empis
df_outcome_oi_filtered_rp_postive = df_outcome_oi_filtered_rp_postive.loc[
set(df_outcome_oi_filtered_rp_postive.index) -
both_rp_radiation_empis]
df_outcome_oi_rp_negative = df_outcome_oi_rp_negative.loc[
set(df_outcome_oi_rp_negative.index)
& radiation_empis - multirp_empis]
df_outcome_oi_filtered_total = pd.concat(
[df_outcome_oi_filtered_rp_postive, df_outcome_oi_rp_negative])
else: # treated (radiation and rp) vs AS
df_outcome_oi_treated_postive = pd.concat([
df_outcome_oi_filtered_rp_postive,
df_outcome_oi_rp_negative.loc[set(df_outcome_oi_rp_negative.index)
& radiation_empis]
])
# df_outcome_oi_filtered_rp_postive
df_outcome_oi_treated_negative = df_outcome_oi_rp_negative.loc[
set(df_outcome_oi_rp_negative.index) - radiation_empis]
df_outcome_oi_filtered_total = pd.concat(
[df_outcome_oi_treated_postive, df_outcome_oi_treated_negative])
# filter out negative time to death
df_outcome_oi_filtered_final = df_outcome_oi_filtered_total.loc[
df_outcome_oi_filtered_total.time_to_death_in_month > 0]
# df_outcome_oi_filtered_final.set_index('EMPI', inplace = True)
# merge comorbidity data and psa prior data
empi_common = set(df_merged_comorb.index) & set(df_merged_psa_prior.index)
df_merged_psa_comorb = pd.concat([
df_merged_comorb.loc[empi_common],
df_merged_psa_prior.loc[empi_common].psa_prior_to_rp
],
axis=1)
df_merged_psa_comorb.drop(columns=['wscore_agg'], inplace=True)
# merge outcome and feature dfs
empi_common_outcome = set(df_outcome_oi_filtered_final.index) & set(
df_merged_psa_comorb.index)
outcome_cols_oi = ['death_ind', 'time_to_death_in_month']
df_cox = pd.concat([
df_merged_psa_comorb.loc[empi_common_outcome],
df_outcome_oi_filtered_final.loc[empi_common_outcome][outcome_cols_oi]
],
axis=1)
if not rp_vs_radiation:
df_cox.loc[df_cox.index.isin(df_outcome_oi_treated_postive.index),
'rp_indicator'] = 1
df_cox.rename(columns={'rp_indicator': 'treated'}, inplace=True)
# get biopsy date range
# biopsy_date_list = []
# for empi in data_merged.index:
# biopsy_date = empi_to_rp_date_dic[empi]
# for yr_idx, yr_range in enumerate(rp_date_range):
# if biopsy_date.year in yr_range:
# biopsy_date_list.append(yr_idx)
# break
# data_merged['rp_date'] = biopsy_date_list
# drop uninformative and extreme minority features
drop_cols = ['benign', 'Unknown/other'] # pre-filtering
# remove metastatic cancer patients
df_cox = df_cox.loc[df_cox.metacanc_agg == 0]
# drop_cols_non_informative = ['cevd_agg', 'rheumd_agg', 'pud_agg', 'mld_agg', 'diabwc_agg', 'aids_agg', 'metacanc_agg']
if rp_vs_radiation:
drop_cols_non_informative = [
'metacanc_agg', 'rheumd_agg', 'copd_agg', 'mld_agg', 'diabwc_agg',
'hp_agg', 'rend_agg', 'aids_agg'
]
else:
drop_cols_non_informative = [
'metacanc_agg', 'cevd_agg', 'rheumd_agg', 'mld_agg', 'diabwc_agg',
'hp_agg', 'aids_agg'
] #, 'rheumd_agg', 'copd_agg', 'mld_agg', 'diabwc_agg', 'hp_agg', 'rend_agg', 'aids_agg']
df_cox_final = df_cox.drop(columns=drop_cols + drop_cols_non_informative)
# standardize age and auxiiliary_mci_score,psa_prior_to_rp
standardize_cols = ['Age at RP', 'auxiiliary_mci_score', 'psa_prior_to_rp']
for col in standardize_cols:
if col == 'psa_prior_to_rp':
breakpoint()
df_cox_final[col] = (df_cox_final[col].values - np.mean(
df_cox_final[col])) / np.std(df_cox_final[col].values)
# df_cox_final = df_cox_final.loc[df_cox_final.overall_grade_merged == 1]
# df_cox_final.drop(columns = ['overall_grade_merged'], inplace = True)
# df_cox_final = df_cox_final.loc[df_cox_final.overall_grade_merged > 1]
# df_cox_final.drop(columns = ['overall_grade_merged'], inplace = True)
print('Final cox df stats : ')
print(df_cox_final.sum())
cph = CoxPHFitter(penalizer=0.00, l1_ratio=0)
cph.fit(df_cox_final,
'time_to_death_in_month',
'death_ind',
show_progress=False,
step_size=0.1)
cph.print_summary()
breakpoint()
# rename colums for downstraem task compatibility
df_cox_final.rename(columns={
'death_ind': 'death',
'rp_indicator': 'rp',
'time_to_death_in_month': 'survtime'
},
inplace=True)
if rp_vs_radiation:
df_cox_final.to_csv(
'../data/df_cox_data_death_causal_inference_rp_vs_radiation.csv')
else:
df_cox_final.to_csv('../data/df_cox_data_death_causal_inference.csv')
breakpoint()
return
def run_coxph(self,
vcf_path,
phenotype_path,
output_path,
id_column,
covar_columns,
event_column,
time_column,
chrom=None,
start=None,
end=None):
def parse_phenotypes(path, id_column, covar_columns, event_column,
time_column):
df = pd.read_csv(path)
df = df.set_index(id_column)
columns_to_keep = covar_columns + [event_column, time_column]
df = df[columns_to_keep]
return df
def gt_types_convert(gt_types):
gt_types = gt_types.astype(float)
# gt_types is array of 0,1,2,3==HOM_REF, HET, UNKNOWN, HOM_ALT
gt_types[gt_types == 2] = np.nan # missing
gt_types[gt_types == 3] = 2 # hom_alt
return gt_types
df_pheno = parse_phenotypes(phenotype_path, id_column, covar_columns,
event_column, time_column)
cph = CoxPHFitter()
vcf = VCF(vcf_path)
sample_list = vcf.samples
# TODO: handle partial information (e.g. chr only)
region = ''
if (chrom) and (start) and (end):
region = f'{chrom}:{start}-{end}'
f = open(output_path, "a")
hdr = 'rsid,chr,start,end,ref,alt,maf,hr,lower_ci,upper_ci,se,z,p'
f.write(hdr + '\n')
for v in vcf(region):
ref = v.REF
alt = ''.join(v.ALT) # assuming biallelics, which is a sin
genotypes_numeric = gt_types_convert(v.gt_types)
df_geno = pd.DataFrame({
'id': sample_list,
'genotype': genotypes_numeric
})
df_geno = df_geno.set_index('id')
df = pd.merge(df_geno, df_pheno, left_index=True, right_index=True)
df = df.dropna()
try:
fit = cph.fit(df,
event_col=event_column,
duration_col=time_column)
genotype_fit = fit.summary.loc['genotype']
f.write(','.join(
str(x) for x in [
v.ID, v.CHROM, v.start, v.end, ref, alt, v.aaf,
genotype_fit["exp(coef)"], genotype_fit["lower 0.95"],
genotype_fit["upper 0.95"], genotype_fit["se(coef)"],
genotype_fit["z"], genotype_fit["p"]
]) + '\n')
except ValueError as e:
print(f'{v.start} {v.end} {v.ID} failed, {str(e)}')
f.close()
def test_cross_validator_with_predictor():
cf = CoxPHFitter()
results = utils.k_fold_cross_validation(
cf, load_regression_dataset(), duration_col="T", event_col="E", k=3, predictor="predict_expectation"
)
assert len(results) == 3
from lifelines.datasets import load_rossi from lifelines import CoxPHFitter import pdb rossi_dataset = load_rossi() cph = CoxPHFitter() cph.fit(rossi_dataset, duration_col='week', event_col='arrest') pdb.set_trace()
return one_hot_df
to_encode = ['edema', 'stage']
one_hot_train = to_one_hot(df_train, to_encode)
one_hot_val = to_one_hot(df_val, to_encode)
one_hot_test = to_one_hot(df_test, to_encode)
print(one_hot_val.columns.tolist())
print(f"There are {len(one_hot_val.columns)} columns")
print(one_hot_train.shape)
one_hot_train.head()
cph = CoxPHFitter()
cph.fit(one_hot_train, duration_col='time', event_col='status', step_size=0.1)
cph.print_summary()
cph.plot_covariate_groups('edema_1.0', values=[0, 1])
def hazard_ratio(case_1, case_2, cox_params):
hr = np.exp(np.dot(cox_params, (case_1 - case_2)))
return hr
i = 1
# This hazard curve shows us that there is low hazard of someone leaving starting off, then it gets worse,
# once you stay for 500 days you stay at least a bit more, then exponentially it gets worse!
# SURVIVAL REGRESSION -- figuring out the influences of other aspects on whether or not someone survives
# Can't use regular linear regression. Want to use Cox's model or Aalen's additive model.
# Cox's Proportional Hazard model
# "The idea behind the model is that the log-hazard of an individual is a linear function of their static covariates
# and a population-level baseline hazard that changes over time" - from https://lifelines.readthedocs.io/en/latest/Survival%20Regression.html
from lifelines.datasets import load_rossi
from lifelines import CoxPHFitter
rossi_dataset = load_rossi()
cph = CoxPHFitter()
cph.fit(rossi_dataset,
duration_col='week',
event_col='arrest',
show_progress=True)
cph.print_summary()
rossi_dataset.info()
rossi_dataset.sample(20)
# Try this with our data
# First have to make categorical columns into number columns and get rid of columns we don't want for regression
data2.head()
# Get rid of join_date, quit_date, event_observed, employee_id and make sure company_id and dept are categorical so they get dummified
data2 = data2.drop(['employee_id', 'join_date', 'quit_date'], axis=1)
data3 = pd.get_dummies(data2)
plt.scatter(toy_none.x.values, np.log(toy_none['T'].values), alpha=0.25)
plt.scatter(toy_lin.x.values, np.log(toy_lin['T'].values), alpha=0.25)
plt.scatter(toy_sq.x.values, np.log(toy_sq['T'].values), alpha=0.25)
plt.show()
# *** Survival is random w.r.t. X input values ***
## run a set of CoxPH fits, generate a boxplot of the outcomes
c_index_list = []
for j in range(100):
# potential X value, but unrelated in this case
x = np.random.poisson(lam=10, size=3000)
toy_dataset = gen_survival(x, x_relation=None)
cph = CoxPHFitter()
cph.fit(toy_dataset,
duration_col='T',
event_col='event_obs',
show_progress=False)
c_index_list.append(cph.score_)
# *** Survival is _linear_ w.r.t. X input values ***
c_index_list_lin = []
for j in range(100):
# potential X value, but unrelated in this case
x = np.random.poisson(lam=10, size=3000)
toy_dataset = gen_survival(x, x_relation='lin')
""" # print cancer['T'].unique() # print cancer['E'].unique() # cancer = cancer.dropna() # the '-1' term # refers to not adding an intercept column (a column of all 1s). # It can be added to the Fitter class. covMatrix = cancer.cov() cf = CoxPHFitter() cf.fit(covMatrix, "T", event_col="E") # extra paramater for categorical , strata=catVar cf.print_summary() curve = cf.predict_survival_function(cancer) curve.plot() plt.show() print "hazard coeff", cf.hazards_ print "baseline ", cf.baseline_hazard_ """ scores = k_fold_cross_validation(cf, covMatrix, 'T', event_col='E', k=3) print scores print np.mean(scores) print np.std(scores)
