def input_process2(self, training_list, clinical):
print("Data processing-II...")
sample, t, f, age = [], [], [], []
for list in tqdm(training_list):
for i in range(len(clinical)):
if clinical.iloc[i]['sample'] + '.png' == str(list):
p_id = clinical.iloc[i]['sample']
time = clinical.iloc[i]['os_time']
status = clinical.iloc[i]['vital_status']
a = clinical.iloc[i]['age']
sample.append(p_id)
t.append(time)
f.append(status)
age.append(a)
continue
else:
pass
t = np.asarray(t)
f = np.asarray(f)
sample = np.asarray(sample)
age = np.asarray(age)
br=np.arange(0.,365.*10,365./4)
nl=len(br)-1
y_t = nnet_survival.make_surv_array(t,f,br)
ind = range(len(f))
print('Done!')
if self.omics=='mrna':
rand_range=[1,2]
if self.omics=='meth':
rand_range=[3,4]
if self.omics=='mirna':
rand_range=[4,5]
if self.omics=='mrna_meth':
rand_range=[6,7]
if self.omics=='mrna_mirna':
rand_range=[8,9]
if self.omics=='mrna_meth_mirna':
rand_range=[10,11]
return t, f, sample, age, br, nl, y_t, ind, rand_range
#Cox model discrimination test set
prediction = cph.predict_partial_hazard(data_test)
print(concordance_index(data_test.time, -prediction, data_test.dead)) #0.735
################################
#Nnet-survival / Our model (flexible version to
#allow non-proportional hazards)
halflife = 365. * 1.4
breaks = -np.log(1 - np.arange(0.0, 0.96, 0.05)) * halflife / np.log(2)
#breaks=-np.log(1-np.arange(0.0,1,0.099))*halflife/np.log(2)
n_intervals = len(breaks) - 1
timegap = breaks[1:] - breaks[:-1]
y_train = nnet_survival.make_surv_array(data_train.time.values,
data_train.dead.values, breaks)
y_test = nnet_survival.make_surv_array(data_test.time.values,
data_test.dead.values, breaks)
hidden_layers_sizes = 7 #Using single hidden layer, with this many neurons
##############################################################
#Our model cross-validation to pick L2 regularization strength
from sklearn.model_selection import KFold
n_folds = 10
kf = KFold(n_splits=n_folds, shuffle=True, random_state=0)
early_stopping = EarlyStopping(monitor='loss', patience=20)
#l2_array = np.concatenate(([0.],np.power(10.,np.arange(-6,-2))))
l2_array = np.power(10., np.arange(-4, 1))
def binary_ANN_surviavl():
breaks = np.arange(0, 5000, 50)
n_intervals = len(breaks) - 1
timegap = breaks[1:] - breaks[:-1]
halflife1 = 200
halflife2 = 400
halflife_cens = 400
n_samples = 5000
np.random.seed(seed=0)
t1 = np.random.exponential(scale=1 / (np.log(2) / halflife1),
size=int(n_samples / 2))
t2 = np.random.exponential(scale=1 / (np.log(2) / halflife2),
size=int(n_samples / 2))
t = np.concatenate((t1, t2))
censtime = np.random.exponential(scale=1 / (np.log(2) / (halflife_cens)),
size=n_samples)
f = t < censtime
t[~f] = censtime[~f]
y_train = nnet_survival.make_surv_array(t, f, breaks)
x_train = np.zeros(n_samples)
x_train[int(n_samples / 2):] = 1
model = Sequential()
# Hidden layers would go here. For this example, using simple linear model with no hidden layers.
model.add(Dense(1, input_dim=1, use_bias=0, kernel_initializer='zeros'))
model.add(nnet_survival.PropHazards(n_intervals))
model.compile(loss=nnet_survival.surv_likelihood(n_intervals),
optimizer=optimizers.RMSprop())
# model.summary()
early_stopping = EarlyStopping(monitor='loss', patience=2)
history = model.fit(x_train,
y_train,
batch_size=32,
epochs=1000,
callbacks=[early_stopping])
y_pred = model.predict_proba(x_train, verbose=0)
kmf = KaplanMeierFitter()
kmf.fit(t[0:int(n_samples / 2)], event_observed=f[0:int(n_samples / 2)])
plt.plot(breaks, np.concatenate(([1], np.cumprod(y_pred[0, :]))), 'bo-')
plt.plot(kmf.survival_function_.index.values,
kmf.survival_function_.KM_estimate,
color='k')
kmf.fit(t[int(n_samples / 2) + 1:],
event_observed=f[int(n_samples / 2) + 1:])
plt.plot(breaks, np.concatenate(([1], np.cumprod(y_pred[-1, :]))), 'ro-')
plt.plot(kmf.survival_function_.index.values,
kmf.survival_function_.KM_estimate,
color='k')
plt.xticks(np.arange(0, 2000.0001, 200))
plt.yticks(np.arange(0, 1.0001, 0.125))
plt.xlim([0, 2000])
plt.ylim([0, 1])
plt.xlabel('Follow-up time (days)')
plt.ylabel('Proportion surviving')
plt.title('One covariate. Actual=black, predicted=blue/red.')
plt.show()
myData = pd.DataFrame({'x_train': x_train, 't': t, 'f': f})
cf = CoxPHFitter()
cf.fit(myData, 't', event_col='f')
# x_train = x_train.astype(np.float64)
# cox_coef = cf.hazards_.x_train.values[0]
cox_coef = cf.hazards_.x_train
nn_coef = model.get_weights()[0][0][0]
print('Cox model coefficient:')
print(cox_coef)
print('Cox model hazard ratio:')
print(np.exp(cox_coef))
print('Neural network coefficient:')
print(nn_coef)
print('Neural network hazard ratio:')
print(np.exp(nn_coef))
breaks = -np.log(1 - np.arange(0.0, 0.96, 0.05)) * halflife / np.log(2)
n_intervals = len(breaks) - 1
timegap = breaks[1:] - breaks[:-1]
##################################################################
#Flexible model (non-proportional hazards).
#All pts with same exponential survival distribution, no censoring
#Not described in paper.
halflife1 = 365.
n_samples = 1000
np.random.seed(seed=0)
t = np.random.exponential(scale=1 / (np.log(2) / halflife1), size=n_samples)
f = np.ones(n_samples) #all patients failed (none censored)
#y_train=nnet_survival.make_surv_array(t,f)
y_train = nnet_survival.make_surv_array(t, f, breaks)
x_train = np.zeros(n_samples)
model = Sequential()
#Hidden layers would go here. For this example, using simple linear model with no hidden layers.
model.add(
Dense(n_intervals,
input_dim=1,
kernel_initializer='zeros',
bias_initializer='zeros'))
model.add(Activation('sigmoid'))
model.compile(loss=nnet_survival.surv_likelihood(n_intervals),
optimizer=optimizers.RMSprop())
#model.summary()
early_stopping = EarlyStopping(monitor='loss', patience=2)
history = model.fit(x_train,
def ANN_survival_model():
#################################################################
print('-------------------------------------------------------------')
print(
'start cross-validation to pick L2 regularization strength for training'
)
print('-------------------------------------------------------------')
halflife = 365. * 2.8
breaks = -np.log(1 - np.arange(0.0, 0.96, 0.05)) * halflife / np.log(2)
n_intervals = len(breaks) - 1
timegap = breaks[1:] - breaks[:-1]
# y_train = nnet_survival.make_surv_array(data_train.time.values, data_train.dead.values, breaks)
# y_test = nnet_survival.make_surv_array(data_test.time.values, data_test.dead.values, breaks)
y_train = nnet_survival.make_surv_array(data_train.duration_d.values,
data_train.CVD.values, breaks)
y_test = nnet_survival.make_surv_array(data_test.duration_d.values,
data_test.CVD.values, breaks)
# uncensored 데이터와 censored 데이터를 구분
# uncensored 데이터는 2번째 배열에서 dead 인터벌에 1값
# censored 데이터는 2번째 배열에서 0 값
hidden_layers_sizes = 7 # Using single hidden layer, with this many neurons
from sklearn.model_selection import KFold
n_folds = 10
kf = KFold(n_splits=n_folds, shuffle=True, random_state=0)
early_stopping = EarlyStopping(monitor='loss', patience=20)
# l2_array = np.concatenate(([0.],np.power(10.,np.arange(-6,-2))))
l2_array = np.power(10., np.arange(-4, 1))
grid_search_train = np.zeros((len(l2_array), n_folds))
grid_search_test = np.zeros((len(l2_array), n_folds))
print('execution of 10-fold validation for five times\n')
for i in range(1):
# for i in range(len(l2_array)):
print(str(i + 1) + ' / ' + str(len(l2_array)) + " times")
j = 0
cv_folds = kf.split(x_train)
for traincv, testcv in cv_folds:
x_train_cv = x_train[traincv]
y_train_cv = y_train[traincv]
x_test_cv = x_train[testcv]
y_test_cv = y_train[testcv]
# 활성함수는 렐루, 마지막 레이어에 시그모이드, iterator 1000, 7차원 hidden layer
model = Sequential()
# model.add(Dense(n_intervals,input_dim=x_train.shape[1],bias_initializer='zeros',kernel_regularizer=regularizers.l2(l2_array[i])))
# 입력층 개수는 변수의 개수
model.add(
Dense(hidden_layers_sizes,
input_dim=x_train.shape[1],
bias_initializer='zeros',
activation='relu',
kernel_regularizer=regularizers.l2(l2_array[i])))
# model.add(Activation('relu'))
model.add(Dense(n_intervals))
model.add(Activation('sigmoid'))
model.compile(loss=nnet_survival.surv_likelihood(n_intervals),
optimizer=optimizers.RMSprop()) # lr=0.0001))
history = model.fit(x_train_cv,
y_train_cv,
batch_size=256,
epochs=100000,
callbacks=[early_stopping],
verbose=0)
# model.summary()
print(model.metrics_names)
grid_search_train[i, j] = model.evaluate(x_train_cv,
y_train_cv,
verbose=0)
print(grid_search_train[i, j])
grid_search_test[i, j] = model.evaluate(x_test_cv,
y_test_cv,
verbose=0)
print(grid_search_test[i, j])
j = j + 1
print(np.average(grid_search_train, axis=1))
print(np.average(grid_search_test, axis=1))
l2_final = l2_array[np.argmax(-np.average(grid_search_test, axis=1))]
############################### plot ######################################
fig, loss_ax = plt.subplots()
acc_ax = loss_ax.twinx()
loss_ax.plot(history.history['loss'], 'y', label='train loss')
loss_ax.plot(history.history['val_loss'], 'r', label='test loss')
acc_ax.plot(history.history['acc'], 'b', label='train acc')
acc_ax.plot(history.history['val_acc'], 'g', label='test acc')
loss_ax.set_xlabel('epoch')
loss_ax.set_ylabel('loss')
acc_ax.set_ylabel('accuray')
loss_ax.legend(loc='upper left')
acc_ax.legend(loc='lower left')
plt.show()
###########################################################################
score = model.evaluate(x_test, y_test, batch_size=2, verbose=1)
# print('Test loss: ', score[0])
# print('Test accuracy: ', score[1])
# Discrimination performance
y_pred = model.predict_proba(x_train, verbose=1)
oneyr_surv = np.cumprod(y_pred[:, 0:np.nonzero(breaks > 365)[0][0]],
axis=1)[:, -1]
print('================================')
print('Training data with concordance_index ')
print(concordance_index(data_train.duration_d, oneyr_surv, data_train.CVD))
print('================================')
y_pred = model.predict_proba(x_test, verbose=1)
oneyr_surv = np.cumprod(y_pred[:, 0:np.nonzero(breaks > 365)[0][0]],
axis=1)[:, -1]
print('================================')
print('Test data with concordance_index ')
print(concordance_index(data_test.duration_d, oneyr_surv, data_test.CVD))
print('================================')
