import numpy as np
from sklearn.preprocessing import normalize
from keras.layers import Input, Dense,concatenate,Dropout,average
from keras.models import Model
from keras import backend as K
from sklearn.metrics import roc_auc_score, f1_score, accuracy_score
import numpy as np
from sklearn.model_selection import StratifiedKFold
from keras.layers import Input, Dense,concatenate,Dropout,average
from keras.models import Model
import keras
from sklearn.metrics import classification_report
#训练三个神经网络
def build_NN_model1(omics):
omics1=omics[0]
omics2=omics[1]
omics3=omics[2]
input1_dim=omics1.shape[1]
input2_dim = omics2.shape[1]
input3_dim = omics3.shape[1]
class_num = 4
#omics1
input_factor1 = Input(shape=(input1_dim,),name='omics1')
# NN
omics1_nn = Dense(500, activation='relu')(input_factor1)
omics1_nn = Dropout(0.1)(omics1_nn)
# omics1_nn = Dense(500, activation='relu')(omics1_nn)
# omics1_nn = Dropout(0.1)(omics1_nn)
omics1_nn = Dense(100, activation='relu')(omics1_nn)
omics1_nn = Dropout(0.1)(omics1_nn)
# omics2
input_factor2 = Input(shape=(input2_dim,), name='omics2')
# NN
omics2_nn = Dense(500, activation='relu')(input_factor2)
omics2_nn = Dropout(0.1)(omics2_nn)
# omics2_nn = Dense(100, activation='relu')(omics2_nn)
# omics2_nn = Dropout(0.1)(omics2_nn)
omics2_nn = Dense(100, activation='relu')(omics2_nn)
omics2_nn = Dropout(0.1)(omics2_nn)
# omics3
input_factor3 = Input(shape=(input3_dim,), name='omics3')
# NN
omics3_nn = Dense(500, activation='relu')(input_factor2)
omics3_nn = Dropout(0.1)(omics3_nn)
# omics3_nn = Dense(100, activation='relu')(omics3_nn)
# omics3_nn = Dropout(0.1)(omics3_nn)
omics3_nn = Dense(100, activation='relu')(omics3_nn)
omics3_nn = Dropout(0.1)(omics3_nn)
mid_concat=concatenate([omics1_nn, omics2_nn, omics3_nn])
# classifier
nn_classifier = Dense(100, activation='relu')(mid_concat)
nn_classifier=Dropout(0.1)(nn_classifier)
nn_classifier = Dense(50, activation='relu')(nn_classifier)
nn_classifier = Dropout(0.1)(nn_classifier)
# nn_classifier = Dense(50, activation='relu')(nn_classifier)
# nn_classifier = Dropout(0.1)(nn_classifier)
nn_classifier = Dense(10, activation='relu')(nn_classifier)
#nn_classifier = Dropout(0.1)(nn_classifier)
nn_classifier = Dense(class_num, activation='softmax', name='classifier')(nn_classifier)
my_metrics = {
'classifier': ['acc']
}
my_loss = {
'classifier': 'categorical_crossentropy', \
}
adam=keras.optimizers.Adam(lr=0.0001, beta_1=0.9, beta_2=0.999, epsilon=1e-08)
zlyNN = Model(inputs=[input_factor1,input_factor2,input_factor3], outputs=nn_classifier)
zlyNN.compile(optimizer=adam, loss=my_loss, metrics=my_metrics)
return zlyNN
def build_NN_model2(omics,class_num):
input_dim=omics.shape[1]
#class_num = 5
#omics1
input_factor1 = Input(shape=(input_dim,),name='omics')
# NN
omics1_nn = Dense(500, activation='relu')(input_factor1)
omics1_nn = Dropout(0.1)(omics1_nn)
omics1_nn = Dense(100, activation='relu')(omics1_nn)
omics1_nn = Dropout(0.1)(omics1_nn)
# omics1_nn1 = Dense(100, activation='relu')(omics1_nn1)
# omics1_nn1 = Dropout(0.1)(omics1_nn1)
# omics1_nn = Dense(10, activation='relu')(omics1_nn)
# omics1_nn = Dropout(0.1)(omics1_nn)
# omics1_nn = average([omics1_nn1,omics1_nn])
# omics1_nn = Dense(100, activation='relu')(omics1_nn)
# omics1_nn = Dropout(0.1)(omics1_nn)
nn_classifier = Dense(50, activation='relu')(omics1_nn)
# nn_classifier = Dropout(0.1)(nn_classifier)
if class_num==2:
nn_classifier = Dense(1, activation='sigmoid', name='classifier')(nn_classifier)
else:
nn_classifier = Dense(class_num, activation='softmax', name='classifier')(nn_classifier)
my_metrics_multi = {
'classifier': ['acc']
}
my_loss_multi = {
'classifier': 'categorical_crossentropy', \
}
my_metrics_bi = {
'classifier': ['acc']
}
my_loss_bi = {
'classifier': 'binary_crossentropy', \
}
# compile autoencoder
# self.autoencoder.compile(optimizer='adam', loss='mse')
zlyNN = Model(inputs=[input_factor1], outputs=nn_classifier)
if class_num==2:
zlyNN.compile(optimizer='adam', loss=my_loss_bi, metrics=my_metrics_bi)
else:
zlyNN.compile(optimizer='adam', loss=my_loss_multi, metrics=my_metrics_multi)
return zlyNN
if __name__ == '__main__':
# files = ['breast2']
# # files = ['gbm']
# for f in files:
# datapath='./data/cancer_d2d/{f}'.format(f=f)
# omics1 = np.loadtxt('{}/after_log_exp.txt'.format(datapath),str)
# omics1 = np.delete(omics1, 0, axis=1)
# #omics1 = np.transpose(omics1)
# omics1 = omics1.astype(np.float)
# omics1 = normalize(omics1, axis=0, norm='max')
# print(omics1.shape)
# omics2 = np.loadtxt('{}/after_log_mirna.txt'.format(datapath),str)
# omics2= np.delete(omics2, 0, axis=1)
# #omics2 = np.transpose(omics2)
# omics2 = omics2.astype(np.float)
# omics2 = normalize(omics2, axis=0, norm='max')
# print(omics2.shape)
# omics3 = np.loadtxt('{}/after_methy.txt'.format(datapath),str)
# omics3= np.delete(omics3,0,axis=1)
# #omics3 = np.transpose(omics3)
# omics3 = omics3.astype(np.float)
# omics3 = normalize(omics3, axis=0, norm='max')
# print(omics3.shape)
# labels = np.loadtxt('{datapath}/after_labels.txt'.format(datapath=datapath), str)
# labels = np.delete(labels, 0, axis=1)
# labels = labels.astype(np.int)
# labels = np.squeeze(labels,axis=1)
# # k折交叉验证
# all_acc = []
# all_f1_macro = []
# all_f1_weighted = []
# all_auc_macro = []
# all_auc_weighted = []
# #omics = np.loadtxt('./result/nmf/mf_em.txt')
# omics = np.concatenate((omics1, omics2, omics3), axis=1)
# #labels = np.loadtxt('./data/BRCA/labels_all.csv', delimiter=',')
# # data=np.concatenate([])
# kfold = StratifiedKFold(n_splits=4, shuffle=True, random_state=1)
# for train_ix, test_ix in kfold.split(omics, labels):
# # select rows
# train_X, test_X = omics[train_ix], omics[test_ix]
# train_y, test_y = labels[train_ix], labels[test_ix]
# # summarize train and test composition
# unique, count = np.unique(train_y, return_counts=True)
# train_data_count = dict(zip(unique, count))
# print('train:' + str(train_data_count))
# unique, count = np.unique(test_y, return_counts=True)
# test_data_count = dict(zip(unique, count))
# print('test:' + str(test_data_count))
# # 多分类的输出
# train_y = list(np.int_(train_y))
# # groundtruth = np.int_(groundtruth)
# y = []
# num = len(train_y)
# for i in range(num):
# tmp = np.zeros(4, dtype='uint8')
# tmp[train_y[i]] = 1
# y.append(tmp)
# train_y = np.array(y)
# test_y = list(np.int_(test_y))
# # groundtruth = np.int_(groundtruth)
# y = []
# num = len(test_y)
# for i in range(num):
# tmp = np.zeros(4, dtype='uint8')
# tmp[test_y[i]] = 1
# y.append(tmp)
# test_y = np.array(y)
# model = build_NN_model2(omics, 4)
# history = model.fit(train_X, train_y, epochs=50, verbose=2, batch_size=8, shuffle=True,
# validation_data=(test_X, test_y))
# y_true = []
# for i in range(len(test_y)):
# y_true.append(np.argmax(test_y[i]))
# predictions = model.predict(test_X)
# y_pred = []
# for i in range(len(predictions)):
# y_pred.append(np.argmax(predictions[i]))
# acc = accuracy_score(y_true, y_pred)
# f1_macro = f1_score(y_true, y_pred, average='macro')
# # f1_micro=f1_score(y_true, y_pred, average='micro')
# f1_weighted = f1_score(y_true, y_pred, average='weighted')
# auc_macro = roc_auc_score(y_true, predictions, multi_class='ovr', average='macro')
# auc_weighted = roc_auc_score(y_true, predictions, multi_class='ovr', average='weighted')
# all_acc.append(acc)
# all_f1_macro.append(f1_macro)
# all_f1_weighted.append(f1_weighted)
# all_auc_macro.append(auc_macro)
# all_auc_weighted.append(auc_weighted)
# print(classification_report(y_true, y_pred))
# print(acc, f1_macro, f1_weighted, auc_macro, auc_weighted)
# # print_precison_recall_f1(y_true, y_pred)
# print('caicai' * 20)
# print(
# 'acc:{all_acc}\nf1_macro:{all_f1_macro}\nf1_weighted:{all_f1_weighted}\nauc_macro:{all_auc_macro}\nauc_weighted:{all_auc_weighted}'. \
# format(all_acc=all_acc, all_f1_macro=all_f1_macro, all_f1_weighted=all_f1_weighted,
# all_auc_macro=all_auc_macro, all_auc_weighted=all_auc_weighted))
# avg_acc = np.mean(all_acc)
# avg_f1_macro = np.mean(all_f1_macro)
# avg_f1_weighted = np.mean(all_f1_weighted)
# avg_auc_macro = np.mean(all_auc_macro)
# avg_auc_weighted = np.mean(all_auc_weighted)
# print(
# 'acc:{avg_acc}\nf1_macro:{avg_f1_macro}\nf1_weighted:{avg_f1_weighted}\nauc_macro:{avg_auc_macro}\nauc_weighted:{avg_auc_weighted}'. \
# format(avg_acc=avg_acc, avg_f1_macro=avg_f1_macro, avg_f1_weighted=avg_f1_weighted,
# avg_auc_macro=avg_auc_macro, avg_auc_weighted=avg_auc_weighted))
#files = ['breast2']
files = ['gbm']
for f in files:
datapath='./data/cancer_d2d/{f}'.format(f=f)
omics1 = np.loadtxt('{}/after_log_exp.txt'.format(datapath),str)
omics1 = np.delete(omics1, 0, axis=1)
#omics1 = np.transpose(omics1)
omics1 = omics1.astype(np.float)
omics1 = normalize(omics1, axis=0, norm='max')
print(omics1.shape)
omics2 = np.loadtxt('{}/after_log_mirna.txt'.format(datapath),str)
omics2= np.delete(omics2, 0, axis=1)
#omics2 = np.transpose(omics2)
omics2 = omics2.astype(np.float)
omics2 = normalize(omics2, axis=0, norm='max')
print(omics2.shape)
omics3 = np.loadtxt('{}/after_methy.txt'.format(datapath),str)
omics3= np.delete(omics3,0,axis=1)
#omics3 = np.transpose(omics3)
omics3 = omics3.astype(np.float)
omics3 = normalize(omics3, axis=0, norm='max')
print(omics3.shape)
labels = np.loadtxt('{datapath}/after_labels.txt'.format(datapath=datapath), str)
labels = np.delete(labels, 0, axis=1)
labels = labels.astype(np.int)
labels = np.squeeze(labels,axis=1)
# datapath = 'data/BRCA'
# omics1 = np.loadtxt('{}/1_all.csv'.format(datapath),delimiter=',')
# #omics1 = np.transpose(omics1)
# omics1 = normalize(omics1, axis=0, norm='max')
# omics2 = np.loadtxt('{}/2_all.csv'.format(datapath),delimiter=',')
# #omics2 = np.transpose(omics2)
# omics2 = normalize(omics2, axis=0, norm='max')
# omics3 = np.loadtxt('{}/3_all.csv'.format(datapath),delimiter=',')
# #omics3 = np.transpose(omics3)
# omics3 = normalize(omics3, axis=0, norm='max')
# k折交叉验证
all_acc = []
all_f1_macro = []
all_f1_weighted = []
all_auc_macro = []
all_auc_weighted = []
#omics = np.loadtxt('./result/nmf/mf_em.txt')
omics = np.concatenate((omics1, omics2, omics3), axis=1)
# labels = np.loadtxt('./data/BRCA/labels_all.csv', delimiter=',')
# data=np.concatenate([])
kfold = StratifiedKFold(n_splits=4, shuffle=True, random_state=1)
for train_ix, test_ix in kfold.split(omics1, labels):
omics_tobuild=[omics1,omics2,omics3]
train_X_1=omics1[train_ix]
train_X_2=omics2[train_ix]
train_X_3=omics3[train_ix]
test_X_1=omics1[test_ix]
test_X_2=omics2[test_ix]
test_X_3=omics3[test_ix]
# select rows
train_X, test_X = [train_X_1,train_X_2,train_X_3],[test_X_1,test_X_2,test_X_3]
#train_X, test_X = (train_X_1,train_X_2,train_X_3),(test_X_1,test_X_2,test_X_3)
train_y, test_y = labels[train_ix], labels[test_ix]
# summarize train and test composition
unique, count = np.unique(train_y, return_counts=True)
train_data_count = dict(zip(unique, count))
print('train:' + str(train_data_count))
unique, count = np.unique(test_y, return_counts=True)
test_data_count = dict(zip(unique, count))
print('test:' + str(test_data_count))
class_num=4
# 多分类的输出
train_y = list(np.int_(train_y))
# groundtruth = np.int_(groundtruth)
y = []
num = len(train_y)
for i in range(num):
tmp = np.zeros(class_num, dtype='uint8')
tmp[train_y[i]] = 1
y.append(tmp)
train_y = np.array(y)
test_y = list(np.int_(test_y))
# groundtruth = np.int_(groundtruth)
y = []
num = len(test_y)
for i in range(num):
tmp = np.zeros(class_num, dtype='uint8')
tmp[test_y[i]] = 1
y.append(tmp)
test_y = np.array(y)
model = build_NN_model1(omics_tobuild)
history = model.fit(train_X, train_y, epochs=50, verbose=2, batch_size=16, shuffle=True,
validation_data=(test_X, test_y))
y_true = []
for i in range(len(test_y)):
y_true.append(np.argmax(test_y[i]))
predictions = model.predict(test_X)
y_pred = []
for i in range(len(predictions)):
y_pred.append(np.argmax(predictions[i]))
acc = accuracy_score(y_true, y_pred)
f1_macro = f1_score(y_true, y_pred, average='macro')
# f1_micro=f1_score(y_true, y_pred, average='micro')
f1_weighted = f1_score(y_true, y_pred, average='weighted')
auc_macro = roc_auc_score(y_true, predictions, multi_class='ovr', average='macro')
auc_weighted = roc_auc_score(y_true, predictions, multi_class='ovr', average='weighted')
all_acc.append(acc)
all_f1_macro.append(f1_macro)
all_f1_weighted.append(f1_weighted)
all_auc_macro.append(auc_macro)
all_auc_weighted.append(auc_weighted)
print(classification_report(y_true, y_pred))
print(acc, f1_macro, f1_weighted, auc_macro, auc_weighted)
# print_precison_recall_f1(y_true, y_pred)
print('caicai' * 20)
print(
'acc:{all_acc}\nf1_macro:{all_f1_macro}\nf1_weighted:{all_f1_weighted}\nauc_macro:{all_auc_macro}\nauc_weighted:{all_auc_weighted}'. \
format(all_acc=all_acc, all_f1_macro=all_f1_macro, all_f1_weighted=all_f1_weighted,
all_auc_macro=all_auc_macro, all_auc_weighted=all_auc_weighted))
avg_acc = np.mean(all_acc)
avg_f1_macro = np.mean(all_f1_macro)
avg_f1_weighted = np.mean(all_f1_weighted)
avg_auc_macro = np.mean(all_auc_macro)
avg_auc_weighted = np.mean(all_auc_weighted)
print(
'acc:{avg_acc}\nf1_macro:{avg_f1_macro}\nf1_weighted:{avg_f1_weighted}\nauc_macro:{avg_auc_macro}\nauc_weighted:{avg_auc_weighted}'. \
format(avg_acc=avg_acc, avg_f1_macro=avg_f1_macro, avg_f1_weighted=avg_f1_weighted,
avg_auc_macro=avg_auc_macro, avg_auc_weighted=avg_auc_weighted))
Datasets
Models
