def train():
dataloaders = list()
if 'big_exam' in wandb.config.datasets:
dataloaders.append(AbnormalBigExamLoader(wandb_config=wandb.config))
if 'audicor_10s' in wandb.config.datasets:
dataloaders.append(AbnormalAudicor10sLoader(wandb_config=wandb.config))
g = BaseDataGenerator(dataloaders=dataloaders,
wandb_config=wandb.config,
preprocessing_fn=preprocessing)
train_set, valid_set, test_set = g.get()
big_data = np.load('big_signal_label_634_5_28.npy')
hht_set_signal = np.load(
'./abnormal_detection/imf0_2_set_hht.npy')[:, 2000:8000]
hht_set_signal = np.delete(hht_set_signal, 433, axis=0)
hht_set_signal = np.delete(hht_set_signal, 525, axis=0)
hht_set_signal_h2 = np.load('./abnormal_detection/h2_imf.npy')[:,
2000:8000]
amp = np.load('./abnormal_detection/set_hht_am.npy')[:, 2000:8000]
amp = np.delete(amp, 433, axis=0)
amp = np.delete(amp, 525, axis=0)
amp_h2 = np.load('./abnormal_detection/h2_amp.npy')[:, 2000:8000]
hht_set_signal = np.array([
np.array(hht_set_signal),
np.array(hht_set_signal_h2),
np.array(amp),
np.array(amp_h2)
])
hht_set_signal = np.transpose(hht_set_signal, (1, 2, 0))
#hht_set_signal=np.vstack((hht_set_signal,amp))
print('hht_set_signal', hht_set_signal.shape)
a = big_data[:, 1:3]
b = np.zeros((big_data.shape[0], 1))
for i in range(big_data.shape[0]):
#print('a[i,0]',a[i,0])
if (a[i, 0] == '1.0'):
b[i] = 1
if (a[i, 1] == '1.0'):
b[i] = 1
#print(a[:5,0],a[:5,1])
#print(a[:5],a.shape)
b = np.delete(b, 433, axis=0)
b = np.delete(b, 525, axis=0)
print(b[:5], b.shape)
duration = 10.0
fs = 1000.0
samples = int(fs * duration)
t = np.arange(samples) / fs
train_set_size = int(big_data.shape[0] / 2)
valid_set_size = int(train_set_size + big_data.shape[0] * 0.2)
#print('set_size',train_set_size,valid_set_size)
train_set_signal = np.array((hht_set_signal[:train_set_size]),
dtype=np.float) #0.5
valid_set_signal = np.array(
(hht_set_signal[train_set_size:valid_set_size]), dtype=np.float) #0.2
test_set_signal = np.array((hht_set_signal[valid_set_size:]),
dtype=np.float) #0.3
#train_set_label=np.array((big_data[:298,1:2]), dtype=np.float)
#valid_set_label=np.array((big_data[298:418,1:2]), dtype=np.float)
#test_set_label=np.array((big_data[418:,1:2]), dtype=np.float)
train_set_label = np.array((b[:train_set_size]), dtype=np.float)
valid_set_label = np.array((b[train_set_size:valid_set_size]),
dtype=np.float)
test_set_label = np.array((b[valid_set_size:]), dtype=np.float)
print('test_set_label', np.sum(test_set_label), test_set_label.shape,
test_set_signal.shape)
#print('*',train_set_label[:5],train_set_label.shape)
train_set_label = onehot(train_set_label)
#print(train_set_label[:5],train_set_label.shape)
valid_set_label = onehot(valid_set_label)
test_set_label = onehot(test_set_label)
#train_set_signal=train_set_signal[:,:,np.newaxis]
#valid_set_signal=valid_set_signal[:,:,np.newaxis]
#test_set_signal=test_set_signal[:,:,np.newaxis]
'''
train_set = combine(train_set_signal, train_set_label)
valid_set = combine(valid_set_signal, valid_set_label)
test_set = combine(test_set_signal, test_set_label)
'''
train_set = [np.array(train_set_signal), np.array(train_set_label)]
valid_set = [np.array(valid_set_signal), np.array(valid_set_label)]
test_set = [np.array(test_set_signal), np.array(test_set_label)]
train_set[0], means_and_stds = normalize(train_set[0])
valid_set[0], _ = normalize(valid_set[0], means_and_stds)
test_set[0], _ = normalize(test_set[0], means_and_stds)
#print(test_set_label[0])
#print(valid_set[0][0][:5])
print('have', train_set[1][:, 0].sum() / train_set[1][:, 0].shape[0],
valid_set[1][:, 0].sum() / valid_set[1][:, 0].shape[0],
test_set[1][:, 0].sum() / test_set[1][:, 0].shape[0])
print('have', train_set[1][:, 1].sum() / train_set[1][:, 0].shape[0],
valid_set[1][:, 1].sum() / valid_set[1][:, 0].shape[0],
test_set[1][:, 1].sum() / test_set[1][:, 0].shape[0])
print('train_set[0]', train_set[0].shape)
print('valid_set[0]', valid_set[0].shape)
print('test_set[0]', test_set[0].shape)
# save means and stds to wandb
#with open(os.path.join(wandb.run.dir, 'means_and_stds.pl'), 'wb') as f:
#pickle.dump(g.means_and_stds, f)
model = backbone(wandb.config,
include_top=True,
classification=True,
classes=2)
model.compile(RAdam(1e-4) if wandb.config.radam else Adam(amsgrad=True),
'binary_crossentropy',
metrics=['acc'])
model.summary()
wandb.log({'model_params': model.count_params()}, commit=False)
callbacks = [
EarlyStopping(monitor='val_loss', patience=50),
# ReduceLROnPlateau(patience=10, cooldown=5, verbose=1),
LogBest(),
WandbCallback(log_gradients=False, training_data=train_set),
]
model.fit(train_set[0],
train_set[1],
batch_size=64,
epochs=800,
validation_data=(valid_set[0], valid_set[1]),
callbacks=callbacks,
shuffle=True)
model.save(os.path.join(wandb.run.dir, 'final_model.h5'))
# load best model from wandb and evaluate
print('Evaluate the BEST model!')
from tensorflow.keras.models import load_model
from ekg.layers import LeftCropLike, CenterCropLike
from ekg.layers.sincnet import SincConv1D
custom_objects = {
'SincConv1D': SincConv1D,
'LeftCropLike': LeftCropLike,
'CenterCropLike': CenterCropLike
}
model = load_model(os.path.join(wandb.run.dir, 'model-best.h5'),
custom_objects=custom_objects,
compile=False)
evaluation.evaluation(model, test_set)
def train():
dataloaders = list()
if 'big_exam' in wandb.config.datasets:
dataloaders.append(AbnormalBigExamLoader(wandb_config=wandb.config))
if 'audicor_10s' in wandb.config.datasets:
dataloaders.append(AbnormalAudicor10sLoader(wandb_config=wandb.config))
'''
g = BaseDataGenerator(dataloaders=dataloaders,
wandb_config=wandb.config,
preprocessing_fn=preprocessing)
train_set, valid_set, test_set = g.get()
'''
audicor_hs_s3s4 = np.load(
'./abnormal_detection/audicor_10s/audicor_hs_s3s4.npy')
#hht_set_signal=np.transpose(hht_set_signal,(1,2,0))
#hht_set_signal=np.vstack((hht_set_signal,amp))
print('audicor_hs_s3s4', audicor_hs_s3s4.shape)
a = audicor_hs_s3s4[:, 3:5]
audicor_hs_s3s4 = audicor_hs_s3s4[:, 5:]
b = np.zeros((audicor_hs_s3s4.shape[0], 1))
for i in range(audicor_hs_s3s4.shape[0]):
if (a[i, 0] == '1.0'):
b[i] = 1
if (a[i, 1] == '1.0'):
b[i] = 1
print(b[:5], b.shape, np.sum(b))
duration = 10.0
fs = 1000.0
samples = int(fs * duration)
t = np.arange(samples) / fs
train_set_size = int(audicor_hs_s3s4.shape[0] / 2)
valid_set_size = int(train_set_size + audicor_hs_s3s4.shape[0] * 0.2)
print('set_size', train_set_size, valid_set_size)
train_set_signal = np.array((audicor_hs_s3s4[:train_set_size]),
dtype=np.float) #0.5
valid_set_signal = np.array(
(audicor_hs_s3s4[train_set_size:valid_set_size]), dtype=np.float) #0.2
test_set_signal = np.array((audicor_hs_s3s4[valid_set_size:]),
dtype=np.float) #0.3
train_set_signal = train_set_signal[:, :, np.newaxis]
valid_set_signal = valid_set_signal[:, :, np.newaxis]
test_set_signal = test_set_signal[:, :, np.newaxis]
#train_set_label=np.array((big_data[:298,1:2]), dtype=np.float)
#valid_set_label=np.array((big_data[298:418,1:2]), dtype=np.float)
#test_set_label=np.array((big_data[418:,1:2]), dtype=np.float)
train_set_label = np.array((b[:train_set_size]), dtype=np.float)
valid_set_label = np.array((b[train_set_size:valid_set_size]),
dtype=np.float)
test_set_label = np.array((b[valid_set_size:]), dtype=np.float)
print('test_set_label', np.sum(test_set_label), test_set_label.shape,
test_set_signal.shape)
train_set_label = onehot(train_set_label)
valid_set_label = onehot(valid_set_label)
test_set_label = onehot(test_set_label)
train_set = [np.array(train_set_signal), np.array(train_set_label)]
valid_set = [np.array(valid_set_signal), np.array(valid_set_label)]
test_set = [np.array(test_set_signal), np.array(test_set_label)]
train_set[0], means_and_stds = normalize(train_set[0])
valid_set[0], _ = normalize(valid_set[0], means_and_stds)
test_set[0], _ = normalize(test_set[0], means_and_stds)
#train_set[0] = multi_input_format(train_set[0], wandb.config.include_info)
#valid_set[0] = multi_input_format(valid_set[0], wandb.config.include_info)
#test_set[0] = multi_input_format(test_set[0], wandb.config.include_info)
print('have', train_set[1][:, 0].sum() / train_set[1][:, 0].shape[0],
valid_set[1][:, 0].sum() / valid_set[1][:, 0].shape[0],
test_set[1][:, 0].sum() / test_set[1][:, 0].shape[0])
print('have', train_set[1][:, 1].sum() / train_set[1][:, 0].shape[0],
valid_set[1][:, 1].sum() / valid_set[1][:, 0].shape[0],
test_set[1][:, 1].sum() / test_set[1][:, 0].shape[0])
print(train_set[1][:, 0].shape[0], valid_set[1][:, 0].shape[0],
test_set[1][:, 0].shape[0])
'''for X in [train_set[0], valid_set[0], test_set[0]]:
if wandb.config.n_ekg_channels != 0:
X['ekg_input'] = X['ekg_hs_input'][..., :wandb.config.n_ekg_channels]
if wandb.config.n_hs_channels != 0:
print('X',X['ekg_hs_input'].shape)
hs = X['ekg_hs_input'][..., -wandb.config.n_hs_channels:] # (?, n_samples, n_channels)
X['hs_input'] = mp_generate_wavelet(hs,wandb.config.sampling_rate,
wandb.config.wavelet_scale_length,
'Generate Wavelets')
X.pop('ekg_hs_input')
'''
# save means and stds to wandb
#with open(os.path.join(wandb.run.dir, 'means_and_stds.pl'), 'wb') as f:
#pickle.dump(g.means_and_stds, f)
model = backbone(wandb.config,
include_top=True,
classification=True,
classes=2)
model.compile(RAdam(1e-4) if wandb.config.radam else Adam(amsgrad=True),
'binary_crossentropy',
metrics=['acc'])
model.summary()
wandb.log({'model_params': model.count_params()}, commit=False)
callbacks = [
EarlyStopping(monitor='val_loss', patience=50),
# ReduceLROnPlateau(patience=10, cooldown=5, verbose=1),
LogBest(),
WandbCallback(log_gradients=False, training_data=train_set),
]
model.fit(train_set[0],
train_set[1],
batch_size=64,
epochs=800,
validation_data=(valid_set[0], valid_set[1]),
callbacks=callbacks,
shuffle=True)
model.save(os.path.join(wandb.run.dir, 'final_model.h5'))
# load best model from wandb and evaluate
print('Evaluate the BEST model!')
from tensorflow.keras.models import load_model
from ekg.layers import LeftCropLike, CenterCropLike
from ekg.layers.sincnet import SincConv1D
custom_objects = {
'SincConv1D': SincConv1D,
'LeftCropLike': LeftCropLike,
'CenterCropLike': CenterCropLike
}
model = load_model(os.path.join(wandb.run.dir, 'model-best.h5'),
custom_objects=custom_objects,
compile=False)
evaluation.evaluation(model, test_set)
def train():
dataloaders = list()
if 'big_exam' in wandb.config.datasets:
dataloaders.append(AbnormalBigExamLoader(wandb_config=wandb.config))
if 'audicor_10s' in wandb.config.datasets:
dataloaders.append(AbnormalAudicor10sLoader(wandb_config=wandb.config))
'''
g = BaseDataGenerator(dataloaders=dataloaders,
wandb_config=wandb.config,
preprocessing_fn=preprocessing)
train_set, valid_set, test_set = g.get()
print(len(train_set),train_set[0].shape,train_set[1].shape)
print_statistics(train_set, valid_set, test_set)
'''
big_data = np.load('big_data_signal_label.npy')
#print('big_data',big_data.shape,big_data[:5])
a = big_data[:, 1:3]
b = np.zeros((595, 1))
for i in range(595):
if (a[i, 0] == '1'):
b[i] = 1
if (a[i, 1] == '1'):
b[i] = 1
#print(a[:5,0],a[:5,1])
#print(a[:5],a.shape)
#print(b[:5],b.shape)
train_set_signal = np.array((big_data[:298, 3:]), dtype=np.float)
valid_set_signal = np.array((big_data[298:418, 3:]), dtype=np.float)
test_set_signal = np.array((big_data[418:, 3:]), dtype=np.float)
#train_set_label=np.array((big_data[:298,1:2]), dtype=np.float)
#valid_set_label=np.array((big_data[298:418,1:2]), dtype=np.float)
#test_set_label=np.array((big_data[418:,1:2]), dtype=np.float)
train_set_label = np.array((b[:298]), dtype=np.float)
valid_set_label = np.array((b[298:418]), dtype=np.float)
test_set_label = np.array((b[418:]), dtype=np.float)
#print('*',train_set_label[:5],train_set_label.shape)
train_set_label = onehot(train_set_label)
#print(train_set_label[:5],train_set_label.shape)
valid_set_label = onehot(valid_set_label)
test_set_label = onehot(test_set_label)
train_set_signal = train_set_signal[:, :, np.newaxis]
valid_set_signal = valid_set_signal[:, :, np.newaxis]
test_set_signal = test_set_signal[:, :, np.newaxis]
'''
train_set = combine(train_set_signal, train_set_label)
valid_set = combine(valid_set_signal, valid_set_label)
test_set = combine(test_set_signal, test_set_label)
'''
train_set = [np.array(train_set_signal), np.array(train_set_label)]
valid_set = [np.array(valid_set_signal), np.array(valid_set_label)]
test_set = [np.array(test_set_signal), np.array(test_set_label)]
train_set[0], means_and_stds = normalize(train_set[0])
valid_set[0], _ = normalize(valid_set[0], means_and_stds)
test_set[0], _ = normalize(test_set[0], means_and_stds)
plt.figure()
plt.plot(range(10000), train_set[0][0])
plt.show()
#print(train_set[0][0][:5])
#print(valid_set[0][0][:5])
print('have', train_set[1][:, 0].sum() / train_set[1][:, 0].shape[0],
valid_set[1][:, 0].sum() / valid_set[1][:, 0].shape[0],
test_set[1][:, 0].sum() / test_set[1][:, 0].shape[0])
print('have', train_set[1][:, 1].sum() / train_set[1][:, 0].shape[0],
valid_set[1][:, 1].sum() / valid_set[1][:, 0].shape[0],
test_set[1][:, 1].sum() / test_set[1][:, 0].shape[0])
# save means and stds to wandb
#with open(os.path.join(wandb.run.dir, 'means_and_stds.pl'), 'wb') as f:
#pickle.dump(g.means_and_stds, f)
model = backbone(wandb.config,
include_top=True,
classification=True,
classes=1)
model.compile(RAdam(1e-4) if wandb.config.radam else Adam(amsgrad=True),
'binary_crossentropy',
metrics=['acc'])
weights = class_weight.compute_class_weight('balanced',
np.unique(train_set[1][:, 0]),
train_set[1][:, 0])
class_weight_dict = dict(enumerate(weights))
print('weights', weights)
#weights2 = {0:0.64 , 1:2.19}
print(class_weight_dict)
model.summary()
wandb.log({'model_params': model.count_params()}, commit=False)
callbacks = [
EarlyStopping(monitor='val_loss', patience=50),
# ReduceLROnPlateau(patience=10, cooldown=5, verbose=1),
LogBest(),
WandbCallback(log_gradients=False, training_data=train_set),
]
model.fit(train_set[0],
train_set[1][:, 0],
batch_size=64,
class_weight=class_weight_dict,
epochs=300,
validation_data=(valid_set[0], valid_set[1][:, 0]),
callbacks=callbacks,
shuffle=True) #valid_set[1]), callbacks=callbacks
model.save(os.path.join(wandb.run.dir, 'final_model.h5'))
# load best model from wandb and evaluate
print('Evaluate the BEST model!')
from tensorflow.keras.models import load_model
from ekg.layers import LeftCropLike, CenterCropLike
from ekg.layers.sincnet import SincConv1D
custom_objects = {
'SincConv1D': SincConv1D,
'LeftCropLike': LeftCropLike,
'CenterCropLike': CenterCropLike
}
model = load_model('model-best.h5',
custom_objects=custom_objects,
compile=False)
model.summary()
evaluation.evaluation(model, train_set)
evaluation.evaluation(model, valid_set)
evaluation.evaluation(model, test_set)
def train():
dataloaders = list()
if 'big_exam' in wandb.config.datasets:
dataloaders.append(AbnormalBigExamLoader(wandb_config=wandb.config))
if 'audicor_10s' in wandb.config.datasets:
dataloaders.append(AbnormalAudicor10sLoader(wandb_config=wandb.config))
g = AbnormalDataGenerator(dataloaders=dataloaders,
wandb_config=wandb.config,
preprocessing_fn=preprocessing)
train_set, valid_set, test_set = g.get()
print_statistics(train_set, valid_set, test_set)
# save means and stds to wandb
with open(os.path.join(wandb.run.dir, 'means_and_stds.pl'), 'wb') as f:
pickle.dump(g.means_and_stds, f)
model = backbone(wandb.config,
include_top=True,
classification=True,
classes=2)
model.compile(RAdam(1e-4) if wandb.config.radam else Adam(amsgrad=True),
'binary_crossentropy',
metrics=['acc'])
model.summary()
wandb.log({'model_params': model.count_params()}, commit=False)
callbacks = [
# ReduceLROnPlateau(patience=10, cooldown=5, verbose=1),
LogBest(),
WandbCallback(),
GarbageCollector(),
EarlyStopping(monitor='val_loss', patience=50),
]
model.fit(train_set[0],
train_set[1],
batch_size=wandb.config.batch_size,
epochs=200,
validation_data=(valid_set[0], valid_set[1]),
callbacks=callbacks,
shuffle=True)
model.save(os.path.join(wandb.run.dir, 'final_model.h5'))
# load best model from wandb and evaluate
print('Evaluate the BEST model!')
from tensorflow.keras.models import load_model
from ekg.layers import LeftCropLike, CenterCropLike
from ekg.layers.sincnet import SincConv1D
custom_objects = {
'SincConv1D': SincConv1D,
'LeftCropLike': LeftCropLike,
'CenterCropLike': CenterCropLike
}
model = load_model(os.path.join(wandb.run.dir, 'model-best.h5'),
custom_objects=custom_objects,
compile=False)
evaluation.evaluation([model], test_set)
def train():
dataloaders = list()
if 'big_exam' in wandb.config.datasets:
dataloaders.append(HazardBigExamLoader(wandb_config=wandb.config))
if 'audicor_10s' in wandb.config.datasets:
dataloaders.append(HazardAudicor10sLoader(wandb_config=wandb.config))
g = HazardDataGenerator(dataloaders=dataloaders,
wandb_config=wandb.config,
preprocessing_fn=preprocessing)
train_set, valid_set, test_set = g.get()
print_statistics(train_set, valid_set, test_set, wandb.config.events)
# save means and stds to wandb
with open(os.path.join(wandb.run.dir, 'means_and_stds.pl'), 'wb') as f:
pickle.dump(g.means_and_stds, f)
if wandb.config.include_info and wandb.config.info_apply_noise:
wandb.config.info_norm_noise_std = np.array(
wandb.config.info_noise_stds) / np.array(g.means_and_stds[1][1])
prediction_model = backbone(wandb.config,
include_top=True,
classification=False,
classes=len(wandb.config.events))
trainable_model = get_trainable_model(prediction_model,
get_loss_layer(wandb.config.loss))
trainable_model.compile(
RAdam(1e-4) if wandb.config.radam else Adam(amsgrad=True), loss=None)
trainable_model.summary()
wandb.log({'model_params': trainable_model.count_params()}, commit=False)
c_index_reverse, scatter_exp = (wandb.config.loss !=
'AFT'), (wandb.config.loss == 'AFT')
scatter_xlabel = 'predicted survival time (days)' if wandb.config.loss == 'AFT' else 'predicted risk'
callbacks = [
# ReduceLROnPlateau(patience=10, cooldown=5, verbose=1),
LossVariableChecker(wandb.config.events),
ConcordanceIndex(train_set,
valid_set,
wandb.config.events,
prediction_model,
reverse=c_index_reverse),
LogBest(records=['val_loss', 'loss'] + [
'{}_cindex'.format(event_name)
for event_name in wandb.config.events
] + [
'val_{}_cindex'.format(event_name)
for event_name in wandb.config.events
] + [
'{}_sigma'.format(event_name) for event_name in wandb.config.events
]),
WandbCallback(),
EarlyStopping(
monitor='val_loss',
patience=50), # must be placed last otherwise it won't work
]
X_train, y_train, X_valid, y_valid = to_trainable_X(
train_set), None, to_trainable_X(valid_set), None
dataset_shuffle(X_train)
dataset_shuffle(X_valid)
trainable_model.fit(X_train,
y_train,
batch_size=wandb.config.batch_size,
epochs=1000,
validation_data=(X_valid, y_valid),
callbacks=callbacks,
shuffle=True)
trainable_model.save(os.path.join(wandb.run.dir, 'final_model.h5'))
# load best model from wandb and evaluate
print('Evaluate the BEST model!')
custom_objects = {
'SincConv1D': SincConv1D,
'LeftCropLike': LeftCropLike,
'CenterCropLike': CenterCropLike,
'AFTLoss': AFTLoss,
'CoxLoss': CoxLoss,
}
model = load_model(os.path.join(wandb.run.dir, 'model-best.h5'),
custom_objects=custom_objects,
compile=False)
prediction_model = to_prediction_model(model, wandb.config.include_info)
print('Training set:')
evaluation(prediction_model,
train_set,
wandb.config.events,
reverse=c_index_reverse)
print('Testing set:')
evaluation(prediction_model,
test_set,
wandb.config.events,
reverse=c_index_reverse)
evaluation_plot(prediction_model,
train_set,
train_set,
'training - ',
reverse=c_index_reverse,
scatter_exp=scatter_exp,
scatter_xlabel=scatter_xlabel)
evaluation_plot(prediction_model,
train_set,
valid_set,
'validation - ',
reverse=c_index_reverse,
scatter_exp=scatter_exp,
scatter_xlabel=scatter_xlabel)
evaluation_plot(prediction_model,
train_set,
test_set,
'testing - ',
reverse=c_index_reverse,
scatter_exp=scatter_exp,
scatter_xlabel=scatter_xlabel)
def train():
dataloaders = list()
if 'big_exam' in wandb.config.datasets:
dataloaders.append(AbnormalBigExamLoader(wandb_config=wandb.config))
if 'audicor_10s' in wandb.config.datasets:
dataloaders.append(AbnormalAudicor10sLoader(wandb_config=wandb.config))
g = BaseDataGenerator(dataloaders=dataloaders,
wandb_config=wandb.config,
preprocessing_fn=preprocessing)
train_set, valid_set, test_set = g.get()
big_data = np.load('big_data_signal_label.npy')
#print(a[:5,0],a[:5,1])
#print(a[:5],a.shape)
#print(b[:5],b.shape)
duration = 10.0
fs = 1000.0
samples = int(fs * duration)
t = np.arange(samples) / fs
train_set_signal = np.array((big_data[:298, 3:]), dtype=np.float)
valid_set_signal = np.array((big_data[298:418, 3:]), dtype=np.float)
test_set_signal = np.array((big_data[418:, 3:]), dtype=np.float)
train_set_label = np.array((big_data[:298, 1:2]), dtype=np.float)
valid_set_label = np.array((big_data[298:418, 1:2]), dtype=np.float)
test_set_label = np.array((big_data[418:, 1:2]), dtype=np.float)
print('label', np.sum(train_set_label), np.sum(valid_set_label),
np.sum(test_set_label))
train_set_label = onehot(train_set_label)
valid_set_label = onehot(valid_set_label)
test_set_label = onehot(test_set_label)
train_set_signal = train_set_signal[:, :, np.newaxis]
valid_set_signal = valid_set_signal[:, :, np.newaxis]
test_set_signal = test_set_signal[:, :, np.newaxis]
'''
train_set = combine(train_set_signal, train_set_label)
valid_set = combine(valid_set_signal, valid_set_label)
test_set = combine(test_set_signal, test_set_label)
'''
train_set = [np.array(train_set_signal), np.array(train_set_label)]
valid_set = [np.array(valid_set_signal), np.array(valid_set_label)]
test_set = [np.array(test_set_signal), np.array(test_set_label)]
train_set[0], means_and_stds = normalize(train_set[0])
valid_set[0], _ = normalize(valid_set[0], means_and_stds)
test_set[0], _ = normalize(test_set[0], means_and_stds)
#print(test_set_label[0])
#print(valid_set[0][0][:5])
print('have', train_set[1][:, 0].sum() / train_set[1][:, 0].shape[0],
valid_set[1][:, 0].sum() / valid_set[1][:, 0].shape[0],
test_set[1][:, 0].sum() / test_set[1][:, 0].shape[0])
print('have', train_set[1][:, 1].sum() / train_set[1][:, 0].shape[0],
valid_set[1][:, 1].sum() / valid_set[1][:, 0].shape[0],
test_set[1][:, 1].sum() / test_set[1][:, 0].shape[0])
# save means and stds to wandb
#with open(os.path.join(wandb.run.dir, 'means_and_stds.pl'), 'wb') as f:
#pickle.dump(g.means_and_stds, f)
model = backbone(wandb.config,
include_top=True,
classification=True,
classes=2)
model.compile(RAdam(1e-4) if wandb.config.radam else Adam(amsgrad=True),
'binary_crossentropy',
metrics=['acc'])
model.summary()
wandb.log({'model_params': model.count_params()}, commit=False)
callbacks = [
EarlyStopping(monitor='val_loss', patience=50),
# ReduceLROnPlateau(patience=10, cooldown=5, verbose=1),
LogBest(),
WandbCallback(log_gradients=False, training_data=train_set),
]
model.fit(train_set[0],
train_set[1],
batch_size=64,
epochs=700,
validation_data=(valid_set[0], valid_set[1]),
callbacks=callbacks,
shuffle=True)
model.save(os.path.join(wandb.run.dir, 'final_model.h5'))
# load best model from wandb and evaluate
print('Evaluate the BEST model!')
from tensorflow.keras.models import load_model
from ekg.layers import LeftCropLike, CenterCropLike
from ekg.layers.sincnet import SincConv1D
custom_objects = {
'SincConv1D': SincConv1D,
'LeftCropLike': LeftCropLike,
'CenterCropLike': CenterCropLike
}
model = load_model(os.path.join(wandb.run.dir, 'model-best.h5'),
custom_objects=custom_objects,
compile=False)
evaluation.evaluation(model, test_set)