def run(hyper_parameter_map):
logger = get_logger()
logger.debug("run()...")
framework = hyper_parameter_map['framework']
model_name = hyper_parameter_map['model_name']
pkg = import_pkg(framework, model_name)
runner_utils.format_params(hyper_parameter_map)
# params is python dictionary
params = pkg.initialize_parameters()
for k, v in hyper_parameter_map.items():
#if not k in params:
# raise Exception("Parameter '{}' not found in set of valid arguments".format(k))
params[k] = v
try:
runner_utils.write_params(params, hyper_parameter_map)
history = pkg.run(params)
runner_utils.keras_clear_session(framework)
# use the last validation_loss as the value to minimize
val_loss = history.history['val_loss']
result = val_loss[-1]
except:
print('benchmark failed')
result = 1.797693e+308
print("result: ", result)
return result
def run(hyper_parameter_map):
framework = hyper_parameter_map['framework']
if framework == 'keras':
import p3b1_baseline_keras2
pkg = p3b1_baseline_keras2
else:
raise ValueError("Unsupported framework: {}".format(framework))
# params is python dictionary
params = pkg.initialize_parameters()
runner_utils.format_params(hyper_parameter_map)
for k, v in hyper_parameter_map.items():
#if not k in params:
# raise Exception("Parameter '{}' not found in set of valid arguments".format(k))
params[k] = v
runner_utils.write_params(params, hyper_parameter_map)
avg_loss = pkg.do_n_fold(params)
if framework == 'keras':
# works around this error:
# https://github.com/tensorflow/tensorflow/issues/3388
try:
from keras import backend as K
K.clear_session()
except AttributeError: # theano does not have this function
pass
return avg_loss
def run(hyper_parameter_map):
framework = hyper_parameter_map['framework']
model_name = hyper_parameter_map['model_name']
pkg = import_pkg(framework, model_name)
runner_utils.format_params(hyper_parameter_map)
# params is python dictionary
params = pkg.initialize_parameters()
for k, v in hyper_parameter_map.items():
#if not k in params:
# raise Exception("Parameter '{}' not found in set of valid arguments".format(k))
params[k] = v
runner_utils.write_params(params, hyper_parameter_map)
history = pkg.run(params)
if framework == 'keras':
# works around this error:
# https://github.com/tensorflow/tensorflow/issues/3388
try:
from keras import backend as K
K.clear_session()
except AttributeError: # theano does not have this function
pass
# use the last validation_loss as the value to minimize
val_loss = history.history['val_loss']
return val_loss[-1]
def run(hyper_parameter_map, callbacks):
global logger
logger = log_tools.get_logger(logger, __name__)
framework = hyper_parameter_map['framework']
model_name = hyper_parameter_map['model_name']
pkg = import_pkg(framework, model_name)
runner_utils.format_params(hyper_parameter_map)
# params is python dictionary
params = pkg.initialize_parameters()
for k, v in hyper_parameter_map.items():
#if not k in params:
# raise Exception("Parameter '{}' not found in set of valid arguments".format(k))
params[k] = v
runner_utils.write_params(params, hyper_parameter_map)
history = pkg.run(params, callbacks)
runner_utils.keras_clear_session(framework)
# use the last validation_loss as the value to minimize
val_loss = history.history['val_loss']
result = val_loss[-1]
print("result: ", result)
return result
def run(hyper_parameter_map, obj_return):
global logger
logger = log_tools.get_logger(logger, __name__)
framework = hyper_parameter_map['framework']
model_name = hyper_parameter_map['model_name']
pkg = import_pkg(framework, model_name)
runner_utils.format_params(hyper_parameter_map)
# params is python dictionary
params = pkg.initialize_parameters()
for k,v in hyper_parameter_map.items():
#if not k in params:
# raise Exception("Parameter '{}' not found in set of valid arguments".format(k))
if(k=="dense"):
if(type(v) != list):
v=v.split(" ")
v = [int(i) for i in v]
if(k=="dense_feature_layers"):
if(type(v) != list):
v=v.split(" ")
v = [int(i) for i in v]
if(k=="cell_features"):
cp_str = v
v = list()
v.append(cp_str)
params[k] = v
logger.debug("WRITE_PARAMS START")
runner_utils.write_params(params, hyper_parameter_map)
logger.debug("WRITE_PARAMS STOP")
history = pkg.run(params)
runner_utils.keras_clear_session(framework)
# Default result if there is no val_loss (as in infer.py)
result = 0
if history != None:
# Return the history entry that the user requested.
val_loss = history.history[obj_return]
# Return a large number for nan and flip sign for val_corr
if(obj_return == "val_loss"):
if(math.isnan(val_loss[-1])):
result = 999999999
else:
result = val_loss[-1]
elif(obj_return == "val_corr"):
if(math.isnan(val_loss[-1])):
result = 999999999
else:
result = -val_loss[-1] #Note negative sign
else:
raise ValueError("Unsupported objective function (use obj_param to specify val_corr or val_loss): {}".format(framework))
print("result: " + str(result))
return result
def run(hyper_parameter_map, obj_param):
logger = get_logger()
framework = hyper_parameter_map['framework']
logger.debug("IMPORT START " + str(time.time()))
if framework == 'keras':
import p1b1_baseline_keras2
pkg = p1b1_baseline_keras2
else:
raise ValueError("Unsupported framework: {}".format(framework))
logger.debug("IMPORT STOP")
runner_utils.format_params(hyper_parameter_map)
# params is python dictionary
params = pkg.initialize_parameters()
for k, v in hyper_parameter_map.items():
#if not k in params:
# raise Exception("Parameter '{}' not found in set of valid arguments".format(k))
params[k] = v
logger.debug("WRITE_PARAMS START")
runner_utils.write_params(params, hyper_parameter_map)
logger.debug("WRITE_PARAMS STOP")
history = pkg.run(params)
if framework == 'keras':
# works around this error:
# https://github.com/tensorflow/tensorflow/issues/3388
try:
from keras import backend as K
K.clear_session()
except AttributeError: # theano does not have this function
pass
# use the last validation_loss as the value to minimize
obj_corr = history.history['val_corr']
obj_loss = history.history['val_loss']
if (obj_param == "val_loss"):
if (math.isnan(obj_loss[-1]) or math.isnan(obj_corr[-1])):
last_val = 999999999
else:
last_val = obj_loss[-1]
elif (obj_param == "val_corr"):
if (math.isnan(obj_loss[-1]) or math.isnan(obj_corr[-1])):
last_val = 999999999
else:
last_val = -obj_corr[-1] #Note negative sign
else:
raise ValueError(
"Unsupported objective function (use obj_param to specify val_corr or val_loss): {}"
.format(framework))
return last_val
def run(hyper_parameter_map, obj_return):
global logger
logger = log_tools.get_logger(logger, __name__)
framework = hyper_parameter_map['framework']
model_name = hyper_parameter_map['model_name']
pkg = import_pkg(framework, model_name)
runner_utils.format_params(hyper_parameter_map)
# params is python dictionary
params = pkg.initialize_parameters()
for k,v in hyper_parameter_map.items():
#if not k in params:
# raise Exception("Parameter '{}' not found in set of valid arguments".format(k))
if(k=="dense"):
if(type(v) != list):
v=v.split(" ")
v = [int(i) for i in v]
if(k=="dense_feature_layers"):
if(type(v) != list):
v=v.split(" ")
v = [int(i) for i in v]
if(k=="cell_features"):
cp_str = v
v = list()
v.append(cp_str)
params[k] = v
logger.debug("WRITE_PARAMS START")
runner_utils.write_params(params, hyper_parameter_map)
logger.debug("WRITE_PARAMS STOP")
history = pkg.run(params)
runner_utils.keras_clear_session(framework)
# Default result if there is no val_loss (as in infer.py)
result = 0
if history != None:
# Return the history entry that the user requested.
val_loss = history.history[obj_return]
result = val_loss[-1]
print("result: " + result)
return result
def run(hyper_parameter_map, obj_param):
global logger
logger = log_tools.get_logger(logger, __name__)
framework = hyper_parameter_map['framework']
model_name = hyper_parameter_map['model_name']
pkg = import_pkg(framework, model_name)
runner_utils.format_params(hyper_parameter_map)
# params is python dictionary
params = pkg.initialize_parameters()
for k, v in hyper_parameter_map.items():
#if not k in params:
# raise Exception("Parameter '{}' not found in set of valid arguments".format(k))
if (k == "dense"):
if (type(v) != list):
v = v.split(" ")
v = [int(i) for i in v]
if (k == "dense_feature_layers"):
if (type(v) != list):
v = v.split(" ")
v = [int(i) for i in v]
if (k == "cell_features"):
cp_str = v
v = list()
v.append(cp_str)
params[k] = v
logger.debug("WRITE_PARAMS START")
runner_utils.write_params(params, hyper_parameter_map)
logger.debug("WRITE_PARAMS STOP")
history = pkg.run(params)
runner_utils.keras_clear_session(framework)
# use the last validation_loss as the value to minimize
# val_loss = history.history['val_loss']
# result = val_loss[-1]
result = history
print("result: ", result)
return result
def setup_params(pkg, hyper_parameter_map, params_arg):
params = pkg.initialize_parameters(**params_arg)
log("PARAM UPDATE START")
for k, v in hyper_parameter_map.items():
if k == "dense" or k == "dense_feature_layers":
if (type(v) != list):
v = v.split(" ")
v = [int(i) for i in v]
if k == "cell_features":
cp_str = v
v = list()
v.append(cp_str)
log(str(k) + " = " + str(v))
params[k] = v
log("PARAM UPDATE STOP")
log("WRITE_PARAMS START")
runner_utils.write_params(params, hyper_parameter_map)
log("WRITE_PARAMS STOP")
return params
def run(hyper_parameter_map):
logger = get_logger()
framework = hyper_parameter_map['framework']
logger.debug("IMPORT START " + str(time.time()))
if framework == 'keras':
import p3b1_baseline_keras2
pkg = p3b1_baseline_keras2
else:
raise ValueError("Unsupported framework: {}".format(framework))
logger.debug("IMPORT STOP")
# params is python dictionary
params = pkg.initialize_parameters()
runner_utils.format_params(hyper_parameter_map)
for k, v in hyper_parameter_map.items():
#if not k in params:
# raise Exception("Parameter '{}' not found in set of valid arguments".format(k))
params[k] = v
logger.debug("WRITE_PARAMS START")
runner_utils.write_params(params, hyper_parameter_map)
logger.debug("WRITE_PARAMS STOP")
logger.debug("DO_N_FOLD START " + str(time.time()))
avg_loss = pkg.do_n_fold(params, verbose=0)
logger.debug("DO_N_FOLD STOP")
if framework == 'keras':
# works around this error:
# https://github.com/tensorflow/tensorflow/issues/3388
try:
from keras import backend as K
K.clear_session()
except AttributeError: # theano does not have this function
pass
return avg_loss