def cli(sys_argv):
parser = argparse.ArgumentParser(description='This script trains a model.',
prog='ludwig train',
usage='%(prog)s [options]')
# ----------------------------
# Experiment naming parameters
# ----------------------------
parser.add_argument('--output_directory',
type=str,
default='results',
help='directory that contains the results')
parser.add_argument('--experiment_name',
type=str,
default='experiment',
help='experiment name')
parser.add_argument('--model_name',
type=str,
default='run',
help='name for the model')
# ---------------
# Data parameters
# ---------------
parser.add_argument(
'--data_csv',
help='input data CSV file. '
'If it has a split column, it will be used for splitting '
'(0: train, 1: validation, 2: test), '
'otherwise the dataset will be randomly split')
parser.add_argument('--data_train_csv', help='input train data CSV file')
parser.add_argument('--data_validation_csv',
help='input validation data CSV file')
parser.add_argument('--data_test_csv', help='input test data CSV file')
parser.add_argument(
'--data_hdf5',
help='input data HDF5 file. It is an intermediate preprocess version of'
' the input CSV created the first time a CSV file is used in the '
'same directory with the same name and a hdf5 extension')
parser.add_argument(
'--data_train_hdf5',
help='input train data HDF5 file. It is an intermediate preprocess '
'version of the input CSV created the first time a CSV file is '
'used in the same directory with the same name and a hdf5 '
'extension')
parser.add_argument(
'--data_validation_hdf5',
help='input validation data HDF5 file. It is an intermediate preprocess'
' version of the input CSV created the first time a CSV file is '
'used in the same directory with the same name and a hdf5 '
'extension')
parser.add_argument(
'--data_test_hdf5',
help='input test data HDF5 file. It is an intermediate preprocess '
'version of the input CSV created the first time a CSV file is '
'used in the same directory with the same name and a hdf5 '
'extension')
parser.add_argument(
'--train_set_metadata_json',
help='input metadata JSON file. It is an intermediate preprocess file '
'containing the mappings of the input CSV created the first time a'
' CSV file is used in the same directory with the same name and a '
'json extension')
parser.add_argument('-sspi',
'--skip_save_processed_input',
help='skips saving intermediate HDF5 and JSON files',
action='store_true',
default=False)
# ----------------
# Model parameters
# ----------------
model_definition = parser.add_mutually_exclusive_group(required=True)
model_definition.add_argument('-md',
'--model_definition',
type=yaml.safe_load,
help='model definition')
model_definition.add_argument(
'-mdf',
'--model_definition_file',
help='YAML file describing the model. Ignores --model_hyperparameters')
parser.add_argument(
'-mlp',
'--model_load_path',
help='path of a pretrained model to load as initialization')
parser.add_argument(
'-mrp',
'--model_resume_path',
help='path of a the model directory to resume training of')
parser.add_argument(
'-ssm',
'--skip_save_model',
action='store_true',
default=False,
help='disables saving weights each time the model imrpoves. '
'By default Ludwig saves weights after each epoch '
'the validation measure imrpvoes, but if the model is really big '
'that can be time consuming if you do not want to keep '
'the weights and just find out what performance can a model get '
'with a set of hyperparameters, use this parameter to skip it.')
parser.add_argument(
'-ssp',
'--skip_save_progress',
action='store_true',
default=False,
help='disables saving weights after each epoch. By default ludwig saves '
'weights after each epoch for enabling resuming of training, but '
'if the model is really big that can be time consuming and will '
'save twice as much space, use this parameter to skip it.')
parser.add_argument(
'-ssl',
'--skip_save_log',
action='store_true',
default=False,
help='disables saving TensorBoard logs. By default Ludwig saves '
'logs for the TensorBoard, but if it is not needed turning it off '
'can slightly increase the overall speed.')
# ------------------
# Runtime parameters
# ------------------
parser.add_argument(
'-rs',
'--random_seed',
type=int,
default=42,
help='a random seed that is going to be used anywhere there is a call '
'to a random number generator: data splitting, parameter '
'initialization and training set shuffling')
parser.add_argument('-g',
'--gpus',
nargs='+',
type=int,
default=None,
help='list of gpus to use')
parser.add_argument(
'-gf',
'--gpu_fraction',
type=float,
default=1.0,
help='fraction of gpu memory to initialize the process with')
parser.add_argument('-uh',
'--use_horovod',
action='store_true',
default=False,
help='uses horovod for distributed training')
parser.add_argument('-dbg',
'--debug',
action='store_true',
default=False,
help='enables debugging mode')
parser.add_argument(
'-l',
'--logging_level',
default='info',
help='the level of logging to use',
choices=['critical', 'error', 'warning', 'info', 'debug', 'notset'])
args = parser.parse_args(sys_argv)
logging.getLogger('ludwig').setLevel(
logging_level_registry[args.logging_level])
set_on_master(args.use_horovod)
if is_on_master():
print_ludwig('Train', LUDWIG_VERSION)
full_train(**vars(args))
def cli(sys_argv):
parser = argparse.ArgumentParser(
description='This script trains and tests a model',
prog='ludwig experiment',
usage='%(prog)s [options]')
# ----------------------------
# Experiment naming parameters
# ----------------------------
parser.add_argument('--output_directory',
type=str,
default='results',
help='directory that contains the results')
parser.add_argument('--experiment_name',
type=str,
default='experiment',
help='experiment name')
parser.add_argument('--model_name',
type=str,
default='run',
help='name for the model')
# ---------------
# Data parameters
# ---------------
parser.add_argument(
'--data_csv',
help='input data CSV file. If it has a split column, it will be used '
'for splitting (0: train, 1: validation, 2: test), otherwise the '
'dataset will be randomly split')
parser.add_argument('--data_train_csv', help='input train data CSV file')
parser.add_argument('--data_validation_csv',
help='input validation data CSV file')
parser.add_argument('--data_test_csv', help='input test data CSV file')
parser.add_argument(
'--data_hdf5',
help='input data HDF5 file. It is an intermediate preprocess version of'
' the input CSV created the first time a CSV file is used in the '
'same directory with the same name and a hdf5 extension')
parser.add_argument(
'--data_train_hdf5',
help='input train data HDF5 file. It is an intermediate preprocess '
'version of the input CSV created the first time a CSV file is '
'used in the same directory with the same name and a hdf5 '
'extension')
parser.add_argument(
'--data_validation_hdf5',
help='input validation data HDF5 file. It is an intermediate preprocess'
' version of the input CSV created the first time a CSV file is '
'used in the same directory with the same name and a hdf5 '
'extension')
parser.add_argument(
'--data_test_hdf5',
help='input test data HDF5 file. It is an intermediate preprocess '
'version of the input CSV created the first time a CSV file is '
'used in the same directory with the same name and a hdf5 '
'extension')
parser.add_argument(
'--train_set_metadata_json',
help='input metadata JSON file. It is an intermediate preprocess file'
' containing the mappings of the input CSV created the first time '
'a CSV file is used in the same directory with the same name and a'
' json extension')
parser.add_argument('-sspi',
'--skip_save_processed_input',
help='skips saving intermediate HDF5 and JSON files',
action='store_true',
default=False)
parser.add_argument('-ssuo',
'--skip_save_unprocessed_output',
help='skips saving intermediate NPY output files',
action='store_true',
default=False)
# -----------------
# K-fold parameters
# -----------------
parser.add_argument(
'-kf',
'--k_fold',
type=int,
default=None,
help='number of folds for a k-fold cross validation run ')
parser.add_argument(
'-skfsi',
'--skip_save_k_fold_split_indices',
action='store_true',
default=False,
help='disables saving indices generated to split training data set '
'for the k-fold cross validation run, but if it is not needed '
'turning it off can slightly increase the overall speed')
# ----------------
# Model parameters
# ----------------
model_definition = parser.add_mutually_exclusive_group(required=True)
model_definition.add_argument('-md',
'--model_definition',
type=yaml.safe_load,
help='model definition')
model_definition.add_argument(
'-mdf',
'--model_definition_file',
help='YAML file describing the model. Ignores --model_hyperparameters')
parser.add_argument(
'-mlp',
'--model_load_path',
help='path of a pretrained model to load as initialization')
parser.add_argument(
'-mrp',
'--model_resume_path',
help='path of a the model directory to resume training of')
parser.add_argument('-sstd',
'--skip_save_training_description',
action='store_true',
default=False,
help='disables saving the description JSON file')
parser.add_argument('-ssts',
'--skip_save_training_statistics',
action='store_true',
default=False,
help='disables saving training statistics JSON file')
parser.add_argument('-sstp',
'--skip_save_test_predictions',
help='skips saving test predictions CSV files',
action='store_true',
default=False)
parser.add_argument('-sstes',
'--skip_save_test_statistics',
help='skips saving test statistics JSON file',
action='store_true',
default=False)
parser.add_argument(
'-ssm',
'--skip_save_model',
action='store_true',
default=False,
help='disables saving model weights and hyperparameters each time '
'the model improves. '
'By default Ludwig saves model weights after each epoch '
'the validation metric imprvoes, but if the model is really big '
'that can be time consuming if you do not want to keep '
'the weights and just find out what performance can a model get '
'with a set of hyperparameters, use this parameter to skip it,'
'but the model will not be loadable later on')
parser.add_argument(
'-ssp',
'--skip_save_progress',
action='store_true',
default=False,
help='disables saving progress each epoch. By default Ludwig saves '
'weights and stats after each epoch for enabling resuming '
'of training, but if the model is really big that can be '
'time consuming and will uses twice as much space, use '
'this parameter to skip it, but training cannot be resumed '
'later on')
parser.add_argument(
'-ssl',
'--skip_save_log',
action='store_true',
default=False,
help='disables saving TensorBoard logs. By default Ludwig saves '
'logs for the TensorBoard, but if it is not needed turning it off '
'can slightly increase the overall speed')
# ------------------
# Runtime parameters
# ------------------
parser.add_argument(
'-rs',
'--random_seed',
type=int,
default=42,
help='a random seed that is going to be used anywhere there is a call '
'to a random number generator: data splitting, parameter '
'initialization and training set shuffling')
parser.add_argument('-g',
'--gpus',
nargs='+',
type=int,
default=None,
help='list of GPUs to use')
parser.add_argument('-gml',
'--gpu_memory_limit',
type=int,
default=None,
help='maximum memory in MB to allocate per GPU device')
parser.add_argument(
'-dpt',
'--disable_parallel_threads',
action='store_false',
dest='allow_parallel_threads',
help='disable TensorFlow from using multithreading for reproducibility'
)
parser.add_argument('-uh',
'--use_horovod',
action='store_true',
default=None,
help='uses horovod for distributed training')
parser.add_argument('-dbg',
'--debug',
action='store_true',
default=False,
help='enables debugging mode')
parser.add_argument(
'-l',
'--logging_level',
default='info',
help='the level of logging to use',
choices=['critical', 'error', 'warning', 'info', 'debug', 'notset'])
args = parser.parse_args(sys_argv)
logging.getLogger('ludwig').setLevel(
logging_level_registry[args.logging_level])
global logger
logger = logging.getLogger('ludwig.experiment')
set_on_master(args.use_horovod)
if is_on_master():
print_ludwig('Experiment', LUDWIG_VERSION)
if args.k_fold is None:
full_experiment(**vars(args))
else:
full_kfold_cross_validate(**vars(args))
def cli(sys_argv):
parser = argparse.ArgumentParser(
description="This script searches for optimal Hyperparameters",
prog="ludwig hyperopt",
usage="%(prog)s [options]",
)
# -------------------
# Hyperopt parameters
# -------------------
parser.add_argument(
"-sshs",
"--skip_save_hyperopt_statistics",
help="skips saving hyperopt statistics file",
action="store_true",
default=False,
)
# ----------------------------
# Experiment naming parameters
# ----------------------------
parser.add_argument(
"--output_directory",
type=str,
default="results",
help="directory that contains the results",
)
parser.add_argument("--experiment_name",
type=str,
default="hyperopt",
help="experiment name")
parser.add_argument("--model_name",
type=str,
default="run",
help="name for the model")
# ---------------
# Data parameters
# ---------------
parser.add_argument(
"--data_csv",
help="input data CSV file. "
"If it has a split column, it will be used for splitting "
"(0: train, 1: validation, 2: test), "
"otherwise the dataset will be randomly split",
)
parser.add_argument("--data_train_csv", help="input train data CSV file")
parser.add_argument("--data_validation_csv",
help="input validation data CSV file")
parser.add_argument("--data_test_csv", help="input test data CSV file")
parser.add_argument(
"--data_hdf5",
help="input data HDF5 file. It is an intermediate preprocess version of"
" the input CSV created the first time a CSV file is used in the "
"same directory with the same name and a hdf5 extension",
)
parser.add_argument(
"--data_train_hdf5",
help="input train data HDF5 file. It is an intermediate preprocess "
"version of the input CSV created the first time a CSV file is "
"used in the same directory with the same name and a hdf5 "
"extension",
)
parser.add_argument(
"--data_validation_hdf5",
help="input validation data HDF5 file. It is an intermediate preprocess"
" version of the input CSV created the first time a CSV file is "
"used in the same directory with the same name and a hdf5 "
"extension",
)
parser.add_argument(
"--data_test_hdf5",
help="input test data HDF5 file. It is an intermediate preprocess "
"version of the input CSV created the first time a CSV file is "
"used in the same directory with the same name and a hdf5 "
"extension",
)
parser.add_argument(
"--train_set_metadata_json",
help="input metadata JSON file. It is an intermediate preprocess file "
"containing the mappings of the input CSV created the first time a"
" CSV file is used in the same directory with the same name and a "
"json extension",
)
parser.add_argument(
"-sspi",
"--skip_save_processed_input",
help="skips saving intermediate HDF5 and JSON files",
action="store_true",
default=False,
)
# ----------------
# Model parameters
# ----------------
model_definition = parser.add_mutually_exclusive_group(required=True)
model_definition.add_argument("-md",
"--model_definition",
type=yaml.safe_load,
help="model definition")
model_definition.add_argument(
"-mdf",
"--model_definition_file",
help="YAML file describing the model. Ignores --model_hyperparameters",
)
parser.add_argument(
"-mlp",
"--model_load_path",
help="path of a pretrained model to load as initialization",
)
parser.add_argument(
"-mrp",
"--model_resume_path",
help="path of a the model directory to resume training of",
)
parser.add_argument(
"-sstd",
"--skip_save_training_description",
action="store_true",
default=False,
help="disables saving the description JSON file",
)
parser.add_argument(
"-ssts",
"--skip_save_training_statistics",
action="store_true",
default=False,
help="disables saving training statistics JSON file",
)
parser.add_argument(
"-ssm",
"--skip_save_model",
action="store_true",
default=False,
help="disables saving weights each time the model imrpoves. "
"By default Ludwig saves weights after each epoch "
"the validation metric imrpvoes, but if the model is really big "
"that can be time consuming if you do not want to keep "
"the weights and just find out what performance can a model get "
"with a set of hyperparameters, use this parameter to skip it",
)
parser.add_argument(
"-ssp",
"--skip_save_progress",
action="store_true",
default=False,
help="disables saving weights after each epoch. By default ludwig saves "
"weights after each epoch for enabling resuming of training, but "
"if the model is really big that can be time consuming and will "
"save twice as much space, use this parameter to skip it",
)
parser.add_argument(
"-ssl",
"--skip_save_log",
action="store_true",
default=False,
help="disables saving TensorBoard logs. By default Ludwig saves "
"logs for the TensorBoard, but if it is not needed turning it off "
"can slightly increase the overall speed",
)
# ------------------
# Runtime parameters
# ------------------
parser.add_argument(
"-rs",
"--random_seed",
type=int,
default=42,
help="a random seed that is going to be used anywhere there is a call "
"to a random number generator: data splitting, parameter "
"initialization and training set shuffling",
)
parser.add_argument("-g",
"--gpus",
nargs="+",
type=int,
default=None,
help="list of gpus to use")
parser.add_argument('-gml',
'--gpu_memory_limit',
type=int,
default=None,
help='maximum memory in MB to allocate per GPU device')
parser.add_argument(
"-uh",
"--use_horovod",
action="store_true",
default=False,
help="uses horovod for distributed training",
)
parser.add_argument(
"-dbg",
"--debug",
action="store_true",
default=False,
help="enables debugging mode",
)
parser.add_argument(
"-l",
"--logging_level",
default="info",
help="the level of logging to use",
choices=["critical", "error", "warning", "info", "debug", "notset"],
)
args = parser.parse_args(sys_argv)
logging.getLogger('ludwig').setLevel(
logging_level_registry[args.logging_level])
global logger
logger = logging.getLogger('ludwig.hyperopt')
set_on_master(args.use_horovod)
if is_on_master():
print_ludwig("Hyperopt", LUDWIG_VERSION)
hyperopt(**vars(args))
def full_experiment(model_definition,
model_definition_file=None,
data_df=None,
data_train_df=None,
data_validation_df=None,
data_test_df=None,
data_csv=None,
data_train_csv=None,
data_validation_csv=None,
data_test_csv=None,
data_hdf5=None,
data_train_hdf5=None,
data_validation_hdf5=None,
data_test_hdf5=None,
train_set_metadata_json=None,
experiment_name='experiment',
model_name='run',
model_load_path=None,
model_resume_path=None,
skip_save_training_description=False,
skip_save_training_statistics=False,
skip_save_model=False,
skip_save_progress=False,
skip_save_log=False,
skip_save_processed_input=False,
skip_save_unprocessed_output=False,
skip_save_test_predictions=False,
skip_save_test_statistics=False,
output_directory='results',
gpus=None,
gpu_memory_limit=None,
allow_parallel_threads=True,
use_horovod=None,
random_seed=default_random_seed,
debug=False,
**kwargs):
"""Trains a model on a dataset's training and validation splits and
uses it to predict on the test split.
It saves the trained model and the statistics of training and testing.
:param model_definition: Model definition which defines the different
parameters of the model, features, preprocessing and training.
:type model_definition: Dictionary
:param model_definition_file: The file that specifies the model definition.
It is a yaml file.
:type model_definition_file: filepath (str)
:param data_csv: A CSV file containing the input data which is used to
train, validate and test a model. The CSV either contains a
split column or will be split.
:type data_csv: filepath (str)
:param data_train_csv: A CSV file containing the input data which is used
to train a model.
:type data_train_csv: filepath (str)
:param data_validation_csv: A CSV file containing the input data which is used
to validate a model..
:type data_validation_csv: filepath (str)
:param data_test_csv: A CSV file containing the input data which is used
to test a model.
:type data_test_csv: filepath (str)
:param data_hdf5: If the dataset is in the hdf5 format, this is used instead
of the csv file.
:type data_hdf5: filepath (str)
:param data_train_hdf5: If the training set is in the hdf5 format, this is
used instead of the csv file.
:type data_train_hdf5: filepath (str)
:param data_validation_hdf5: If the validation set is in the hdf5 format,
this is used instead of the csv file.
:type data_validation_hdf5: filepath (str)
:param data_test_hdf5: If the test set is in the hdf5 format, this is
used instead of the csv file.
:type data_test_hdf5: filepath (str)
:param train_set_metadata_json: If the dataset is in hdf5 format, this is
the associated json file containing metadata.
:type train_set_metadata_json: filepath (str)
:param experiment_name: The name for the experiment.
:type experiment_name: Str
:param model_name: Name of the model that is being used.
:type model_name: Str
:param model_load_path: If this is specified the loaded model will be used
as initialization (useful for transfer learning).
:type model_load_path: filepath (str)
:param model_resume_path: Resumes training of the model from the path
specified. The difference with model_load_path is that also training
statistics like the current epoch and the loss and performance so
far are also resumed effectively continuing a previously interrupted
training process.
:type model_resume_path: filepath (str)
:param skip_save_training_description: Disables saving
the description JSON file.
:type skip_save_training_description: Boolean
:param skip_save_training_statistics: Disables saving
training statistics JSON file.
:type skip_save_training_statistics: Boolean
:param skip_save_model: Disables
saving model weights and hyperparameters each time the model
improves. By default Ludwig saves model weights after each epoch
the validation metric improves, but if the model is really big
that can be time consuming if you do not want to keep
the weights and just find out what performance can a model get
with a set of hyperparameters, use this parameter to skip it,
but the model will not be loadable later on.
:type skip_save_model: Boolean
:param skip_save_progress: Disables saving
progress each epoch. By default Ludwig saves weights and stats
after each epoch for enabling resuming of training, but if
the model is really big that can be time consuming and will uses
twice as much space, use this parameter to skip it, but training
cannot be resumed later on.
:type skip_save_progress: Boolean
:param skip_save_log: Disables saving TensorBoard
logs. By default Ludwig saves logs for the TensorBoard, but if it
is not needed turning it off can slightly increase the
overall speed..
:type skip_save_log: Boolean
:param skip_save_processed_input: If a CSV dataset is provided it is
preprocessed and then saved as an hdf5 and json to avoid running
the preprocessing again. If this parameter is False,
the hdf5 and json file are not saved.
:type skip_save_processed_input: Boolean
:param skip_save_unprocessed_output: By default predictions and
their probabilities are saved in both raw unprocessed numpy files
containing tensors and as postprocessed CSV files
(one for each output feature). If this parameter is True,
only the CSV ones are saved and the numpy ones are skipped.
:type skip_save_unprocessed_output: Boolean
:param skip_save_test_predictions: skips saving test predictions CSV files
:type skip_save_test_predictions: Boolean
:param skip_save_test_statistics: skips saving test statistics JSON file
:type skip_save_test_statistics: Boolean
:param output_directory: The directory that will contain the training
statistics, the saved model and the training progress files.
:type output_directory: filepath (str)
:param gpus: List of GPUs that are available for training.
:type gpus: List
:param gpu_memory_limit: maximum memory in MB to allocate per GPU device.
:type gpu_memory_limit: Integer
:param allow_parallel_threads: allow TensorFlow to use multithreading parallelism
to improve performance at the cost of determinism.
:type allow_parallel_threads: Boolean
:param use_horovod: Flag for using horovod
:type use_horovod: Boolean
:param random_seed: Random seed used for weights initialization,
splits and any other random function.
:type random_seed: Integer
:param debug: If true turns on tfdbg with inf_or_nan checks.
:type debug: Boolean
"""
set_on_master(use_horovod)
(
model,
preprocessed_data,
experiment_dir_name,
_, # train_stats
model_definition,
test_results) = experiment(
model_definition,
model_definition_file=model_definition_file,
data_df=data_df,
data_train_df=data_train_df,
data_validation_df=data_validation_df,
data_test_df=data_test_df,
data_csv=data_csv,
data_train_csv=data_train_csv,
data_validation_csv=data_validation_csv,
data_test_csv=data_test_csv,
data_hdf5=data_hdf5,
data_train_hdf5=data_train_hdf5,
data_validation_hdf5=data_validation_hdf5,
data_test_hdf5=data_test_hdf5,
train_set_metadata_json=train_set_metadata_json,
experiment_name=experiment_name,
model_name=model_name,
model_load_path=model_load_path,
model_resume_path=model_resume_path,
skip_save_training_description=skip_save_training_description,
skip_save_training_statistics=skip_save_training_statistics,
skip_save_model=skip_save_model,
skip_save_progress=skip_save_progress,
skip_save_log=skip_save_log,
skip_save_processed_input=skip_save_processed_input,
output_directory=output_directory,
gpus=gpus,
gpu_memory_limit=gpu_memory_limit,
allow_parallel_threads=allow_parallel_threads,
use_horovod=use_horovod,
random_seed=random_seed,
debug=debug,
**kwargs)
(training_set, validation_set, test_set,
train_set_metadata) = preprocessed_data
if test_set is not None:
# check if we need to create the output dir
if is_on_master():
if not (skip_save_unprocessed_output and skip_save_test_predictions
and skip_save_test_statistics):
if not os.path.exists(experiment_dir_name):
os.makedirs(experiment_dir_name)
# postprocess
postprocessed_output = postprocess(
test_results, model_definition['output_features'],
train_set_metadata, experiment_dir_name,
skip_save_unprocessed_output or not is_on_master())
if is_on_master():
print_test_results(test_results)
if not skip_save_test_predictions:
save_prediction_outputs(postprocessed_output,
experiment_dir_name)
if not skip_save_test_statistics:
save_test_statistics(test_results, experiment_dir_name)
if is_on_master():
logger.info('\nFinished: {0}_{1}'.format(experiment_name, model_name))
logger.info('Saved to: {}'.format(experiment_dir_name))
contrib_command("experiment_save", experiment_dir_name)
return experiment_dir_name
def cli(sys_argv):
parser = argparse.ArgumentParser(
description='This script loads a pretrained model '
'and tests its performance by comparing'
'its predictions with ground truth.',
prog='ludwig test',
usage='%(prog)s [options]')
# ---------------
# Data parameters
# ---------------
group = parser.add_mutually_exclusive_group(required=True)
group.add_argument(
'--data_csv',
help='input data CSV file. '
'If it has a split column, it will be used for splitting '
'(0: train, 1: validation, 2: test), '
'otherwise the dataset will be randomly split')
group.add_argument(
'--data_hdf5',
help='input data HDF5 file. It is an intermediate preprocess version of'
' the input CSV created the first time a CSV file is used in the '
'same directory with the same name and a hdf5 extension')
parser.add_argument(
'--train_set_metadata_json',
help='input metadata JSON file. It is an intermediate preprocess file '
'containing the mappings of the input CSV created the first time '
'a CSV file is used in the same directory with the same name and '
'a json extension')
parser.add_argument('-s',
'--split',
default=TEST,
choices=[TRAINING, VALIDATION, TEST, FULL],
help='the split to test the model on')
# ----------------
# Model parameters
# ----------------
parser.add_argument('-m',
'--model_path',
help='model to load',
required=True)
# -------------------------
# Output results parameters
# -------------------------
parser.add_argument('-od',
'--output_directory',
type=str,
default='results',
help='directory that contains the results')
parser.add_argument('-ssuo',
'--skip_save_unprocessed_output',
help='skips saving intermediate NPY output files',
action='store_true',
default=False)
# ------------------
# Generic parameters
# ------------------
parser.add_argument('-bs',
'--batch_size',
type=int,
default=128,
help='size of batches')
# ------------------
# Runtime parameters
# ------------------
parser.add_argument('-g',
'--gpus',
type=int,
default=0,
help='list of gpu to use')
parser.add_argument(
'-gf',
'--gpu_fraction',
type=float,
default=1.0,
help='fraction of gpu memory to initialize the process with')
parser.add_argument('-uh',
'--use_horovod',
action='store_true',
default=False,
help='uses horovod for distributed training')
parser.add_argument('-dbg',
'--debug',
action='store_true',
default=False,
help='enables debugging mode')
parser.add_argument(
'-l',
'--logging_level',
default='info',
help='the level of logging to use',
choices=['critical', 'error', 'warning', 'info', 'debug', 'notset'])
args = parser.parse_args(sys_argv)
args.evaluate_performance = True
logging.getLogger('ludwig').setLevel(
logging_level_registry[args.logging_level])
set_on_master(args.use_horovod)
if is_on_master():
print_ludwig('Test', LUDWIG_VERSION)
full_predict(**vars(args))
def full_predict(model_path,
data_csv=None,
data_hdf5=None,
split=TEST,
batch_size=128,
skip_save_unprocessed_output=False,
skip_save_test_predictions=False,
skip_save_test_statistics=False,
output_directory='results',
evaluate_performance=True,
gpus=None,
gpu_memory_limit=None,
allow_parallel_threads=True,
use_horovod=None,
debug=False,
**kwargs):
set_on_master(use_horovod)
if is_on_master():
logger.info('Dataset path: {}'.format(
data_csv if data_csv is not None else data_hdf5))
logger.info('Model path: {}'.format(model_path))
logger.info('')
train_set_metadata_json_fp = os.path.join(model_path,
TRAIN_SET_METADATA_FILE_NAME)
# preprocessing
dataset, train_set_metadata = preprocess_for_prediction(
model_path, split, data_csv, data_hdf5, train_set_metadata_json_fp,
evaluate_performance)
# run the prediction
if is_on_master():
print_boxed('LOADING MODEL')
model, model_definition = load_model_and_definition(
model_path,
use_horovod=use_horovod,
gpus=gpus,
gpu_memory_limit=gpu_memory_limit,
allow_parallel_threads=allow_parallel_threads)
prediction_results = predict(dataset, train_set_metadata, model,
model_definition, batch_size,
evaluate_performance, debug)
if is_on_master():
# setup directories and file names
experiment_dir_name = find_non_existing_dir_by_adding_suffix(
output_directory)
# if we are skipping all saving,
# there is no need to create a directory that will remain empty
should_create_exp_dir = not (skip_save_unprocessed_output
and skip_save_test_predictions
and skip_save_test_statistics)
if should_create_exp_dir:
os.makedirs(experiment_dir_name)
# postprocess
postprocessed_output = postprocess(
prediction_results, model_definition['output_features'],
train_set_metadata, experiment_dir_name,
skip_save_unprocessed_output or not is_on_master())
if not skip_save_test_predictions:
save_prediction_outputs(postprocessed_output, experiment_dir_name)
if evaluate_performance:
print_test_results(prediction_results)
if not skip_save_test_statistics:
save_test_statistics(prediction_results, experiment_dir_name)
logger.info('Saved to: {0}'.format(experiment_dir_name))
def cli(sys_argv):
parser = argparse.ArgumentParser(
description='This script trains and tests a model.',
prog='ludwig experiment',
usage='%(prog)s [options]'
)
# ----------------------------
# Experiment naming parameters
# ----------------------------
parser.add_argument(
'--output_directory',
type=str,
default='results',
help='directory that contains the results'
)
parser.add_argument(
'--experiment_name',
type=str,
default='experiment',
help='experiment name'
)
parser.add_argument(
'--model_name',
type=str,
default='run',
help='name for the model'
)
# ---------------
# Data parameters
# ---------------
parser.add_argument(
'--data_csv',
help='input data CSV file. If it has a split column, it will be used '
'for splitting (0: train, 1: validation, 2: test), otherwise the '
'dataset will be randomly split'
)
parser.add_argument('--data_train_csv', help='input train data CSV file')
parser.add_argument(
'--data_validation_csv',
help='input validation data CSV file'
)
parser.add_argument('--data_test_csv', help='input test data CSV file')
parser.add_argument(
'--data_hdf5',
help='input data HDF5 file. It is an intermediate preprocess version of'
' the input CSV created the first time a CSV file is used in the '
'same directory with the same name and a hdf5 extension'
)
parser.add_argument(
'--data_train_hdf5',
help='input train data HDF5 file. It is an intermediate preprocess '
'version of the input CSV created the first time a CSV file is '
'used in the same directory with the same name and a hdf5 '
'extension'
)
parser.add_argument(
'--data_validation_hdf5',
help='input validation data HDF5 file. It is an intermediate preprocess'
' version of the input CSV created the first time a CSV file is '
'used in the same directory with the same name and a hdf5 '
'extension'
)
parser.add_argument(
'--data_test_hdf5',
help='input test data HDF5 file. It is an intermediate preprocess '
'version of the input CSV created the first time a CSV file is '
'used in the same directory with the same name and a hdf5 '
'extension'
)
parser.add_argument(
'--metadata_json',
help='input metadata JSON file. It is an intermediate preprocess file'
' containing the mappings of the input CSV created the first time '
'a CSV file is used in the same directory with the same name and a'
' json extension'
)
parser.add_argument(
'-sspi',
'--skip_save_processed_input',
help='skips saving intermediate HDF5 and JSON files',
action='store_true',
default=False
)
parser.add_argument(
'-ssuo',
'--skip_save_unprocessed_output',
help='skips saving intermediate NPY output files',
action='store_true',
default=False
)
# ----------------
# Model parameters
# ----------------
model_definition = parser.add_mutually_exclusive_group(required=True)
model_definition.add_argument(
'-md',
'--model_definition',
type=yaml.load,
help='model definition'
)
model_definition.add_argument(
'-mdf',
'--model_definition_file',
help='YAML file describing the model. Ignores --model_hyperparameters'
)
parser.add_argument(
'-mlp',
'--model_load_path',
help='path of a pretrained model to load as initialization'
)
parser.add_argument(
'-mrp',
'--model_resume_path',
help='path of a the model directory to resume training of'
)
parser.add_argument(
'-sspw',
'--skip_save_progress_weights',
help='does not save weights after each epoch. By default Ludwig saves '
'weights after each epoch for enabling resuming of training, but '
'if the model is really big that can be time consuming and will '
'use twice as much storage space, use this parameter to skip it.'
)
# ------------------
# Runtime parameters
# ------------------
parser.add_argument(
'-rs',
'--random_seed',
type=int,
default=42,
help='a random seed that is going to be used anywhere there is a call '
'to a random number generator: data splitting, parameter '
'initialization and training set shuffling'
)
parser.add_argument(
'-g',
'--gpus',
nargs='+',
type=int,
default=None,
help='list of GPUs to use'
)
parser.add_argument(
'-gf',
'--gpu_fraction',
type=float,
default=1.0,
help='fraction of gpu memory to initialize the process with'
)
parser.add_argument(
'-uh',
'--use_horovod',
action='store_true',
default=False,
help='uses horovod for distributed training'
)
parser.add_argument(
'-dbg',
'--debug',
action='store_true',
default=False,
help='enables debugging mode'
)
parser.add_argument(
'-l',
'--logging_level',
default='info',
help='the level of logging to use',
choices=['critical', 'error', 'warning', 'info', 'debug', 'notset']
)
args = parser.parse_args(sys_argv)
logging.basicConfig(
stream=sys.stdout,
level=logging_level_registry[args.logging_level],
format='%(message)s'
)
set_on_master(args.use_horovod)
if is_on_master():
print_ludwig('Experiment', LUDWIG_VERSION)
experiment(**vars(args))
def full_train(
model_definition=None,
model_definition_file=None,
data_df=None,
data_train_df=None,
data_validation_df=None,
data_test_df=None,
data_csv=None,
data_train_csv=None,
data_validation_csv=None,
data_test_csv=None,
data_hdf5=None,
data_train_hdf5=None,
data_validation_hdf5=None,
data_test_hdf5=None,
train_set_metadata_json=None,
experiment_name='experiment',
model_name='run',
model_load_path=None,
model_resume_path=None,
skip_save_training_description=False,
skip_save_training_statistics=False,
skip_save_model=False,
skip_save_progress=False,
skip_save_log=False,
skip_save_processed_input=False,
output_directory='results',
gpus=None,
gpu_memory_limit=None,
allow_parallel_threads=True,
use_horovod=None,
random_seed=42,
debug=False,
**kwargs
):
"""*full_train* defines the entire training procedure used by Ludwig's
internals. Requires most of the parameters that are taken into the model.
Builds a full ludwig model and performs the training.
:param data_test_df:
:param data_df:
:param data_train_df:
:param data_validation_df:
:param model_definition: Model definition which defines the different
parameters of the model, features, preprocessing and training.
:type model_definition: Dictionary
:param model_definition_file: The file that specifies the model definition.
It is a yaml file.
:type model_definition_file: filepath (str)
:param data_csv: A CSV file containing the input data which is used to
train, validate and test a model. The CSV either contains a
split column or will be split.
:type data_csv: filepath (str)
:param data_train_csv: A CSV file containing the input data which is used
to train a model.
:type data_train_csv: filepath (str)
:param data_validation_csv: A CSV file containing the input data which is used
to validate a model..
:type data_validation_csv: filepath (str)
:param data_test_csv: A CSV file containing the input data which is used
to test a model.
:type data_test_csv: filepath (str)
:param data_hdf5: If the dataset is in the hdf5 format, this is used instead
of the csv file.
:type data_hdf5: filepath (str)
:param data_train_hdf5: If the training set is in the hdf5 format, this is
used instead of the csv file.
:type data_train_hdf5: filepath (str)
:param data_validation_hdf5: If the validation set is in the hdf5 format,
this is used instead of the csv file.
:type data_validation_hdf5: filepath (str)
:param data_test_hdf5: If the test set is in the hdf5 format, this is
used instead of the csv file.
:type data_test_hdf5: filepath (str)
:param train_set_metadata_json: If the dataset is in hdf5 format, this is
the associated json file containing metadata.
:type train_set_metadata_json: filepath (str)
:param experiment_name: The name for the experiment.
:type experiment_name: Str
:param model_name: Name of the model that is being used.
:type model_name: Str
:param model_load_path: If this is specified the loaded model will be used
as initialization (useful for transfer learning).
:type model_load_path: filepath (str)
:param model_resume_path: Resumes training of the model from the path
specified. The difference with model_load_path is that also training
statistics like the current epoch and the loss and performance so
far are also resumed effectively cotinuing a previously interrupted
training process.
:type model_resume_path: filepath (str)
:param skip_save_training_description: Disables saving
the description JSON file.
:type skip_save_training_description: Boolean
:param skip_save_training_statistics: Disables saving
training statistics JSON file.
:type skip_save_training_statistics: Boolean
:param skip_save_model: Disables saving model weights
and hyperparameters each time the model
improves. By default Ludwig saves model weights after each epoch
the validation metric improves, but if the model is really big
that can be time consuming if you do not want to keep
the weights and just find out what performance can a model get
with a set of hyperparameters, use this parameter to skip it,
but the model will not be loadable later on.
:type skip_save_model: Boolean
:param skip_save_progress: Disables saving
progress each epoch. By default Ludwig saves weights and stats
after each epoch for enabling resuming of training, but if
the model is really big that can be time consuming and will uses
twice as much space, use this parameter to skip it, but training
cannot be resumed later on.
:type skip_save_progress: Boolean
:param skip_save_processed_input: If a CSV dataset is provided it is
preprocessed and then saved as an hdf5 and json to avoid running
the preprocessing again. If this parameter is False,
the hdf5 and json file are not saved.
:type skip_save_processed_input: Boolean
:param skip_save_log: Disables saving TensorBoard
logs. By default Ludwig saves logs for the TensorBoard, but if it
is not needed turning it off can slightly increase the
overall speed..
:type skip_save_progress: Boolean
:param output_directory: The directory that will contain the training
statistics, the saved model and the training progress files.
:type output_directory: filepath (str)
:param gpus: (string, default: `None`) list of GPUs to use (it uses the
same syntax of CUDA_VISIBLE_DEVICES)
:type gpus: str
:param gpu_memory_limit: maximum memory in MB to allocate per GPU device.
:type gpu_memory_limit: Integer
:param allow_parallel_threads: allow TensorFlow to use multithreading parallelism
to improve performance at the cost of determinism.
:type allow_parallel_threads: Boolean
:param random_seed: Random seed used for weights initialization,
splits and any other random function.
:type random_seed: Integer
:param debug: If true turns on tfdbg with inf_or_nan checks.
:type debug: Boolean
:returns: None
"""
set_on_master(use_horovod)
# check for model_definition and model_definition_file
if model_definition is None and model_definition_file is None:
raise ValueError(
'Either model_definition of model_definition_file have to be'
'not None to initialize a LudwigModel'
)
if model_definition is not None and model_definition_file is not None:
raise ValueError(
'Only one between model_definition and '
'model_definition_file can be provided'
)
# merge with default model definition to set defaults
if model_definition_file is not None:
with open(model_definition_file, 'r') as def_file:
model_definition = merge_with_defaults(yaml.safe_load(def_file))
else:
model_definition = merge_with_defaults(model_definition)
# setup directories and file names
experiment_dir_name = None
if model_resume_path is not None:
if os.path.exists(model_resume_path):
experiment_dir_name = model_resume_path
else:
if is_on_master():
logger.info(
'Model resume path does not exists, '
'starting training from scratch'
)
model_resume_path = None
if model_resume_path is None:
if is_on_master():
experiment_dir_name = get_experiment_dir_name(
output_directory,
experiment_name,
model_name
)
else:
experiment_dir_name = None
# if model_load_path is not None, load its train_set_metadata
if model_load_path is not None:
train_set_metadata_json = os.path.join(
model_load_path,
TRAIN_SET_METADATA_FILE_NAME
)
# if we are skipping all saving,
# there is no need to create a directory that will remain empty
should_create_exp_dir = not (
skip_save_training_description and
skip_save_training_statistics and
skip_save_model and
skip_save_progress and
skip_save_log and
skip_save_processed_input
)
description_fn = training_stats_fn = model_dir = None
if is_on_master():
if should_create_exp_dir:
if not os.path.exists(experiment_dir_name):
os.makedirs(experiment_dir_name, exist_ok=True)
description_fn, training_stats_fn, model_dir = get_file_names(
experiment_dir_name)
# save description
description = get_experiment_description(
model_definition,
data_csv=data_csv,
data_train_csv=data_train_csv,
data_validation_csv=data_validation_csv,
data_test_csv=data_test_csv,
data_hdf5=data_hdf5,
data_train_hdf5=data_train_hdf5,
data_validation_hdf5=data_validation_hdf5,
data_test_hdf5=data_test_hdf5,
metadata_json=train_set_metadata_json,
random_seed=random_seed
)
if is_on_master():
if not skip_save_training_description:
save_json(description_fn, description)
# print description
logger.info('Experiment name: {}'.format(experiment_name))
logger.info('Model name: {}'.format(model_name))
logger.info('Output path: {}'.format(experiment_dir_name))
logger.info('\n')
for key, value in description.items():
logger.info('{}: {}'.format(key, pformat(value, indent=4)))
logger.info('\n')
# preprocess
preprocessed_data = preprocess_for_training(
model_definition,
data_df=data_df,
data_train_df=data_train_df,
data_validation_df=data_validation_df,
data_test_df=data_test_df,
data_csv=data_csv,
data_train_csv=data_train_csv,
data_validation_csv=data_validation_csv,
data_test_csv=data_test_csv,
data_hdf5=data_hdf5,
data_train_hdf5=data_train_hdf5,
data_validation_hdf5=data_validation_hdf5,
data_test_hdf5=data_test_hdf5,
train_set_metadata_json=train_set_metadata_json,
skip_save_processed_input=skip_save_processed_input,
preprocessing_params=model_definition['preprocessing'],
random_seed=random_seed
)
(training_set,
validation_set,
test_set,
train_set_metadata) = preprocessed_data
if is_on_master():
logger.info('Training set: {0}'.format(training_set.size))
if validation_set is not None:
logger.info('Validation set: {0}'.format(validation_set.size))
if test_set is not None:
logger.info('Test set: {0}'.format(test_set.size))
# update model definition with metadata properties
update_model_definition_with_metadata(
model_definition,
train_set_metadata
)
if is_on_master():
if not skip_save_model:
# save train set metadata
os.makedirs(model_dir, exist_ok=True)
save_json(
os.path.join(
model_dir,
TRAIN_SET_METADATA_FILE_NAME
),
train_set_metadata
)
contrib_command("train_init", experiment_directory=experiment_dir_name,
experiment_name=experiment_name, model_name=model_name,
output_directory=output_directory,
resume=model_resume_path is not None)
# run the experiment
model, result = train(
training_set=training_set,
validation_set=validation_set,
test_set=test_set,
model_definition=model_definition,
save_path=model_dir,
model_load_path=model_load_path,
resume=model_resume_path is not None,
skip_save_model=skip_save_model,
skip_save_progress=skip_save_progress,
skip_save_log=skip_save_log,
gpus=gpus,
gpu_memory_limit=gpu_memory_limit,
allow_parallel_threads=allow_parallel_threads,
use_horovod=use_horovod,
random_seed=random_seed,
debug=debug
)
train_trainset_stats, train_valisest_stats, train_testset_stats = result
train_stats = {
TRAINING: train_trainset_stats,
VALIDATION: train_valisest_stats,
TEST: train_testset_stats
}
# save training statistics
if is_on_master():
if not skip_save_training_statistics:
save_json(training_stats_fn, train_stats)
# grab the results of the model with highest validation test performance
validation_field = model_definition[TRAINING]['validation_field']
validation_metric = model_definition[TRAINING]['validation_metric']
validation_field_result = train_valisest_stats[validation_field]
best_function = get_best_function(validation_metric)
# results of the model with highest validation test performance
if is_on_master() and validation_set is not None:
epoch_best_vali_metric, best_vali_metric = best_function(
enumerate(validation_field_result[validation_metric]),
key=lambda pair: pair[1]
)
logger.info(
'Best validation model epoch: {0}'.format(
epoch_best_vali_metric + 1)
)
logger.info(
'Best validation model {0} on validation set {1}: {2}'.format(
validation_metric, validation_field, best_vali_metric
))
if test_set is not None:
best_vali_metric_epoch_test_metric = train_testset_stats[
validation_field][validation_metric][epoch_best_vali_metric]
logger.info(
'Best validation model {0} on test set {1}: {2}'.format(
validation_metric,
validation_field,
best_vali_metric_epoch_test_metric
)
)
logger.info('\nFinished: {0}_{1}'.format(experiment_name, model_name))
logger.info('Saved to: {0}'.format(experiment_dir_name))
contrib_command("train_save", experiment_dir_name)
return (
model,
preprocessed_data,
experiment_dir_name,
train_stats,
model_definition
)
