def test_retrieve_cv_folds():
"""
Test to make sure that the fold ids get returned correctly after cross-validation
"""
# Setup
learner = Learner('LogisticRegression')
num_folds = 5
cv_fs, custom_cv_folds = make_cv_folds_data(num_examples_per_fold=2, num_folds=num_folds)
# Test 1: learner.cross_validate() makes the folds itself.
expected_fold_ids = {'EXAMPLE_0': '0',
'EXAMPLE_1': '4',
'EXAMPLE_2': '3',
'EXAMPLE_3': '1',
'EXAMPLE_4': '2',
'EXAMPLE_5': '2',
'EXAMPLE_6': '1',
'EXAMPLE_7': '0',
'EXAMPLE_8': '4',
'EXAMPLE_9': '3'}
_, _, _, skll_fold_ids = learner.cross_validate(cv_fs,
stratified=True,
cv_folds=num_folds,
grid_search=True,
grid_objective='f1_score_micro',
shuffle=False,
save_cv_folds=True)
assert_equal(skll_fold_ids, expected_fold_ids)
# Test 2: if we pass in custom fold ids, those are also preserved.
_, _, _, skll_fold_ids = learner.cross_validate(cv_fs,
stratified=True,
cv_folds=custom_cv_folds,
grid_search=True,
grid_objective='f1_score_micro',
shuffle=False,
save_cv_folds=True)
assert_equal(skll_fold_ids, custom_cv_folds)
# Test 3: when learner.cross_validate() makes the folds but stratified=False
# and grid_search=False, so that KFold is used.
expected_fold_ids = {'EXAMPLE_0': '0',
'EXAMPLE_1': '0',
'EXAMPLE_2': '1',
'EXAMPLE_3': '1',
'EXAMPLE_4': '2',
'EXAMPLE_5': '2',
'EXAMPLE_6': '3',
'EXAMPLE_7': '3',
'EXAMPLE_8': '4',
'EXAMPLE_9': '4'}
_, _, _, skll_fold_ids = learner.cross_validate(cv_fs,
stratified=False,
cv_folds=num_folds,
grid_search=False,
shuffle=False,
save_cv_folds=True)
assert_equal(skll_fold_ids, custom_cv_folds)
def test_retrieve_cv_folds():
"""
Test to make sure that the fold ids get returned correctly after cross-validation
"""
# Setup
learner = Learner('LogisticRegression')
num_folds = 5
cv_fs, custom_cv_folds = make_cv_folds_data(num_examples_per_fold=2, num_folds=num_folds)
# Test 1: learner.cross_validate() makes the folds itself.
expected_fold_ids = {'EXAMPLE_0': '0',
'EXAMPLE_1': '4',
'EXAMPLE_2': '3',
'EXAMPLE_3': '1',
'EXAMPLE_4': '2',
'EXAMPLE_5': '2',
'EXAMPLE_6': '1',
'EXAMPLE_7': '0',
'EXAMPLE_8': '4',
'EXAMPLE_9': '3'}
_, _, _, skll_fold_ids, _ = learner.cross_validate(cv_fs,
stratified=True,
cv_folds=num_folds,
grid_search=True,
grid_objective='f1_score_micro',
shuffle=False,
save_cv_folds=True)
assert_equal(skll_fold_ids, expected_fold_ids)
# Test 2: if we pass in custom fold ids, those are also preserved.
_, _, _, skll_fold_ids, _ = learner.cross_validate(cv_fs,
stratified=True,
cv_folds=custom_cv_folds,
grid_search=True,
grid_objective='f1_score_micro',
shuffle=False,
save_cv_folds=True)
assert_equal(skll_fold_ids, custom_cv_folds)
# Test 3: when learner.cross_validate() makes the folds but stratified=False
# and grid_search=False, so that KFold is used.
expected_fold_ids = {'EXAMPLE_0': '0',
'EXAMPLE_1': '0',
'EXAMPLE_2': '1',
'EXAMPLE_3': '1',
'EXAMPLE_4': '2',
'EXAMPLE_5': '2',
'EXAMPLE_6': '3',
'EXAMPLE_7': '3',
'EXAMPLE_8': '4',
'EXAMPLE_9': '4'}
_, _, _, skll_fold_ids, _ = learner.cross_validate(cv_fs,
stratified=False,
cv_folds=num_folds,
grid_search=False,
shuffle=False,
save_cv_folds=True)
assert_equal(skll_fold_ids, custom_cv_folds)
def check_bad_xval_float_classes(do_stratified_xval):
float_class_fs = make_float_class_data()
prediction_prefix = join(_my_dir, 'output', 'float_class')
learner = Learner('LogisticRegression')
learner.cross_validate(float_class_fs,
stratified=do_stratified_xval,
grid_objective='accuracy',
prediction_prefix=prediction_prefix)
def check_bad_xval_float_classes(do_stratified_xval):
float_class_fs = make_float_class_data()
prediction_prefix = join(_my_dir, 'output', 'float_class')
learner = Learner('LogisticRegression')
learner.cross_validate(float_class_fs,
stratified=do_stratified_xval,
grid_search=True,
grid_objective='accuracy',
prediction_prefix=prediction_prefix)
def test_rare_class():
"""
Test cross-validation when some labels are very rare
"""
rare_class_fs = make_rare_class_data()
prediction_prefix = join(_my_dir, 'output', 'rare_class')
learner = Learner('LogisticRegression')
learner.cross_validate(rare_class_fs,
grid_objective='unweighted_kappa',
prediction_prefix=prediction_prefix)
with open(prediction_prefix + '_predictions.tsv', 'r') as f:
reader = csv.reader(f, dialect='excel-tab')
next(reader)
pred = [row[1] for row in reader]
eq_(len(pred), 15)
def test_xval_float_classes_as_strings():
"""
Test that classification with float labels encoded as strings works
"""
float_class_fs = make_float_class_data(labels_as_strings=True)
prediction_prefix = join(_my_dir, 'output', 'float_class')
learner = Learner('LogisticRegression')
learner.cross_validate(float_class_fs,
grid_objective='accuracy',
prediction_prefix=prediction_prefix)
with open(prediction_prefix + '_predictions.tsv', 'r') as f:
reader = csv.reader(f, dialect='excel-tab')
next(reader)
pred = [row[1] for row in reader]
for p in pred:
assert p in ['1.2', '1.5', '1.8']
def test_rare_class():
"""
Test cross-validation when some labels are very rare
"""
rare_class_fs = make_rare_class_data()
prediction_prefix = join(_my_dir, 'output', 'rare_class')
learner = Learner('LogisticRegression')
learner.cross_validate(rare_class_fs,
grid_objective='unweighted_kappa',
prediction_prefix=prediction_prefix)
with open(prediction_prefix + '_predictions.tsv', 'r') as f:
reader = csv.reader(f, dialect='excel-tab')
next(reader)
pred = [row[1] for row in reader]
eq_(len(pred), 15)
def test_float_classes():
"""
Test classification with labels that look like floats
Make sure that they have been converted to strings as expected
"""
float_class_fs = make_float_class_data()
prediction_prefix = join(_my_dir, 'output', 'float_class')
learner = Learner('LogisticRegression')
learner.cross_validate(float_class_fs,
grid_objective='accuracy',
prediction_prefix=prediction_prefix)
with open(prediction_prefix + '.predictions', 'r') as f:
reader = csv.reader(f, dialect='excel-tab')
next(reader)
pred = [row[1] for row in reader]
for p in pred:
assert p in ['1.2', '1.5', '1.8']
def test_xval_float_classes_as_strings():
"""
Test that classification with float labels encoded as strings works
"""
float_class_fs = make_float_class_data(labels_as_strings=True)
prediction_prefix = join(_my_dir, 'output', 'float_class')
learner = Learner('LogisticRegression')
learner.cross_validate(float_class_fs,
grid_search=True,
grid_objective='accuracy',
prediction_prefix=prediction_prefix)
with open(prediction_prefix + '_predictions.tsv', 'r') as f:
reader = csv.reader(f, dialect='excel-tab')
next(reader)
pred = [row[1] for row in reader]
for p in pred:
assert p in ['1.2', '1.5', '1.8']
def test_float_classes():
"""
Test classification with labels that look like floats
Make sure that they have been converted to strings as expected
"""
float_class_fs = make_float_class_data()
prediction_prefix = join(_my_dir, 'output', 'float_class')
learner = Learner('LogisticRegression')
learner.cross_validate(float_class_fs,
grid_objective='accuracy',
prediction_prefix=prediction_prefix)
with open(prediction_prefix + '.predictions', 'r') as f:
reader = csv.reader(f, dialect='excel-tab')
next(reader)
pred = [row[1] for row in reader]
for p in pred:
assert p in ['1.2', '1.5', '1.8']
def check_learner_api_grid_search_no_objective(task='train'):
(train_fs, test_fs) = make_classification_data(num_examples=500,
train_test_ratio=0.7,
num_features=5,
use_feature_hashing=False,
non_negative=True)
learner = Learner('LogisticRegression')
if task == 'train':
_ = learner.train(train_fs)
else:
_ = learner.cross_validate(train_fs)
def check_learner_api_grid_search_no_objective(task='train'):
(train_fs,
test_fs) = make_classification_data(num_examples=500,
train_test_ratio=0.7,
num_features=5,
use_feature_hashing=False,
non_negative=True)
learner = Learner('LogisticRegression')
if task == 'train':
_ = learner.train(train_fs)
else:
_ = learner.cross_validate(train_fs)
def test_retrieve_cv_folds():
"""
Test to make sure that the fold ids get returned correctly after cross-validation
"""
learner = Learner('LogisticRegression')
num_folds = 5
cv_fs, custom_cv_folds = make_cv_folds_data(num_examples_per_fold=2,
num_folds=num_folds)
# First test where learner.cross_validate makes the folds itself
expected_fold_ids = {
'EXAMPLE_0': '0',
'EXAMPLE_1': '4',
'EXAMPLE_2': '3',
'EXAMPLE_3': '1',
'EXAMPLE_4': '2',
'EXAMPLE_5': '2',
'EXAMPLE_6': '1',
'EXAMPLE_7': '0',
'EXAMPLE_8': '4',
'EXAMPLE_9': '3'
}
_, _, skll_fold_ids = learner.cross_validate(cv_fs,
cv_folds=num_folds,
save_cv_folds=True,
grid_search=True)
assert_equal(skll_fold_ids, expected_fold_ids)
# Now test that if we pass in custom fold ids, those are also preserved
_, _, skll_fold_ids = learner.cross_validate(cv_fs,
cv_folds=custom_cv_folds,
save_cv_folds=True,
grid_search=True)
assert_equal(skll_fold_ids, custom_cv_folds)
def test_retrieve_cv_folds():
"""
Test to make sure that the fold ids get returned correctly after cross-validation
"""
learner = Learner('LogisticRegression')
num_folds = 5
cv_fs, custom_cv_folds = make_cv_folds_data(num_examples_per_fold=2, num_folds=num_folds)
# First test where learner.cross_validate makes the folds itself
expected_fold_ids = {'EXAMPLE_0': '0', 'EXAMPLE_1': '4', 'EXAMPLE_2': '3', 'EXAMPLE_3': '1',
'EXAMPLE_4': '2', 'EXAMPLE_5': '2', 'EXAMPLE_6': '1', 'EXAMPLE_7': '0',
'EXAMPLE_8': '4', 'EXAMPLE_9': '3'}
_, _, skll_fold_ids = learner.cross_validate(cv_fs, cv_folds=num_folds, save_cv_folds=True,
grid_search=True)
assert_equal(skll_fold_ids, expected_fold_ids)
# Now test that if we pass in custom fold ids, those are also preserved
_, _, skll_fold_ids = learner.cross_validate(cv_fs, cv_folds=custom_cv_folds, save_cv_folds=True,
grid_search=True)
assert_equal(skll_fold_ids, custom_cv_folds)
def test_specified_cv_folds():
"""
Test to check cross-validation results with specified folds, feature hashing, and RBFSampler
"""
# This runs four tests.
# The first does not use feature hashing with 9 features (3 numeric, 6
# binary) has pre-specified folds and has less than 60% accuracy for each
# of the 3 folds.
# The second uses feature hashing with 4 features, uses 10 folds (not pre-
# specified) and has more than 70% accuracy accuracy for each of the 10
# folds.
# The third is the same as the first but uses an RBFSampler.
# The fourth is the same as the second but uses an RBFSampler.
for test_value, assert_func, expected_folds, use_hashing, use_sampler in \
[(0.58, assert_less, 3, False, False),
(0.1, assert_greater, 10, True, False),
(0.57, assert_less, 3, False, True),
(0.69, assert_greater, 10, True, True)]:
sampler = 'RBFSampler' if use_sampler else None
learner = Learner('LogisticRegression', sampler=sampler)
cv_fs, custom_cv_folds = make_cv_folds_data(
use_feature_hashing=use_hashing)
folds = custom_cv_folds if not use_hashing else 10
(grid_scores, _, _, _) = \
learner.cross_validate(cv_fs,
cv_folds=folds,
grid_search=True,
grid_objective='f1_score_micro')
fold_test_scores = [t[-2] for t in grid_scores]
overall_score = np.mean(fold_test_scores)
assert_func(overall_score, test_value)
eq_(len(fold_test_scores), expected_folds)
for fold_score in fold_test_scores:
assert_func(fold_score, test_value)
def test_specified_cv_folds():
"""
Test to check cross-validation results with specified folds, feature hashing, and RBFSampler
"""
# This runs four tests.
# The first does not use feature hashing with 9 features (3 numeric, 6
# binary) has pre-specified folds and has less than 60% accuracy for each
# of the 3 folds.
# The second uses feature hashing with 4 features, uses 10 folds (not pre-
# specified) and has more than 70% accuracy accuracy for each of the 10
# folds.
# The third is the same as the first but uses an RBFSampler.
# The fourth is the same as the second but uses an RBFSampler.
for test_value, assert_func, expected_folds, use_hashing, use_sampler in \
[(0.58, assert_less, 3, False, False),
(0.1, assert_greater, 10, True, False),
(0.57, assert_less, 3, False, True),
(0.69, assert_greater, 10, True, True)]:
sampler = 'RBFSampler' if use_sampler else None
learner = Learner('LogisticRegression', sampler=sampler)
cv_fs, custom_cv_folds = make_cv_folds_data(
use_feature_hashing=use_hashing)
folds = custom_cv_folds if not use_hashing else 10
(grid_scores, _, _, _) = \
learner.cross_validate(cv_fs,
cv_folds=folds,
grid_search=True,
grid_objective='f1_score_micro')
fold_test_scores = [t[-2] for t in grid_scores]
overall_score = np.mean(fold_test_scores)
assert_func(overall_score, test_value)
eq_(len(fold_test_scores), expected_folds)
for fold_score in fold_test_scores:
assert_func(fold_score, test_value)
def test_specified_cv_folds():
"""
Test to check cross-validation results with specified folds, feature hashing, and RBFSampler
"""
# This runs four tests.
# The first does not use feature hashing with 9 features (3 numeric, 6
# binary) has pre-specified folds and has less than 60% accuracy for each
# of the 3 folds.
# The second uses feature hashing with 4 features, uses 10 folds (not pre-
# specified) and has more than 70% accuracy accuracy for each of the 10
# folds.
# The third is the same as the first but uses an RBFSampler.
# The fourth is the same as the second but uses an RBFSampler.
for test_value, assert_func, grid_size, use_hashing, use_sampler in [
(0.55, assert_less, 3, False, False),
(0.1, assert_greater, 10, True, False),
(0.53, assert_less, 3, False, True),
(0.7, assert_greater, 10, True, True),
]:
sampler = "RBFSampler" if use_sampler else None
learner = Learner("LogisticRegression", sampler=sampler)
cv_fs, custom_cv_folds = make_cv_folds_data(use_feature_hashing=use_hashing)
folds = custom_cv_folds if not use_hashing else 10
cv_output = learner.cross_validate(cv_fs, cv_folds=folds, grid_search=True)
fold_test_scores = [t[-1] for t in cv_output[0]]
overall_score = np.mean(fold_test_scores)
assert_func(overall_score, test_value)
eq_(len(fold_test_scores), grid_size)
for fold_score in fold_test_scores:
assert_func(fold_score, test_value)
def _classify_featureset(args):
"""
Classification job to be submitted to grid.
Parameters
----------
args : dict
A dictionary with arguments for classifying the
``FeatureSet`` instance.
Returns
-------
res : list of dicts
The results of the classification, in the format
of a list of dictionaries.
Raises
------
ValueError
If extra unknown arguments are passed to the function.
"""
# Extract all the arguments.
# (There doesn't seem to be a better way to do this since one can't specify
# required keyword arguments.)
experiment_name = args.pop("experiment_name")
task = args.pop("task")
sampler = args.pop("sampler")
feature_hasher = args.pop("feature_hasher")
hasher_features = args.pop("hasher_features")
job_name = args.pop("job_name")
featureset = args.pop("featureset")
featureset_name = args.pop("featureset_name")
learner_name = args.pop("learner_name")
train_path = args.pop("train_path")
test_path = args.pop("test_path")
train_set_name = args.pop("train_set_name")
test_set_name = args.pop("test_set_name")
shuffle = args.pop('shuffle')
model_path = args.pop("model_path")
prediction_prefix = args.pop("prediction_prefix")
grid_search = args.pop("grid_search")
grid_objective = args.pop("grid_objective")
output_metrics = args.pop("output_metrics")
suffix = args.pop("suffix")
job_log_file = args.pop("log_file")
job_log_level = args.pop("log_level")
probability = args.pop("probability")
pipeline = args.pop("pipeline")
results_path = args.pop("results_path")
fixed_parameters = args.pop("fixed_parameters")
sampler_parameters = args.pop("sampler_parameters")
param_grid = args.pop("param_grid")
pos_label_str = args.pop("pos_label_str")
overwrite = args.pop("overwrite")
feature_scaling = args.pop("feature_scaling")
min_feature_count = args.pop("min_feature_count")
folds_file = args.pop("folds_file")
grid_search_jobs = args.pop("grid_search_jobs")
grid_search_folds = args.pop("grid_search_folds")
cv_folds = args.pop("cv_folds")
save_cv_folds = args.pop("save_cv_folds")
save_cv_models = args.pop("save_cv_models")
use_folds_file_for_grid_search = args.pop("use_folds_file_for_grid_search")
stratified_folds = args.pop("do_stratified_folds")
label_col = args.pop("label_col")
id_col = args.pop("id_col")
ids_to_floats = args.pop("ids_to_floats")
class_map = args.pop("class_map")
custom_learner_path = args.pop("custom_learner_path")
custom_metric_path = args.pop("custom_metric_path")
quiet = args.pop('quiet', False)
learning_curve_cv_folds = args.pop("learning_curve_cv_folds")
learning_curve_train_sizes = args.pop("learning_curve_train_sizes")
if args:
raise ValueError(("Extra arguments passed to _classify_featureset: "
"{}").format(args.keys()))
start_timestamp = datetime.datetime.now()
# create a new SKLL logger for this specific job and
# use the given log level
logger = get_skll_logger(job_name, job_log_file, log_level=job_log_level)
try:
# log messages
logger.info("Task: {}".format(task))
# check if we have any possible custom metrics
possible_custom_metric_names = []
for metric_name in output_metrics + [grid_objective]:
# metrics that are not in `SCORERS` or `None` are candidates
# (the `None` is a by-product of how jobs with single tuning
# objectives are created)
if metric_name not in SCORERS and metric_name is not None:
possible_custom_metric_names.append(metric_name)
# if the metric is already in `SCORERS`, is it a custom one
# that we already registered? if so, log that
elif metric_name in _CUSTOM_METRICS:
logger.info(
f"custom metric '{metric_name}' is already registered")
# initialize list that will hold any invalid metrics
# that we could not register as custom metrics
invalid_metric_names = []
# if we have possible custom metrics
if possible_custom_metric_names:
# check that we have a file to load them from
if not custom_metric_path:
raise ValueError(
f"invalid metrics specified: {possible_custom_metric_names}"
)
else:
# try to register each possible custom metric
# raise an exception if we fail, if we don't then
# add the custom metric function to `globals()` so
# that it serializes properly for gridmap
for custom_metric_name in possible_custom_metric_names:
try:
custom_metric_func = register_custom_metric(
custom_metric_path, custom_metric_name)
except (AttributeError, NameError, ValueError):
invalid_metric_names.append(custom_metric_name)
else:
logger.info(f"registered '{custom_metric_name}' as a "
f"custom metric")
globals()[custom_metric_name] = custom_metric_func
# raise an error if we have any invalid metrics
if invalid_metric_names:
raise ValueError(
f"invalid metrics specified: {invalid_metric_names}. "
f"If these are custom metrics, check the function "
f"names.")
if task == 'cross_validate':
if isinstance(cv_folds, int):
num_folds = cv_folds
else: # folds_file was used, so count the unique fold ids.
num_folds = len(set(cv_folds.values()))
logger.info("Cross-validating ({} folds) on {}, feature "
"set {} ...".format(num_folds, train_set_name,
featureset))
elif task == 'evaluate':
logger.info("Training on {}, Test on {}, "
"feature set {} ...".format(train_set_name,
test_set_name, featureset))
elif task == 'train':
logger.info("Training on {}, feature set {} ...".format(
train_set_name, featureset))
elif task == 'learning_curve':
logger.info("Generating learning curve "
"({} 80/20 folds, sizes={}, objective={}) on {}, "
"feature set {} ...".format(
learning_curve_cv_folds,
learning_curve_train_sizes, grid_objective,
train_set_name, featureset))
else: # predict
logger.info("Training on {}, Making predictions on {}, "
"feature set {} ...".format(train_set_name,
test_set_name, featureset))
# check whether a trained model on the same data with the same
# featureset already exists if so, load it and then use it on test data
modelfile = join(model_path, '{}.model'.format(job_name))
if (task in ['cross_validate', 'learning_curve']
or not exists(modelfile) or overwrite):
train_examples = load_featureset(train_path,
featureset,
suffix,
label_col=label_col,
id_col=id_col,
ids_to_floats=ids_to_floats,
quiet=quiet,
class_map=class_map,
feature_hasher=feature_hasher,
num_features=hasher_features,
logger=logger)
train_set_size = len(train_examples.ids)
if not train_examples.has_labels:
raise ValueError('Training examples do not have labels')
# initialize a classifer object
learner = Learner(learner_name,
probability=probability,
pipeline=pipeline,
feature_scaling=feature_scaling,
model_kwargs=fixed_parameters,
pos_label_str=pos_label_str,
min_feature_count=min_feature_count,
sampler=sampler,
sampler_kwargs=sampler_parameters,
custom_learner_path=custom_learner_path,
logger=logger)
# load the model if it already exists
else:
# import custom learner into global namespace if we are reusing
# a saved model
if custom_learner_path:
globals()[learner_name] = load_custom_learner(
custom_learner_path, learner_name)
train_set_size = 'unknown'
if exists(modelfile) and not overwrite:
logger.info("Loading pre-existing {} model: {}".format(
learner_name, modelfile))
learner = Learner.from_file(modelfile)
# attach the job logger to this learner
learner.logger = logger
# Load test set if there is one
if task == 'evaluate' or task == 'predict':
test_examples = load_featureset(test_path,
featureset,
suffix,
label_col=label_col,
id_col=id_col,
ids_to_floats=ids_to_floats,
quiet=quiet,
class_map=class_map,
feature_hasher=feature_hasher,
num_features=hasher_features)
test_set_size = len(test_examples.ids)
else:
test_set_size = 'n/a'
# compute information about xval and grid folds that can be put in results
# in readable form
if isinstance(cv_folds, dict):
cv_folds_to_print = '{} via folds file'.format(
len(set(cv_folds.values())))
else:
cv_folds_to_print = str(cv_folds)
if isinstance(grid_search_folds, dict):
grid_search_folds_to_print = \
'{} via folds file'.format(len(set(grid_search_folds.values())))
else:
grid_search_folds_to_print = str(grid_search_folds)
# create a list of dictionaries of the results information
learner_result_dict_base = {
'experiment_name':
experiment_name,
'train_set_name':
train_set_name,
'train_set_size':
train_set_size,
'test_set_name':
test_set_name,
'test_set_size':
test_set_size,
'featureset':
json.dumps(featureset),
'featureset_name':
featureset_name,
'shuffle':
shuffle,
'learner_name':
learner_name,
'task':
task,
'start_timestamp':
start_timestamp.strftime('%d %b %Y %H:%M:'
'%S.%f'),
'version':
__version__,
'feature_scaling':
feature_scaling,
'folds_file':
folds_file,
'grid_search':
grid_search,
'grid_objective':
grid_objective,
'grid_search_folds':
grid_search_folds_to_print,
'min_feature_count':
min_feature_count,
'cv_folds':
cv_folds_to_print,
'using_folds_file':
isinstance(cv_folds, dict) or isinstance(grid_search_folds, dict),
'save_cv_folds':
save_cv_folds,
'save_cv_models':
save_cv_models,
'use_folds_file_for_grid_search':
use_folds_file_for_grid_search,
'stratified_folds':
stratified_folds,
'scikit_learn_version':
SCIKIT_VERSION
}
# check if we're doing cross-validation, because we only load/save
# models when we're not.
task_results = None
if task == 'cross_validate':
logger.info('Cross-validating')
(
task_results, grid_scores, grid_search_cv_results_dicts,
skll_fold_ids, models
) = learner.cross_validate(
train_examples,
shuffle=shuffle,
stratified=stratified_folds,
prediction_prefix=prediction_prefix,
grid_search=grid_search,
grid_search_folds=grid_search_folds,
cv_folds=cv_folds,
grid_objective=grid_objective,
output_metrics=output_metrics,
param_grid=param_grid,
grid_jobs=grid_search_jobs,
save_cv_folds=save_cv_folds,
save_cv_models=save_cv_models,
use_custom_folds_for_grid_search=use_folds_file_for_grid_search
)
if models:
for index, m in enumerate(models, start=1):
modelfile = join(model_path,
'{}_fold{}.model'.format(job_name, index))
m.save(modelfile)
elif task == 'learning_curve':
logger.info("Generating learning curve(s)")
(curve_train_scores, curve_test_scores,
computed_curve_train_sizes) = learner.learning_curve(
train_examples,
grid_objective,
cv_folds=learning_curve_cv_folds,
train_sizes=learning_curve_train_sizes)
else:
# if we have do not have a saved model, we need to train one.
if not exists(modelfile) or overwrite:
logger.info("Featurizing and training new {} model".format(
learner_name))
(best_score, grid_search_cv_results) = learner.train(
train_examples,
shuffle=shuffle,
grid_search=grid_search,
grid_search_folds=grid_search_folds,
grid_objective=grid_objective,
param_grid=param_grid,
grid_jobs=grid_search_jobs)
grid_scores = [best_score]
grid_search_cv_results_dicts = [grid_search_cv_results]
# save model
if model_path:
learner.save(modelfile)
if grid_search:
logger.info("Best {} grid search score: {}".format(
grid_objective, round(best_score, 3)))
else:
grid_scores = [None]
grid_search_cv_results_dicts = [None]
# print out the parameters
param_out = ('{}: {}'.format(param_name, param_value)
for param_name, param_value in
learner.model.get_params().items())
logger.info("Hyperparameters: {}".format(', '.join(param_out)))
# run on test set or cross-validate on training data,
# depending on what was asked for
if task == 'evaluate':
logger.info("Evaluating predictions")
task_results = [
learner.evaluate(test_examples,
prediction_prefix=prediction_prefix,
grid_objective=grid_objective,
output_metrics=output_metrics)
]
elif task == 'predict':
logger.info("Writing predictions")
# we set `class_labels` to `False` so that if the learner is
# probabilistic, probabilities are written instead of labels
learner.predict(test_examples,
prediction_prefix=prediction_prefix,
class_labels=False)
# do nothing here for train
end_timestamp = datetime.datetime.now()
learner_result_dict_base['end_timestamp'] = end_timestamp.strftime(
'%d %b %Y %H:%M:%S.%f')
total_time = end_timestamp - start_timestamp
learner_result_dict_base['total_time'] = str(total_time)
if task == 'cross_validate' or task == 'evaluate':
results_json_path = join(results_path,
'{}.results.json'.format(job_name))
res = _create_learner_result_dicts(task_results, grid_scores,
grid_search_cv_results_dicts,
learner_result_dict_base)
# write out the result dictionary to a json file
with open(results_json_path, 'w') as json_file:
json.dump(res, json_file, cls=NumpyTypeEncoder)
with open(join(results_path, '{}.results'.format(job_name)),
'w') as output_file:
_print_fancy_output(res, output_file)
elif task == 'learning_curve':
results_json_path = join(results_path,
'{}.results.json'.format(job_name))
res = {}
res.update(learner_result_dict_base)
res.update({
'learning_curve_cv_folds':
learning_curve_cv_folds,
'given_curve_train_sizes':
learning_curve_train_sizes,
'learning_curve_train_scores_means':
np.mean(curve_train_scores, axis=1),
'learning_curve_test_scores_means':
np.mean(curve_test_scores, axis=1),
'learning_curve_train_scores_stds':
np.std(curve_train_scores, axis=1, ddof=1),
'learning_curve_test_scores_stds':
np.std(curve_test_scores, axis=1, ddof=1),
'computed_curve_train_sizes':
computed_curve_train_sizes
})
# we need to return and write out a list of dictionaries
res = [res]
# write out the result dictionary to a json file
with open(results_json_path, 'w') as json_file:
json.dump(res, json_file, cls=NumpyTypeEncoder)
# For all other tasks, i.e. train or predict
else:
if results_path:
results_json_path = join(results_path,
'{}.results.json'.format(job_name))
assert len(grid_scores) == 1
assert len(grid_search_cv_results_dicts) == 1
grid_search_cv_results_dict = {"grid_score": grid_scores[0]}
grid_search_cv_results_dict["grid_search_cv_results"] = \
grid_search_cv_results_dicts[0]
grid_search_cv_results_dict.update(learner_result_dict_base)
# write out the result dictionary to a json file
with open(results_json_path, 'w') as json_file:
json.dump(grid_search_cv_results_dict,
json_file,
cls=NumpyTypeEncoder)
res = [learner_result_dict_base]
# write out the cv folds if required
if task == 'cross_validate' and save_cv_folds:
skll_fold_ids_file = experiment_name + '_skll_fold_ids.csv'
with open(join(results_path, skll_fold_ids_file),
'w') as output_file:
_write_skll_folds(skll_fold_ids, output_file)
finally:
close_and_remove_logger_handlers(logger)
return res
def _classify_featureset(args):
""" Classification job to be submitted to grid """
# Extract all the arguments.
# (There doesn't seem to be a better way to do this since one can't specify
# required keyword arguments.)
experiment_name = args.pop("experiment_name")
task = args.pop("task")
sampler = args.pop("sampler")
feature_hasher = args.pop("feature_hasher")
hasher_features = args.pop("hasher_features")
job_name = args.pop("job_name")
featureset = args.pop("featureset")
featureset_name = args.pop("featureset_name")
learner_name = args.pop("learner_name")
train_path = args.pop("train_path")
test_path = args.pop("test_path")
train_set_name = args.pop("train_set_name")
test_set_name = args.pop("test_set_name")
shuffle = args.pop('shuffle')
model_path = args.pop("model_path")
prediction_prefix = args.pop("prediction_prefix")
grid_search = args.pop("grid_search")
grid_objective = args.pop("grid_objective")
suffix = args.pop("suffix")
log_path = args.pop("log_path")
probability = args.pop("probability")
results_path = args.pop("results_path")
fixed_parameters = args.pop("fixed_parameters")
sampler_parameters = args.pop("sampler_parameters")
param_grid = args.pop("param_grid")
pos_label_str = args.pop("pos_label_str")
overwrite = args.pop("overwrite")
feature_scaling = args.pop("feature_scaling")
min_feature_count = args.pop("min_feature_count")
grid_search_jobs = args.pop("grid_search_jobs")
grid_search_folds = args.pop("grid_search_folds")
cv_folds = args.pop("cv_folds")
stratified_folds = args.pop("do_stratified_folds")
label_col = args.pop("label_col")
id_col = args.pop("id_col")
ids_to_floats = args.pop("ids_to_floats")
class_map = args.pop("class_map")
custom_learner_path = args.pop("custom_learner_path")
quiet = args.pop('quiet', False)
if args:
raise ValueError(("Extra arguments passed to _classify_featureset: "
"{}").format(args.keys()))
start_timestamp = datetime.datetime.now()
with open(log_path, 'w') as log_file:
# logging
print("Task:", task, file=log_file)
if task == 'cross_validate':
print(("Cross-validating ({} folds) on {}, feature " +
"set {} ...").format(cv_folds, train_set_name, featureset),
file=log_file)
elif task == 'evaluate':
print(("Training on {}, Test on {}, " +
"feature set {} ...").format(train_set_name, test_set_name,
featureset),
file=log_file)
elif task == 'train':
print("Training on {}, feature set {} ...".format(train_set_name,
featureset),
file=log_file)
else: # predict
print(("Training on {}, Making predictions about {}, " +
"feature set {} ...").format(train_set_name, test_set_name,
featureset),
file=log_file)
# check whether a trained model on the same data with the same
# featureset already exists if so, load it and then use it on test data
modelfile = join(model_path, '{}.model'.format(job_name))
if task == 'cross_validate' or (not exists(modelfile) or
overwrite):
train_examples = _load_featureset(train_path, featureset, suffix,
label_col=label_col,
id_col=id_col,
ids_to_floats=ids_to_floats,
quiet=quiet, class_map=class_map,
feature_hasher=feature_hasher,
num_features=hasher_features)
train_set_size = len(train_examples.ids)
if not train_examples.has_labels:
raise ValueError('Training examples do not have labels')
# initialize a classifer object
learner = Learner(learner_name,
probability=probability,
feature_scaling=feature_scaling,
model_kwargs=fixed_parameters,
pos_label_str=pos_label_str,
min_feature_count=min_feature_count,
sampler=sampler,
sampler_kwargs=sampler_parameters,
custom_learner_path=custom_learner_path)
# load the model if it already exists
else:
# import the custom learner path here in case we are reusing a
# saved model
if custom_learner_path:
_import_custom_learner(custom_learner_path, learner_name)
train_set_size = 'unknown'
if exists(modelfile) and not overwrite:
print(('\tloading pre-existing %s model: %s') % (learner_name,
modelfile))
learner = Learner.from_file(modelfile)
# Load test set if there is one
if task == 'evaluate' or task == 'predict':
test_examples = _load_featureset(test_path, featureset, suffix,
label_col=label_col,
id_col=id_col,
ids_to_floats=ids_to_floats,
quiet=quiet, class_map=class_map,
feature_hasher=feature_hasher,
num_features=hasher_features)
test_set_size = len(test_examples.ids)
else:
test_set_size = 'n/a'
# create a list of dictionaries of the results information
learner_result_dict_base = {'experiment_name': experiment_name,
'train_set_name': train_set_name,
'train_set_size': train_set_size,
'test_set_name': test_set_name,
'test_set_size': test_set_size,
'featureset': json.dumps(featureset),
'featureset_name': featureset_name,
'shuffle': shuffle,
'learner_name': learner_name,
'task': task,
'start_timestamp':
start_timestamp.strftime('%d %b %Y %H:%M:'
'%S.%f'),
'version': __version__,
'feature_scaling': feature_scaling,
'grid_search': grid_search,
'grid_objective': grid_objective,
'grid_search_folds': grid_search_folds,
'min_feature_count': min_feature_count,
'cv_folds': cv_folds,
'stratified_folds': stratified_folds,
'scikit_learn_version': SCIKIT_VERSION}
# check if we're doing cross-validation, because we only load/save
# models when we're not.
task_results = None
if task == 'cross_validate':
print('\tcross-validating', file=log_file)
task_results, grid_scores = learner.cross_validate(
train_examples, shuffle=shuffle, stratified=stratified_folds,
prediction_prefix=prediction_prefix, grid_search=grid_search,
grid_search_folds=grid_search_folds, cv_folds=cv_folds,
grid_objective=grid_objective, param_grid=param_grid,
grid_jobs=grid_search_jobs)
else:
# if we have do not have a saved model, we need to train one.
if not exists(modelfile) or overwrite:
print(('\tfeaturizing and training new ' +
'{} model').format(learner_name),
file=log_file)
if not isinstance(cv_folds, int):
grid_search_folds = cv_folds
best_score = learner.train(train_examples,
shuffle=shuffle,
grid_search=grid_search,
grid_search_folds=grid_search_folds,
grid_objective=grid_objective,
param_grid=param_grid,
grid_jobs=grid_search_jobs)
grid_scores = [best_score]
# save model
if model_path:
learner.save(modelfile)
if grid_search:
# note: bankers' rounding is used in python 3,
# so these scores may be different between runs in
# python 2 and 3 at the final decimal place.
print('\tbest {} grid search score: {}'
.format(grid_objective, round(best_score, 3)),
file=log_file)
else:
grid_scores = [None]
# print out the tuned parameters and best CV score
param_out = ('{}: {}'.format(param_name, param_value)
for param_name, param_value in
iteritems(learner.model.get_params()))
print('\thyperparameters: {}'.format(', '.join(param_out)),
file=log_file)
# run on test set or cross-validate on training data,
# depending on what was asked for
if task == 'evaluate':
print('\tevaluating predictions', file=log_file)
task_results = [learner.evaluate(
test_examples, prediction_prefix=prediction_prefix,
grid_objective=grid_objective)]
elif task == 'predict':
print('\twriting predictions', file=log_file)
learner.predict(test_examples,
prediction_prefix=prediction_prefix)
# do nothing here for train
end_timestamp = datetime.datetime.now()
learner_result_dict_base['end_timestamp'] = end_timestamp.strftime(
'%d %b %Y %H:%M:%S.%f')
total_time = end_timestamp - start_timestamp
learner_result_dict_base['total_time'] = str(total_time)
if task == 'cross_validate' or task == 'evaluate':
results_json_path = join(results_path,
'{}.results.json'.format(job_name))
res = _create_learner_result_dicts(task_results, grid_scores,
learner_result_dict_base)
# write out the result dictionary to a json file
file_mode = 'w' if sys.version_info >= (3, 0) else 'wb'
with open(results_json_path, file_mode) as json_file:
json.dump(res, json_file, cls=NumpyTypeEncoder)
with open(join(results_path,
'{}.results'.format(job_name)),
'w') as output_file:
_print_fancy_output(res, output_file)
else:
res = [learner_result_dict_base]
return res
def _classify_featureset(args):
''' Classification job to be submitted to grid '''
# Extract all the arguments.
# (There doesn't seem to be a better way to do this since one can't specify
# required keyword arguments.)
experiment_name = args.pop("experiment_name")
task = args.pop("task")
job_name = args.pop("job_name")
featureset = args.pop("featureset")
learner_name = args.pop("learner_name")
train_path = args.pop("train_path")
test_path = args.pop("test_path")
train_set_name = args.pop("train_set_name")
test_set_name = args.pop("test_set_name")
model_path = args.pop("model_path")
prediction_prefix = args.pop("prediction_prefix")
grid_search = args.pop("grid_search")
grid_objective = args.pop("grid_objective")
suffix = args.pop("suffix")
log_path = args.pop("log_path")
probability = args.pop("probability")
results_path = args.pop("results_path")
fixed_parameters = args.pop("fixed_parameters")
param_grid = args.pop("param_grid")
pos_label_str = args.pop("pos_label_str")
overwrite = args.pop("overwrite")
feature_scaling = args.pop("feature_scaling")
min_feature_count = args.pop("min_feature_count")
grid_search_jobs = args.pop("grid_search_jobs")
cv_folds = args.pop("cv_folds")
label_col = args.pop("label_col")
ids_to_floats = args.pop("ids_to_floats")
class_map = args.pop("class_map")
quiet = args.pop('quiet', False)
if args:
raise ValueError(("Extra arguments passed to _classify_featureset: " +
"{}").format(args.keys()))
timestamp = datetime.datetime.now().strftime('%d %b %Y %H:%M:%S')
with open(log_path, 'w') as log_file:
# logging
print("Task:", task, file=log_file)
if task == 'cross_validate':
print(("Cross-validating on {}, feature " +
"set {} ...").format(train_set_name, featureset),
file=log_file)
elif task == 'evaluate':
print(("Training on {}, Test on {}, " +
"feature set {} ...").format(train_set_name, test_set_name,
featureset),
file=log_file)
elif task == 'train':
print("Training on {}, feature set {} ...".format(train_set_name,
featureset),
file=log_file)
else: # predict
print(("Training on {}, Making predictions about {}, " +
"feature set {} ...").format(train_set_name, test_set_name,
featureset),
file=log_file)
# check whether a trained model on the same data with the same
# featureset already exists if so, load it and then use it on test data
modelfile = os.path.join(model_path, '{}.model'.format(job_name))
# load the training and test examples
if task == 'cross_validate' or (not os.path.exists(modelfile) or
overwrite):
train_examples = _load_featureset(train_path, featureset, suffix,
label_col=label_col,
ids_to_floats=ids_to_floats,
quiet=quiet, class_map=class_map)
# initialize a classifer object
learner = Learner(learner_name,
probability=probability,
feature_scaling=feature_scaling,
model_kwargs=fixed_parameters,
pos_label_str=pos_label_str,
min_feature_count=min_feature_count)
# load the model if it already exists
else:
if os.path.exists(modelfile) and not overwrite:
print(('\tloading pre-existing {} ' +
'model: {}').format(learner_name, modelfile))
learner = Learner.from_file(modelfile)
# Load test set if there is one
if task == 'evaluate' or task == 'predict':
test_examples = _load_featureset(test_path, featureset, suffix,
label_col=label_col,
ids_to_floats=ids_to_floats,
quiet=quiet, class_map=class_map,
unlabelled=True)
# create a list of dictionaries of the results information
learner_result_dict_base = {'experiment_name': experiment_name,
'train_set_name': train_set_name,
'test_set_name': test_set_name,
'featureset': json.dumps(featureset),
'learner_name': learner_name,
'task': task,
'timestamp': timestamp,
'version': __version__,
'feature_scaling': feature_scaling,
'grid_search': grid_search,
'grid_objective': grid_objective,
'min_feature_count': min_feature_count}
# check if we're doing cross-validation, because we only load/save
# models when we're not.
task_results = None
if task == 'cross_validate':
print('\tcross-validating', file=log_file)
task_results, grid_scores = learner.cross_validate(train_examples,
prediction_prefix=prediction_prefix,
grid_search=grid_search,
cv_folds=cv_folds,
grid_objective=grid_objective,
param_grid=param_grid,
grid_jobs=grid_search_jobs)
else:
# if we have do not have a saved model, we need to train one.
if not os.path.exists(modelfile) or overwrite:
print(('\tfeaturizing and training new ' +
'{} model').format(learner_name),
file=log_file)
grid_search_folds = 5
if not isinstance(cv_folds, int):
grid_search_folds = cv_folds
best_score = learner.train(train_examples,
grid_search=grid_search,
grid_search_folds=grid_search_folds,
grid_objective=grid_objective,
param_grid=param_grid,
grid_jobs=grid_search_jobs)
grid_scores = [best_score]
# save model
if model_path:
learner.save(modelfile)
if grid_search:
print('\tbest {} grid search score: {}'
.format(grid_objective, round(best_score, 3)),
file=log_file)
else:
grid_scores = [None]
# print out the tuned parameters and best CV score
param_out = ('{}: {}'.format(param_name, param_value)
for param_name, param_value in
iteritems(learner.model.get_params()))
print('\thyperparameters: {}'.format(', '.join(param_out)),
file=log_file)
# run on test set or cross-validate on training data,
# depending on what was asked for
if task == 'evaluate':
print('\tevaluating predictions', file=log_file)
task_results = [learner.evaluate(
test_examples, prediction_prefix=prediction_prefix,
grid_objective=grid_objective)]
elif task == 'predict':
print('\twriting predictions', file=log_file)
learner.predict(test_examples,
prediction_prefix=prediction_prefix)
# do nothing here for train
if task == 'cross_validate' or task == 'evaluate':
results_json_path = os.path.join(results_path,
'{}.results.json'.format(job_name))
res = _create_learner_result_dicts(task_results, grid_scores,
learner_result_dict_base)
# write out the result dictionary to a json file
file_mode = 'w' if sys.version_info >= (3, 0) else 'wb'
with open(results_json_path, file_mode) as json_file:
json.dump(res, json_file)
with open(os.path.join(results_path, '{}.results'.format(job_name)),
'w') as output_file:
_print_fancy_output(res, output_file)
else:
res = [learner_result_dict_base]
return res
def _classify_featureset(args):
''' Classification job to be submitted to grid '''
# Extract all the arguments.
# (There doesn't seem to be a better way to do this since one can't specify
# required keyword arguments.)
experiment_name = args.pop("experiment_name")
task = args.pop("task")
job_name = args.pop("job_name")
featureset = args.pop("featureset")
learner_name = args.pop("learner_name")
train_path = args.pop("train_path")
test_path = args.pop("test_path")
train_set_name = args.pop("train_set_name")
test_set_name = args.pop("test_set_name")
model_path = args.pop("model_path")
prediction_prefix = args.pop("prediction_prefix")
grid_search = args.pop("grid_search")
grid_objective = args.pop("grid_objective")
suffix = args.pop("suffix")
log_path = args.pop("log_path")
probability = args.pop("probability")
results_path = args.pop("results_path")
fixed_parameters = args.pop("fixed_parameters")
param_grid = args.pop("param_grid")
pos_label_str = args.pop("pos_label_str")
overwrite = args.pop("overwrite")
feature_scaling = args.pop("feature_scaling")
min_feature_count = args.pop("min_feature_count")
grid_search_jobs = args.pop("grid_search_jobs")
cv_folds = args.pop("cv_folds")
label_col = args.pop("label_col")
ids_to_floats = args.pop("ids_to_floats")
class_map = args.pop("class_map")
quiet = args.pop('quiet', False)
if args:
raise ValueError(("Extra arguments passed to _classify_featureset: " +
"{}").format(args.keys()))
timestamp = datetime.datetime.now().strftime('%d %b %Y %H:%M:%S')
with open(log_path, 'w') as log_file:
# logging
print("Task:", task, file=log_file)
if task == 'cross_validate':
print(("Cross-validating on {}, feature " + "set {} ...").format(
train_set_name, featureset),
file=log_file)
elif task == 'evaluate':
print(
("Training on {}, Test on {}, " + "feature set {} ...").format(
train_set_name, test_set_name, featureset),
file=log_file)
elif task == 'train':
print("Training on {}, feature set {} ...".format(
train_set_name, featureset),
file=log_file)
else: # predict
print(("Training on {}, Making predictions about {}, " +
"feature set {} ...").format(train_set_name, test_set_name,
featureset),
file=log_file)
# check whether a trained model on the same data with the same
# featureset already exists if so, load it and then use it on test data
modelfile = os.path.join(model_path, '{}.model'.format(job_name))
# load the training and test examples
if task == 'cross_validate' or (not os.path.exists(modelfile)
or overwrite):
train_examples = _load_featureset(train_path,
featureset,
suffix,
label_col=label_col,
ids_to_floats=ids_to_floats,
quiet=quiet,
class_map=class_map)
# initialize a classifer object
learner = Learner(learner_name,
probability=probability,
feature_scaling=feature_scaling,
model_kwargs=fixed_parameters,
pos_label_str=pos_label_str,
min_feature_count=min_feature_count)
# load the model if it already exists
else:
if os.path.exists(modelfile) and not overwrite:
print(('\tloading pre-existing {} ' + 'model: {}').format(
learner_name, modelfile))
learner = Learner.from_file(modelfile)
# Load test set if there is one
if task == 'evaluate' or task == 'predict':
test_examples = _load_featureset(test_path,
featureset,
suffix,
label_col=label_col,
ids_to_floats=ids_to_floats,
quiet=quiet,
class_map=class_map,
unlabelled=True)
# create a list of dictionaries of the results information
learner_result_dict_base = {
'experiment_name': experiment_name,
'train_set_name': train_set_name,
'test_set_name': test_set_name,
'featureset': json.dumps(featureset),
'learner_name': learner_name,
'task': task,
'timestamp': timestamp,
'version': __version__,
'feature_scaling': feature_scaling,
'grid_search': grid_search,
'grid_objective': grid_objective,
'min_feature_count': min_feature_count
}
# check if we're doing cross-validation, because we only load/save
# models when we're not.
task_results = None
if task == 'cross_validate':
print('\tcross-validating', file=log_file)
task_results, grid_scores = learner.cross_validate(
train_examples,
prediction_prefix=prediction_prefix,
grid_search=grid_search,
cv_folds=cv_folds,
grid_objective=grid_objective,
param_grid=param_grid,
grid_jobs=grid_search_jobs)
else:
# if we have do not have a saved model, we need to train one.
if not os.path.exists(modelfile) or overwrite:
print(('\tfeaturizing and training new ' +
'{} model').format(learner_name),
file=log_file)
grid_search_folds = 5
if not isinstance(cv_folds, int):
grid_search_folds = cv_folds
best_score = learner.train(train_examples,
grid_search=grid_search,
grid_search_folds=grid_search_folds,
grid_objective=grid_objective,
param_grid=param_grid,
grid_jobs=grid_search_jobs)
grid_scores = [best_score]
# save model
if model_path:
learner.save(modelfile)
if grid_search:
# note: bankers' rounding is used in python 3,
# so these scores may be different between runs in
# python 2 and 3 at the final decimal place.
print('\tbest {} grid search score: {}'.format(
grid_objective, round(best_score, 3)),
file=log_file)
else:
grid_scores = [None]
# print out the tuned parameters and best CV score
param_out = ('{}: {}'.format(param_name, param_value)
for param_name, param_value in iteritems(
learner.model.get_params()))
print('\thyperparameters: {}'.format(', '.join(param_out)),
file=log_file)
# run on test set or cross-validate on training data,
# depending on what was asked for
if task == 'evaluate':
print('\tevaluating predictions', file=log_file)
task_results = [
learner.evaluate(test_examples,
prediction_prefix=prediction_prefix,
grid_objective=grid_objective)
]
elif task == 'predict':
print('\twriting predictions', file=log_file)
learner.predict(test_examples,
prediction_prefix=prediction_prefix)
# do nothing here for train
if task == 'cross_validate' or task == 'evaluate':
results_json_path = os.path.join(
results_path, '{}.results.json'.format(job_name))
res = _create_learner_result_dicts(task_results, grid_scores,
learner_result_dict_base)
# write out the result dictionary to a json file
file_mode = 'w' if sys.version_info >= (3, 0) else 'wb'
with open(results_json_path, file_mode) as json_file:
json.dump(res, json_file)
with open(
os.path.join(results_path, '{}.results'.format(job_name)),
'w') as output_file:
_print_fancy_output(res, output_file)
else:
res = [learner_result_dict_base]
return res
def _classify_featureset(args):
""" Classification job to be submitted to grid """
# Extract all the arguments.
# (There doesn't seem to be a better way to do this since one can't specify
# required keyword arguments.)
experiment_name = args.pop("experiment_name")
task = args.pop("task")
sampler = args.pop("sampler")
feature_hasher = args.pop("feature_hasher")
hasher_features = args.pop("hasher_features")
job_name = args.pop("job_name")
featureset = args.pop("featureset")
featureset_name = args.pop("featureset_name")
learner_name = args.pop("learner_name")
train_path = args.pop("train_path")
test_path = args.pop("test_path")
train_set_name = args.pop("train_set_name")
test_set_name = args.pop("test_set_name")
shuffle = args.pop('shuffle')
model_path = args.pop("model_path")
prediction_prefix = args.pop("prediction_prefix")
grid_search = args.pop("grid_search")
grid_objective = args.pop("grid_objective")
suffix = args.pop("suffix")
log_path = args.pop("log_path")
probability = args.pop("probability")
results_path = args.pop("results_path")
fixed_parameters = args.pop("fixed_parameters")
sampler_parameters = args.pop("sampler_parameters")
param_grid = args.pop("param_grid")
pos_label_str = args.pop("pos_label_str")
overwrite = args.pop("overwrite")
feature_scaling = args.pop("feature_scaling")
min_feature_count = args.pop("min_feature_count")
grid_search_jobs = args.pop("grid_search_jobs")
grid_search_folds = args.pop("grid_search_folds")
cv_folds = args.pop("cv_folds")
save_cv_folds = args.pop("save_cv_folds")
stratified_folds = args.pop("do_stratified_folds")
label_col = args.pop("label_col")
id_col = args.pop("id_col")
ids_to_floats = args.pop("ids_to_floats")
class_map = args.pop("class_map")
custom_learner_path = args.pop("custom_learner_path")
quiet = args.pop('quiet', False)
if args:
raise ValueError(("Extra arguments passed to _classify_featureset: "
"{}").format(args.keys()))
start_timestamp = datetime.datetime.now()
with open(log_path, 'w') as log_file:
# logging
print("Task:", task, file=log_file)
if task == 'cross_validate':
print(("Cross-validating ({} folds) on {}, feature " +
"set {} ...").format(cv_folds, train_set_name, featureset),
file=log_file)
elif task == 'evaluate':
print(("Training on {}, Test on {}, " +
"feature set {} ...").format(train_set_name, test_set_name,
featureset),
file=log_file)
elif task == 'train':
print("Training on {}, feature set {} ...".format(train_set_name,
featureset),
file=log_file)
else: # predict
print(("Training on {}, Making predictions about {}, " +
"feature set {} ...").format(train_set_name, test_set_name,
featureset),
file=log_file)
# check whether a trained model on the same data with the same
# featureset already exists if so, load it and then use it on test data
modelfile = join(model_path, '{}.model'.format(job_name))
if task == 'cross_validate' or (not exists(modelfile) or
overwrite):
train_examples = _load_featureset(train_path, featureset, suffix,
label_col=label_col,
id_col=id_col,
ids_to_floats=ids_to_floats,
quiet=quiet, class_map=class_map,
feature_hasher=feature_hasher,
num_features=hasher_features)
train_set_size = len(train_examples.ids)
if not train_examples.has_labels:
raise ValueError('Training examples do not have labels')
# initialize a classifer object
learner = Learner(learner_name,
probability=probability,
feature_scaling=feature_scaling,
model_kwargs=fixed_parameters,
pos_label_str=pos_label_str,
min_feature_count=min_feature_count,
sampler=sampler,
sampler_kwargs=sampler_parameters,
custom_learner_path=custom_learner_path)
# load the model if it already exists
else:
# import the custom learner path here in case we are reusing a
# saved model
if custom_learner_path:
_import_custom_learner(custom_learner_path, learner_name)
train_set_size = 'unknown'
if exists(modelfile) and not overwrite:
print(('\tloading pre-existing %s model: %s') % (learner_name,
modelfile))
learner = Learner.from_file(modelfile)
# Load test set if there is one
if task == 'evaluate' or task == 'predict':
test_examples = _load_featureset(test_path, featureset, suffix,
label_col=label_col,
id_col=id_col,
ids_to_floats=ids_to_floats,
quiet=quiet, class_map=class_map,
feature_hasher=feature_hasher,
num_features=hasher_features)
test_set_size = len(test_examples.ids)
else:
test_set_size = 'n/a'
# create a list of dictionaries of the results information
learner_result_dict_base = {'experiment_name': experiment_name,
'train_set_name': train_set_name,
'train_set_size': train_set_size,
'test_set_name': test_set_name,
'test_set_size': test_set_size,
'featureset': json.dumps(featureset),
'featureset_name': featureset_name,
'shuffle': shuffle,
'learner_name': learner_name,
'task': task,
'start_timestamp':
start_timestamp.strftime('%d %b %Y %H:%M:'
'%S.%f'),
'version': __version__,
'feature_scaling': feature_scaling,
'grid_search': grid_search,
'grid_objective': grid_objective,
'grid_search_folds': grid_search_folds,
'min_feature_count': min_feature_count,
'cv_folds': cv_folds,
'save_cv_folds': save_cv_folds,
'stratified_folds': stratified_folds,
'scikit_learn_version': SCIKIT_VERSION}
# check if we're doing cross-validation, because we only load/save
# models when we're not.
task_results = None
if task == 'cross_validate':
print('\tcross-validating', file=log_file)
task_results, grid_scores, skll_fold_ids = learner.cross_validate(
train_examples, shuffle=shuffle, stratified=stratified_folds,
prediction_prefix=prediction_prefix, grid_search=grid_search,
grid_search_folds=grid_search_folds, cv_folds=cv_folds,
grid_objective=grid_objective, param_grid=param_grid,
grid_jobs=grid_search_jobs, save_cv_folds=save_cv_folds)
else:
# if we have do not have a saved model, we need to train one.
if not exists(modelfile) or overwrite:
print(('\tfeaturizing and training new ' +
'{} model').format(learner_name),
file=log_file)
if not isinstance(cv_folds, int):
grid_search_folds = cv_folds
best_score = learner.train(train_examples,
shuffle=shuffle,
grid_search=grid_search,
grid_search_folds=grid_search_folds,
grid_objective=grid_objective,
param_grid=param_grid,
grid_jobs=grid_search_jobs)
grid_scores = [best_score]
# save model
if model_path:
learner.save(modelfile)
if grid_search:
# note: bankers' rounding is used in python 3,
# so these scores may be different between runs in
# python 2 and 3 at the final decimal place.
print('\tbest {} grid search score: {}'
.format(grid_objective, round(best_score, 3)),
file=log_file)
else:
grid_scores = [None]
# print out the tuned parameters and best CV score
param_out = ('{}: {}'.format(param_name, param_value)
for param_name, param_value in
iteritems(learner.model.get_params()))
print('\thyperparameters: {}'.format(', '.join(param_out)),
file=log_file)
# run on test set or cross-validate on training data,
# depending on what was asked for
if task == 'evaluate':
print('\tevaluating predictions', file=log_file)
task_results = [learner.evaluate(
test_examples, prediction_prefix=prediction_prefix,
grid_objective=grid_objective)]
elif task == 'predict':
print('\twriting predictions', file=log_file)
learner.predict(test_examples,
prediction_prefix=prediction_prefix)
# do nothing here for train
end_timestamp = datetime.datetime.now()
learner_result_dict_base['end_timestamp'] = end_timestamp.strftime(
'%d %b %Y %H:%M:%S.%f')
total_time = end_timestamp - start_timestamp
learner_result_dict_base['total_time'] = str(total_time)
if task == 'cross_validate' or task == 'evaluate':
results_json_path = join(results_path,
'{}.results.json'.format(job_name))
res = _create_learner_result_dicts(task_results, grid_scores,
learner_result_dict_base)
# write out the result dictionary to a json file
file_mode = 'w' if sys.version_info >= (3, 0) else 'wb'
with open(results_json_path, file_mode) as json_file:
json.dump(res, json_file, cls=NumpyTypeEncoder)
with open(join(results_path,
'{}.results'.format(job_name)),
'w') as output_file:
_print_fancy_output(res, output_file)
else:
res = [learner_result_dict_base]
# write out the cv folds if required
if task == 'cross_validate' and save_cv_folds:
skll_fold_ids_file = experiment_name + '_skll_fold_ids.csv'
file_mode = 'w' if sys.version_info >= (3, 0) else 'wb'
with open(join(results_path, skll_fold_ids_file),
file_mode) as output_file:
_write_skll_folds(skll_fold_ids, output_file)
return res
