def test_features(feature_extraction, split_ta):
if feature_extraction in REQUIRES_EXTRA_DEPS and not ADVANCED_DEPS[
"tensorflow"]:
pytest.skip()
embedding_fp = os.path.join("tests", "demo_data", "generic.vec")
data_fp = os.path.join("tests", "demo_data", "generic.csv")
as_data = ASReviewData.from_file(data_fp)
texts = as_data.texts
if feature_extraction.startswith("embedding-"):
model = get_feature_model(feature_extraction,
split_ta=split_ta,
embedding_fp=embedding_fp)
else:
model = get_feature_model(feature_extraction, split_ta=split_ta)
X = model.fit_transform(texts,
titles=as_data.title,
abstracts=as_data.abstract)
assert X.shape[0] == len(as_data.title)
assert X.shape[1] > 0
assert isinstance(model.param, dict)
assert model.name == feature_extraction
def get_hyper_space(self):
model_hs, model_hc = get_model(self.model_name).hyper_space()
query_hs, query_hc = get_query_model(self.query_name).hyper_space()
balance_hs, balance_hc = get_balance_model(
self.balance_name).hyper_space()
feature_hs, feature_hc = get_feature_model(
self.feature_name).hyper_space()
hyper_space = {**model_hs, **query_hs, **balance_hs, **feature_hs}
hyper_choices = {**model_hc, **query_hc, **balance_hc, **feature_hc}
return hyper_space, hyper_choices
def test_features(feature_extraction, split_ta):
embedding_fp = os.path.join("test", "demo_data", "generic.vec")
data_fp = os.path.join("test", "demo_data", "generic.csv")
as_data = ASReviewData.from_file(data_fp)
texts = as_data.texts
if feature_extraction.startswith("embedding-"):
model = get_feature_model(feature_extraction,
split_ta=split_ta,
embedding_fp=embedding_fp)
else:
model = get_feature_model(feature_extraction, split_ta=split_ta)
X = model.fit_transform(texts,
titles=as_data.title,
abstracts=as_data.abstract)
assert X.shape[0] == len(as_data.title)
assert X.shape[1] > 0
assert isinstance(model.param, dict)
assert model.name == feature_extraction
def from_file(self, config_file):
""" Fill the contents of settings by reading a config file.
Arguments
---------
config_file: str
Source configuration file.
"""
if config_file is None or not os.path.isfile(config_file):
if config_file is not None:
print(f"Didn't find configuration file: {config_file}")
return
config = ConfigParser()
config.optionxform = str
config.read(config_file)
# Read the each of the sections.
for sect in config:
if sect == "global_settings":
for key, value in config.items(sect):
try:
setattr(self, key, SETTINGS_TYPE_DICT[key](value))
except (KeyError, TypeError):
print(f"Warning: value with key '{key}' is ignored "
"(spelling mistake, wrong type?).")
elif sect in [
"model_param", "query_param", "balance_param",
"feature_param"
]:
setattr(self, sect, dict(config.items(sect)))
elif sect != "DEFAULT":
print(f"Warning: section [{sect}] is ignored in "
f"config file {config_file}")
model = get_model(self.model)
_convert_types(model.default_param, self.model_param)
balance_model = get_balance_model(self.balance_strategy)
_convert_types(balance_model.default_param, self.balance_param)
query_model = get_query_model(self.query_strategy)
_convert_types(query_model.default_param, self.query_param)
feature_model = get_feature_model(self.feature_extraction)
_convert_types(feature_model.default_param, self.feature_param)
def get_reviewer(dataset,
mode="simulate",
model=DEFAULT_MODEL,
query_strategy=DEFAULT_QUERY_STRATEGY,
balance_strategy=DEFAULT_BALANCE_STRATEGY,
feature_extraction=DEFAULT_FEATURE_EXTRACTION,
n_instances=DEFAULT_N_INSTANCES,
n_papers=None,
n_queries=None,
embedding_fp=None,
verbose=0,
prior_idx=None,
n_prior_included=DEFAULT_N_PRIOR_INCLUDED,
n_prior_excluded=DEFAULT_N_PRIOR_EXCLUDED,
config_file=None,
state_file=None,
model_param=None,
query_param=None,
balance_param=None,
feature_param=None,
abstract_only=False,
included_dataset=[],
excluded_dataset=[],
prior_dataset=[],
new=False,
**kwargs):
"""Get a review object from arguments.
See __main__.py for a description of the arguments.
"""
as_data = create_as_data(dataset,
included_dataset,
excluded_dataset,
prior_dataset,
new=new)
if len(as_data) == 0:
raise ValueError("Supply at least one dataset"
" with at least one record.")
cli_settings = ASReviewSettings(model=model,
n_instances=n_instances,
n_queries=n_queries,
n_papers=n_papers,
n_prior_included=n_prior_included,
n_prior_excluded=n_prior_excluded,
query_strategy=query_strategy,
balance_strategy=balance_strategy,
feature_extraction=feature_extraction,
mode=mode,
data_fp=None,
abstract_only=abstract_only)
cli_settings.from_file(config_file)
if state_file is not None:
with open_state(state_file) as state:
if state.is_empty():
state.settings = cli_settings
settings = state.settings
else:
settings = cli_settings
if n_queries is not None:
settings.n_queries = n_queries
if n_papers is not None:
settings.n_papers = n_papers
if model_param is not None:
settings.model_param = model_param
if query_param is not None:
settings.query_param = query_param
if balance_param is not None:
settings.balance_param = balance_param
if feature_param is not None:
settings.feature_param = feature_param
# Check if mode is valid
if mode in AVAILABLE_REVIEW_CLASSES:
logging.info(f"Start review in '{mode}' mode.")
else:
raise ValueError(f"Unknown mode '{mode}'.")
logging.debug(settings)
train_model = get_model(settings.model, **settings.model_param)
query_model = get_query_model(settings.query_strategy,
**settings.query_param)
balance_model = get_balance_model(settings.balance_strategy,
**settings.balance_param)
feature_model = get_feature_model(settings.feature_extraction,
**settings.feature_param)
if train_model.name.startswith("lstm-"):
texts = as_data.texts
train_model.embedding_matrix = feature_model.get_embedding_matrix(
texts, embedding_fp)
# Initialize the review class.
if mode == "simulate":
reviewer = ReviewSimulate(as_data,
model=train_model,
query_model=query_model,
balance_model=balance_model,
feature_model=feature_model,
n_papers=settings.n_papers,
n_instances=settings.n_instances,
n_queries=settings.n_queries,
verbose=verbose,
prior_idx=prior_idx,
n_prior_included=settings.n_prior_included,
n_prior_excluded=settings.n_prior_excluded,
state_file=state_file,
data_fp=dataset,
**kwargs)
elif mode == "minimal":
reviewer = MinimalReview(as_data,
model=train_model,
query_model=query_model,
balance_model=balance_model,
feature_model=feature_model,
n_papers=settings.n_papers,
n_instances=settings.n_instances,
n_queries=settings.n_queries,
verbose=verbose,
state_file=state_file,
data_fp=dataset,
**kwargs)
else:
raise ValueError("Error finding mode, should never come here...")
return reviewer
def get_reviewer(dataset,
mode='oracle',
model=DEFAULT_MODEL,
query_strategy=DEFAULT_QUERY_STRATEGY,
balance_strategy=DEFAULT_BALANCE_STRATEGY,
feature_extraction=DEFAULT_FEATURE_EXTRACTION,
n_instances=DEFAULT_N_INSTANCES,
n_papers=None,
n_queries=None,
embedding_fp=None,
verbose=0,
prior_included=None,
prior_excluded=None,
n_prior_included=DEFAULT_N_PRIOR_INCLUDED,
n_prior_excluded=DEFAULT_N_PRIOR_EXCLUDED,
config_file=None,
log_file=None,
model_param=None,
query_param=None,
balance_param=None,
feature_param=None,
abstract_only=False,
extra_dataset=[],
**kwargs
):
""" Get a review object from arguments. See __main__.py for a description
Of the arguments.
"""
# Find the URL of the datasets if the dataset is an example dataset.
if dataset in DEMO_DATASETS.keys():
dataset = DEMO_DATASETS[dataset]
cli_settings = ASReviewSettings(
model=model, n_instances=n_instances, n_queries=n_queries,
n_papers=n_papers, n_prior_included=n_prior_included,
n_prior_excluded=n_prior_excluded, query_strategy=query_strategy,
balance_strategy=balance_strategy,
feature_extraction=feature_extraction,
mode=mode, data_fp=dataset,
abstract_only=abstract_only)
cli_settings.from_file(config_file)
if log_file is not None:
with open_logger(log_file) as logger:
if logger.is_empty():
logger.add_settings(cli_settings)
settings = logger.settings
else:
settings = cli_settings
logger = None
if n_queries is not None:
settings.n_queries = n_queries
if n_papers is not None:
settings.n_papers = n_papers
if model_param is not None:
settings.model_param = model_param
if query_param is not None:
settings.query_param = query_param
if balance_param is not None:
settings.balance_param = balance_param
if feature_param is not None:
settings.feature_param = feature_param
# Check if mode is valid
if mode in AVAILABLE_REVIEW_CLASSES:
logging.info(f"Start review in '{mode}' mode.")
else:
raise ValueError(f"Unknown mode '{mode}'.")
logging.debug(settings)
as_data = ASReviewData.from_file(dataset, extra_dataset=extra_dataset,
abstract_only=settings.abstract_only)
texts = as_data.texts
y = as_data.labels
data_prior_included, data_prior_excluded = as_data.get_priors()
if len(data_prior_included) != 0:
if prior_included is None:
prior_included = []
prior_included.extend(data_prior_included.tolist())
if len(data_prior_excluded) != 0:
if prior_excluded is None:
prior_excluded = []
prior_excluded.extend(data_prior_excluded.tolist())
if as_data.final_labels is not None:
with open_logger(log_file) as logger:
logger.set_final_labels(as_data.final_labels)
train_model = get_model(settings.model, **settings.model_param)
query_model = get_query_model(settings.query_strategy,
**settings.query_param)
balance_model = get_balance_model(settings.balance_strategy,
**settings.balance_param)
feature_model = get_feature_model(settings.feature_extraction,
**settings.feature_param)
X = feature_model.fit_transform(texts, as_data.title, as_data.abstract)
if train_model.name.startswith("lstm-"):
train_model.embedding_matrix = feature_model.get_embedding_matrix(
texts, embedding_fp)
# Initialize the review class.
if mode == "simulate":
reviewer = ReviewSimulate(
X, y,
model=train_model,
query_model=query_model,
balance_model=balance_model,
feature_model=feature_model,
n_papers=settings.n_papers,
n_instances=settings.n_instances,
n_queries=settings.n_queries,
verbose=verbose,
prior_included=prior_included,
prior_excluded=prior_excluded,
n_prior_included=settings.n_prior_included,
n_prior_excluded=settings.n_prior_excluded,
log_file=log_file,
final_labels=as_data.final_labels,
data_fp=dataset,
**kwargs)
elif mode == "oracle":
reviewer = ReviewOracle(
X,
model=train_model,
query_model=query_model,
balance_model=balance_model,
feature_model=feature_model,
as_data=as_data,
n_papers=settings.n_papers,
n_instances=settings.n_instances,
n_queries=settings.n_queries,
verbose=verbose,
prior_included=prior_included,
prior_excluded=prior_excluded,
log_file=log_file,
data_fp=dataset,
**kwargs)
elif mode == "minimal":
reviewer = MinimalReview(
X,
model=model,
query_model=query_model,
balance_model=balance_model,
feature_model=feature_model,
n_papers=settings.n_papers,
n_instances=settings.n_instances,
n_queries=settings.n_queries,
verbose=verbose,
prior_included=prior_included,
prior_excluded=prior_excluded,
log_file=log_file,
data_fp=dataset,
**kwargs)
else:
raise ValueError("Error finding mode, should never come here...")
return reviewer