def test_query(query_strategy,
n_features=50,
n_sample=100,
n_instances_list=[0, 1, 5, 50],
n_train_idx=[0, 1, 5, 50]):
classifier = get_classifier("rf")
query_model = get_query_model(query_strategy)
X = np.random.rand(n_sample, n_features)
y = np.concatenate((np.zeros(n_sample // 2), np.ones(n_sample // 2)),
axis=0)
print(X.shape, y.shape)
order = np.random.permutation(n_sample)
print(order.shape)
X = X[order]
y = y[order]
sources = query_strategy.split('_')
classifier.fit(X, y)
assert isinstance(query_model.param, dict)
assert query_model.name == query_strategy
for n_instances in n_instances_list:
for n_train in n_train_idx:
shared = {"query_src": {}, "current_queries": {}}
train_idx = np.random.choice(np.arange(n_sample),
n_train,
replace=False)
pool_idx = np.delete(np.arange(n_sample), train_idx)
query_idx, X_query = query_model.query(X, classifier, pool_idx,
n_instances, shared)
check_integrity(query_idx, X_query, X, pool_idx, shared,
n_instances, sources)
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_classifier(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,
prior_record_id=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,
seed=None,
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)
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)
# Initialize models.
random_state = get_random_state(seed)
train_model = get_classifier(settings.model,
**settings.model_param,
random_state=random_state)
query_model = get_query_model(settings.query_strategy,
**settings.query_param,
random_state=random_state)
balance_model = get_balance_model(settings.balance_strategy,
**settings.balance_param,
random_state=random_state)
feature_model = get_feature_model(settings.feature_extraction,
**settings.feature_param,
random_state=random_state)
# LSTM models need embedding matrices.
if train_model.name.startswith("lstm-"):
texts = as_data.texts
train_model.embedding_matrix = feature_model.get_embedding_matrix(
texts, embedding_fp)
# prior knowledge
if prior_idx is not None and prior_record_id is not None and \
len(prior_idx) > 0 and len(prior_record_id) > 0:
raise ValueError(
"Not possible to provide both prior_idx and prior_record_id")
if prior_record_id is not None and len(prior_record_id) > 0:
prior_idx = convert_id_to_idx(as_data, prior_record_id)
# 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,
prior_idx=prior_idx,
n_prior_included=settings.n_prior_included,
n_prior_excluded=settings.n_prior_excluded,
state_file=state_file,
**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,
state_file=state_file,
**kwargs)
else:
raise ValueError("Error finding mode, should never come here...")
return reviewer