def cfg():
description = 'covid_xray'
source = '/home/lybarger/clinical_extractors/analyses_pulmonary/step005_text_import/covid_xray/corpus.pkl'
include = None
exclude = None
as_stem = True
model_dir = '/home/lybarger/clinical_extractors/analyses_pulmonary/step320_pulmonary_modeling/fit/sent1+concat0+run1/'
fast_run = True
output_dir = paths_pulmonary.predict
if fast_run:
destination = os.path.join(output_dir, description + '_FAST_RUN')
else:
destination = os.path.join(output_dir, description)
# Scratch directory
make_and_clear(destination)
device = 0
# Create observers
file_observ = FileStorageObserver.create(destination)
cust_observ = CustomObserver(destination)
ex.observers.append(file_observ)
ex.observers.append(cust_observ)
def cfg():
description = 'basic'
source_dir = paths_pulmonary.brat_import
source = constants_pulmonary.COVID_XRAY
file = constants.CORPUS_FILE
source = os.path.join(source_dir, source, file)
labels = [INFILTRATES, EXTRAPARENCHYMAL]
doc_map = constants_pulmonary.DOC_MAP
doc_label_order = [INFILTRATES, EXTRAPARENCHYMAL]
assertion_label_order = [NONE, PRESENT, UNILATERAL, BILATERAL]
'''
Paths
'''
destination = os.path.join(paths_pulmonary.stats, description)
# Scratch directory
make_and_clear(destination)
# Create observers
file_observ = FileStorageObserver.create(destination)
cust_observ = CustomObserver(destination)
ex.observers.append(file_observ)
ex.observers.append(cust_observ)
def cfg():
#mode = CV
mode = FIT
#mode = PREDICT
#mode = SCORE
#file_doc_scores = ["scores_doc_labels.csv", "scores_doc_labels_summary.csv", "scores_sent_labels_summary.csv"] #"scores_entities.csv", "scores_relations.csv"]
file_doc_scores = "scores_doc_labels.csv" #"scores_entities.csv", "scores_relations.csv"]
file_sent_scores = "scores_sent_labels_summary.csv"
source_dirs = [os.path.join(paths_pulmonary.modeling, mode)]
discrete_dir = '/home/lybarger/clinical_extractors/analyses_pulmonary/step322_pulmonary_discrete/ngrams/'
if mode == FIT:
source_dirs.append(discrete_dir)
metric = F1
destination = os.path.join(paths_pulmonary.summary, mode)
suffix_pat = '\+run\d'
# Destination file for corpus
# Scratch directory
make_and_clear(destination)
# Create observers
file_observ = FileStorageObserver.create(destination)
cust_observ = CustomObserver(destination)
ex.observers.append(file_observ)
ex.observers.append(cust_observ)
def text_to_disk(corpus, destination, sub_dir="text"):
'''
Save corpus to disc as txt files
'''
dir = os.path.join(destination, sub_dir)
make_and_clear(dir, recursive=True)
for doc in corpus.docs():
doc.write_text(dir)
def fit_cv(self,
X,
y,
device=None,
path=None,
n_splits=3,
shuffle=True,
seed=1):
if shuffle:
z = list(zip(X, y))
random.Random(seed).shuffle(z)
X, y = zip(*z)
if not isinstance(X, list):
X = list(X)
if not isinstance(y, list):
y = list(y)
kf = KFold(n_splits=n_splits)
dfs = OrderedDict()
for j, (train_index, test_index) in enumerate(kf.split(X)):
self.reset_parameters()
X_train = [X[i] for i in train_index]
y_train = [y[i] for i in train_index]
X_test = [X[i] for i in test_index]
y_test = [y[i] for i in test_index]
dir = os.path.join(path, f'cross_val_{j}')
make_and_clear(dir)
self.fit(X_train, y_train, device=device, path=dir)
y_pred, scores = self.score(X_test,
y_test,
device=device,
path=dir)
for name, df in scores.items():
if name not in dfs:
dfs[name] = []
dfs[name].append(df)
dfs = self.scorer.combine_cv(dfs, path=path)
return dfs
def tokenization_examples(self, path, n, **kwargs):
make_and_clear(path, recursive=True)
for doc in self.docs(**kwargs)[:n]:
# Output file name
fn = os.path.join(path, '{}_original.{}'.format(doc.id, 'txt'))
# Directory, including path in id
dir_ = os.path.dirname(fn)
if not os.path.exists(dir_):
os.makedirs(dir_)
with open(fn, 'w') as f:
f.write(doc.text())
fn = os.path.join(path, '{}_tokenized.{}'.format(doc.id, 'txt'))
with open(fn, 'w') as f:
f.write('\n====\n====\n'.join(doc.sents()))
def cfg():
description = None
use_binary = False
description = f'binary_{int(use_binary)}'
source = constants_pulmonary.XRAY_IMAGES
source_corpus_text = '/home/lybarger/clinical_extractors/analyses_pulmonary/step005_text_import/covid_xray/corpus.pkl'
source_corpus_anno = '/home/lybarger/clinical_extractors/analyses_pulmonary/step010_brat_import/covid_xray/corpus.pkl'
if use_binary:
source_model = '/home/lybarger/clinical_extractors/analyses_pulmonary/step320_pulmonary_modeling/fit/sent1+concat0+run0+bd1/'
doc_map = constants_pulmonary.DOC_MAP_BINARY
else:
source_model = '/home/lybarger/clinical_extractors/analyses_pulmonary/step320_pulmonary_modeling/fit/sent1+concat0+run0/'
doc_map = constants_pulmonary.DOC_MAP
source_image = paths_pulmonary.xray_quadrant_interp
load_predictions = False
#file = constants.CORPUS_FILE
#source = os.path.join(source_dir, source, file)
device = 0
'''
Paths
'''
destination = os.path.join(paths_pulmonary.image_anno_comp, description)
# Scratch directory
make_and_clear(destination)
# Create observers
file_observ = FileStorageObserver.create(destination)
cust_observ = CustomObserver(destination)
ex.observers.append(file_observ)
ex.observers.append(cust_observ)
def get_predictions(source_model,
device,
text_dict,
target_ids,
path,
load_predictions=False):
logging.info(f"=" * 72)
logging.info(f"Predictions")
logging.info(f"=" * 72)
logging.info(f"Document count, all: {len(text_dict)}")
text = []
for study_id, accession in target_ids:
k = (study_id, accession)
text.append(text_dict[k])
logging.info(f"Document count, target: {len(text)}")
dir = os.path.join(path, 'predictions')
f = os.path.join(dir, PREDICTIONS_FILE)
if load_predictions:
y = joblib.load(f)
else:
model = load_pretrained(ModelXray, source_model)
y = model.predict(X=text, device=device)
make_and_clear(dir)
joblib.dump(y, f)
labels = [y_[constants.DOC_LABELS] for y_ in y]
labels = nest_list(labels)
return labels
def cfg():
# Annotation source
#source = constants.SYMPTOMS
#source = constants.SDOH
source = constants_pulmonary.COVID_XRAY
#source = constants.SDOH_DEID
#source = constants.SDOH_PARTIAL
fast_run = False
fast_count = 50 if fast_run else None
source_dir = None
skip = None
source_tags = None
source_original = None
write_brat = False
write_text = False
map_ids = False
corpus_object = CorpusBrat
update_lb = False
id2tags = None
rm_extra_lb = False
snap_textbounds = False
linebreak_bound = True
if source == constants.SDOH:
source_dir = paths_deid.sdoh_brat
source_tags = paths_deid.sdoh_doc_tags
source_original = paths_deid.sdoh_original
dir = paths_deid.brat_import
write_brat = True
write_text = True
update_lb = True
elif source == constants.SDOH_DEID:
source_dir = paths_deid.sdoh_brat_deid
dir = paths_deid.brat_import
corpus_object = CorpusBratDeid
elif source == constants.SDOH_PARTIAL:
source_dir = paths.sdoh_brat_partial
source_tags = paths.sdoh_doc_tags
source_original = paths.sdoh_original
dir = paths.brat_import
write_brat = True
write_text = True
fast_run = True
elif source == constants.SYMPTOMS:
source_dir = paths_symptoms.symptoms_brat
source_tags = paths_symptoms.symptoms_doc_tags
#source_original = paths_symptoms.symptoms_original
dir = paths_symptoms.brat_import
corpus_object = CorpusBratSymptoms
write_brat = False
write_text = False
elif source == constants_pulmonary.COVID_XRAY:
source_dir = paths_pulmonary.brat_xray
source_tags = paths_pulmonary.pulmonary_doc_tags
dir = paths_pulmonary.brat_import
corpus_object = CorpusBratXray
id2tags = corpus_brat_xray.id2tags
rm_extra_lb = True
snap_textbounds = True
skip = []
else:
ValueError("invalid source: {}".format(source))
'''
Paths
'''
if fast_run:
destination = os.path.join(dir, source + '_FAST_RUN')
else:
destination = os.path.join(dir, source)
# Destination file for corpus
# Scratch directory
make_and_clear(destination)
# Create observers
file_observ = FileStorageObserver.create(destination)
cust_observ = CustomObserver(destination)
ex.observers.append(file_observ)
ex.observers.append(cust_observ)
def cfg():
description = 'bert'
#description = 'baseline+crf'
source = constants_pulmonary.COVID_XRAY
dir = None
mode = CV
#mode = FIT
#mode = PREDICT
#mode = SCORE
model_dir = '/home/lybarger/clinical_extractors/analyses_pulmonary/step320_pulmonary_modeling/fit/baseline/'
fast_run = False
fast_count = 20 if fast_run else None
source_dir = None
n_splits = 3
doc_map = constants_pulmonary.DOC_MAP
if source == constants_pulmonary.COVID_XRAY:
source_dir = paths_pulmonary.brat_import
source = constants_pulmonary.COVID_XRAY
source = os.path.join(source_dir, source, constants.CORPUS_FILE)
output_dir = paths_pulmonary.modeling
else:
ValueError("invalid source: {}".format(source))
side_swap = False
if side_swap:
entity_definition = ENTITY_DEFINITION_SWAP
relation_definition = RELATION_DEFINITION_SWAP
else:
entity_definition = ENTITY_DEFINITION
relation_definition = RELATION_DEFINITION
sent_definition = SENT_DEFINITION
'''
Paths
'''
if fast_run:
destination = os.path.join(output_dir, mode, description + '_FAST_RUN')
else:
destination = os.path.join(output_dir, mode, description)
# Destination file for corpus
# Scratch directory
make_and_clear(destination)
device = 0
use_sent_objective = True
concat_sent_scores = True
span_embed_dim = 50
batch_size = 4
num_workers = 0
max_sent_count = 35
keep_ws = False
linebreak_bound = True
dropout_sent = 0.0
dropout_doc = 0.0
lr = 1e-5
lr_ratio = 1.0
pretrained = "emilyalsentzer/Bio_ClinicalBERT" # 'bert-base-uncased'
doc_definition = DOC_DEFINITION
sent_definition = SENT_DEFINITION
grad_max_norm = 1.0
loss_reduction = "sum"
project_sent = True
project_size = 200
attention_query_dim = 100
max_length = 60
num_workers = 6
num_epochs = 10
# Create observers
file_observ = FileStorageObserver.create(destination)
cust_observ = CustomObserver(destination)
ex.observers.append(file_observ)
ex.observers.append(cust_observ)
def write_brat(self, path, **kwargs):
make_and_clear(path, recursive=True)
for doc in self.docs(**kwargs):
doc.write_brat(path)
def cfg():
description = 'baseline'
source = constants.SYMPTOMS
dir = None
fast_run = True
source_dir = None
include_train = [constants.TRAIN]
if source == constants.SYMPTOMS:
source_dir = paths_symptoms.brat_import
if fast_run:
source += '_FAST_RUN'
source = os.path.join(source_dir, source, constants.CORPUS_FILE)
output_dir = paths_symptoms.modeling
else:
ValueError("invalid source: {}".format(source))
'''
Paths
'''
if fast_run:
destination = os.path.join(output_dir, description + '_FAST_RUN')
else:
destination = os.path.join(output_dir, description)
# Destination file for corpus
# Scratch directory
make_and_clear(destination)
device = 1
use_rnn = True
num_workers = 0
xfmr_dim = 768
lstm_size = 200
h_size = lstm_size * 2 if use_rnn else xfmr_dim
loss_reduction = "sum"
hyperparams = {}
hyperparams['use_rnn'] = use_rnn
rnn = {}
rnn['input_size'] = xfmr_dim
rnn['output_size'] = lstm_size
rnn['type_'] = 'lstm'
rnn['num_layers'] = 1
rnn['dropout_output'] = 0.0
hyperparams['rnn'] = rnn
relation_extractor = {}
relation_extractor[
"entity_definition"] = constants_symptoms.ENTITY_DEFINITION
relation_extractor["input_dim"] = h_size
relation_extractor["span_scorer_type"] = "span"
relation_extractor["span_embed_project"] = True
relation_extractor["span_embed_dim"] = 100
relation_extractor["span_embed_dropout"] = 0.0
relation_extractor["span_scorer_hidden_dim"] = 100
relation_extractor["span_scorer_dropout"] = 0.0
relation_extractor["span_class_weights"] = None
relation_extractor["spans_per_word"] = 2
relation_extractor[
"relation_definition"] = constants_symptoms.RELATION_DEFINITION
relation_extractor["role_hidden_dim"] = 100
relation_extractor["role_output_dim"] = 2
relation_extractor["role_dropout"] = 0.0
relation_extractor["loss_reduction"] = loss_reduction
hyperparams["relation_extractor"] = relation_extractor
hyperparams['grad_max_norm'] = 1.0
hyperparams["loss_reduction"] = loss_reduction
dataset_params = {}
dataset_params["pretrained"] = "emilyalsentzer/Bio_ClinicalBERT"
dataset_params["max_length"] = 30
dataset_params["max_wp_length"] = 60
dataset_params["linebreak_bound"] = True
dataset_params["keep"] = 'mean'
dataset_params["max_span_width"] = 6
dataset_params["entity_definition"] = constants_symptoms.ENTITY_DEFINITION
dataset_params[
"relation_definition"] = constants_symptoms.RELATION_DEFINITION
dataloader_params = {}
dataloader_params['batch_size'] = 100
dataloader_params['num_workers'] = num_workers
optimizer_params = {}
optimizer_params['lr'] = 0.001
num_workers = 6
num_epochs = 100
# Create observers
file_observ = FileStorageObserver.create(destination)
cust_observ = CustomObserver(destination)
ex.observers.append(file_observ)
ex.observers.append(cust_observ)
def main(source, destination, corpus_fn, num_examples, source_params, sampling,
exclude, annotators, id2filename):
# Load and create corpus
logging.info("Corpus loading...")
if source == constants_pulmonary.COVID_XRAY:
corpus = xray.load_corpus(**source_params)
logging.info('-' * 72)
logging.info('Only day 0')
logging.info('-' * 72)
corpus.summary(path=destination, day_range=(0, 0), rep_range=None)
logging.info('-' * 72)
logging.info('Only day in [0-7]')
logging.info('-' * 72)
corpus.summary(path=destination, day_range=(0, 7), rep_range=None)
logging.info('-' * 72)
logging.info('All notes')
logging.info('-' * 72)
corpus.summary(path=destination, day_range=None, rep_range=None)
elif source == constants_pulmonary.EMERGE_XRAY:
corpus = xray.load_emerge_corpus(**source_params)
else:
raise ValueError("Incorrect corpus:\t{}".format(corpus))
logging.info("Corpus loaded")
# Save examples for review
example_dir = os.path.join(destination, "Examples")
make_and_clear(example_dir, recursive=True)
corpus.write_examples(example_dir, num_examples=num_examples)
corpus.summary(path=destination)
corpus.write_ids(destination)
exclude = [tuple(e) for e in exclude]
if sampling is not None:
logging.info('Sampling')
# Sampling
brat_dir = os.path.join(destination, "brat")
make_and_clear(brat_dir, recursive=True)
sampled = []
for params in sampling:
dir_ = os.path.join(brat_dir,
'round{:0>2d}'.format(params['round']))
os.mkdir(dir_)
logging.info('')
logging.info('Round:\t{}'.format(params['round']))
docs = corpus.random_sample( \
size = params['size'],
exclude = exclude,
seed = params['seed'],
path = dir_,
brat = True,
footer = params['footer'],
annotators = annotators,
anno_type = params['anno_type'],
**params['kwargs'])
exclude.extend(list(docs.keys()))
for id in docs:
if id2filename is not None:
id = id2filename(id)
sampled.append((params['round'], id))
sample_check(brat_dir, destination)
fn = os.path.join(destination, 'sampled_documents.csv')
df = pd.DataFrame(sampled, columns=['round', 'id'])
df.to_csv(fn)
# Save corpus
logging.info("Saving to disk...")
joblib.dump(corpus, corpus_fn)
logging.info("Saving complete")
return True
def cfg():
description = 'baseline'
#description = 'baseline+crf'
source = constants_pulmonary.COVID_XRAY
dir = None
#mode = CV
#mode = FIT
#mode = PREDICT
#mode = SCORE
mode = PROB
model_dir='/home/lybarger/clinical_extractors/analyses_pulmonary/step320_pulmonary_modeling/fit/sent1+concat0+run0+bd1/'
fast_run = False
fast_count = 20 if fast_run else None
source_dir = None
n_splits = 3
binary_doc_map = False
if binary_doc_map:
doc_map = constants_pulmonary.DOC_MAP_BINARY
doc_definition = DOC_DEFINITION_BINARY
else:
doc_map = constants_pulmonary.DOC_MAP
doc_definition = DOC_DEFINITION
if source == constants_pulmonary.COVID_XRAY:
source_dir = paths_pulmonary.brat_import
source = constants_pulmonary.COVID_XRAY
source = os.path.join(source_dir, source, constants.CORPUS_FILE)
output_dir = paths_pulmonary.modeling
else:
ValueError("invalid source: {}".format(source))
side_swap = False
if side_swap:
entity_definition = ENTITY_DEFINITION_SWAP
relation_definition = RELATION_DEFINITION_SWAP
else:
entity_definition = ENTITY_DEFINITION
relation_definition = RELATION_DEFINITION
sent_definition = SENT_DEFINITION
'''
Paths
'''
if fast_run:
destination = os.path.join(output_dir, mode, description + '_FAST_RUN')
else:
destination = os.path.join(output_dir, mode, description)
# Destination file for corpus
# Scratch directory
make_and_clear(destination)
device = 0
use_rnn = True
use_doc_classifier = True
use_span_classifier = False
use_doc_features = False
use_sent_objective = True
concat_sent_scores = True
projection_dim = 100
if concat_sent_scores:
assert use_sent_objective
span_embed_dim = 50
dropout_rnn = 0.0
dropout_sent_classifier = 0.0
dropout_doc_classifier = 0.0
batch_size = 30
linebreak_bound = True
max_sent_count = 35
keep_ws = True
num_workers = 0
xfmr_dim = 768
rnn_size = 100
h_size = rnn_size*2 if use_rnn else xfmr_dim
loss_reduction = "sum"
lr = 0.002
hyperparams = {}
hyperparams['use_rnn'] = use_rnn
hyperparams['use_doc_classifier'] = use_doc_classifier
hyperparams['use_span_classifier'] = use_span_classifier
hyperparams['use_doc_features'] = use_doc_features
rnn = {}
rnn['input_size'] = xfmr_dim
rnn['output_size'] = rnn_size
rnn['type_'] = 'lstm'
rnn['num_layers'] = 1
rnn['dropout_output'] = dropout_rnn
rnn['layer_norm'] = True
hyperparams['rnn'] = rnn
span_class_weights = OrderedDict()
w = 100.0
span_class_weights[REGION] = [1.0, w, w] # [NONE, PARENCHYMAL, EXTRAPARENCHYMAL]
span_class_weights[SIDE] = [1.0, w, w] # [NONE, UNILATERAL, BILATERAL]
span_class_weights[SIZE] = [1.0, w, w, w] # [NONE, SMALL, MODERATE, LARGE]
span_class_weights[NEGATION] = [1.0, w] # [NONE, NEGATION]
relation_extractor = {}
relation_extractor["entity_definition"] = entity_definition
relation_extractor["input_dim"] = h_size
relation_extractor["span_scorer_type"] = "span"
relation_extractor["span_embed_project"] = True
relation_extractor["span_embed_dim"] = span_embed_dim
relation_extractor["span_embed_dropout"] = 0
relation_extractor["span_scorer_hidden_dim"] = 50
relation_extractor["span_scorer_dropout"] = 0
relation_extractor["span_class_weights"] = None # span_class_weights
relation_extractor["spans_per_word"] = 2
relation_extractor["relation_definition"] = relation_definition
relation_extractor["role_hidden_dim"] = 50
relation_extractor["role_output_dim"] = 2
relation_extractor["role_dropout"] = 0
relation_extractor["create_doc_vector"] = use_doc_features
relation_extractor["doc_attention_dropout"] = 0
relation_extractor["loss_reduction"] = loss_reduction
hyperparams["relation_extractor"] = relation_extractor
doc_classifier = {}
doc_classifier["doc_definition"] = doc_definition
doc_classifier["input_dim"] = h_size
doc_classifier["query_dim"] = 100
doc_classifier["use_ffnn"] = True
doc_classifier["dropout_sent_classifier"] = dropout_sent_classifier
doc_classifier["dropout_doc_classifier"] = dropout_doc_classifier
doc_classifier["activation"] = 'tanh'
doc_classifier["loss_reduction"] = loss_reduction
doc_classifier["use_sent_objective"] = use_sent_objective
doc_classifier["concat_sent_scores"] = concat_sent_scores
doc_classifier["sent_definition"] = sent_definition
doc_classifier["projection_dim"] = projection_dim
hyperparams['doc_classifier'] = doc_classifier
hyperparams['grad_max_norm'] = 1.0
hyperparams["loss_reduction"] = loss_reduction
dataset_params = {}
dataset_params["pretrained"] = "emilyalsentzer/Bio_ClinicalBERT"
dataset_params["max_length"] = 30
dataset_params["max_wp_length"] = 50
dataset_params["max_sent_count"] = max_sent_count
dataset_params["linebreak_bound"] = linebreak_bound
dataset_params["keep"] = 'mean'
dataset_params["max_span_width"] = 6
dataset_params["document_definition"] = doc_definition
dataset_params["sent_definition"] = sent_definition
dataset_params["entity_definition"] = entity_definition
dataset_params["relation_definition"] = relation_definition
dataset_params["pad_start"] = True
dataset_params["pad_end"] = True
dataset_params["keep_ws"] = False
dataloader_params = {}
dataloader_params['batch_size'] = batch_size
dataloader_params['num_workers'] = num_workers
optimizer_params = {}
optimizer_params['lr'] = lr
tokenization_params = {}
tokenization_params['max_length'] = dataset_params["max_length"]
tokenization_params['max_sent_count'] = dataset_params["max_sent_count"]
tokenization_params['linebreak_bound'] = linebreak_bound
tokenization_params['pad_start'] = dataset_params["pad_start"]
tokenization_params['pad_end'] = dataset_params["pad_end"]
num_workers = 6
num_epochs = 300
# Create observers
file_observ = FileStorageObserver.create(destination)
cust_observ = CustomObserver(destination)
ex.observers.append(file_observ)
ex.observers.append(cust_observ)
def cfg():
# Annotation source
#source = constants.SYMPTOMS
#source = constants.SDOH
source = constants_pulmonary.COVID_XRAY
description = 'all'
fast_run = False
source_dir = None
index_round = 0
index_annotator = 1
index_note = 2
round = None
annotators = None
scorer = Scorer
label_spec = {}
if source == constants.SDOH:
pass
elif source == constants.SDOH_PARTIAL:
pass
elif source == constants.SYMPTOMS:
pass
elif source == constants_pulmonary.COVID_XRAY:
source_dir = paths_pulmonary.brat_import
dir = paths_pulmonary.agreement
if description == 'round01':
target_rounds_aggree = ["round01"]
elif description == 'round04':
target_rounds_aggree = ["round04"]
elif description == 'all':
target_rounds_aggree = ["round01", "round04"]
target_rounds_dist = ["round02"]
#annotator_pairs = [('Mark', 'Linzee'),
# ('Mark', 'Matthew'),
# ('Linzee', 'Matthew')]
annotator_pairs = [('Linzee', 'Matthew')]
scorer = ScorerXray
doc_map = constants_pulmonary.DOC_MAP
label_spec = {'doc_map': doc_map}
else:
ValueError("invalid source: {}".format(source))
source_corpus = os.path.join(source_dir, source, constants.CORPUS_FILE)
'''
Paths55309
'''
destination = os.path.join(dir, source, description)
# Destination file for corpus
# Scratch directory
make_and_clear(destination)
# Create observers
file_observ = FileStorageObserver.create(destination)
cust_observ = CustomObserver(destination)
ex.observers.append(file_observ)
ex.observers.append(cust_observ)
def cfg():
#prediction_type = 'oracle'
run = 0
prediction_type = 'ngrams'
exclude_size = False
exclude = None
description = f"{prediction_type}+run{run}"
fast_run = False
n_splits = 3
doc_map = constants_pulmonary.DOC_MAP
source_dir = paths_pulmonary.brat_import
source = constants_pulmonary.COVID_XRAY
source = os.path.join(source_dir, source, constants.CORPUS_FILE)
output_dir = paths_pulmonary.discrete
labels = [INFILTRATES, EXTRAPARENCHYMAL]
if prediction_type == 'oracle':
model_type = 'random_forest'
hyperparams = OrderedDict()
hyperparams['n_estimators'] = 200
hyperparams['max_depth'] = None
hyperparams['min_samples_split'] = 2
hyperparams['min_samples_leaf'] = 1
hyperparams['min_weight_fraction_leaf'] = 0.0
hyperparams['max_features'] = 'auto'
hyperparams['max_leaf_nodes'] = None
hyperparams['random_state'] = None
hyperparams['ccp_alpha'] = 0.0
hyperparams['n_jobs'] = 1
#hyperparams['class_weight'] = {0:1, 1:1}
tuned_parameters = OrderedDict()
tuned_parameters['max_depth'] = [5, 10, 30] if fast_run else [
2, 4, 6, 8, 10, 15, 20, 25, 30, 35
]
tuned_parameters['min_samples_split'] = [2, 4] if fast_run else [
2, 3, 4, 6, 8, 10, 12
]
tuned_parameters['n_estimators'] = [100] if fast_run else [
50, 100, 200, 500
]
exclude_size = True
if exclude_size:
description = 'exclude_size'
exclude = [SIZE]
elif prediction_type == 'ngrams':
model_type = 'svm'
hyperparams = OrderedDict()
hyperparams['C'] = 1.0
#hyperparams['kernel'] = 'rbf'
#hyperparams['degree'] = 3
#hyperparams['gamma'] = 'scale'
#hyperparams['coef0'] = 0.0
#hyperparams['shrinking'] = True
#hyperparams['probability'] = True
#hyperparams['tol'] = 0.001
#hyperparams['cache_size'] = 200
#hyperparams['class_weight'] = None
#hyperparams['verbose'] = False
#hyperparams['max_iter'] = - 1,
#hyperparams['decision_function_shape'] = 'ovr'
#hyperparams['break_ties'] = False
#hyperparams['random_state'] = None
tuned_parameters = OrderedDict()
tuned_parameters['C'] = [0.0001, 1.0, 1000.0] if fast_run else [
0.0001, 0.0001, 0.001, 0.01, 0.1, 1.0, 10.0, 100.0, 1000.0
]
else:
raise ValueError(f"invalid prediction type: {prediction_type}")
'''
Paths
'''
if fast_run:
destination = os.path.join(output_dir, prediction_type,
description + '_FAST_RUN')
else:
destination = os.path.join(output_dir, prediction_type, description)
# Scratch directory
make_and_clear(destination)
# Create observers
file_observ = FileStorageObserver.create(destination)
cust_observ = CustomObserver(destination)
ex.observers.append(file_observ)
ex.observers.append(cust_observ)
