def test_fit_predict_multi_model(self):
"""
Ensure model training does not error out
Ensure model returns predictions
"""
self.model = SequenceLabeler(batch_size=2,
max_length=256,
lm_loss_coef=0.0,
multi_label_sequences=True)
raw_docs = ["".join(text) for text in self.texts]
texts, annotations = finetune_to_indico_sequence(
raw_docs,
self.texts,
self.labels,
none_value=self.model.config.pad_token)
train_texts, test_texts, train_annotations, _ = train_test_split(
texts, annotations, test_size=0.1)
self.model.fit(train_texts, train_annotations)
self.model.predict(test_texts)
probas = self.model.predict_proba(test_texts)
self.assertIsInstance(probas, list)
self.assertIsInstance(probas[0], list)
self.assertIsInstance(probas[0][0], dict)
self.assertIsInstance(probas[0][0]['confidence'], dict)
self.model.save(self.save_file)
model = SequenceLabeler.load(self.save_file)
model.predict(test_texts)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.model_config.update(
dict(
# general params that differ from finetune
base_model=RoBERTa,
batch_size=4,
predict_batch_size=10,
val_size=0.0,
crf_sequence_labeling=False,
low_memory_mode=True,
class_weights="log",
# auxiliary-specific params
use_auxiliary_info=True,
context_dim=4,
default_context={
'left': 0,
'right': 0,
'top': 0,
'bottom': 0,
},
n_context_embed_per_channel=48,
context_in_base_model=True,
n_layers_with_aux=-1)
)
self.model_config.update(kwargs)
self.model = SequenceLabeler(**self.model_config)
def setUp(self):
self.save_file = 'tests/saved-models/test-save-load'
random.seed(42)
np.random.seed(42)
with open(self.processed_path, 'rt') as fp:
self.texts, self.labels = json.load(fp)
self.model = SequenceLabeler(**self.default_config())
def setUp(self):
self.save_file = 'tests/saved-models/test-save-load'
with open(self.processed_path, 'rt') as fp:
self.texts, self.labels = json.load(fp)
tf.reset_default_graph()
self.model = SequenceLabeler(batch_size=2, max_length=256, verbose=False)
def test_sequence_labeler_auxiliary(self):
"""
Ensure model training does not error out
Ensure model returns reasonable predictions
"""
# here we want to make sure we're actually using context
model = SequenceLabeler(**self.default_config(n_epochs=1500))
model.fit(self.trainX, self.trainY_seq, context=self.train_context)
preds = model.predict(self.trainX, context=self.train_context)
self._evaluate_sequence_preds(preds, includes_context=True)
def test_sequence_labeler_no_auxiliary(self):
"""
Ensure model training does not error out
Ensure model returns reasonable predictions
"""
model = SequenceLabeler(**self.default_config(
use_auxiliary_info=False, val_set=(self.trainX, self.trainY)))
model.fit(self.trainX, self.trainY_seq)
preds = model.predict(self.trainX)
self._evaluate_sequence_preds(preds, includes_context=False)
class FinetuneSequenceLabel(ClassificationExperiment):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.model = SequenceLabeler(val_size=0)
def fit(self, X, y):
self.model.fit(X, y)
def predict(self, X, **kwargs):
return self.model.predict(X)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.model_config = dict(
use_auxiliary_info = False,
n_layers_with_aux = 0,
context_in_base_model = False,
context_dim = 0
)
self.model_config.update(kwargs)
self.model = SequenceLabeler(**self.model_config)
def setUpClass(cls):
cls._download_data()
#dataset preparation
cls.classifier_dataset = pd.read_csv(cls.classifier_dataset_path, nrows=cls.n_sample * 10)
path = os.path.join(os.path.dirname(__file__), "data", "testdata.json")
with open(path, 'rt') as fp:
cls.texts, cls.labels = json.load(fp)
cls.animals = ["dog", "cat", "horse", "cow", "pig", "sheep", "goat", "chicken", "guinea pig", "donkey", "turkey", "duck", "camel", "goose", "llama", "rabbit", "fox"]
cls.numbers = ["one", "two", "three", "four", "five", "six", "seven", "eight", "nine", "ten", "eleven", "twelve", "thirteen", "fourteen", "fifteen", "sixteen"]
#train and save sequence labeler for later use
try:
cls.s = SequenceLabeler.load(cls.sequence_labeler_path, **cls.default_seq_config(cls))
except FileNotFoundError:
cls.s = SequenceLabeler(**cls.default_seq_config(cls))
cls.s.fit(cls.texts * 10, cls.labels * 10)
cls.s.save(cls.sequence_labeler_path)
#train and save classifier for later use
train_sample = cls.classifier_dataset.sample(n=cls.n_sample*10)
try:
cls.cl = Classifier.load(cls.classifier_path)
except FileNotFoundError:
cls.cl = Classifier(**cls.default_config(cls))
cls.cl.fit(train_sample.Text, train_sample.Target)
cls.cl.save(cls.classifier_path)
if cls.do_comparison:
#train and save comparison regressor for use
cls.cr = ComparisonRegressor()
n_per = 150
similar = []
different = []
for dataset in [cls.animals, cls.numbers]:
for i in range(n_per // 2):
similar.append([random.choice(dataset), random.choice(dataset)])
for i in range(n_per):
different.append([random.choice(cls.animals), random.choice(cls.numbers)])
targets = np.asarray([1] * len(similar) + [0] * len(different))
data = similar + different
cls.x_tr, cls.x_te, cls.t_tr, cls.t_te = train_test_split(data, targets, test_size=0.3, random_state=42)
try:
cls.cr = ComparisonRegressor.load(cls.comparison_regressor_path, **cls.default_config(cls))
except FileNotFoundError:
cls.cr = ComparisonRegressor(**cls.default_config(cls))
cls.cr.fit(cls.x_tr, cls.t_tr)
cls.cr.save(cls.comparison_regressor_path)
def test_fit_predict(self):
"""
Ensure model training does not error out
Ensure model returns predictions
Ensure class reweighting behaves as intended
"""
raw_docs = ["".join(text) for text in self.texts]
texts, annotations = finetune_to_indico_sequence(
raw_docs, self.texts, self.labels, none_value=self.model.config.pad_token
)
train_texts, test_texts, train_annotations, test_annotations = train_test_split(
texts, annotations, test_size=0.1
)
reweighted_model = SequenceLabeler(
**self.default_config(class_weights={"Named Entity": 100.0})
)
reweighted_model.fit(train_texts, train_annotations)
reweighted_predictions = reweighted_model.predict(test_texts)
reweighted_token_recall = sequence_labeling_token_recall(
test_annotations, reweighted_predictions
)
self.model.fit(train_texts, train_annotations)
predictions = self.model.predict(test_texts)
probas = self.model.predict_proba(test_texts)
self.assertIsInstance(probas, list)
self.assertIsInstance(probas[0], list)
self.assertIsInstance(probas[0][0], dict)
self.assertIsInstance(probas[0][0]["confidence"], dict)
token_precision = sequence_labeling_token_precision(
test_annotations, predictions
)
token_recall = sequence_labeling_token_recall(test_annotations, predictions)
overlap_precision = sequence_labeling_overlap_precision(
test_annotations, predictions
)
overlap_recall = sequence_labeling_overlap_recall(test_annotations, predictions)
self.assertIn("Named Entity", token_precision)
self.assertIn("Named Entity", token_recall)
self.assertIn("Named Entity", overlap_precision)
self.assertIn("Named Entity", overlap_recall)
self.model.save(self.save_file)
self.assertGreater(
reweighted_token_recall["Named Entity"], token_recall["Named Entity"]
)
def test_train_test_tokenization_consistency(self):
filepath = os.path.abspath(
os.path.join(os.path.dirname(__file__), 'data', 'testdata.csv'))
df = pd.read_csv(filepath)
X = []
Y = []
for i, row in df.iterrows():
X.append(row["text"])
labels = json.loads(row["question_843"])
for label in labels:
label['start'] = label['startOffset']
label['end'] = label['endOffset']
label['text'] = row["text"][label['start']:label['end']]
Y.append(labels)
for multilabel_setting in [True, False]:
for base_model in [GPT, GPT2, BERT]:
model = SequenceLabeler(
chunk_long_sequences=True,
base_model=base_model,
multi_label_sequences=multilabel_setting)
train_encoded = [
x for x in model.input_pipeline._text_to_ids(
X, Y=Y, pad_token=model.config.pad_token)
]
test_encoded = [
x for x in model.input_pipeline._text_to_ids(X)
]
for chunk_id in range(len(train_encoded)):
for train_token_ids, test_token_ids in zip(
train_encoded[chunk_id].token_ids,
test_encoded[chunk_id].token_ids):
self.assertEqual(train_token_ids[0], test_token_ids[0])
def test_fit_lm_only(self):
"""
Ensure model training does not error out
Ensure model returns predictions
"""
raw_docs = ["".join(text) for text in self.texts]
texts, annotations = finetune_to_indico_sequence(
raw_docs, self.texts, self.labels)
train_texts, test_texts, train_annotations, test_annotations = train_test_split(
texts, annotations, test_size=0.1)
self.model.fit(train_texts)
self.model.fit(train_texts, train_annotations)
predictions = self.model.predict(test_texts)
probas = self.model.predict_proba(test_texts)
self.assertIsInstance(probas, list)
self.assertIsInstance(probas[0], list)
self.assertIsInstance(probas[0][0], dict)
self.assertIsInstance(probas[0][0]['confidence'], dict)
token_precision = sequence_labeling_token_precision(
test_annotations, predictions)
token_recall = sequence_labeling_token_recall(test_annotations,
predictions)
overlap_precision = sequence_labeling_overlap_precision(
test_annotations, predictions)
overlap_recall = sequence_labeling_overlap_recall(
test_annotations, predictions)
self.assertIn('Named Entity', token_precision)
self.assertIn('Named Entity', token_recall)
self.assertIn('Named Entity', overlap_precision)
self.assertIn('Named Entity', overlap_recall)
self.model.save(self.save_file)
model = SequenceLabeler.load(self.save_file)
predictions = model.predict(test_texts)
def test_auxiliary_sequence_labeler(self):
"""
Ensure model training does not error out
Ensure model returns reasonable predictions
"""
(trainX, testX, trainY, testY) = self.dataset
model = SequenceLabeler(**self.default_config())
model.fit(trainX, trainY)
preds = model.predict(testX)
token_precision = sequence_labeling_token_precision(preds, testY)
token_recall = sequence_labeling_token_recall(preds, testY)
self.assertIn("Named Entity", token_precision)
self.assertIn("Named Entity", token_recall)
token_precision = np.mean(list(token_precision.values()))
token_recall = np.mean(list(token_recall.values()))
self.assertGreater(token_precision, 0.6)
self.assertGreater(token_recall, 0.6)
class RoBERTaSeqLab(SidekickSeqLab):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.model_config = dict(
use_auxiliary_info = False,
n_layers_with_aux = 0,
context_in_base_model = False,
context_dim = 0
)
self.model_config.update(kwargs)
self.model = SequenceLabeler(**self.model_config)
def fit(self, X, y):
text, context = zip(*X)
self.model.fit(text, y)
def predict(self, X, **kwargs):
text, context = zip(*X)
return self.model.predict(text)
class FinetuneSeqBaselineRationalized(ClassificationExperiment):
param_grid = {}
def __init__(self, *args, **kwargs):
"""Initialize internal classifier."""
super().__init__(auto_resample=False, *args, **kwargs)
self.model = SequenceLabeler(val_size=0)
def fit(self, X, y):
targets = []
for x, l in zip(X, y):
if l[0]:
targets.append([{**label, "label": l[1]} for label in l[0]])
else:
targets.append([{
"start": 0,
"end": len(x),
"label": l[1],
"text": x
}])
idxs, _ = self.resample(list(range(len(X))), [yi[1] for yi in y])
train_x = []
train_y = []
for i in idxs:
train_x.append(X[i])
train_y.append(targets[i])
self.model.fit(train_x, train_y)
def predict(self, X, **kwargs):
preds = self.model.predict_proba(X)
classes = self.model.input_pipeline.label_encoder.classes_[:]
classes.remove("<PAD>")
output = []
for sample in preds:
output.append({
k: safe_mean([s["confidence"][k] for s in sample]) + 1e-10
for k in classes
})
return pd.DataFrame.from_records(output)
def cleanup(self):
del self.model
def test_fit_predict(self):
"""
Ensure model training does not error out
Ensure model returns predictions
"""
raw_docs = ["".join(text) for text in self.texts]
texts, annotations = finetune_to_indico_sequence(raw_docs, self.texts, self.labels)
train_texts, test_texts, train_annotations, test_annotations = train_test_split(texts, annotations)
self.model.fit(train_texts, train_annotations)
predictions = self.model.predict(test_texts)
self.model.save(self.save_file)
model = SequenceLabeler.load(self.save_file)
predictions = model.predict(test_texts)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.model_config.update(dict(
pos_injection=True,
n_layers_with_aux = 0,
context_in_base_model = False
))
self.model_config.update(kwargs)
self.model = SequenceLabeler(**self.model_config)
class TestSequenceLabeler(unittest.TestCase):
n_sample = 100
n_hidden = 768
dataset_path = os.path.join('Data', 'Sequence', 'reuters.xml')
processed_path = os.path.join('Data', 'Sequence', 'reuters.json')
@classmethod
def _download_reuters(cls):
"""
Download Stanford Sentiment Treebank to enso `data` directory
"""
path = Path(cls.dataset_path)
if not path.exists():
path.parent.mkdir(parents=True, exist_ok=True)
if not os.path.exists(cls.dataset_path):
url = "https://raw.githubusercontent.com/dice-group/n3-collection/master/reuters.xml"
r = requests.get(url)
with open(cls.dataset_path, "wb") as fp:
fp.write(r.content)
with codecs.open(cls.dataset_path, "r", "utf-8") as infile:
soup = bs(infile, "html5lib")
docs = []
docs_labels = []
for elem in soup.find_all("document"):
texts = []
labels = []
# Loop through each child of the element under "textwithnamedentities"
for c in elem.find("textwithnamedentities").children:
if type(c) == Tag:
if c.name == "namedentityintext":
label = "Named Entity" # part of a named entity
else:
label = "<PAD>" # irrelevant word
texts.append(c.text)
labels.append(label)
docs.append(texts)
docs_labels.append(labels)
with open(cls.processed_path, 'wt') as fp:
json.dump((docs, docs_labels), fp)
@classmethod
def setUpClass(cls):
cls._download_reuters()
def setUp(self):
self.save_file = 'tests/saved-models/test-save-load'
with open(self.processed_path, 'rt') as fp:
self.texts, self.labels = json.load(fp)
tf.reset_default_graph()
self.model = SequenceLabeler(batch_size=2,
max_length=256,
lm_loss_coef=0.0,
verbose=False)
def test_fit_lm_only(self):
"""
Ensure model training does not error out
Ensure model returns predictions
"""
raw_docs = ["".join(text) for text in self.texts]
texts, annotations = finetune_to_indico_sequence(
raw_docs, self.texts, self.labels)
train_texts, test_texts, train_annotations, test_annotations = train_test_split(
texts, annotations, test_size=0.1)
self.model.fit(train_texts)
self.model.fit(train_texts, train_annotations)
predictions = self.model.predict(test_texts)
probas = self.model.predict_proba(test_texts)
self.assertIsInstance(probas, list)
self.assertIsInstance(probas[0], list)
self.assertIsInstance(probas[0][0], dict)
self.assertIsInstance(probas[0][0]['confidence'], dict)
token_precision = sequence_labeling_token_precision(
test_annotations, predictions)
token_recall = sequence_labeling_token_recall(test_annotations,
predictions)
overlap_precision = sequence_labeling_overlap_precision(
test_annotations, predictions)
overlap_recall = sequence_labeling_overlap_recall(
test_annotations, predictions)
self.assertIn('Named Entity', token_precision)
self.assertIn('Named Entity', token_recall)
self.assertIn('Named Entity', overlap_precision)
self.assertIn('Named Entity', overlap_recall)
self.model.save(self.save_file)
model = SequenceLabeler.load(self.save_file)
predictions = model.predict(test_texts)
def test_fit_predict(self):
"""
Ensure model training does not error out
Ensure model returns predictions
"""
raw_docs = ["".join(text) for text in self.texts]
texts, annotations = finetune_to_indico_sequence(
raw_docs, self.texts, self.labels)
train_texts, test_texts, train_annotations, test_annotations = train_test_split(
texts, annotations, test_size=0.1)
self.model.fit(train_texts, train_annotations)
predictions = self.model.predict(test_texts)
probas = self.model.predict_proba(test_texts)
self.assertIsInstance(probas, list)
self.assertIsInstance(probas[0], list)
self.assertIsInstance(probas[0][0], dict)
self.assertIsInstance(probas[0][0]['confidence'], dict)
token_precision = sequence_labeling_token_precision(
test_annotations, predictions)
token_recall = sequence_labeling_token_recall(test_annotations,
predictions)
overlap_precision = sequence_labeling_overlap_precision(
test_annotations, predictions)
overlap_recall = sequence_labeling_overlap_recall(
test_annotations, predictions)
self.assertIn('Named Entity', token_precision)
self.assertIn('Named Entity', token_recall)
self.assertIn('Named Entity', overlap_precision)
self.assertIn('Named Entity', overlap_recall)
self.model.save(self.save_file)
model = SequenceLabeler.load(self.save_file)
predictions = model.predict(test_texts)
def test_reasonable_predictions(self):
test_sequence = [
"I am a dog. A dog that's incredibly bright. I can talk, read, and write!"
]
path = os.path.join(os.path.dirname(__file__), "testdata.json")
# test ValueError raised when raw text is passed along with character idxs and doesn't match
with self.assertRaises(ValueError):
self.model.fit(["Text about a dog."], [[{
"start": 0,
"end": 5,
"text": "cat",
"label": "dog"
}]])
with open(path, "rt") as fp:
text, labels = json.load(fp)
self.model.finetune(text * 10, labels * 10)
predictions = self.model.predict(test_sequence)
self.assertTrue(1 <= len(predictions[0]) <= 3)
self.assertTrue(any(pred["text"] == "dog" for pred in predictions[0]))
self.model.config.subtoken_predictions = True
predictions = self.model.predict(test_sequence)
self.assertTrue(1 <= len(predictions[0]) <= 3)
self.assertTrue(any(pred["text"] == "dog" for pred in predictions[0]))
def test_chunk_long_sequences(self):
test_sequence = [
"I am a dog. A dog that's incredibly bright. I can talk, read, and write!"
* 10
]
path = os.path.join(os.path.dirname(__file__), "testdata.json")
# test ValueError raised when raw text is passed along with character idxs and doesn't match
self.model.config.chunk_long_sequences = True
self.model.config.max_length = 18
with self.assertRaises(ValueError):
self.model.fit(["Text about a dog."], [[{
"start": 0,
"end": 5,
"text": "cat",
"label": "dog"
}]])
with open(path, "rt") as fp:
text, labels = json.load(fp)
self.model.finetune(text * 10, labels * 10)
predictions = self.model.predict(test_sequence)
print(test_sequence)
print(predictions)
print(len(predictions))
self.assertEqual(len(predictions[0]), 20)
self.assertTrue(any(pred["text"] == "dog" for pred in predictions[0]))
def __init__(self, *args, **kwargs):
"""Initialize internal classifier."""
super().__init__(auto_resample=False, *args, **kwargs)
self.model = SequenceLabeler(val_size=0)
os.remove(XML_PATH)
raw_texts = ["".join(doc) for doc in docs]
texts, annotations = finetune_to_indico_sequence(
raw_texts, docs, docs_labels)
df = pd.DataFrame({
'texts':
texts,
'annotations':
[json.dumps(annotation) for annotation in annotations]
})
df.to_csv(DATA_PATH)
if __name__ == "__main__":
dataset = Reuters(nrows=1000).dataframe
dataset['annotations'] = [
json.loads(annotation) for annotation in dataset['annotations']
]
trainX, testX, trainY, testY = train_test_split(dataset.texts.values,
dataset.annotations.values,
test_size=0.3,
random_state=42)
model = SequenceLabeler(verbose=False,
max_length=64,
chunk_long_sequences=True)
model.fit(trainX, trainY)
predictions = model.predict(testX)
n_sample = 10
for i in range(n_sample):
print(testX[i], predictions[i])
class TestSequenceLabeler(unittest.TestCase):
n_sample = 100
dataset_path = os.path.join('Data', 'Sequence', 'reuters.xml')
processed_path = os.path.join('Data', 'Sequence', 'reuters.json')
@classmethod
def _download_reuters(cls):
"""
Download Stanford Sentiment Treebank to enso `data` directory
"""
path = Path(cls.dataset_path)
if not path.exists():
path.parent.mkdir(parents=True, exist_ok=True)
if not os.path.exists(cls.dataset_path):
url = "https://raw.githubusercontent.com/dice-group/n3-collection/master/reuters.xml"
r = requests.get(url)
with open(cls.dataset_path, "wb") as fp:
fp.write(r.content)
with codecs.open(cls.dataset_path, "r", "utf-8") as infile:
soup = bs(infile, "html.parser")
docs = []
docs_labels = []
for elem in soup.find_all("document"):
texts = []
labels = []
# Loop through each child of the element under "textwithnamedentities"
for c in elem.find("textwithnamedentities").children:
if type(c) == Tag:
if c.name == "namedentityintext":
label = "Named Entity" # part of a named entity
else:
label = "<PAD>" # irrelevant word
texts.append(c.text)
labels.append(label)
docs.append(texts)
docs_labels.append(labels)
with open(cls.processed_path, 'wt') as fp:
json.dump((docs, docs_labels), fp)
@classmethod
def setUpClass(cls):
cls._download_reuters()
def default_config(self, **kwargs):
d = dict(
batch_size=2,
max_length=256,
lm_loss_coef=0.0,
val_size=0,
interpolate_pos_embed=False,
)
d.update(**kwargs)
return d
def setUp(self):
self.save_file = 'tests/saved-models/test-save-load'
random.seed(42)
np.random.seed(42)
with open(self.processed_path, 'rt') as fp:
self.texts, self.labels = json.load(fp)
self.model = SequenceLabeler(**self.default_config())
@pytest.mark.skipif(
SKIP_LM_TESTS,
reason="Bidirectional models do not yet support LM functions")
def test_fit_lm_only(self):
"""
Ensure model training does not error out
Ensure model returns predictions
"""
raw_docs = ["".join(text) for text in self.texts]
texts, annotations = finetune_to_indico_sequence(
raw_docs,
self.texts,
self.labels,
none_value=self.model.config.pad_token)
train_texts, test_texts, train_annotations, test_annotations = train_test_split(
texts, annotations, test_size=0.1)
self.model.fit(train_texts)
self.model.fit(train_texts, train_annotations)
predictions = self.model.predict(test_texts)
probas = self.model.predict_proba(test_texts)
self.assertIsInstance(probas, list)
self.assertIsInstance(probas[0], list)
self.assertIsInstance(probas[0][0], dict)
self.assertIsInstance(probas[0][0]['confidence'], dict)
token_precision = sequence_labeling_token_precision(
test_annotations, predictions)
token_recall = sequence_labeling_token_recall(test_annotations,
predictions)
overlap_precision = sequence_labeling_overlap_precision(
test_annotations, predictions)
overlap_recall = sequence_labeling_overlap_recall(
test_annotations, predictions)
self.assertIn('Named Entity', token_precision)
self.assertIn('Named Entity', token_recall)
self.assertIn('Named Entity', overlap_precision)
self.assertIn('Named Entity', overlap_recall)
self.model.save(self.save_file)
model = SequenceLabeler.load(self.save_file)
predictions = model.predict(test_texts)
def test_fit_predict(self):
"""
Ensure model training does not error out
Ensure model returns predictions
Ensure class reweighting behaves as intended
"""
raw_docs = ["".join(text) for text in self.texts]
texts, annotations = finetune_to_indico_sequence(
raw_docs,
self.texts,
self.labels,
none_value=self.model.config.pad_token)
train_texts, test_texts, train_annotations, test_annotations = train_test_split(
texts, annotations, test_size=0.1, random_state=42)
reweighted_model = SequenceLabeler(**self.default_config(
class_weights={'Named Entity': 10.}))
reweighted_model.fit(train_texts, train_annotations)
reweighted_predictions = reweighted_model.predict(test_texts)
reweighted_token_recall = sequence_labeling_token_recall(
test_annotations, reweighted_predictions)
self.model.fit(train_texts, train_annotations)
predictions = self.model.predict(test_texts)
probas = self.model.predict_proba(test_texts)
self.assertIsInstance(probas, list)
self.assertIsInstance(probas[0], list)
self.assertIsInstance(probas[0][0], dict)
self.assertIsInstance(probas[0][0]['confidence'], dict)
token_precision = sequence_labeling_token_precision(
test_annotations, predictions)
token_recall = sequence_labeling_token_recall(test_annotations,
predictions)
overlap_precision = sequence_labeling_overlap_precision(
test_annotations, predictions)
overlap_recall = sequence_labeling_overlap_recall(
test_annotations, predictions)
self.assertIn('Named Entity', token_precision)
self.assertIn('Named Entity', token_recall)
self.assertIn('Named Entity', overlap_precision)
self.assertIn('Named Entity', overlap_recall)
self.model.save(self.save_file)
self.assertGreater(reweighted_token_recall['Named Entity'],
token_recall['Named Entity'])
def test_cached_predict(self):
"""
Ensure model training does not error out
Ensure model returns predictions
"""
raw_docs = ["".join(text) for text in self.texts]
texts, annotations = finetune_to_indico_sequence(
raw_docs,
self.texts,
self.labels,
none_value=self.model.config.pad_token)
train_texts, test_texts, train_annotations, _ = train_test_split(
texts, annotations, test_size=0.1)
self.model.fit(train_texts, train_annotations)
self.model.config.chunk_long_sequences = True
self.model.config.max_length = 128
uncached_preds = self.model.predict(test_texts[:1])
with self.model.cached_predict():
start = time.time()
self.model.predict(test_texts[:1])
first = time.time()
self.model.predict(test_texts[:1])
second = time.time()
preds = self.model.predict(test_texts[:1])
assert len(preds) == 1
preds = self.model.predict(test_texts[:2])
assert len(preds) == 2
for uncached_pred, cached_pred in zip(uncached_preds, preds):
self.assertEqual(str(uncached_pred), str(cached_pred))
first_prediction_time = (first - start)
second_prediction_time = (second - first)
self.assertLess(second_prediction_time, first_prediction_time / 2.)
def test_reasonable_predictions(self):
test_sequence = [
"I am a dog. A dog that's incredibly bright. I can talk, read, and write!"
]
path = os.path.join(os.path.dirname(__file__), "testdata.json")
# test ValueError raised when raw text is passed along with character idxs and doesn't match
with self.assertRaises(ValueError):
self.model.fit(["Text about a dog."], [[{
"start": 0,
"end": 5,
"text": "cat",
"label": "dog"
}]])
with open(path, "rt") as fp:
text, labels = json.load(fp)
self.model.fit(text * 10, labels * 10)
predictions = self.model.predict(test_sequence)
self.assertTrue(1 <= len(predictions[0]) <= 3)
self.assertTrue(
any(pred["text"].strip() == "dog" for pred in predictions[0]))
predictions = self.model.predict(test_sequence)
self.assertTrue(1 <= len(predictions[0]) <= 3)
self.assertTrue(
any(pred["text"].strip() == "dog" for pred in predictions[0]))
def test_chunk_long_sequences(self):
test_sequence = [
"I am a dog. A dog that's incredibly bright. I can talk, read, and write! "
* 10
]
path = os.path.join(os.path.dirname(__file__), "testdata.json")
# test ValueError raised when raw text is passed along with character idxs and doesn't match
self.model.config.chunk_long_sequences = True
self.model.config.max_length = 18
with self.assertRaises(ValueError):
self.model.fit(["Text about a dog."], [[{
"start": 0,
"end": 5,
"text": "cat",
"label": "dog"
}]])
with open(path, "rt") as fp:
text, labels = json.load(fp)
self.model.finetune(text * 10, labels * 10)
predictions = self.model.predict(test_sequence)
self.assertEqual(len(predictions[0]), 20)
self.assertTrue(
any(pred["text"].strip() == "dog" for pred in predictions[0]))
def test_fit_predict_multi_model(self):
"""
Ensure model training does not error out
Ensure model returns predictions
"""
self.model = SequenceLabeler(batch_size=2,
max_length=256,
lm_loss_coef=0.0,
multi_label_sequences=True)
raw_docs = ["".join(text) for text in self.texts]
texts, annotations = finetune_to_indico_sequence(
raw_docs,
self.texts,
self.labels,
none_value=self.model.config.pad_token)
train_texts, test_texts, train_annotations, _ = train_test_split(
texts, annotations, test_size=0.1)
self.model.fit(train_texts, train_annotations)
self.model.predict(test_texts)
probas = self.model.predict_proba(test_texts)
self.assertIsInstance(probas, list)
self.assertIsInstance(probas[0], list)
self.assertIsInstance(probas[0][0], dict)
self.assertIsInstance(probas[0][0]['confidence'], dict)
self.model.save(self.save_file)
model = SequenceLabeler.load(self.save_file)
model.predict(test_texts)
for c in elem.find("textwithnamedentities").children:
if type(c) == Tag:
if c.name == "namedentityintext":
label = "Named Entity" # part of a named entity
else:
label = "<PAD>" # irrelevant word
texts.append(c.text)
labels.append(label)
docs.append(texts)
docs_labels.append(labels)
fd.close()
os.remove(XML_PATH)
raw_texts = ["".join(doc) for doc in docs]
texts, annotations = finetune_to_indico_sequence(raw_texts, docs, docs_labels)
df = pd.DataFrame({'texts': texts, 'annotations': [json.dumps(annotation) for annotation in annotations]})
df.to_csv(DATA_PATH)
if __name__ == "__main__":
dataset = Reuters(nrows=1000).dataframe
dataset['annotations'] = [json.loads(annotation) for annotation in dataset['annotations']]
trainX, testX, trainY, testY = train_test_split(dataset.texts.values, dataset.annotations.values, test_size=0.3, random_state=42)
model = SequenceLabeler(verbose=False, max_length=64, chunk_long_sequences=True)
model.fit(trainX, trainY)
predictions = model.predict(testX)
n_sample = 10
for i in range(n_sample):
print(testX[i], predictions[i])
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.model = SequenceLabeler(val_size=0)
none_value="<PAD>",
subtoken_predictions=True)
df = pd.DataFrame({
'texts':
texts,
'annotations':
[json.dumps(annotation) for annotation in annotations]
})
df.to_csv(DATA_PATH)
if __name__ == "__main__":
dataset = Reuters().dataframe
dataset['annotations'] = [
json.loads(annotation) for annotation in dataset['annotations']
]
trainX, testX, trainY, testY = train_test_split(dataset.texts.values,
dataset.annotations.values,
test_size=0.7,
random_state=42)
model = SequenceLabeler(base_model=RoBERTa,
batch_size=1,
val_size=0.,
max_length=16,
chunk_long_sequences=True,
subtoken_predictions=True)
model.fit(trainX, trainY)
predictions = model.predict(testX)
print(predictions)
print(annotation_report(testY, predictions))
class TestSequenceLabelerTextCNN(TestModelBase):
n_sample = 100
dataset_path = os.path.join("Data", "Sequence", "reuters.xml")
processed_path = os.path.join("Data", "Sequence", "reuters.json")
base_model = TextCNN
@classmethod
def _download_reuters(cls):
"""
Download Reuters to test directory
"""
path = Path(cls.dataset_path)
if not path.exists():
path.parent.mkdir(parents=True, exist_ok=True)
if not os.path.exists(cls.dataset_path):
url = "https://raw.githubusercontent.com/dice-group/n3-collection/master/reuters.xml"
r = requests.get(url)
with open(cls.dataset_path, "wb") as fp:
fp.write(r.content)
with codecs.open(cls.dataset_path, "r", "utf-8") as infile:
soup = bs(infile, "html.parser")
docs = []
docs_labels = []
for elem in soup.find_all("document"):
texts = []
labels = []
# Loop through each child of the element under "textwithnamedentities"
for c in elem.find("textwithnamedentities").children:
if type(c) == Tag:
if c.name == "namedentityintext":
label = "Named Entity" # part of a named entity
else:
label = "<PAD>" # irrelevant word
texts.append(c.text)
labels.append(label)
docs.append(texts)
docs_labels.append(labels)
with open(cls.processed_path, "wt") as fp:
json.dump((docs, docs_labels), fp)
@classmethod
def setUpClass(cls):
cls._download_reuters()
def setUp(self):
self.save_file = "tests/saved-models/test-save-load"
random.seed(42)
np.random.seed(42)
with open(self.processed_path, "rt") as fp:
self.texts, self.labels = json.load(fp)
self.model = SequenceLabeler(**self.default_config())
def test_fit_predict(self):
"""
Ensure model training does not error out
Ensure model returns predictions
Ensure class reweighting behaves as intended
"""
raw_docs = ["".join(text) for text in self.texts]
texts, annotations = finetune_to_indico_sequence(
raw_docs,
self.texts,
self.labels,
none_value=self.model.config.pad_token)
train_texts, test_texts, train_annotations, test_annotations = train_test_split(
texts, annotations, test_size=0.1)
self.model.fit(train_texts, train_annotations)
predictions = self.model.predict(test_texts)
probas = self.model.predict_proba(test_texts)
self.assertIsInstance(probas, list)
self.assertIsInstance(probas[0], list)
self.assertIsInstance(probas[0][0], dict)
self.assertIsInstance(probas[0][0]["confidence"], dict)
token_precision = sequence_labeling_token_precision(
test_annotations, predictions)
token_recall = sequence_labeling_token_recall(test_annotations,
predictions)
overlap_precision = sequence_labeling_overlap_precision(
test_annotations, predictions)
overlap_recall = sequence_labeling_overlap_recall(
test_annotations, predictions)
self.assertIn("Named Entity", token_precision)
self.assertIn("Named Entity", token_recall)
self.assertIn("Named Entity", overlap_precision)
self.assertIn("Named Entity", overlap_recall)
self.model.save(self.save_file)
def test_cached_predict(self):
"""
Ensure model training does not error out
Ensure model returns predictions
"""
raw_docs = ["".join(text) for text in self.texts]
texts, annotations = finetune_to_indico_sequence(
raw_docs,
self.texts,
self.labels,
none_value=self.model.config.pad_token)
train_texts, test_texts, train_annotations, _ = train_test_split(
texts, annotations, test_size=0.1)
self.model.fit(train_texts, train_annotations)
with self.model.cached_predict():
self.model.predict(test_texts)
self.model.predict(test_texts)
def test_fit_predict_multi_model(self):
"""
Ensure model training does not error out
Ensure model returns predictions
"""
self.model = SequenceLabeler(**self.default_config(
batch_size=2,
max_length=256,
lm_loss_coef=0.0,
multi_label_sequences=True,
))
raw_docs = ["".join(text) for text in self.texts]
texts, annotations = finetune_to_indico_sequence(
raw_docs,
self.texts,
self.labels,
none_value=self.model.config.pad_token)
train_texts, test_texts, train_annotations, _ = train_test_split(
texts, annotations, test_size=0.1)
self.model.fit(train_texts, train_annotations)
self.model.predict(test_texts)
probas = self.model.predict_proba(test_texts)
self.assertIsInstance(probas, list)
self.assertIsInstance(probas[0], list)
self.assertIsInstance(probas[0][0], dict)
self.assertIsInstance(probas[0][0]["confidence"], dict)
self.model.save(self.save_file)
model = SequenceLabeler.load(self.save_file)
model.predict(test_texts)
fd.close()
os.remove(XML_PATH)
raw_texts = ["".join(doc) for doc in docs]
texts, annotations = finetune_to_indico_sequence(
raw_texts, docs, docs_labels)
df = pd.DataFrame({
'texts':
texts,
'annotations':
[json.dumps(annotation) for annotation in annotations]
})
df.to_csv(DATA_PATH)
if __name__ == "__main__":
dataset = Reuters().dataframe
dataset['annotations'] = [
json.loads(annotation) for annotation in dataset['annotations']
]
trainX, testX, trainY, testY = train_test_split(dataset.texts.values,
dataset.annotations.values,
test_size=0.3,
random_state=42)
model = SequenceLabeler(batch_size=2,
val_size=0.,
chunk_long_sequences=True)
model.fit(trainX, trainY)
predictions = model.predict(testX)
print(annotation_report(testY, predictions))
fd.close()
os.remove(XML_PATH)
raw_texts = ["".join(doc) for doc in docs]
texts, annotations = finetune_to_indico_sequence(
raw_texts, docs, docs_labels)
df = pd.DataFrame({
'texts':
texts,
'annotations':
[json.dumps(annotation) for annotation in annotations]
})
df.to_csv(DATA_PATH)
if __name__ == "__main__":
dataset = Reuters(nrows=1000).dataframe
dataset['annotations'] = [
json.loads(annotation) for annotation in dataset['annotations']
]
trainX, testX, trainY, testY = train_test_split(dataset.texts,
dataset.annotations,
test_size=0.3,
random_state=42)
model = SequenceLabeler(verbose=False)
model.fit(trainX, trainY)
predictions = model.predict(testX)
n_sample = 10
for i in range(n_sample):
print(testX.values[i], predictions[i])
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.model_config = dict(val_size=0)
self.model_config.update(kwargs)
self.model = SequenceLabeler(**self.model_config)
class TestSequenceLabeler(unittest.TestCase):
n_sample = 100
dataset_path = os.path.join(
'Data', 'Sequence', 'reuters.xml'
)
processed_path = os.path.join('Data', 'Sequence', 'reuters.json')
@classmethod
def _download_reuters(cls):
"""
Download Stanford Sentiment Treebank to enso `data` directory
"""
path = Path(cls.dataset_path)
if not path.exists():
path.parent.mkdir(parents=True, exist_ok=True)
if not os.path.exists(cls.dataset_path):
url = "https://raw.githubusercontent.com/dice-group/n3-collection/master/reuters.xml"
r = requests.get(url)
with open(cls.dataset_path, "wb") as fp:
fp.write(r.content)
with codecs.open(cls.dataset_path, "r", "utf-8") as infile:
soup = bs(infile, "html.parser")
docs = []
docs_labels = []
for elem in soup.find_all("document"):
texts = []
labels = []
# Loop through each child of the element under "textwithnamedentities"
for c in elem.find("textwithnamedentities").children:
if type(c) == Tag:
if c.name == "namedentityintext":
label = "Named Entity" # part of a named entity
else:
label = "<PAD>" # irrelevant word
texts.append(c.text)
labels.append(label)
docs.append(texts)
docs_labels.append(labels)
with open(cls.processed_path, 'wt') as fp:
json.dump((docs, docs_labels), fp)
@classmethod
def setUpClass(cls):
cls._download_reuters()
def default_config(self, **kwargs):
d = dict(
batch_size=2,
max_length=256,
lm_loss_coef=0.0,
val_size=0,
interpolate_pos_embed=False,
)
d.update(**kwargs)
return d
def setUp(self):
self.save_file = 'tests/saved-models/test-save-load'
random.seed(42)
np.random.seed(42)
with open(self.processed_path, 'rt') as fp:
self.texts, self.labels = json.load(fp)
self.model = SequenceLabeler(
**default_config()
)
def test_fit_predict(self):
"""
Ensure model training does not error out
Ensure model returns predictions
Ensure class reweighting behaves as intended
"""
raw_docs = ["".join(text) for text in self.texts]
texts, annotations = finetune_to_indico_sequence(
raw_docs,
self.texts,
self.labels,
encoder=self.model.input_pipeline.text_encoder,
none_value=self.model.config.pad_token
)
train_texts, test_texts, train_annotations, test_annotations = train_test_split(
texts, annotations, test_size=0.1
)
reweighted_model = SequenceLabeler(
**default_config(class_weights={'Named Entity': 10.})
)
reweighted_model.fit(train_texts, train_annotations)
reweighted_predictions = reweighted_model.predict(test_texts)
reweighted_token_recall = sequence_labeling_token_recall(test_annotations, reweighted_predictions)
self.model.fit(train_texts, train_annotations)
predictions = self.model.predict(test_texts)
probas = self.model.predict_proba(test_texts)
self.assertIsInstance(probas, list)
self.assertIsInstance(probas[0], list)
self.assertIsInstance(probas[0][0], dict)
self.assertIsInstance(probas[0][0]['confidence'], dict)
token_precision = sequence_labeling_token_precision(test_annotations, predictions)
token_recall = sequence_labeling_token_recall(test_annotations, predictions)
overlap_precision = sequence_labeling_overlap_precision(test_annotations, predictions)
overlap_recall = sequence_labeling_overlap_recall(test_annotations, predictions)
self.assertIn('Named Entity', token_precision)
self.assertIn('Named Entity', token_recall)
self.assertIn('Named Entity', overlap_precision)
self.assertIn('Named Entity', overlap_recall)
self.model.save(self.save_file)
self.assertGreater(reweighted_token_recall['Named Entity'], token_recall['Named Entity'])
def test_cached_predict(self):
"""
Ensure model training does not error out
Ensure model returns predictions
"""
raw_docs = ["".join(text) for text in self.texts]
texts, annotations = finetune_to_indico_sequence(
raw_docs,
self.texts,
self.labels,
encoder=self.model.input_pipeline.text_encoder,
none_value=self.model.config.pad_token
)
train_texts, test_texts, train_annotations, _ = train_test_split(texts, annotations, test_size=0.1)
self.model.fit(train_texts, train_annotations)
with self.model.cached_predict():
self.model.predict(test_texts)
self.model.predict(test_texts)
def test_fit_predict_multi_model(self):
"""
Ensure model training does not error out
Ensure model returns predictions
"""
self.model = SequenceLabeler(batch_size=2, max_length=256, lm_loss_coef=0.0, multi_label_sequences=True)
raw_docs = ["".join(text) for text in self.texts]
texts, annotations = finetune_to_indico_sequence(
raw_docs,
self.texts,
self.labels,
encoder=self.model.input_pipeline.text_encoder,
none_value=self.model.config.pad_token
)
train_texts, test_texts, train_annotations, _ = train_test_split(texts, annotations, test_size=0.1)
self.model.fit(train_texts, train_annotations)
self.model.predict(test_texts)
probas = self.model.predict_proba(test_texts)
self.assertIsInstance(probas, list)
self.assertIsInstance(probas[0], list)
self.assertIsInstance(probas[0][0], dict)
self.assertIsInstance(probas[0][0]['confidence'], dict)
self.model.save(self.save_file)
model = SequenceLabeler.load(self.save_file)
model.predict(test_texts)
subtoken_predictions=True)
df = pd.DataFrame({
'texts':
texts,
'annotations':
[json.dumps(annotation) for annotation in annotations]
})
df.to_csv(DATA_PATH)
if __name__ == "__main__":
dataset = Reuters().dataframe
dataset['annotations'] = [
json.loads(annotation) for annotation in dataset['annotations']
]
trainX, testX, trainY, testY = train_test_split(dataset.texts.values,
dataset.annotations.values,
test_size=0.3,
random_state=42)
model = SequenceLabeler(base_model=GPT2,
batch_size=2,
val_size=0.,
max_length=16,
chunk_long_sequences=True,
subtoken_predictions=True,
filter_empty_examples=True)
model.fit(trainX, trainY)
predictions = model.predict(testX)
print(predictions)
print(annotation_report(testY, predictions))
class TestSequenceLabeler(unittest.TestCase):
n_sample = 100
n_hidden = 768
dataset_path = os.path.join(
'Data', 'Sequence', 'reuters.xml'
)
processed_path = os.path.join('Data', 'Sequence', 'reuters.json')
@classmethod
def _download_reuters(cls):
"""
Download Stanford Sentiment Treebank to enso `data` directory
"""
path = Path(cls.dataset_path)
if not path.exists():
path.parent.mkdir(parents=True, exist_ok=True)
if not os.path.exists(cls.dataset_path):
url = "https://raw.githubusercontent.com/dice-group/n3-collection/master/reuters.xml"
r = requests.get(url)
with open(cls.dataset_path, "wb") as fp:
fp.write(r.content)
with codecs.open(cls.dataset_path, "r", "utf-8") as infile:
soup = bs(infile, "html5lib")
docs = []
docs_labels = []
for elem in soup.find_all("document"):
texts = []
labels = []
# Loop through each child of the element under "textwithnamedentities"
for c in elem.find("textwithnamedentities").children:
if type(c) == Tag:
if c.name == "namedentityintext":
label = "Named Entity" # part of a named entity
else:
label = "<PAD>" # irrelevant word
texts.append(c.text)
labels.append(label)
docs.append(texts)
docs_labels.append(labels)
with open(cls.processed_path, 'wt') as fp:
json.dump((docs, docs_labels), fp)
@classmethod
def setUpClass(cls):
cls._download_reuters()
def setUp(self):
self.save_file = 'tests/saved-models/test-save-load'
with open(self.processed_path, 'rt') as fp:
self.texts, self.labels = json.load(fp)
tf.reset_default_graph()
self.model = SequenceLabeler(batch_size=2, max_length=256, verbose=False)
def test_fit_predict(self):
"""
Ensure model training does not error out
Ensure model returns predictions
"""
raw_docs = ["".join(text) for text in self.texts]
texts, annotations = finetune_to_indico_sequence(raw_docs, self.texts, self.labels)
train_texts, test_texts, train_annotations, test_annotations = train_test_split(texts, annotations)
self.model.fit(train_texts, train_annotations)
predictions = self.model.predict(test_texts)
self.model.save(self.save_file)
model = SequenceLabeler.load(self.save_file)
predictions = model.predict(test_texts)
