def test_infer_from_data():
X = ["One", "Two words", "Three words here"]
keras_vectorizer = KerasVectorizer()
keras_vectorizer.fit(X)
assert keras_vectorizer.sequence_length == 3
def test_build_embedding_matrix_word_vectors():
X = ["One", "Two", "Three"]
vocab_size = 1
keras_vectorizer = KerasVectorizer(vocab_size=vocab_size)
keras_vectorizer.fit(X)
embedding_matrix = keras_vectorizer.build_embedding_matrix(
embeddings_name_or_path="glove-twitter-25")
assert embedding_matrix.shape == (5, 25)
def test_build_embedding_matrix():
X = ["One", "Two", "Three"]
vocab_size = 1
keras_vectorizer = KerasVectorizer(vocab_size=vocab_size)
keras_vectorizer.fit(X)
with tempfile.TemporaryDirectory() as tmp_dir:
embeddings_path = os.path.join(tmp_dir, "embeddings.csv")
embeddings = [
"one 0 1 0 0 0",
"two 0 0 1 0 0",
"three 0 0 0 1 0",
"four 0 0 0 0 1",
]
with open(embeddings_path, "w") as embeddings_path_tmp:
for line in embeddings:
embeddings_path_tmp.write(line)
embeddings_path_tmp.write("\n")
embedding_matrix = keras_vectorizer.build_embedding_matrix(
embeddings_name_or_path=embeddings_path)
assert embedding_matrix.shape == (5, 5)
class MeshCNN:
def __init__(
self,
threshold=0.5,
batch_size=256,
shuffle=True,
buffer_size=1000,
data_cache=None,
random_seed=42,
):
"""
threshold: float, default 0.5. Probability threshold on top of which a tag should be assigned.
batch_size: int, default 256. Size of batches used for training and prediction.
shuffle: bool, default True. Flag on whether to shuffle data before fit.
buffer_size: int, default 1000. Buffer size used for shuffling or transforming data before fit.
data_cache: path, default None. Path to use for caching data transformations.
random_seed: int, default 42. Random seed that controls reproducibility.
"""
self.threshold = threshold
self.batch_size = batch_size
self.shuffle = shuffle
self.buffer_size = buffer_size
self.data_cache = data_cache
self.random_seed = random_seed
def _yield_data(self, X, vectorizer, Y=None):
"""
Generator to yield vectorized X and Y data one by one
X: list of texts
vectorizer: vectorizer class that implements transform which transforms texts to integers
Y: 2d numpy array or sparse csr_matrix that represents targets (tags) assigned.
If Y is missing, for example when called by predict, yield_data yields only X vectorized
"""
def yield_transformed_data(X_buffer, Y_buffer):
# TODO: This could move to WellcomeML to enable CNN to receive generators
Y_den = None
X_vec = self.vectorizer.transform(X_buffer)
if Y_buffer:
# Y_buffer list of np or sparse arrays
if type(Y_buffer[0]) == np.ndarray:
Y_den = np.vstack(Y_buffer)
else: # sparse
Y_buffer = sp.vstack(Y_buffer)
Y_den = np.asarray(Y_buffer.todense())
for i in range(len(X_buffer)):
if Y_den is not None:
yield X_vec[i], Y_den[i]
else:
yield X_vec[i]
def data_gen():
"""
Wrapper on top of yield_transformed_data to get a callable function
which enables to restart the iterator.
This function also implements buffering for more efficient transformations
"""
X_buffer = []
Y_buffer = []
X_gen = X()
if Y:
Y_gen = Y()
data_zip = zip(X_gen, Y_gen)
else:
data_zip = X_gen
for data_example in data_zip:
if Y:
x, y = data_example
Y_buffer.append(y)
else:
x = data_example
X_buffer.append(x)
if len(X_buffer) >= self.buffer_size:
yield from yield_transformed_data(X_buffer, Y_buffer)
X_buffer = []
Y_buffer = []
if X_buffer:
yield from yield_transformed_data(X_buffer, Y_buffer)
output_types = (tf.int32, tf.int32) if Y else (tf.int32)
data = tf.data.Dataset.from_generator(data_gen,
output_types=output_types)
if self.data_cache:
data = data.cache(self.data_cache)
return data
def _init_vectorizer(self):
self.vectorizer = KerasVectorizer(vocab_size=5_000,
sequence_length=400)
def _init_classifier(self):
self.classifier = CNNClassifier(
learning_rate=0.01,
dropout=0.1,
sparse_y=True,
nb_epochs=20,
nb_layers=4,
multilabel=True,
threshold=self.threshold,
batch_size=self.batch_size,
)
def set_params(self, **params):
if not hasattr(self, "vectorizer"):
self._init_vectorizer()
if not hasattr(self, "classifier"):
self._init_classifier()
vec_params = get_params_for_component(params, "vec")
clf_params = get_params_for_component(params, "cnn")
self.vectorizer.set_params(**vec_params)
self.classifier.set_params(**clf_params)
def fit(self, X, Y):
"""
X: list or generator of texts
Y: 2d numpy array or sparse csr_matrix or generator of 2d numpy array of tags assigned
If X is a generator it need to be callable i.e. return
the generator by calling it X_gen = X(). This is so
we can iterate on the data again.
"""
if not hasattr(self, "vectorizer"):
self._init_vectorizer()
if not hasattr(self, "classifier"):
self._init_classifier()
if type(X) in [list, np.ndarray]:
print("Fitting vectorizer")
self.vectorizer.fit(X)
X_vec = self.vectorizer.transform(X)
print(X_vec.shape)
print("Fitting classifier")
self.classifier.fit(X_vec, Y)
else:
print("Fitting vectorizer")
X_gen = X()
self.vectorizer.fit(X_gen)
print("Fitting classifier")
params_from_vectorizer = {
"sequence_length": self.vectorizer.sequence_length,
"vocab_size": self.vectorizer.vocab_size,
}
self.classifier.set_params(**params_from_vectorizer)
train_data = self._yield_data(X, self.vectorizer, Y)
# TODO: This should move inside CNNClassifier
if self.shuffle:
train_data = train_data.shuffle(self.buffer_size,
seed=self.random_seed)
self.classifier.fit(train_data)
return self
def predict(self, X):
if type(X) in [list, np.ndarray]:
X_vec = self.vectorizer.transform(X)
Y_pred = self.classifier.predict(X_vec)
else:
pred_data = self._yield_data(X, self.vectorizer)
Y_pred = self.classifier.predict(pred_data)
return Y_pred
def predict_proba(self, X):
if type(X) in [list, np.ndarray]:
X_vec = self.vectorizer.transform(X)
Y_pred_proba = []
for i in range(0, X_vec.shape[0], self.batch_size):
Y_pred_proba_batch = self.classifier.predict_proba(
X_vec[i:i + self.batch_size])
Y_pred_proba.append(Y_pred_proba_batch)
Y_pred_proba = np.hstack(Y_pred_proba)
else:
pred_data = self._yield_data(X, self.vectorizer)
Y_pred_proba = self.classifier.predict_proba(pred_data)
return Y_pred_proba
def save(self, model_path):
if not os.path.exists(model_path):
os.mkdir(model_path)
meta = {"name": "MeshCNN", "approach": "mesh-cnn"}
meta_path = os.path.join(model_path, "meta.json")
with open(meta_path, "w") as f:
f.write(json.dumps(meta))
vectorizer_path = os.path.join(model_path, "vectorizer.pkl")
save_pickle(vectorizer_path, self.vectorizer)
self.classifier.save(model_path)
def load(self, model_path):
meta_path = os.path.join(model_path, "meta.json")
with open(meta_path, "r") as f:
meta = json.loads(f.read())
self.set_params(**meta)
vectorizer_path = os.path.join(model_path, "vectorizer.pkl")
self.vectorizer = load_pickle(vectorizer_path)
self._init_classifier()
self.classifier.load(model_path)
