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Commit 42da7864 authored by Christopher Shallue's avatar Christopher Shallue
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Move tensorflow_models/research/astronet to google-research/exoplanet-ml

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research/astronet/astronet/ops/dataset_ops_test.py deleted 100644 → 0
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research/astronet/astronet/ops/input_ops.py deleted 100644 → 0
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# Copyright 2018 The TensorFlow Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Operations for feeding input data using TensorFlow placeholders."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import tensorflow as tf
def prepare_feed_dict(model, features, labels=None, is_training=None):
"""Prepares a feed_dict for sess.run() given a batch of features and labels.
Args:
model: An instance of AstroModel.
features: Dictionary containing "time_series_features" and "aux_features".
Each is a dictionary of named numpy arrays of shape [batch_size, length].
labels: (Optional). Numpy array of shape [batch_size].
is_training: (Optional). Python boolean to feed to the model.is_training
Tensor (if None, no value is fed).
Returns:
feed_dict: A dictionary of input Tensor to numpy array.
"""
feed_dict = {}
for feature, tensor in model.time_series_features.items():
feed_dict[tensor] = features["time_series_features"][feature]
for feature, tensor in model.aux_features.items():
feed_dict[tensor] = features["aux_features"][feature]
if labels is not None:
feed_dict[model.labels] = labels
if is_training is not None:
feed_dict[model.is_training] = is_training
return feed_dict
def build_feature_placeholders(config):
"""Builds tf.Placeholder ops for feeding model features and labels.
Args:
config: ConfigDict containing the feature configurations.
Returns:
features: A dictionary containing "time_series_features" and "aux_features",
each of which is a dictionary of tf.Placeholders of features from the
input configuration. All features have dtype float32 and shape
[batch_size, length].
"""
batch_size = None # Batch size will be dynamically specified.
features = {"time_series_features": {}, "aux_features": {}}
for feature_name, feature_spec in config.items():
placeholder = tf.placeholder(
dtype=tf.float32,
shape=[batch_size, feature_spec.length],
name=feature_name)
if feature_spec.is_time_series:
features["time_series_features"][feature_name] = placeholder
else:
features["aux_features"][feature_name] = placeholder
return features
def build_labels_placeholder():
"""Builds a tf.Placeholder op for feeding model labels.
Returns:
labels: An int64 tf.Placeholder with shape [batch_size].
"""
batch_size = None # Batch size will be dynamically specified.
return tf.placeholder(dtype=tf.int64, shape=[batch_size], name="labels")
research/astronet/astronet/ops/input_ops_test.py deleted 100644 → 0
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# Copyright 2018 The TensorFlow Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Tests for input_ops."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import tensorflow as tf
from astronet.ops import input_ops
from tf_util import configdict
class InputOpsTest(tf.test.TestCase):
def assertFeatureShapesEqual(self, expected_shapes, features):
"""Asserts that a dict of feature placeholders has the expected shapes.
Args:
expected_shapes: Dictionary of expected Tensor shapes, as lists,
corresponding to the structure of 'features'.
features: Dictionary of feature placeholders of the format returned by
input_ops.build_feature_placeholders().
"""
actual_shapes = {}
for feature_type in features:
actual_shapes[feature_type] = {
feature: tensor.shape.as_list()
for feature, tensor in features[feature_type].items()
}
self.assertDictEqual(expected_shapes, actual_shapes)
def testBuildFeaturePlaceholders(self):
# One time series feature.
config = configdict.ConfigDict({
"time_feature_1": {
"length": 14,
"is_time_series": True,
}
})
expected_shapes = {
"time_series_features": {
"time_feature_1": [None, 14],
},
"aux_features": {}
}
features = input_ops.build_feature_placeholders(config)
self.assertFeatureShapesEqual(expected_shapes, features)
# Two time series features.
config = configdict.ConfigDict({
"time_feature_1": {
"length": 14,
"is_time_series": True,
},
"time_feature_2": {
"length": 5,
"is_time_series": True,
}
})
expected_shapes = {
"time_series_features": {
"time_feature_1": [None, 14],
"time_feature_2": [None, 5],
},
"aux_features": {}
}
features = input_ops.build_feature_placeholders(config)
self.assertFeatureShapesEqual(expected_shapes, features)
# One aux feature.
config = configdict.ConfigDict({
"time_feature_1": {
"length": 14,
"is_time_series": True,
},
"aux_feature_1": {
"length": 1,
"is_time_series": False,
}
})
expected_shapes = {
"time_series_features": {
"time_feature_1": [None, 14],
},
"aux_features": {
"aux_feature_1": [None, 1]
}
}
features = input_ops.build_feature_placeholders(config)
self.assertFeatureShapesEqual(expected_shapes, features)
# Two aux features.
config = configdict.ConfigDict({
"time_feature_1": {
"length": 14,
"is_time_series": True,
},
"aux_feature_1": {
"length": 1,
"is_time_series": False,
},
"aux_feature_2": {
"length": 6,
"is_time_series": False,
},
})
expected_shapes = {
"time_series_features": {
"time_feature_1": [None, 14],
},
"aux_features": {
"aux_feature_1": [None, 1],
"aux_feature_2": [None, 6]
}
}
features = input_ops.build_feature_placeholders(config)
self.assertFeatureShapesEqual(expected_shapes, features)
if __name__ == "__main__":
tf.test.main()
research/astronet/astronet/ops/metrics.py deleted 100644 → 0
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# Copyright 2018 The TensorFlow Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Functions for computing evaluation metrics."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import tensorflow as tf
def _metric_variable(name, shape, dtype):
"""Creates a Variable in LOCAL_VARIABLES and METRIC_VARIABLES collections."""
return tf.get_variable(
name,
initializer=tf.zeros(shape, dtype),
trainable=False,
collections=[tf.GraphKeys.LOCAL_VARIABLES, tf.GraphKeys.METRIC_VARIABLES])
def _build_metrics(labels, predictions, weights, batch_losses, output_dim=1):
"""Builds TensorFlow operations to compute model evaluation metrics.
Args:
labels: Tensor with shape [batch_size].
predictions: Tensor with shape [batch_size, output_dim].
weights: Tensor with shape [batch_size].
batch_losses: Tensor with shape [batch_size].
output_dim: Dimension of model output
Returns:
A dictionary {metric_name: (metric_value, update_op).
"""
# Compute the predicted labels.
assert len(predictions.shape) == 2
binary_classification = output_dim == 1
if binary_classification:
assert predictions.shape[1] == 1
predictions = tf.squeeze(predictions, axis=[1])
predicted_labels = tf.to_int32(
tf.greater(predictions, 0.5), name="predicted_labels")
else:
predicted_labels = tf.argmax(
predictions, 1, name="predicted_labels", output_type=tf.int32)
metrics = {}
with tf.variable_scope("metrics"):
# Total number of examples.
num_examples = _metric_variable("num_examples", [], tf.float32)
update_num_examples = tf.assign_add(num_examples, tf.reduce_sum(weights))
metrics["num_examples"] = (num_examples.read_value(), update_num_examples)
# Accuracy metrics.
num_correct = _metric_variable("num_correct", [], tf.float32)
is_correct = weights * tf.to_float(tf.equal(labels, predicted_labels))
update_num_correct = tf.assign_add(num_correct, tf.reduce_sum(is_correct))
metrics["accuracy/num_correct"] = (num_correct.read_value(),
update_num_correct)
accuracy = tf.div(num_correct, num_examples, name="accuracy")
metrics["accuracy/accuracy"] = (accuracy, tf.no_op())
# Weighted cross-entropy loss.
metrics["losses/weighted_cross_entropy"] = tf.metrics.mean(
batch_losses, weights=weights, name="cross_entropy_loss")
def _count_condition(name, labels_value, predicted_value):
"""Creates a counter for given values of predictions and labels."""
count = _metric_variable(name, [], tf.float32)
is_equal = tf.to_float(
tf.logical_and(
tf.equal(labels, labels_value),
tf.equal(predicted_labels, predicted_value)))
update_op = tf.assign_add(count, tf.reduce_sum(weights * is_equal))
return count.read_value(), update_op
# Confusion matrix metrics.
num_labels = 2 if binary_classification else output_dim
for gold_label in range(num_labels):
for pred_label in range(num_labels):
metric_name = "confusion_matrix/label_{}_pred_{}".format(
gold_label, pred_label)
metrics[metric_name] = _count_condition(
metric_name, labels_value=gold_label, predicted_value=pred_label)
# Possibly create AUC metric for binary classification.
if binary_classification:
labels = tf.cast(labels, dtype=tf.bool)
metrics["auc"] = tf.metrics.auc(
labels, predictions, weights=weights, num_thresholds=1000)
return metrics
def create_metric_fn(model):
"""Creates a tuple (metric_fn, metric_fn_inputs).
This function is primarily used for creating a TPUEstimator.
The result of calling metric_fn(**metric_fn_inputs) is a dictionary
{metric_name: (metric_value, update_op)}.
Args:
model: Instance of AstroModel.
Returns:
A tuple (metric_fn, metric_fn_inputs).
"""
weights = model.weights
if weights is None:
weights = tf.ones_like(model.labels, dtype=tf.float32)
metric_fn_inputs = {
"labels": model.labels,
"predictions": model.predictions,
"weights": weights,
"batch_losses": model.batch_losses,
}
def metric_fn(labels, predictions, weights, batch_losses):
return _build_metrics(
labels,
predictions,
weights,
batch_losses,
output_dim=model.hparams.output_dim)
return metric_fn, metric_fn_inputs
def create_metrics(model):
"""Creates a dictionary {metric_name: (metric_value, update_op)}.
This function is primarily used for creating an Estimator.
Args:
model: Instance of AstroModel.
Returns:
A dictionary {metric_name: (metric_value, update_op).
"""
metric_fn, metric_fn_inputs = create_metric_fn(model)
return metric_fn(**metric_fn_inputs)
research/astronet/astronet/ops/metrics_test.py deleted 100644 → 0
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# Copyright 2018 The TensorFlow Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Tests for metrics.py."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import tensorflow as tf
from astronet.ops import metrics
def _unpack_metric_map(names_to_tuples):
"""Unpacks {metric_name: (metric_value, update_op)} into separate dicts."""
metric_names = names_to_tuples.keys()
value_ops, update_ops = zip(*names_to_tuples.values())
return dict(zip(metric_names, value_ops)), dict(zip(metric_names, update_ops))
class _MockHparams(object):
"""Mock Hparams class to support accessing with dot notation."""
pass
class _MockModel(object):
"""Mock model for testing."""
def __init__(self, labels, predictions, weights, batch_losses, output_dim):
self.labels = tf.constant(labels, dtype=tf.int32)
self.predictions = tf.constant(predictions, dtype=tf.float32)
self.weights = None if weights is None else tf.constant(
weights, dtype=tf.float32)
self.batch_losses = tf.constant(batch_losses, dtype=tf.float32)
self.hparams = _MockHparams()
self.hparams.output_dim = output_dim
class MetricsTest(tf.test.TestCase):
def testMultiClassificationWithoutWeights(self):
labels = [0, 1, 2, 3]
predictions = [
[0.7, 0.2, 0.1, 0.0], # Predicted label = 0
[0.2, 0.4, 0.2, 0.2], # Predicted label = 1
[0.0, 0.0, 0.0, 1.0], # Predicted label = 3
[0.1, 0.1, 0.7, 0.1], # Predicted label = 2
]
weights = None
batch_losses = [0, 0, 4, 2]
model = _MockModel(labels, predictions, weights, batch_losses, output_dim=4)
metric_map = metrics.create_metrics(model)
value_ops, update_ops = _unpack_metric_map(metric_map)
initializer = tf.local_variables_initializer()
with self.test_session() as sess:
sess.run(initializer)
sess.run(update_ops)
self.assertAllClose({
"num_examples": 4,
"accuracy/num_correct": 2,
"accuracy/accuracy": 0.5,
"losses/weighted_cross_entropy": 1.5,
"confusion_matrix/label_0_pred_0": 1,
"confusion_matrix/label_0_pred_1": 0,
"confusion_matrix/label_0_pred_2": 0,
"confusion_matrix/label_0_pred_3": 0,
"confusion_matrix/label_1_pred_0": 0,
"confusion_matrix/label_1_pred_1": 1,
"confusion_matrix/label_1_pred_2": 0,
"confusion_matrix/label_1_pred_3": 0,
"confusion_matrix/label_2_pred_0": 0,
"confusion_matrix/label_2_pred_1": 0,
"confusion_matrix/label_2_pred_2": 0,
"confusion_matrix/label_2_pred_3": 1,
"confusion_matrix/label_3_pred_0": 0,
"confusion_matrix/label_3_pred_1": 0,
"confusion_matrix/label_3_pred_2": 1,
"confusion_matrix/label_3_pred_3": 0
}, sess.run(value_ops))
sess.run(update_ops)
self.assertAllClose({
"num_examples": 8,
"accuracy/num_correct": 4,
"accuracy/accuracy": 0.5,
"losses/weighted_cross_entropy": 1.5,
"confusion_matrix/label_0_pred_0": 2,
"confusion_matrix/label_0_pred_1": 0,
"confusion_matrix/label_0_pred_2": 0,
"confusion_matrix/label_0_pred_3": 0,
"confusion_matrix/label_1_pred_0": 0,
"confusion_matrix/label_1_pred_1": 2,
"confusion_matrix/label_1_pred_2": 0,
"confusion_matrix/label_1_pred_3": 0,
"confusion_matrix/label_2_pred_0": 0,
"confusion_matrix/label_2_pred_1": 0,
"confusion_matrix/label_2_pred_2": 0,
"confusion_matrix/label_2_pred_3": 2,
"confusion_matrix/label_3_pred_0": 0,
"confusion_matrix/label_3_pred_1": 0,
"confusion_matrix/label_3_pred_2": 2,
"confusion_matrix/label_3_pred_3": 0
}, sess.run(value_ops))
def testMultiClassificationWithWeights(self):
labels = [0, 1, 2, 3]
predictions = [
[0.7, 0.2, 0.1, 0.0], # Predicted label = 0
[0.2, 0.4, 0.2, 0.2], # Predicted label = 1
[0.0, 0.0, 0.0, 1.0], # Predicted label = 3
[0.1, 0.1, 0.7, 0.1], # Predicted label = 2
]
weights = [0, 1, 0, 1]
batch_losses = [0, 0, 4, 2]
model = _MockModel(labels, predictions, weights, batch_losses, output_dim=4)
metric_map = metrics.create_metrics(model)
value_ops, update_ops = _unpack_metric_map(metric_map)
initializer = tf.local_variables_initializer()
with self.test_session() as sess:
sess.run(initializer)
sess.run(update_ops)
self.assertAllClose({
"num_examples": 2,
"accuracy/num_correct": 1,
"accuracy/accuracy": 0.5,
"losses/weighted_cross_entropy": 1,
"confusion_matrix/label_0_pred_0": 0,
"confusion_matrix/label_0_pred_1": 0,
"confusion_matrix/label_0_pred_2": 0,
"confusion_matrix/label_0_pred_3": 0,
"confusion_matrix/label_1_pred_0": 0,
"confusion_matrix/label_1_pred_1": 1,
"confusion_matrix/label_1_pred_2": 0,
"confusion_matrix/label_1_pred_3": 0,
"confusion_matrix/label_2_pred_0": 0,
"confusion_matrix/label_2_pred_1": 0,
"confusion_matrix/label_2_pred_2": 0,
"confusion_matrix/label_2_pred_3": 0,
"confusion_matrix/label_3_pred_0": 0,
"confusion_matrix/label_3_pred_1": 0,
"confusion_matrix/label_3_pred_2": 1,
"confusion_matrix/label_3_pred_3": 0
}, sess.run(value_ops))
sess.run(update_ops)
self.assertAllClose({
"num_examples": 4,
"accuracy/num_correct": 2,
"accuracy/accuracy": 0.5,
"losses/weighted_cross_entropy": 1,
"confusion_matrix/label_0_pred_0": 0,
"confusion_matrix/label_0_pred_1": 0,
"confusion_matrix/label_0_pred_2": 0,
"confusion_matrix/label_0_pred_3": 0,
"confusion_matrix/label_1_pred_0": 0,
"confusion_matrix/label_1_pred_1": 2,
"confusion_matrix/label_1_pred_2": 0,
"confusion_matrix/label_1_pred_3": 0,
"confusion_matrix/label_2_pred_0": 0,
"confusion_matrix/label_2_pred_1": 0,
"confusion_matrix/label_2_pred_2": 0,
"confusion_matrix/label_2_pred_3": 0,
"confusion_matrix/label_3_pred_0": 0,
"confusion_matrix/label_3_pred_1": 0,
"confusion_matrix/label_3_pred_2": 2,
"confusion_matrix/label_3_pred_3": 0
}, sess.run(value_ops))
def testBinaryClassificationWithoutWeights(self):
labels = [0, 1, 1, 0]
predictions = [
[0.4], # Predicted label = 0
[0.6], # Predicted label = 1
[0.0], # Predicted label = 0
[1.0], # Predicted label = 1
]
weights = None
batch_losses = [0, 0, 4, 2]
model = _MockModel(labels, predictions, weights, batch_losses, output_dim=1)
metric_map = metrics.create_metrics(model)
value_ops, update_ops = _unpack_metric_map(metric_map)
initializer = tf.local_variables_initializer()
with self.test_session() as sess:
sess.run(initializer)
sess.run(update_ops)
self.assertAllClose({
"num_examples": 4,
"accuracy/num_correct": 2,
"accuracy/accuracy": 0.5,
"losses/weighted_cross_entropy": 1.5,
"auc": 0.25,
"confusion_matrix/label_0_pred_0": 1,
"confusion_matrix/label_0_pred_1": 1,
"confusion_matrix/label_1_pred_0": 1,
"confusion_matrix/label_1_pred_1": 1,
}, sess.run(value_ops))
sess.run(update_ops)
self.assertAllClose({
"num_examples": 8,
"accuracy/num_correct": 4,
"accuracy/accuracy": 0.5,
"losses/weighted_cross_entropy": 1.5,
"auc": 0.25,
"confusion_matrix/label_0_pred_0": 2,
"confusion_matrix/label_0_pred_1": 2,
"confusion_matrix/label_1_pred_0": 2,
"confusion_matrix/label_1_pred_1": 2,
}, sess.run(value_ops))
def testBinaryClassificationWithWeights(self):
labels = [0, 1, 1, 0]
predictions = [
[0.4], # Predicted label = 0
[0.6], # Predicted label = 1
[0.0], # Predicted label = 0
[1.0], # Predicted label = 1
]
weights = [0, 1, 0, 1]
batch_losses = [0, 0, 4, 2]
model = _MockModel(labels, predictions, weights, batch_losses, output_dim=1)
metric_map = metrics.create_metrics(model)
value_ops, update_ops = _unpack_metric_map(metric_map)
initializer = tf.local_variables_initializer()
with self.test_session() as sess:
sess.run(initializer)
sess.run(update_ops)
self.assertAllClose({
"num_examples": 2,
"accuracy/num_correct": 1,
"accuracy/accuracy": 0.5,
"losses/weighted_cross_entropy": 1,
"auc": 0,
"confusion_matrix/label_0_pred_0": 0,
"confusion_matrix/label_0_pred_1": 1,
"confusion_matrix/label_1_pred_0": 0,
"confusion_matrix/label_1_pred_1": 1,
}, sess.run(value_ops))
sess.run(update_ops)
self.assertAllClose({
"num_examples": 4,
"accuracy/num_correct": 2,
"accuracy/accuracy": 0.5,
"losses/weighted_cross_entropy": 1,
"auc": 0,
"confusion_matrix/label_0_pred_0": 0,
"confusion_matrix/label_0_pred_1": 2,
"confusion_matrix/label_1_pred_0": 0,
"confusion_matrix/label_1_pred_1": 2,
}, sess.run(value_ops))
if __name__ == "__main__":
tf.test.main()
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package(default_visibility = ["//visibility:public"])
licenses(["notice"]) # Apache 2.0
py_library(
name = "estimator_util",
srcs = ["estimator_util.py"],
srcs_version = "PY2AND3",
deps = [
"//astronet/ops:dataset_ops",
"//astronet/ops:metrics",
"//astronet/ops:training",
],
)
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# Copyright 2018 The TensorFlow Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
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