I've implemented the following model using the DNNClassifier class. The model is paramatrized as follows
classifier = tf.estimator.DNNClassifier(
hidden_units=[60, 30, 20],
feature_columns=feature_columns,
n_classes=len(labels),
label_vocabulary=labels,
batch_norm=True,
optimizer=lambda: tf.keras.optimizers.Adam(
learning_rate=tf.compat.v1.train.exponential_decay(
learning_rate=0.1,
global_step=tf.compat.v1.train.get_global_step(),
decay_steps=10000,
decay_rate=0.96)
)
)
Now I would like to do some hyperparameters tuning (e.g. learning rate, number of units, etc).
DNNClassifier, being a premade estimator class, inherits from the Estimator class.
But while Estimator has a params argument to pass hyperparameters, DNNClassifier has none.
So what should be the preferred way to do hyperparameter tuning using DNNClassifier?
First of all you need an input function for your estimator, assuming you are using pandas dataframes to keep your data, (data_df and label_df are dataframes) you can write something like:
def make_input_fn(data_df, label_df, num_epochs=10, shuffle=True, batch_size=32):
def input_function():
ds = tf.data.Dataset.from_tensor_slices((dict(data_df), label_df))
if shuffle:
ds = ds.shuffle(1024)
ds = ds.batch(batch_size).repeat(num_epochs)
return ds
return input_function
Then use the code above to create two input functions, one for training and one for validation like this:
train_input_fn = make_input_fn(X_train, y_train)
val_input_fn = make_input_fn(X_val, y_val, num_epochs=1, shuffle=False)
Finally train the classifier you defined and evaluate it using the validation set. Run this pipeline multiple times to tune your hyperparameters.
classifier = tf.estimator.DNNClassifier(
hidden_units=[60, 30, 20],
feature_columns=feature_columns,
n_classes=len(labels),
label_vocabulary=labels,
batch_norm=True,
optimizer=lambda: tf.keras.optimizers.Adam(
learning_rate=tf.compat.v1.train.exponential_decay(
learning_rate=0.1,
global_step=tf.compat.v1.train.get_global_step(),
decay_steps=10000,
decay_rate=0.96)
)
)
# Train Classifier.
classifier.train(train_input_fn)
# Evaluate Classifier.
result = classifier.evaluate(val_input_fn)
print(result)
Related
Problem
As the title suggests I have been trying to create a pipeline for training an Autoencoder model using TFX. The problem I'm having is fitting the tf.Dataset returned by the DataAccessor.tf_dataset_factory object to the Autoencoder.
Below I summarise the steps I've taken through this project, and have some Questions at the bottom if you wish to skip the background information.
Intro
TFX Pipeline
The TFX components I have used so far have been:
CsvExampleGenerator (the dataset has 82 columns, all numeric, and the sample csv has 739 rows)
StatisticsGenerator / SchemaGenerator, the schema has been edited as is now loaded in using an Importer
Transform
Trainer (this is the component I am currently having problems with)
Model
The model that I am attempting to train is based off of the example laid out here https://www.tensorflow.org/tutorials/generative/autoencoder. However, my model is being trained on tabular data, searching for anomalous results, as opposed to image data.
As I have tried a couple of solutions I have tried using both the Keras.layers and Keras.model format for defining the model and I outline both below:
Subclassing Keras.Model
class Autoencoder(keras.models.Model):
def __init__(self, features):
super(Autoencoder, self).__init__()
self.encoder = tf.keras.Sequential([
keras.layers.Dense(82, activation = 'relu'),
keras.layers.Dense(32, activation = 'relu'),
keras.layers.Dense(16, activation = 'relu'),
keras.layers.Dense(8, activation = 'relu')
])
self.decoder = tf.keras.Sequential([
keras.layers.Dense(16, activation = 'relu'),
keras.layers.Dense(32, activation = 'relu'),
keras.layers.Dense(len(features), activation = 'sigmoid')
])
def call(self, x):
inputs = [keras.layers.Input(shape = (1,), name = f) for f in features]
dense = keras.layers.concatenate(inputs)
encoded = self.encoder(dense)
decoded = self.decoder(encoded)
return decoded
Subclassing Keras.Layers
def _build_keras_model(features: List[str]) -> tf.keras.Model:
inputs = [keras.layers.Input(shape = (1,), name = f) for f in features]
dense = keras.layers.concatenate(inputs)
dense = keras.layers.Dense(32, activation = 'relu')(dense)
dense = keras.layers.Dense(16, activation = 'relu')(dense)
dense = keras.layers.Dense(8, activation = 'relu')(dense)
dense = keras.layers.Dense(16, activation = 'relu')(dense)
dense = keras.layers.Dense(32, activation = 'relu')(dense)
outputs = keras.layers.Dense(len(features), activation = 'sigmoid')(dense)
model = keras.Model(inputs = inputs, outputs = outputs)
model.compile(
optimizer = 'adam',
loss = 'mae'
)
return model
TFX Trainer Component
For creating the Trainer Component I have been mainly following the implementation details laid out here: https://www.tensorflow.org/tfx/guide/trainer
As well as following the default penguins example: https://www.tensorflow.org/tfx/tutorials/tfx/penguin_simple#write_model_training_code
run_fn defintion
def run_fn(fn_args: tfx.components.FnArgs) -> None:
tft_output = tft.TFTransformOutput(fn_args.transform_output)
train_dataset = _input_fn(
file_pattern = fn_args.train_files,
data_accessor = fn_args.data_accessor,
tf_transform_output = tft_output,
batch_size = fn_args.train_steps
)
eval_dataset = _input_fn(
file_pattern = fn_args.eval_files,
data_accessor = fn_args.data_accessor,
tf_transform_output = tft_output,
batch_size = fn_args.custom_config['eval_batch_size']
)
# model = Autoencoder(
# features = fn_args.custom_config['features']
# )
model = _build_keras_model(features = fn_args.custom_config['features'])
model.compile(optimizer = 'adam', loss = 'mse')
model.fit(
train_dataset,
steps_per_epoch = fn_args.train_steps,
validation_data = eval_dataset,
validation_steps = fn_args.eval_steps
)
...
_input_fn definition
def _apply_preprocessing(raw_features, tft_layer):
transformed_features = tft_layer(raw_features)
return transformed_features
def _input_fn(
file_pattern,
data_accessor: tfx.components.DataAccessor,
tf_transform_output: tft.TFTransformOutput,
batch_size: int) -> tf.data.Dataset:
"""
Generates features and label for tuning/training.
Args:
file_pattern: List of paths or patterns of input tfrecord files.
data_accessor: DataAccessor for converting input to RecordBatch.
tf_transform_output: A TFTransformOutput.
batch_size: representing the number of consecutive elements of returned
dataset to combine in a single batch
Returns:
A dataset that contains features where features is a
dictionary of Tensors.
"""
dataset = data_accessor.tf_dataset_factory(
file_pattern,
tfxio.TensorFlowDatasetOptions(batch_size = batch_size),
tf_transform_output.transformed_metadata.schema
)
transform_layer = tf_transform_output.transform_features_layer()
def apply_transform(raw_features):
return _apply_preprocessing(raw_features, transform_layer)
return dataset.map(apply_transform).repeat()
This differs from the _input_fn example given above as I was following the example in the next tfx tutorial found here: https://www.tensorflow.org/tfx/tutorials/tfx/penguin_tft#run_fn
Also for reference, there is no Target within the example data so there is no label_key to be passed to the tfxio.TensorFlowDatasetOptions object.
Error
When trying to run the Trainer component using a TFX InteractiveContext object I receive the following error.
ValueError: No gradients provided for any variable: ['dense_460/kernel:0', 'dense_460/bias:0', 'dense_461/kernel:0', 'dense_461/bias:0', 'dense_462/kernel:0', 'dense_462/bias:0', 'dense_463/kernel:0', 'dense_463/bias:0', 'dense_464/kernel:0', 'dense_464/bias:0', 'dense_465/kernel:0', 'dense_465/bias:0'].
From my own attempts to solve this I believe the problem lies in the way that an Autoencoder is trained. From the Autoencoder example linked here https://www.tensorflow.org/tutorials/generative/autoencoder the data is fitted like so:
autoencoder.fit(x_train, x_train,
epochs=10,
shuffle=True,
validation_data=(x_test, x_test))
therefore it stands to reason that the tf.Dataset should also mimic this behaviour and when testing with plain Tensor objects I have been able to recreate the error above and then solve it when adding the target to be the same as the training data in the .fit() function.
Things I've Tried So Far
Duplicating Train Dataset
model.fit(
train_dataset,
train_dataset,
steps_per_epoch = fn_args.train_steps,
validation_data = eval_dataset,
validation_steps = fn_args.eval_steps
)
Raises error due to Keras not accepting a 'y' value when a dataset is passed.
ValueError: `y` argument is not supported when using dataset as input.
Returning a dataset that is a tuple with itself
def _input_fn(...
dataset = data_accessor.tf_dataset_factory(
file_pattern,
tfxio.TensorFlowDatasetOptions(batch_size = batch_size),
tf_transform_output.transformed_metadata.schema
)
transform_layer = tf_transform_output.transform_features_layer()
def apply_transform(raw_features):
return _apply_preprocessing(raw_features, transform_layer)
dataset = dataset.map(apply_transform)
return dataset.map(lambda x: (x, x))
This raises an error where the keys from the features dictionary don't match the output of the model.
ValueError: Found unexpected keys that do not correspond to any Model output: dict_keys(['feature_string', ...]). Expected: ['dense_477']
At this point I switched to using the keras.model Autoencoder subclass and tried to add output keys to the Model using an output which I tried to create dynamically in the same way as the inputs.
def call(self, x):
inputs = [keras.layers.Input(shape = (1,), name = f) for f in x]
dense = keras.layers.concatenate(inputs)
encoded = self.encoder(dense)
decoded = self.decoder(encoded)
outputs = {}
for feature_name in x:
outputs[feature_name] = keras.layers.Dense(1, activation = 'sigmoid')(decoded)
return outputs
This raises the following error:
TypeError: Cannot convert a symbolic Keras input/output to a numpy array. This error may indicate that you're trying to pass a symbolic value to a NumPy call, which is not supported. Or, you may be trying to pass Keras symbolic inputs/outputs to a TF API that does not register dispatching, preventing Keras from automatically converting the API call to a lambda layer in the Functional Model.
I've been looking into solving this issue but am no longer sure if the data is being passed correctly and am beginning to think I'm getting side-tracked from the actual problem.
Questions
Has anyone managed to get an Autoencoder working when connected via TFX examples?
Did you alter the tf.Dataset or handled the examples in a different way to the _input_fn demonstrated?
So I managed to find an answer to this and wanted to leave what I found here in case anyone else stumbles onto a similar problem.
It turns out my feelings around the error were correct and the solution did indeed lie in how the tf.Dataset object was presented.
This can be demonstrated when I ran some code which simulated the incoming data using randomly generated tensors.
tensors = [tf.random.uniform(shape = (1, 82)) for i in range(739)]
# This gives us a list of 739 tensors which hold 1 value for 82 'features' simulating the dataset I had
dataset = tf.data.Dataset.from_tensor_slices(tensors)
dataset = dataset.map(lambda x : (x, x))
# This returns a dataset which marks the training set and target as the same
# which is what the Autoecnoder model is looking for
model.fit(dataset ...)
Following this I proceeded to do the same thing with the dataset returned by the _input_fn. Given that the tfx DataAccessor object returns a features_dict however I needed to combine the tensors in that dict together to create a single tensor.
This is how my _input_fn looks now:
def create_target_values(features_dict: Dict[str, tf.Tensor]) -> tuple:
value_tensor = tf.concat(list(features_dict.values()), axis = 1)
return (features_dict, value_tensor)
def _input_fn(
file_pattern,
data_accessor: tfx.components.DataAccessor,
tf_transform_output: tft.TFTransformOutput,
batch_size: int) -> tf.data.Dataset:
"""
Generates features and label for tuning/training.
Args:
file_pattern: List of paths or patterns of input tfrecord files.
data_accessor: DataAccessor for converting input to RecordBatch.
tf_transform_output: A TFTransformOutput.
batch_size: representing the number of consecutive elements of returned
dataset to combine in a single batch
Returns:
A dataset that contains (features, target_tensor) tuple where features is a
dictionary of Tensors, and target_tensor is a single Tensor that is a concatenated tensor of all the
feature values.
"""
dataset = data_accessor.tf_dataset_factory(
file_pattern,
tfxio.TensorFlowDatasetOptions(batch_size = batch_size),
tf_transform_output.transformed_metadata.schema
)
dataset = dataset.map(lambda x: create_target_values(features_dict = x))
return dataset.repeat()
I have a Keras model that takes an input layer with shape (n, 288, 1), of which 288 is the number of features. I am using a TensorFlow dataset tf.data.experimental.make_batched_features_dataset and my input layer will be (n, 1, 1) which means it gives one feature to the model at a time. How can I make an input tensor with the shape of (n, 288, 1)? I mean how can I use all my features in one tensor?
You can specify the shape of your input in the Keras input layer. Here an example code demonstrating with dummy data demonstrating the same.
import tensorflow as tf
## Creating dummy data for demo
def make_sample():
return tf.random.normal([288, 1])
n_samples = 100
samples = [make_sample() for _ in range(n_samples)]
labels = [tf.random.uniform([1]) for _ in range(n_samples)]
# Use tf.data to create dataset
batch_size = 4
dataset = tf.data.Dataset.from_tensor_slices((samples, labels))
dataset = dataset.batch(batch_size)
# Build keras function model
inputs = tf.keras.Input(shape=[288, 1], name='input')
x = tf.keras.layers.Dense(1)(inputs)
model = tf.keras.Model(inputs=[inputs], outputs=[x])
# Compile loss and optimizer
model.compile(loss='mse', optimizer='sgd', metrics=['mae'])
model.fit(dataset, epochs=1)
I'm feeding my tf.estimator.DNNClassifier data in batches and I want to visualize the loss as the model is trained. When I use the default SUM loss reduction I see the average loss in a chart in Tensorboard. If I use the SUM_OVER_BATCH_SIZE the loss chart vanishes. Is there a way to see the loss over the training?
What I have is as follows:
import tensorflow as tf
features = ... # all of type tf.feature_column.numeric_column(...)
weight_col = ... # of type tf.feature_column.numeric_column(key=...)
def train_input_fn():
...
def eval_input_fn():
...
config = tf.estimator.RunConfig(model_dir=job_dir).replace(save_summary_steps=5)
estimator = tf.estimator.DNNClassifier(
feature_columns=features,
hidden_units=[50, 100, 50],
weight_column=weight_col,
n_classes=2,
activation_fn=tf.nn.relu,
optimizer=tf.train.AdamOptimizer(learning_rate=0.005),
loss_reduction=tf.losses.Reduction.SUM_OVER_BATCH_SIZE,
dropout=0.001,
config=config)
estimator.train(input_fn=train_input_fn, max_steps=10000)
eval = estimator.evaluate(input_fn=eval_input_fn)
I'm on TensorFlow 1.9.0.
I have a basic classification code for Irish dataset.
import tensorflow as tf
import pandas as pd
COLUMN_NAMES = [
'SepalLength',
'SepalWidth',
'PetalLength',
'PetalWidth',
'Species'
]
# Import training dataset
training_dataset = pd.read_csv('iris_training.csv', names=COLUMN_NAMES, header=0)
train_x = training_dataset.iloc[:, 0:4]
train_y = training_dataset.iloc[:, 4]
# Import testing dataset
test_dataset = pd.read_csv('iris_test.csv', names=COLUMN_NAMES, header=0)
test_x = test_dataset.iloc[:, 0:4]
test_y = test_dataset.iloc[:, 4]
columns_feat = [
tf.feature_column.numeric_column(key='SepalLength'),
tf.feature_column.numeric_column(key='SepalWidth'),
tf.feature_column.numeric_column(key='PetalLength'),
tf.feature_column.numeric_column(key='PetalWidth')
]
classifier = tf.estimator.DNNClassifier(
feature_columns=columns_feat,
# Two hidden layers of 10 nodes each.
hidden_units=[10, 10],
# The model is classifying 3 classes
n_classes=3)
def train_function(inputs, outputs, batch_size):
dataset = tf.data.Dataset.from_tensor_slices((dict(inputs), outputs))
dataset = dataset.shuffle(1000).repeat().batch(batch_size)
return dataset.make_one_shot_iterator().get_next()
# Train the Model.
classifier.train(
input_fn=lambda:train_function(train_x, train_y, 100),
steps=1000)
def evaluation_function(attributes, classes, batch_size):
attributes=dict(attributes)
if classes is None:
inputs = attributes
else:
inputs = (attributes, classes)
dataset = tf.data.Dataset.from_tensor_slices(inputs)
assert batch_size is not None, "batch_size must not be None"
dataset = dataset.batch(batch_size)
return dataset.make_one_shot_iterator().get_next()
# Evaluate the model.
eval_result = classifier.evaluate(
input_fn=lambda:evaluation_function(test_x, test_y, 100))
I evaluate the result but how can i make a prediction on my data because now i get only console info of loss and epochs, accuracy. For example if i have everything except species. I want to give my own sepal length and etc so i can get prediction of the species and it will be another variable. Do i have to create variables like pred_x or pred_y(pandas dataframe) and then put them into eval_result?
Is that what you mean? for example:new_samples = np.array([[6.4, 3.2, 4.5, 1.5], [5.8, 3.1, 5.0, 1.7]], dtype=np.float32) If you want new data like this to make predictions, then you can refer to this code.TensorFlow-Iris-Classification
Like all estimator classes, the DNNClassifier class has a predict method that makes real-world predictions. The documentation is here.
I use Estimator and I train model in the loop to feed data. Every step is the final step. The checkpoints are saved for every final step too. I want to avoid saving checkpoint in every iteration to increase the performance (speed) of the training.
I can not find any information how to do this. Do you have any ideas/suggestions/solutions?
classifier = Estimator(
model_fn=cnn_model_fn,
model_dir="./temp_model_Adam",
config=tf.contrib.learn.RunConfig(
save_checkpoints_secs=None,
save_checkpoints_steps=100,
save_summary_steps=None
)
)
# Train the model
for e in range(0, 10):
numbers = np.arange(10000)
np.random.shuffle(numbers)
for step in range(0, 2000):
classifier.fit(
input_fn=lambda: read_images_for_training_as_batch(step, path, 5, numbers),
steps=1
)
Nowadays the api got changed a bit but from what I see you were using the fit (currently train) method incorrectly, you should put steps=2000 and have your input function return an iterator over your dataset. Today you have tf.estimator.inputs.numpy_input_fn at your disposal that can help you when you have small data sets, otherwise you have to use tf.data.DataSet api.
Something like this (it loads .wav files):
from tensorflow.contrib.framework.python.ops import audio_ops as contrib_audio
from tensorflow.python.ops import io_ops
# ...
def input_fn(num_epochs, batch_size, shuffle=False, mode='training')
def input_fn_bound():
def _read_file(fn, label):
return io_ops.read_file(fn), label
def _decode(data, label):
pcm = contrib_audio.decode_wav(data,
desired_channels=1,
desired_samples=desired_samples)
return pcm.audio, label
filenames = get_files(mode)
classes = get_classes(mode)
labels = {'class': np.array(classes)}
dataset = tf.data.Dataset.from_tensor_slices((filenames, labels))
if shuffle:
dataset = dataset.shuffle(buffer_size=len(labels))
dataset = dataset.map(_read_file, num_parallel_calls=num_map_threads)
dataset = dataset.map(_decode, num_parallel_calls=num_map_threads)
dataset = dataset.map(lambda wav, label: ({'wav': wav}, label))
dataset = dataset.repeat(num_epochs)
dataset = dataset.batch(batch_size)
dataset = dataset.prefetch(2) # To load next batch while the first one is being processed on GPU
iter = dataset.make_one_shot_iterator()
features, labels = iter.get_next()
return features, labels
return input_fn_bound
# ....
estimator.train(input_fn=input_fn(
num_epoths=None,
batch_size=64,
shuffle=True,
mode='training'),
steps=10000)