Preprocessing data with TensorFlow Transform

The Feature Engineering Component of TensorFlow Extended (TFX)

This example colab notebook provides a somewhat more advanced example of how TensorFlow Transform (tf.Transform) can be used to preprocess data using exactly the same code for both training a model and serving inferences in production.

TensorFlow Transform is a library for preprocessing input data for TensorFlow, including creating features that require a full pass over the training dataset. For example, using TensorFlow Transform you could:

  • Normalize an input value by using the mean and standard deviation
  • Convert strings to integers by generating a vocabulary over all of the input values
  • Convert floats to integers by assigning them to buckets, based on the observed data distribution

TensorFlow has built-in support for manipulations on a single example or a batch of examples. tf.Transform extends these capabilities to support full passes over the entire training dataset.

The output of tf.Transform is exported as a TensorFlow graph which you can use for both training and serving. Using the same graph for both training and serving can prevent skew, since the same transformations are applied in both stages.

What we're doing in this example

In this example we'll be processing a widely used dataset containing census data, and training a model to do classification. Along the way we'll be transforming the data using tf.Transform.

Python check, imports, and globals

First we'll make sure that we're using Python 2, and then go ahead and install and import the stuff we need.

import sys
from __future__ import print_function

# Confirm that we're using Python 2
assert sys.version_info.major is 2, 'Oops, not running Python 2'
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function

import argparse
import os
import pprint
import tempfile
import urllib
import zipfile

temp = tempfile.gettempdir()
zip, headers = urllib.urlretrieve('')

train = os.path.join(temp, 'census/')
test = os.path.join(temp, 'census/adult.test')

  import tensorflow_transform as tft
  import apache_beam as beam
except ImportError:
  print('Installing TensorFlow Transform.  This will take a minute, ignore the warnings')
  !pip install -q tensorflow_transform
  print('Installing Apache Beam.  This will take a minute, ignore the warnings')
  !pip install -q apache_beam
  import tensorflow_transform as tft
  import apache_beam as beam

import tensorflow as tf
import tensorflow_transform.beam as tft_beam
from tensorflow_transform.tf_metadata import dataset_metadata
from tensorflow_transform.tf_metadata import dataset_schema
Installing TensorFlow Transform.  This will take a minute, ignore the warnings
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Installing Apache Beam.  This will take a minute, ignore the warnings
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.

WARNING: Logging before flag parsing goes to stderr.
W0515 18:37:57.428355 139851846362880] From /usr/local/lib/python2.7/dist-packages/tensorflow_transform/beam/ The name tf.ConfigProto is deprecated. Please use tf.compat.v1.ConfigProto instead.

W0515 18:37:57.438539 139851846362880] From /usr/local/lib/python2.7/dist-packages/tensorflow_transform/beam/ The name tf.SparseTensorValue is deprecated. Please use tf.compat.v1.SparseTensorValue instead.

Name our columns

We'll create some handy lists for referencing the columns in our dataset.

LABEL_KEY = 'label'

Define our features and schema

Let's define a schema based on what types the columns are in our input. Among other things this will help with importing them correctly.

    [(name, tf.FixedLenFeature([], tf.string))
     for name in CATEGORICAL_FEATURE_KEYS] +
    [(name, tf.FixedLenFeature([], tf.float32))
     for name in NUMERIC_FEATURE_KEYS] +
    [(name, tf.VarLenFeature(tf.float32))
    [(LABEL_KEY, tf.FixedLenFeature([], tf.string))]

RAW_DATA_METADATA = dataset_metadata.DatasetMetadata(

Setting hyperparameters and basic housekeeping

Constants and hyperparameters used for training. The bucket size includes all listed categories in the dataset description as well as one extra for "?" which represents unknown.

testing = os.getenv("WEB_TEST_BROWSER", False)
if testing:

# Names of temp files
EXPORTED_MODEL_DIR = 'exported_model_dir'


Create a Beam Transform for cleaning our input data

We'll create a Beam Transform by creating a subclass of Apache Beam's PTransform class and overriding the expand method to specify the actual processing logic. A PTransform represents a data processing operation, or a step, in your pipeline. Every PTransform takes one or more PCollection objects as input, performs a processing function that you provide on the elements of that PCollection, and produces zero or more output PCollection objects.

Our transform class will apply Beam's ParDo on the input PCollection containing our census dataset, producing clean data in an output PCollection.

class MapAndFilterErrors(beam.PTransform):
  """Like beam.Map but filters out erros in the map_fn."""

  class _MapAndFilterErrorsDoFn(beam.DoFn):
    """Count the bad examples using a beam metric."""

    def __init__(self, fn):
      self._fn = fn
      # Create a counter to measure number of bad elements.
      self._bad_elements_counter = beam.metrics.Metrics.counter(
          'census_example', 'bad_elements')

    def process(self, element):
        yield self._fn(element)
      except Exception:  # pylint: disable=broad-except
        # Catch any exception the above call.

  def __init__(self, fn):
    self._fn = fn

  def expand(self, pcoll):
    return pcoll | beam.ParDo(self._MapAndFilterErrorsDoFn(self._fn))

Preprocessing with tf.Transform

Create a tf.Transform preprocessing_fn

The preprocessing function is the most important concept of tf.Transform. A preprocessing function is where the transformation of the dataset really happens. It accepts and returns a dictionary of tensors, where a tensor means a Tensor or SparseTensor. There are two main groups of API calls that typically form the heart of a preprocessing function:

  1. TensorFlow Ops: Any function that accepts and returns tensors, which usually means TensorFlow ops. These add TensorFlow operations to the graph that transforms raw data into transformed data one feature vector at a time. These will run for every example, during both training and serving.
  2. TensorFlow Transform Analyzers: Any of the analyzers provided by tf.Transform. Analyzers also accept and return tensors, but unlike TensorFlow ops they only run once, during training, and typically make a full pass over the entire training dataset. They create tensor constants, which are added to your graph. For example, tft.min computes the minimum of a tensor over the training dataset. tf.Transform provides a fixed set of analyzers, but this will be extended in future versions.
def preprocessing_fn(inputs):
  """Preprocess input columns into transformed columns."""
  # Since we are modifying some features and leaving others unchanged, we
  # start by setting `outputs` to a copy of `inputs.
  outputs = inputs.copy()

  # Scale numeric columns to have range [0, 1].
    outputs[key] = tft.scale_to_0_1(outputs[key])

    # This is a SparseTensor because it is optional. Here we fill in a default
    # value when it is missing.
    dense = tf.sparse_to_dense(outputs[key].indices,
                               [outputs[key].dense_shape[0], 1],
                               outputs[key].values, default_value=0.)
    # Reshaping from a batch of vectors of size 1 to a batch to scalars.
    dense = tf.squeeze(dense, axis=1)
    outputs[key] = tft.scale_to_0_1(dense)

  # For all categorical columns except the label column, we generate a
  # vocabulary but do not modify the feature.  This vocabulary is instead
  # used in the trainer, by means of a feature column, to convert the feature
  # from a string to an integer id.
    tft.vocabulary(inputs[key], vocab_filename=key)

  # For the label column we provide the mapping from string to index.
  table = tf.contrib.lookup.index_table_from_tensor(['>50K', '<=50K'])
  outputs[LABEL_KEY] = table.lookup(outputs[LABEL_KEY])

  return outputs

Transform the data

Now we're ready to start transforming our data in an Apache Beam pipeline.

  1. Read in the data using the CSV reader
  2. Clean it using our new MapAndFilterErrors transform
  3. Transform it using a preprocessing pipeline that scales numeric data and converts categorical data from strings to int64 values indices, by creating a vocabulary for each category
  4. Write out the result as a TFRecord of Example protos, which we will use for training a model later
def transform_data(train_data_file, test_data_file, working_dir):
  """Transform the data and write out as a TFRecord of Example protos.

  Read in the data using the CSV reader, and transform it using a
  preprocessing pipeline that scales numeric data and converts categorical data
  from strings to int64 values indices, by creating a vocabulary for each

    train_data_file: File containing training data
    test_data_file: File containing test data
    working_dir: Directory to write transformed data and metadata to

  # The "with" block will create a pipeline, and run that pipeline at the exit
  # of the block.
  with beam.Pipeline() as pipeline:
    with tft_beam.Context(temp_dir=tempfile.mkdtemp()):
      # Create a coder to read the census data with the schema.  To do this we
      # need to list all columns in order since the schema doesn't specify the
      # order of columns in the csv.
      ordered_columns = [
          'age', 'workclass', 'fnlwgt', 'education', 'education-num',
          'marital-status', 'occupation', 'relationship', 'race', 'sex',
          'capital-gain', 'capital-loss', 'hours-per-week', 'native-country',
      converter = tft.coders.CsvCoder(ordered_columns, RAW_DATA_METADATA.schema)

      # Read in raw data and convert using CSV converter.  Note that we apply
      # some Beam transformations here, which will not be encoded in the TF
      # graph since we don't do the from within tf.Transform's methods
      # (AnalyzeDataset, TransformDataset etc.).  These transformations are just
      # to get data into a format that the CSV converter can read, in particular
      # removing spaces after commas.
      # We use MapAndFilterErrors instead of Map to filter out decode errors in
      # convert.decode which should only occur for the trailing blank line.
      raw_data = (
          | 'ReadTrainData' >>
          | 'FixCommasTrainData' >> beam.Map(
              lambda line: line.replace(', ', ','))
          | 'DecodeTrainData' >> MapAndFilterErrors(converter.decode))

      # Combine data and schema into a dataset tuple.  Note that we already used
      # the schema to read the CSV data, but we also need it to interpret
      # raw_data.
      raw_dataset = (raw_data, RAW_DATA_METADATA)
      transformed_dataset, transform_fn = (
          raw_dataset | tft_beam.AnalyzeAndTransformDataset(preprocessing_fn))
      transformed_data, transformed_metadata = transformed_dataset
      transformed_data_coder = tft.coders.ExampleProtoCoder(

      _ = (
          | 'EncodeTrainData' >> beam.Map(transformed_data_coder.encode)
          | 'WriteTrainData' >>
              os.path.join(working_dir, TRANSFORMED_TRAIN_DATA_FILEBASE)))

      # Now apply transform function to test data.  In this case we remove the
      # trailing period at the end of each line, and also ignore the header line
      # that is present in the test data file.
      raw_test_data = (
          | 'ReadTestData' >>,
          | 'FixCommasTestData' >> beam.Map(
              lambda line: line.replace(', ', ','))
          | 'RemoveTrailingPeriodsTestData' >> beam.Map(lambda line: line[:-1])
          | 'DecodeTestData' >> MapAndFilterErrors(converter.decode))

      raw_test_dataset = (raw_test_data, RAW_DATA_METADATA)

      transformed_test_dataset = (
          (raw_test_dataset, transform_fn) | tft_beam.TransformDataset())
      # Don't need transformed data schema, it's the same as before.
      transformed_test_data, _ = transformed_test_dataset

      _ = (
          | 'EncodeTestData' >> beam.Map(transformed_data_coder.encode)
          | 'WriteTestData' >>
              os.path.join(working_dir, TRANSFORMED_TEST_DATA_FILEBASE)))

      # Will write a SavedModel and metadata to working_dir, which can then
      # be read by the tft.TFTransformOutput class.
      _ = (
          | 'WriteTransformFn' >> tft_beam.WriteTransformFn(working_dir))

Using our preprocessed data to train a model

To show how tf.Transform enables us to use the same code for both training and serving, and thus prevent skew, we're going to train a model. To train our model and prepare our trained model for production we need to create input functions. The main difference between our training input function and our serving input function is that training data contains the labels, and production data does not. The arguments and returns are also somewhat different.

Create an input function for training

def _make_training_input_fn(tf_transform_output, transformed_examples,
  """Creates an input function reading from transformed data.

    tf_transform_output: Wrapper around output of tf.Transform.
    transformed_examples: Base filename of examples.
    batch_size: Batch size.

    The input function for training or eval.
  def input_fn():
    """Input function for training and eval."""
    dataset =

    transformed_features = dataset.make_one_shot_iterator().get_next()

    # Extract features and label from the transformed tensors.
    transformed_labels = transformed_features.pop(LABEL_KEY)

    return transformed_features, transformed_labels

  return input_fn

Create an input function for serving

Let's create an input function that we could use in production, and prepare our trained model for serving.

def _make_serving_input_fn(tf_transform_output):
  """Creates an input function reading from raw data.

    tf_transform_output: Wrapper around output of tf.Transform.

    The serving input function.
  raw_feature_spec = RAW_DATA_METADATA.schema.as_feature_spec()
  # Remove label since it is not available during serving.

  def serving_input_fn():
    """Input function for serving."""
    # Get raw features by generating the basic serving input_fn and calling it.
    # Here we generate an input_fn that expects a parsed Example proto to be fed
    # to the model at serving time.  See also
    # tf.estimator.export.build_raw_serving_input_receiver_fn.
    raw_input_fn = tf.estimator.export.build_parsing_serving_input_receiver_fn(
        raw_feature_spec, default_batch_size=None)
    serving_input_receiver = raw_input_fn()

    # Apply the transform function that was used to generate the materialized
    # data.
    raw_features = serving_input_receiver.features
    transformed_features = tf_transform_output.transform_raw_features(

    return tf.estimator.export.ServingInputReceiver(
        transformed_features, serving_input_receiver.receiver_tensors)

  return serving_input_fn

Wrap our input data in FeatureColumns

Our model will expect our data in TensorFlow FeatureColumns.

def get_feature_columns(tf_transform_output):
  """Returns the FeatureColumns for the model.

    tf_transform_output: A `TFTransformOutput` object.

    A list of FeatureColumns.
  # Wrap scalars as real valued columns.
  real_valued_columns = [tf.feature_column.numeric_column(key, shape=())
                         for key in NUMERIC_FEATURE_KEYS]

  # Wrap categorical columns.
  one_hot_columns = [

  return real_valued_columns + one_hot_columns

Train, Evaluate, and Export our model

def train_and_evaluate(working_dir, num_train_instances=NUM_TRAIN_INSTANCES,
  """Train the model on training data and evaluate on test data.

    working_dir: Directory to read transformed data and metadata from and to
        write exported model to.
    num_train_instances: Number of instances in train set
    num_test_instances: Number of instances in test set

    The results from the estimator's 'evaluate' method
  tf_transform_output = tft.TFTransformOutput(working_dir)
  run_config = tf.estimator.RunConfig()

  estimator = tf.estimator.LinearClassifier(

  # Fit the model using the default optimizer.
  train_input_fn = _make_training_input_fn(
      os.path.join(working_dir, TRANSFORMED_TRAIN_DATA_FILEBASE + '*'),
      max_steps=TRAIN_NUM_EPOCHS * num_train_instances / TRAIN_BATCH_SIZE)

  # Evaluate model on test dataset.
  eval_input_fn = _make_training_input_fn(
      os.path.join(working_dir, TRANSFORMED_TEST_DATA_FILEBASE + '*'),

  # Export the model.
  serving_input_fn = _make_serving_input_fn(tf_transform_output)
  exported_model_dir = os.path.join(working_dir, EXPORTED_MODEL_DIR)
  estimator.export_savedmodel(exported_model_dir, serving_input_fn)

  return estimator.evaluate(input_fn=eval_input_fn, steps=num_test_instances)

Put it all together

We've created all the stuff we need to preprocess our census data, train a model, and prepare it for serving. So far we've just been getting things ready. It's time to start running!

import time

start = time.time()
  transform_data(train, test, temp)
  print('Transform took {:.2f} seconds'.format(time.time() - start))
  results = train_and_evaluate(temp)
  print('Transform and training took {:.2f} seconds'.format(time.time() - start))
  # cleanup
  import shutil
  if os.path.isdir(temp) and not testing:
W0515 18:38:06.332725 139851846362880] Couldn't find python-snappy so the implementation of _TFRecordUtil._masked_crc32c is not as fast as it could be.

Transform took 9.73 seconds
Transform and training took 61.30 seconds
{'accuracy': 0.8097783,
 'accuracy_baseline': 0.7596585,
 'auc': 0.855185,
 'auc_precision_recall': 0.94773537,
 'average_loss': 0.441462,
 'global_step': 4071,
 'label/mean': 0.7596585,
 'loss': 0.441462,
 'precision': 0.8718216,
 'prediction/mean': 0.7424,
 'recall': 0.87880015}

What we did

In this example we used tf.Transform to preprocess a dataset of census data, and train a model with the cleaned and transformed data. We also created an input function that we could use when we deploy our trained model in a production environment to perform inference. By using the same code for both training and inference we avoid any issues with data skew. Along the way we learned about creating an Apache Beam transform to perform the transformation that we needed for cleaing the data, and wrapped our data in TensorFlow FeatureColumns. This is just a small piece of what TensorFlow Transform can do! We encourage you to dive into tf.Transform and discover what it can do for you.