Spark MLlib Tutorial – Feature Transformation

Feature Transformation

In the previous article we talked about MLlib and how to use it for training a regression model. This article focus on Feature Transformation. We will understand the concepts and how to implement them directly in MLlib.

Feature Transformation

Feature transformation is simply a function that transforms features from one representation to another. But why would we transform our features? Well there are many reasons, such as:

  1. data types are not suitable to be fed into a machine learning algorithm, e.g. text, categories
  2. feature values may cause problems during the learning process, e.g. data represented in different scales
  3. we want to reduce the number of features to plot and visualize data, speed up training or improve the accuracy of a specific model

In this article we will focus on three main transformation techniques:

  • Handling categorical variables
  • Feature scaling
  • Principal Component Analysis

Handling Categorical Variables

Categorical Data

Categorical values are values that can be represented as categories or groups. They can be grouped into two main types: Nominal and Ordinal.

  • Nominal values are simply names or labels with no ordering defined. Example: gender, color.
  • Ordinal values are categories where order does matter. Example: t-shirt size, rank, grade.

Machine learning algorithms can not handle data represented as categories or labels. Therefore, we need to transform the values into a more relevant format.

Dataset

We will work with a very simple dataset so that we put total focus on the techniques we are going to learn. The dataset is simply a CSV file with two fields: ID and Color. [Download it from here]

Setting up the Environment

For the rest of the article, the following steps are common to setup the development environment:

  1. open a Jupyter notebook
  2. import findspark and initialize it
  3. create a spark session
  4. load and show the data
import findspark
findspark.init('/opt/spark')
from pyspark.sql import SparkSession
spark = SparkSession.builder.getOrCreate()
data = spark.read.csv('./datasets/titanic.csv', header=True, inferSchema=True)
data.show()
Data

Even thought the data is very simple, we can not work with the color column as it is, since it contains categorical data.

In order to solve this problem, we will introduce two main methods and how implement them in MLlib: String Indexing and One Hot Encoding.

String Indexing

The concept behind String Indexing is very intuitive. We simply replace each category with a number. Then we use this number in our models instead of the label.

Here is how we do it. First, we need to define a StringIndexer.

from pyspark.ml.feature import StringIndexer
indexer = StringIndexer(inputCol="color", outputCol="color_indexed")

Note that indexer here is an object of type Estimator.

An Estimator abstracts the concept of a learning algorithm or any algorithm that fits or trains on data. Technically, an Estimator implements a method fit(), which accepts a DataFrame and produces a Model, which is a Transformer.
source: https://spark.apache.org/docs/1.6.1/ml-guide.html#estimators

The objective of an estimator here is to learn the mappings from a color label to a color index.

Next we call the fit() method to initiate the learning process.

indexer_model = indexer.fit(data)

The returned indexer_model is an object of type Transformer.

Transformer is an abstraction that includes feature transformers and learned models. It implements a method transform(), which converts one DataFrame into another, generally by appending one or more columns.
source: https://spark.apache.org/docs/1.6.1/ml-guide.html#transformers

After fitting the estimator and getting our transformer, it is time to use it on our data by calling transform().

indexed_data= indexer_model.transform(data)
# to view the data
indexed_data.show()

Notice how a new column “color_indexed” is added as specified in our outputCol field.

Data after running the StringIndexer

The new column represents an index for each color value. Similar color values have similar indices. Here we see that red, white, orange and blue where given the numbers 0, 1, 2 and 3 respectively.

These numbers will be the ones collected in the features vector with the VectorAssembler to be passed to the machine learning algorithm.

But wait! We still have a problem. A color is a nominal value not an ordinal one. This means that there is no order between the color names. For example: red is not greater, less than or equal to green. However, based on the current representation the machine learning model may consider somehow that there is an order based on the values given. Don’t worry we will fix this with another technique called One Hot Encoding.

One Hot Encoding

We use One Hot Encoding (OHE) to break the ordering within a categorical column. The process to apply OHE is the following:

  1. break the categorical column into n different columns, where n is the number of uniques categories in the column
  2. assign a binary value (0 or 1) in each column that represents the existence of the color in the data point

Going back to our example, we have four unique colors: red, white, orange and blue. Therefore, we need four columns. We will name them: is_red, is_white, is_orange and is_blue. Now instead of having a value x for the color red we will put 1 in the is_red column and 0 in the others. Then, we will group the values in an array to be used as the color feature instead of the single-value index calculated by StringIndexer. [See the table below to get a better idea]

One Hot Encoding Process

To apply OHE in MLlib, we first import the OneHotEncoderEstimator class and create an estimator variable.

from pyspark.ml.feature import OneHotEncoderEstimator
ohe = OneHotEncoderEstimator(inputCols=["color_indexed"], outputCols=["color_ohe"])

Now we fit the estimator on the data to learn how many categories it needs to encode.

ohe_model = ohe.fit(indexed_data)

We got our trained model, time to apply it on our data.

encoded_data = ohe_model.transform(indexed_data)
encoded_data.show()
Data after applying the One Hot Encoder

Done! We have the color_ohe column that contains our one-hot-encoded data. But what is this weird representation? It is called a DenseVector data type, used to reduce storage space. For example the numbers (3, [0], [1]) mean we have an array of 3 values such that we got the value 1 at index 0, and the value 0 in all other positions. But again, why 3 values while we have four unique categories? Well this is how MLlib does it. It omits the final category to break the correlation between features. Normally you do not have to worry about it. But in case you want to force MLlib not to drop the last column, simply add dropLast=False in the constructor.

ohe = OneHotEncoderEstimator(inputCols=["color_indexed"], outputCols=["color_ohe"], dropLast=False)

Now the color_ohe column is ready to be collected by your VectorAssemblerwithout worrying about the ordinal relationship between colors.

Feature Scaling

Let us move from categorical values to numerical ones. But why do we need to bother? This kind of data is already numerical and could be used directly in a machine learning model, right? Unfortunately, this is not always the case. Next we will understand what is feature scaling, and how it could improve our models.

Dataset

We will work with the popular Wine Data Set [Download from here]. Let us load it and have a look.

Note: I have omitted the column names for space purposes.

data = spark.read.csv('./datasets/wine.csv', header=False, inferSchema=True)
data.show()
Wine dataset

You might ask what is wrong with the data? Well, have a closer look at the values in each column. Some values are small fractions < 1, some range between 10 and 20 and others are in thousands. Notice for each column, the difference in means, standard deviations, minimum and maximum values. [Calculated with data.describe().show() method]

Wine data statistics

This diversity in scale could cause a lot of problems in some machine learning algorithms e.g. KMeans. This is because the algorithm may treat some variables as more dominant according to their value range. For example: consider a dataset about employees. We may have a years of experience column that ranges between 0 → 30 and a salary column with values in thousands. But this does not mean that the salary column is more dominant!

To solve this problem we transform the values to be at the same scale. There are a lot of transformation methods, we will look at two of them.

Note that scalers are applied on Vector Data Types that is why we need to collect the features using a VectorAssembler first:

from pyspark.ml.feature import VectorAssembler
assembler = VectorAssembler(inputCols=data.columns[1:], outputCol="features")
data_2 = assembler.transform(data)

Important: We omitted the _c0 column since it is a categorical column. Scaler should be applied only on numerical values.

Here we got our features column.

StandardScaler

StandardScaler standardizes features by removing the mean and scaling to unit standard deviation using column-summary-statistics.

To define a StandardScaler:

from pyspark.ml.feature import StandardScaler
scaler = StandardScaler(inputCol="features", outputCol="scaled_features")

StandardScaler can take two additional parameters:

  • withStd: True by default. Scales the data to unit standard deviation.
  • withMean: False by default. Centers the data with mean before scaling.

Now we fit our estimator on the dataset.

scaler_model = scaler.fit(data_2)

Finally, we apply our transformer on the data to get our scaled features.

scaled_data = scaler_model.transform(data_2)

Done! We have our scaled features ready.

MinMaxScaler

Applying any other scaler is doing the exact same process as above, but with a different class name and its relevant parameters.

MinMaxScaler transforms data values to a specific range ([0, 1] by default).

Full example:

from pyspark.ml.feature import MinMaxScaler
scaler = MinMaxScaler(min=0, max=1, inputCol='features', outputCol='features_minmax')
scaler_model = scaler.fit(data_2)
data_3 = scaler_model.transform(data_2)

Principal Component Analysis

Principal Component Analysis (PCA) is a procedure that converts a set of observations from m to n dimensions (m > n), after analyzing the correlated features of the variables. It is used to move the data from high to a low dimension for visualization or dimensionality reduction purposes. I will not go much into details since my goal here is to teach you how to apply it in MLlib.

Applying PCA is no different than applying other estimators:

  1. create an estimator,
  2. fit it on the model to get a transformer,
  3. apply the transformer to the data.

To see how powerful PCA is, we will apply it on a dataset of handwritten images [Download from here]. The data has 785 columns. The first column represents a label defining the digit class (0 →9), the other 784 columns represent the pixel values of the 28*28 image.

It is too difficult for our minds to visualize something higher that 3 dimensions. Here our data has 784 dimensions! So it would be impossible for use to make sense of it in this representation. Luckily we could use PCA to reduce the dimensions to only 2!

First, we read the data and collect the pixels into a features column:

data = spark.read.csv('./datasets/digits.csv', header=True, inferSchema=True)
from pyspark.ml.feature import VectorAssembler
assembler = VectorAssembler(inputCols=data.columns[1:], outputCol='features')
data_2 = assembler.transform(data)

We create our PCA model given k = 2 (number of output dimensions):

pca = PCA(k=2, inputCol='features', outputCol='features_pca')

We train the estimator:

pca_model = pca.fit(data_2)

Finally, we apply the model on the data:

pca_data = pca_model.transform(data_2).select('features_pca')

Notice how the features_pca column only has two values. These values are the reduced dimensions from 784 → 2.

PCA features with K = 2

Now, notice what happens when we plot these values and label them by each digit label.

Digits plotted with 2 dimensions

See how we beautifully were able to plot the distribution of digits only using 2 dimensions. We see that similar digits form a cluster, and this insight is very useful for later processing.

PCA is very powerful when used properly. It helps you visualize data or prepare it for other machine learning algorithms.

Final Thoughts

In this article we covered the basics of Feature Transformation. A set of techniques that help transforming our data into more relevant or optimized formats for machine learning algorithms. We covered the most common approaches and how to implement them in MLlib. Next we are going to learn how to put these techniques in practice and how to organize them in a full work flow. Stay tuned…

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