Preprocessing

Sometimes, one or more preprocessing steps may need to be taken before handing a dataset off to a Learner. In some cases, data may not be in the correct format and in others you may want to process the data to aid in training.

Transformers

Transformers are objects that perform various preprocessing steps to the samples in a dataset. They take a dataset object as input and transform it in place. Stateful transformers are a type of transformer that must be fitted to a dataset. Fitting a dataset to a transformer is much like training a learner but in the context of preprocessing rather than inference. After fitting a stateful transformer, it will expect the features to be present in the same order when transforming subsequent datasets. A few transformers are supervised meaning they must be fitted with a Labeled dataset. Elastic transformers can have their fittings updated with new data after an initial fitting.

Transform a Dataset

An example of a transformation is one that converts the categorical features of a dataset to continuous ones using a one hot encoding. To accomplish this with the library, pass a One Hot Encoder instance as an argument to the Dataset object's apply() method. Note that the apply() method also handles fitting a Stateful transformer automatically.

use Rubix\ML\Transformers\OneHotEncoder;

$dataset->apply(new OneHotEncoder());

Transformations can be chained by calling the apply() method fluently.

use Rubix\ML\Transformers\HotDeckImputer;
use Rubix\ML\Transformers\OneHotEncoder;
use Rubix\ML\Transformers\MinMaxNormalizer;

$dataset->apply(new HotDeckImputer(5))
    ->apply(new OneHotEncoder())
    ->apply(new MinMaxNormalizer());

Transforming the Labels

Transformers do not alter the labels in a dataset. For that we can pass a callback function to the transformLabels() method on a Labeled dataset instance. The callback accepts a single argument that is the value of the label to be transformed. In this example, we'll convert the categorical labels of a dataset to integer ordinals.

$dataset->transformLabels('intval');

Manually Fitting

If you need to fit a Stateful transformer to a dataset other than the one it was meant to transform, you can fit the transformer manually by calling the fit() method before applying the transformation.

use Rubix\ML\Transformers\WordCountVectorizer;

$transformer = new WordCountVectorizer(5000);

$transformer->fit($dataset1);

$dataset2->apply($transformer);

Update Fitting

To update the fitting of an Elastic transformer call the update() method with a new dataset.

$transformer->update($dataset);

Types of Preprocessing

Here we dive into the different types of data preprocessing that Transformers are capable of.

Standardization and Normalization

Oftentimes, the continuous features of a dataset will be on different scales because they were measured by different methods. For example, age (0 - 100) and income (0 - 9,999,999) are on two widely different scales. Standardization is the processes of transforming a dataset such that the features are all on one common scale. Normalization is the special case where the transformed features have a range between 0 and 1. Depending on the transformer, it may operate on the columns or the rows of the dataset.

Transformer	Operates	Output Range	Stateful	Elastic
L1 Normalizer	Row-wise	[0, 1]
L2 Normalizer	Row-wise	[0, 1]
Max Absolute Scaler	Column-wise	[-1, 1]	●	●
Min Max Normalizer	Column-wise	[min, max]	●	●
Robust Standardizer	Column-wise	[-∞, ∞]	●
Z Scale Standardizer	Column-wise	[-∞, ∞]	●	●

Feature Conversion

Feature converters are transformers that convert feature columns of one data type to another by changing their representation.

Transformer	From	To	Stateful	Elastic
Interval Discretizer	Continuous	Categorical	●
One Hot Encoder	Categorical	Continuous	●
Numeric String Converter	Categorical	Continuous
Boolean Converter	Other	Categorical or Continuous

Dimensionality Reduction

Dimensionality reduction is a preprocessing technique for projecting a dataset onto a lower dimensional vector space. It allows a learner to train and infer quicker by producing a training set with fewer but more informative features. Dimensionality reducers can also be used to visualize datasets by outputting low (1 - 3) dimensionality embeddings for use in plotting software.

Transformer	Supervised	Stateful	Elastic
Gaussian Random Projector		●
Linear Discriminant Analysis	●	●
Principal Component Analysis		●
Sparse Random Projector		●
Truncated SVD		●
t-SNE

Feature Expansion

Feature expansion aims to add flexibility to a model by deriving additional features from a dataset. It can be thought of as the opposite of dimensionality reduction.

Transformer	Supervised	Stateful	Elastic
Polynomial Expander

Imputation

Imputation is a technique for handling missing values in a dataset by replacing them with a pretty good guess.

Transformer	Compatibility	Supervised	Stateful	Elastic
KNN Imputer	Depends on distance kernel		●
Missing Data Imputer	Categorical, Continuous		●
Hot Deck Imputer	Depends on distance kernel		●

Natural Language

The library provides a number of transformers for Natural Language Processing (NLP) and Information Retrieval (IR) tasks such as text cleaning, feature extraction, and term weighting.

Transformer	Supervised	Stateful	Elastic
Regex Filter
Text Normalizer
Multibyte Text Normalizer
Stop Word Filter
TF-IDF Transformer		●	●
Token Hashing Vectorizer
Word Count Vectorizer		●

Images

These transformers operate on the high-level image data type.

Transformer	Supervised	Stateful	Elastic
Image Resizer
Image Vectorizer		●

Custom Transformations

In additional to providing specialized Transformers for common preprocessing tasks, the library includes a Lambda Function transformer that allows you to apply custom data transformations using a callback. The callback function accepts a sample passed by reference so that the transformation occurs in-place. In the following example, let's write a callback to binarize the continuous features just at column offset 3 of the dataset.

use Rubix\ML\Transformers\LambdaFunction;

$binarize = function (&$sample) {
    $sample[3] = $sample[3] > 182 ? 'tall' : 'not tall';
}

$dataset->apply(new LambdaFunction($binarize));

Another technique we can employ using the Lambda Function transformer is to perform a categorical feature cross between two feature columns of a dataset. A cross feature is a higher-order feature that represents the presence of two or more features simultaneously. For example, we may want to represent the combination of someone's gender and education level as it's own feature. We'll choose to represent the new feature as a CRC32 hash to save on memory and storage but you could just concatenate both categories to represent the new feature as well.

use Rubix\ML\Transformers\LambdaFunction;
use function hash;

$crossFeatures = function (&$sample) {
    $sample[] = hash('crc32b', "{$sample[6]} and {$sample[7]}");
};

$dataset->apply(new LambdaFunction($crossFeatures));

Advanced Preprocessing

In some cases, certain features of a dataset may require a different set of preprocessing steps than the others. In such a case, we can extract a certain set of features, preprocess them, and then join them with the rest of the dataset later. In the example below, we'll extract just the text reviews and their sentiment labels into a dataset object and put the sample's category, number of clicks, and ratings into another one using two Column Pickers. Then, we can apply a separate set of transformations to each set of features and use the join() method to combine them into a single dataset. We can even apply another set of transformations to the joined dataset after that.

use Rubix\ML\Dataset\Labeled;
use Rubix\ML\Extractors\ColumnPicker;
use Rubix\ML\Extractors\NDJSON;
use Rubix\ML\Dataset\Unlabeled;
use Rubix\ML\Transformers\TextNormalizer;
use Rubix\ML\Transformers\WordCountVectorizer;
use Rubix\ML\Transformers\TfIdfTransformer;
use Rubix\ML\Transformers\OneHotEncoder;
use Rubix\ML\Transformers\ZScaleStandardizer;

$extractor1 = new ColumnPicker(new NDJSON('example.ndjson'), [
    'review', 'sentiment',
]);

$extractor2 = new ColumnPicker(new NDJSON('example.ndjson'), [
    'category', 'clicks', 'rating',
]);

$dataset1 = Labeled::fromIterator($extractor1)
    ->apply(new TextNormalizer())
    ->apply(new WordCountVectorizer(5000))
    ->apply(new TfIdfTransformer());

$dataset2 = Unlabeled::fromIterator($extractor2)
    ->apply(new OneHotEncoder());

$dataset = $dataset1->join($dataset2)
    ->apply(new ZScaleStandardizer());

Transformer Pipelines

The Pipeline meta-estimator helps you automate a series of transformations applied to the input dataset to an estimator. With a Pipeline, any dataset object passed to will automatically be fitted and/or transformed before it arrives in the estimator's context. In addition, transformer fittings can be saved alongside the model data when the Pipeline is persisted.

use Rubix\ML\Pipeline;
use Rubix\ML\Transformers\HotDeckImputer;
use Rubix\ML\Transformers\OneHotEncoder;
use Rubix\ML\Transformers\ZScaleStandardizer;
use Rubix\ML\Clusterers\KMeans;

$estimator = new Pipeline([
    new HotDeckImputer(5),
    new OneHotEncoder(),
    new ZScaleStandardizer(),
], new KMeans(10));

Calling train() or partial() will result in the transformers being fitted or updated before being passed to the Softmax Classifier.

$estimator->train($dataset); // Transformers fitted and applied

$estimator->partial($dataset); // Transformers updated and applied

Any time a dataset is passed to the Pipeline it will automatically be transformed before being handed to the underlying estimator.

$predictions = $estimator->predict($dataset); // Dataset transformed automatically

Filtering Records

In some cases, you may want to remove entire rows from the dataset. For example, you may want to remove records that contain features with abnormally low/high values as these samples can be interpreted as noise. The filter() method on the dataset object uses a callback function to determine if a row should be included in the return dataset. In this example, we'll filter all the samples whose value for feature at offset 3 is greater than some amount.

$tallPeople = function ($record) {
    return $record[3] > 178.5;
};

$dataset = $dataset->filter($tallPeople);

Let's say we wanted to train a classifier with our Labeled dataset but only on a subset of the possible class outcomes. We could filter the samples that correspond to undesirable outcomes by targetting the label with our callback.

use function in_array;

$dogsAndCats = function ($record) {
    return in_array(end($record), ['dog', 'cat']);
}

$training = $dataset->filter($dogsAndCats);

Note

For Labeled datasets the label column is always the last column of the record.

In the next example, we'll filter all the records that have missing feature values. We can detect missing continuous variables by calling the custom library function iterator_contains_nan() on each record. Additionally, we can filter records with missing categorical values by looking for a special placeholder category, in this case we'll use the value '?', to denote missing categorical variables.

use function Rubix\ML\iterator_contains_nan;
use function in_array;

$noMissingValues = function ($record) {
    return !iterator_contains_nan($record) and !in_array('?', $record);
};

$complete = $dataset->filter($noMissingValues);

Note

The standard PHP library function in_array() does not handle NAN comparisons.

De-duplication

When it is undesirable for a dataset to contain duplicate records, you can remove all duplicates by calling the deduplicate() method on the dataset object.

$dataset->deduplicate();

Note

The O(N^2) time complexity of de-duplication may be prohibitive for large datasets.

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Last update: 2021-06-05