2.2. Data

Data input to run_cross_validation()

Julearn deals with data in the form of pandas DataFrames. This is the kind of data structure that the run_cross_validation() uses to input the data and output some of the results.

The input DataFrame must contain the features and the target or label. This will be communicated to run_cross_validation() by specifying the following parameters:

• data: Name of the dataframe containing the features and the target or

  label.

• X: List of strings containing the column names of the features.

• y: String containing the name of the column with the target or label.

For example, using the well known iris dataset, we can specify the data input as follows:

First, we load the data into a pandas dataframe called df and specify X and y:

from seaborn import load_dataset

df = load_dataset('iris')

Let’s inspect what our dataframe looks like.

df.head()

	sepal_length	sepal_width	petal_length	petal_width	species
0	5.1	3.5	1.4	0.2	setosa
1	4.9	3.0	1.4	0.2	setosa
2	4.7	3.2	1.3	0.2	setosa
3	4.6	3.1	1.5	0.2	setosa
4	5.0	3.6	1.4	0.2	setosa

Given this data, we can now specify the X and y parameters:

X = ["sepal_length", "sepal_width", "petal_length", "petal_width"]
y = "species"

Julearn’s run_cross_validation() function so far would look like this:

run_cross_validation(X=X, y=y, data=df)

This is not yet very useful to do machine learning, but we will come to it step by step.

Giving types to features

A nice add-on that Julearn offers is the capacity to specify colum-based types for the features. This comes in handy if within the pipeline, one wants to manipulate only certain columns.

To specify column types, we must provide a dictionary with the column types as keys and the column names as values. The type can be anything, but it is recommended to use a string that is meaningful to you.

Important

Every column can only have one type!

In the case of the iris dataset, we could specify the type of the columns related to the _sepal_ and _petal_ information as "sepal" and "petal" respectively.

X_types = {
    "petal": ["petal_length", "petal_width"],
    "sepal": ["sepal_length", "sepal_width"],
}

Importantly, Julearn also allows to specify the column names as regular expressions. This comes in handy when we are dealing with hundreds or thousands of features and we do not want to specify all the names by hand. For example, we could specify the type of the _sepal_ columns as follows:

X_types = {
    "petal": ["petal.*"],
    "sepal": ["sepal.*"],
}

Adding an X_types specification to run_cross_validation() will make it look like this:

run_cross_validation(X=X, y=y, data=df, X_types=X_types)

Important

If no X_types is specified, all the columns will be considered as "continuous" and a warning will be raised.

Up to now, we saw how to parametrize run_cross_validation() in terms of the input data. In the next section we will see how to specify the output In the next section we will focus on basic options to use run_cross_validation() to evaluate different pipelines in a cross-validation consistent manner.

Advanced uses cases regarding X_types selective processing are covered in Selective preprocessing using feature types