Input Data

julearn supports two kinds of data input configuration. The function run_cross_validation() takes as input the following variables:

• X: Features

• y: Target or labels

• confounds: Confounds to remove (optional)

• pos_labels: Labels to be considered as positive (optional, needed for some

  metrics)

• groups: Grouping variables to avoid data leakage in some cross-validation

  schemes. See Cross Validation for more information.

julearn interprets data using two kinds of combinations:

Using Pandas dataframes (recommended)

This method interprets X, y, confounds and groups as columns in the dataframe (specified in df).

For example, using the ‘iris’ dataset, we can specify:

df_iris = load_dataset('iris')
X = ['sepal_length', 'sepal_width', 'petal_length']
y = 'species'
confounds = 'petal_width'

And finally call run_cross_validation() with the following parameters:

scores = run_cross_validation(X=X, y=y, data=df_iris, confounds=confounds)

Using regular expressions

It might be the case that the number of elements of X and confounds are too many to specify manually all the column names. For this purpose, julearn provides the option of using regular expressions to match columns names.

In the previous example, we can pick both sepal_width and sepal_length by using sepal_.*.

df_iris = load_dataset('iris')
X = ['sepal_.*', 'petal_length']
y = 'species'
confounds = 'petal_width'

Additionally, we also provide a way to select all the columns, except for the ones used for y, confounds and groups. That is, using X = [‘:’].

df_iris = load_dataset('iris')
X = [':']
y = 'species'
confounds = 'petal_width'

For more information, check python’s Regular Expressions. Keep in mind that julearn uses fullmatch, so it requires that the regular expression matches the whole string and not part of it.

Using Numpy arrays

This method allows X, y, confounds and groups to be specified as n-dimensional arrays. In this case, the number of samples for X, y, confounds and groups must match:

X.shape[0] == y.shape[0] == confunds.shape[0] == groups.shape[0]

X (and confounds) can be one- or two-dimensional, with each element in the second dimension representing a feature (or confound):

if X.ndim == 1:
    n_features == 1
else:
    n_features == X.shape[1]

Additionally, y and groups must be one-dimensional:

y.ndim == 1
groups.ndim == 1

The previous example can be also written as numpy arrays:

df_iris = load_dataset('iris')
features = ['sepal_length', 'sepal_width', 'petal_length']
target = 'species'
confound_names = 'petal_width'

X = df_iris[features].values
y = df_iris[target].values
confounds = df_iris[confound_names].values

And finally call run_cross_validation() without specifying the df parameter:

scores = run_cross_validation(X=X, y=y, confounds=confounds)