Example

This page illustrates how to use the MIset library by an example.

First, lets load in the Breast Cancer Wisconsin (Diagnostic) dataset.

>>> from ucimlrepo import fetch_ucirepo

>>> breast_cancer_wisconsin_diagnostic = fetch_ucirepo(id=17)

>>> X = breast_cancer_wisconsin_diagnostic.data.features
>>> y = breast_cancer_wisconsin_diagnostic.data.targets

Let us combine both the core data and the target variable into a single dataframe:

>>> import pandas as pd
>>> pd.set_option('display.max_columns',None)

>>> df=pd.concat([X,y],axis=1)
>>> df.head()

    radius1  texture1  perimeter1   area1  smoothness1  compactness1  concavity1  concave_points1  symmetry1  fractal_dimension1  radius2  texture2  perimeter2   area2  smoothness2  compactness2  concavity2  concave_points2  symmetry2  fractal_dimension2  radius3  texture3  perimeter3   area3  smoothness3  compactness3  concavity3  concave_points3  symmetry3  fractal_dimension3 Diagnosis
  17.99     10.38      122.80  1001.0      0.11840       0.27760      0.3001          0.14710     0.2419             0.07871   1.0950    0.9053       8.589  153.40     0.006399       0.04904     0.05373          0.01587    0.03003            0.006193    25.38     17.33      184.60  2019.0       0.1622        0.6656      0.7119           0.2654     0.4601             0.11890         M
  20.57     17.77      132.90  1326.0      0.08474       0.07864      0.0869          0.07017     0.1812             0.05667   0.5435    0.7339       3.398   74.08     0.005225       0.01308     0.01860          0.01340    0.01389            0.003532    24.99     23.41      158.80  1956.0       0.1238        0.1866      0.2416           0.1860     0.2750             0.08902         M
  19.69     21.25      130.00  1203.0      0.10960       0.15990      0.1974          0.12790     0.2069             0.05999   0.7456    0.7869       4.585   94.03     0.006150       0.04006     0.03832          0.02058    0.02250            0.004571    23.57     25.53      152.50  1709.0       0.1444        0.4245      0.4504           0.2430     0.3613             0.08758         M
  11.42     20.38       77.58   386.1      0.14250       0.28390      0.2414          0.10520     0.2597             0.09744   0.4956    1.1560       3.445   27.23     0.009110       0.07458     0.05661          0.01867    0.05963            0.009208    14.91     26.50       98.87   567.7       0.2098        0.8663      0.6869           0.2575     0.6638             0.17300         M
  20.29     14.34      135.10  1297.0      0.10030       0.13280      0.1980          0.10430     0.1809             0.05883   0.7572    0.7813       5.438   94.44     0.011490       0.02461     0.05688          0.01885    0.01756            0.005115    22.54     16.67      152.20  1575.0       0.1374        0.2050      0.4000           0.1625     0.2364             0.07678         M

This dataset contains many columns having continuous values. Before we implement our feature selection algorithm, let us first perform binning on these features.

>>> from sklearn.preprocessing import KBinsDiscretizer

>>> kbd=KBinsDiscretizer(n_bins=10,encode='ordinal',strategy='uniform')

>>> cont_columns=list(df.columns)
>>> cont_columns.remove('Diagnosis') # This is our target variable
>>> df[cont_columns]=kbd.fit_transform(df[cont_columns])

Now, let us perform feature selection. We select the Joint Mutual Information Maximization algorithm to perform feature selection and retrieve the top 3 most relevant features out of the entire dataset.

We initialize the class object and call the MIset.fit() method to fit the feature selection algorithm on our dataset.

>>> from MIset import MIset

>>> miset=MIset(max_features=3,variant='jmim',verbose=False,n_jobs=-1)
>>> miset.fit(df=df,feature_list=cont_columns,class_feature_name='Diagnosis')

Now that feature selection is done, we use MIset.feature_ranking() method to get the top 3 relevant features found by the feature selection algorithm from our entire dataset.

MIset.feature_ranking() gives a dictionary where the dictionary key is the iteration number and the dictionary value is the most important feature found in that iteration.

>>> miset.feature_selection_order()
{1: 'concave_points3', 2: 'radius3', 3: 'texture3'}