clfutils4r 1.0.2

Wrapper around some basic sklearn and scikit-plot utilities for classification.

Classification Utilities

This packages provides a simple convenience wrapper around some basic sklearn and scikit-plot utilities for classification. There are two modules available - gridsearch_classification and eval_classification.

Installation

pip install clfutils4r

Module gridsearch_classification:

Only function available is gridsearch_classification()

Available Parameters

X: dataset.

gt_labels: ground truth labels.

best_model_metric: metric to use to choose the best model.

For plotting

show: whether to display the plots; this is used in a notebook.

save: whether to save the plots.

save_dir: if save=True, directory to save results in.

Module eval_classification:

Only function available is eval_classification()

Metrics plotted -

1. Confusion Matrix
2. Class-wise PR curve
3. Class-wise ROC curve

Additional metrics plotted if binary classification -

1. KS Statistic Plot
2. Lift Curve
3. Cumulative Gain Plot
4. Cross-validated PR curve
5. Cross-validated ROC curve

Available Parameters

For cross-validation on full dataset

untrained_model: classifier object (untrained); this is used for cross-validation

X: Pandas DataFrame containing preprocessed, normalized, complete dataset

y: Pandas Series containing encoded labels for X

For single run evaluation

y_test: ground-truth encoded labels of test set

y_pred: binary predicted labels for test set

y_pred_proba: probabilist predictions per class for test set

For Shapley analysis

make_shap_plot: set True if you want to perform Shapley analysis

trained_model: classifier object (trained)

X_train: Pandas DataFrame containing preprocessed, normalized, complete train set

X_test: Pandas DataFrame containing preprocessed, normalized, complete test set

For plotting

class_names: list of unique classes

RESULTS_DIR: location to store results; directory will be created if it does not exist

save: set True if you want to save all results in RESULTS_DIR; defaults to False

show: display all results; useful in notebooks; defaults to False

Example Usage

import collections
import matplotlib.pyplot as plt
%matplotlib inline
import numpy as np
import pandas as pd
import os

from sklearn import datasets
from sklearn.preprocessing import StandardScaler
scaler = StandardScaler()

## Load dataset: Example - breast cancer prediction
data = datasets.load_breast_cancer()
class_names = [str(x) for x in data.target_names]
feature_names = [str(x) for x in data.feature_names]

X, y = data.data, data.target
X = scaler.fit_transform(X)

## Split into train and test sets
from sklearn.model_selection import train_test_split
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.30, random_state=42)

## Grid search for best model
from gridsearch_classification import gridsearch_classification
save_dir = "gridsearch_results"
os.makedirs(save_dir, exist_ok=True)
best_model, grid_search_results = gridsearch_classification(X=X_train,                    # dataset
                                                            gt_labels=y_train,            # ground truth labels
                                                            best_model_metric="F1",       # metric to use to choose the best model
                                                            show=True,                    # whether to display the plots; this is used in a notebook
                                                            save=True, save_dir=save_dir  # whether to save the plots
                                                        )

## Predict on test set
y_pred = best_model.predict(X_test)
y_pred_proba = best_model.predict_proba(X_test)

## Evaluate best model on test set
from eval_classification import eval_classification
## Make metrics plots
eval_classification(make_metrics_plots=True, y_test=y_test, y_pred=y_pred, y_pred_proba=y_pred_proba,  
                    class_names=class_names, feature_names=feature_names,
                    titlestr="Breast Cancer Classification",
                    show=True, save=True, 
                    RESULTS_DIR=os.getcwd()+'/test_results')

Developer Notes:

This package is the updated version of bcutils4r which supported only binary classification. bcutils4r is now defunct.

Credits:

1. For pretty confusion matrix - https://github.com/phongsathorn1/pretty-confusion-matrix
2. Scikit Plot package - https://scikit-plot.readthedocs.io/en/stable
3. Shapley Analysis - https://shap-lrjball.readthedocs.io/en/latest/